Daily Papers

Three-dimensional microscopy is often limited by anisotropic spatial resolution, resulting in lower axial resolution than lateral resolution. Current State-of-The-Art (SoTA) isotropic reconstruction methods utilizing deep neural networks can achieve impressive super-resolution performance in fixed imaging settings. However, their generality in practical use is limited by degraded performance caused by artifacts and blurring when facing unseen anisotropic factors. To address these issues, we propose DiffuseIR, an unsupervised method for isotropic reconstruction based on diffusion models. First, we pre-train a diffusion model to learn the structural distribution of biological tissue from lateral microscopic images, resulting in generating naturally high-resolution images. Then we use low-axial-resolution microscopy images to condition the generation process of the diffusion model and generate high-axial-resolution reconstruction results. Since the diffusion model learns the universal structural distribution of biological tissues, which is independent of the axial resolution, DiffuseIR can reconstruct authentic images with unseen low-axial resolutions into a high-axial resolution without requiring re-training. The proposed DiffuseIR achieves SoTA performance in experiments on EM data and can even compete with supervised methods.

Clinical decision-making relies heavily on understanding relative positions of anatomical structures and anomalies. Therefore, for Vision-Language Models (VLMs) to be applicable in clinical practice, the ability to accurately determine relative positions on medical images is a fundamental prerequisite. Despite its importance, this capability remains highly underexplored. To address this gap, we evaluate the ability of state-of-the-art VLMs, GPT-4o, Llama3.2, Pixtral, and JanusPro, and find that all models fail at this fundamental task. Inspired by successful approaches in computer vision, we investigate whether visual prompts, such as alphanumeric or colored markers placed on anatomical structures, can enhance performance. While these markers provide moderate improvements, results remain significantly lower on medical images compared to observations made on natural images. Our evaluations suggest that, in medical imaging, VLMs rely more on prior anatomical knowledge than on actual image content for answering relative position questions, often leading to incorrect conclusions. To facilitate further research in this area, we introduce the MIRP , Medical Imaging Relative Positioning, benchmark dataset, designed to systematically evaluate the capability to identify relative positions in medical images.

Accurate segmentation of regions of interest in biomedical images holds substantial value in image analysis. Although several foundation models for biomedical segmentation have currently achieved excellent performance on certain datasets, they typically demonstrate sub-optimal performance on unseen domain data. We owe the deficiency to lack of vision-language knowledge before segmentation. Multimodal Large Language Models (MLLMs) bring outstanding understanding and reasoning capabilities to multimodal tasks, which inspires us to leverage MLLMs to inject Vision-Language Knowledge (VLK), thereby enabling vision models to demonstrate superior generalization capabilities on cross-domain datasets. In this paper, we propose using MLLMs to guide SAM in learning microscopy crose-domain data, unifying Segment Anything in Microscopy, named uLLSAM. Specifically, we propose the Vision-Language Semantic Alignment (VLSA) module, which injects VLK into Segment Anything Model (SAM). We find that after SAM receives global VLK prompts, its performance improves significantly, but there are deficiencies in boundary contour perception. Therefore, we further propose Semantic Boundary Regularization (SBR) to prompt SAM. Our method achieves performance improvements of 7.71% in Dice and 12.10% in SA across 9 in-domain microscopy datasets, achieving state-of-the-art performance. Our method also demonstrates improvements of 6.79% in Dice and 10.08% in SA across 10 out-ofdomain datasets, exhibiting strong generalization capabilities. Code is available at https://github.com/ieellee/uLLSAM.

Halo artifacts significantly impact display quality. We propose a method to reduce halos in Local Histogram Equalization (LHE) algorithms by separately addressing dark and light variants. This approach results in visually natural images by exploring the relationship between lateral inhibition and halo artifacts in the human visual system.

Unlike color photography images, which are consistently encoded into RGB channels, biological images encompass various modalities, where the type of microscopy and the meaning of each channel varies with each experiment. Importantly, the number of channels can range from one to a dozen and their correlation is often comparatively much lower than RGB, as each of them brings specific information content. This aspect is largely overlooked by methods designed out of the bioimage field, and current solutions mostly focus on intra-channel spatial attention, often ignoring the relationship between channels, yet crucial in most biological applications. Importantly, the variable channel type and count prevent the projection of several experiments to a unified representation for large scale pre-training. In this study, we propose ChAda-ViT, a novel Channel Adaptive Vision Transformer architecture employing an Inter-Channel Attention mechanism on images with an arbitrary number, order and type of channels. We also introduce IDRCell100k, a bioimage dataset with a rich set of 79 experiments covering 7 microscope modalities, with a multitude of channel types, and channel counts varying from 1 to 10 per experiment. Our proposed architecture, trained in a self-supervised manner, outperforms existing approaches in several biologically relevant downstream tasks. Additionally, it can be used to bridge the gap for the first time between assays with different microscopes, channel numbers or types by embedding various image and experimental modalities into a unified biological image representation. The latter should facilitate interdisciplinary studies and pave the way for better adoption of deep learning in biological image-based analyses. Code and Data to be released soon.

Pathology is the study of microscopic inspection of tissue, and a pathology diagnosis is often the medical gold standard to diagnose disease. Pathology images provide a unique challenge for computer-vision-based analysis: a single pathology Whole Slide Image (WSI) is gigapixel-sized and often contains hundreds of thousands to millions of objects of interest across multiple resolutions. In this work, we propose PathoLogy Universal TransfOrmer (PLUTO): a light-weight pathology FM that is pre-trained on a diverse dataset of 195 million image tiles collected from multiple sites and extracts meaningful representations across multiple WSI scales that enable a large variety of downstream pathology tasks. In particular, we design task-specific adaptation heads that utilize PLUTO's output embeddings for tasks which span pathology scales ranging from subcellular to slide-scale, including instance segmentation, tile classification, and slide-level prediction. We compare PLUTO's performance to other state-of-the-art methods on a diverse set of external and internal benchmarks covering multiple biologically relevant tasks, tissue types, resolutions, stains, and scanners. We find that PLUTO matches or outperforms existing task-specific baselines and pathology-specific foundation models, some of which use orders-of-magnitude larger datasets and model sizes when compared to PLUTO. Our findings present a path towards a universal embedding to power pathology image analysis, and motivate further exploration around pathology foundation models in terms of data diversity, architectural improvements, sample efficiency, and practical deployability in real-world applications.

Recent advances in microscopy have enabled the rapid generation of terabytes of image data in cell biology and biomedical research. Vision-language models (VLMs) offer a promising solution for large-scale biological image analysis, enhancing researchers' efficiency, identifying new image biomarkers, and accelerating hypothesis generation and scientific discovery. However, there is a lack of standardized, diverse, and large-scale vision-language benchmarks to evaluate VLMs' perception and cognition capabilities in biological image understanding. To address this gap, we introduce {\mu}-Bench, an expert-curated benchmark encompassing 22 biomedical tasks across various scientific disciplines (biology, pathology), microscopy modalities (electron, fluorescence, light), scales (subcellular, cellular, tissue), and organisms in both normal and abnormal states. We evaluate state-of-the-art biomedical, pathology, and general VLMs on {\mu}-Bench and find that: i) current models struggle on all categories, even for basic tasks such as distinguishing microscopy modalities; ii) current specialist models fine-tuned on biomedical data often perform worse than generalist models; iii) fine-tuning in specific microscopy domains can cause catastrophic forgetting, eroding prior biomedical knowledge encoded in their base model. iv) weight interpolation between fine-tuned and pre-trained models offers one solution to forgetting and improves general performance across biomedical tasks. We release {\mu}-Bench under a permissive license to accelerate the research and development of microscopy foundation models.

Extracting single-cell information from microscopy data requires accurate instance-wise segmentations. Obtaining pixel-wise segmentations from microscopy imagery remains a challenging task, especially with the added complexity of microstructured environments. This paper presents a novel dataset for segmenting yeast cells in microstructures. We offer pixel-wise instance segmentation labels for both cells and trap microstructures. In total, we release 493 densely annotated microscopy images. To facilitate a unified comparison between novel segmentation algorithms, we propose a standardized evaluation strategy for our dataset. The aim of the dataset and evaluation strategy is to facilitate the development of new cell segmentation approaches. The dataset is publicly available at https://christophreich1996.github.io/yeast_in_microstructures_dataset/ .

Masked image modelling (MIM) is a powerful self-supervised representation learning paradigm, whose potential has not been widely demonstrated in medical image analysis. In this work, we show the capacity of MIM to capture rich semantic representations of Haemotoxylin & Eosin (H&E)-stained images at the nuclear level. Inspired by Bidirectional Encoder representation from Image Transformers (BEiT), we split the images into smaller patches and generate corresponding discrete visual tokens. In addition to the regular grid-based patches, typically used in visual Transformers, we introduce patches of individual cell nuclei. We propose positional encoding of the irregular distribution of these structures within an image. We pre-train the model in a self-supervised manner on H&E-stained whole-slide images of diffuse large B-cell lymphoma, where cell nuclei have been segmented. The pre-training objective is to recover the original discrete visual tokens of the masked image on the one hand, and to reconstruct the visual tokens of the masked object instances on the other. Coupling these two pre-training tasks allows us to build powerful, context-aware representations of nuclei. Our model generalizes well and can be fine-tuned on downstream classification tasks, achieving improved cell classification accuracy on PanNuke dataset by more than 5% compared to current instance segmentation methods.

Radiography imaging protocols focus on particular body regions, therefore producing images of great similarity and yielding recurrent anatomical structures across patients. To exploit this structured information, we propose the use of Space-aware Memory Queues for In-painting and Detecting anomalies from radiography images (abbreviated as SQUID). We show that SQUID can taxonomize the ingrained anatomical structures into recurrent patterns; and in the inference, it can identify anomalies (unseen/modified patterns) in the image. SQUID surpasses 13 state-of-the-art methods in unsupervised anomaly detection by at least 5 points on two chest X-ray benchmark datasets measured by the Area Under the Curve (AUC). Additionally, we have created a new dataset (DigitAnatomy), which synthesizes the spatial correlation and consistent shape in chest anatomy. We hope DigitAnatomy can prompt the development, evaluation, and interpretability of anomaly detection methods.

Computational microscopy, in which hardware and algorithms of an imaging system are jointly designed, shows promise for making imaging systems that cost less, perform more robustly, and collect new types of information. Often, the performance of computational imaging systems, especially those that incorporate machine learning, is sample-dependent. Thus, standardized datasets are an essential tool for comparing the performance of different approaches. Here, we introduce the Berkeley Single Cell Computational Microscopy (BSCCM) dataset, which contains over ~12,000,000 images of 400,000 of individual white blood cells. The dataset contains images captured with multiple illumination patterns on an LED array microscope and fluorescent measurements of the abundance of surface proteins that mark different cell types. We hope this dataset will provide a valuable resource for the development and testing of new algorithms in computational microscopy and computer vision with practical biomedical applications.

Automated and semi-automated techniques in biomedical electron microscopy (EM) enable the acquisition of large datasets at a high rate. Segmentation methods are therefore essential to analyze and interpret these large volumes of data, which can no longer completely be labeled manually. In recent years, deep learning algorithms achieved impressive results in both pixel-level labeling (semantic segmentation) and the labeling of separate instances of the same class (instance segmentation). In this review, we examine how these algorithms were adapted to the task of segmenting cellular and sub-cellular structures in EM images. The special challenges posed by such images and the network architectures that overcame some of them are described. Moreover, a thorough overview is also provided on the notable datasets that contributed to the proliferation of deep learning in EM. Finally, an outlook of current trends and future prospects of EM segmentation is given, especially in the area of label-free learning.

Developing self-supervised learning (SSL) models that can learn universal and transferable representations of H&E gigapixel whole-slide images (WSIs) is becoming increasingly valuable in computational pathology. These models hold the potential to advance critical tasks such as few-shot classification, slide retrieval, and patient stratification. Existing approaches for slide representation learning extend the principles of SSL from small images (e.g., 224 x 224 patches) to entire slides, usually by aligning two different augmentations (or views) of the slide. Yet the resulting representation remains constrained by the limited clinical and biological diversity of the views. Instead, we postulate that slides stained with multiple markers, such as immunohistochemistry, can be used as different views to form a rich task-agnostic training signal. To this end, we introduce Madeleine, a multimodal pretraining strategy for slide representation learning. Madeleine is trained with a dual global-local cross-stain alignment objective on large cohorts of breast cancer samples (N=4,211 WSIs across five stains) and kidney transplant samples (N=12,070 WSIs across four stains). We demonstrate the quality of slide representations learned by Madeleine on various downstream evaluations, ranging from morphological and molecular classification to prognostic prediction, comprising 21 tasks using 7,299 WSIs from multiple medical centers. Code is available at https://github.com/mahmoodlab/MADELEINE.

Following the impressive development of LLMs, vision-language alignment in LLMs is actively being researched to enable multimodal reasoning and visual IO. This direction of research is particularly relevant to medical imaging because medical image analysis and generation consist of reasoning based on a combination of visual features and prior knowledge. Many recent works have focused on training adapter networks that serve as an information bridge between image processing networks and LLMs; but presumably, in order to achieve maximum reasoning potential of LLMs on visual information as well, visual and language features should be allowed to interact more freely. This is especially important in the medical domain because understanding and generating medical images such as chest X-rays (CXR) require not only accurate visual and language-based reasoning but also a more intimate mapping between the two modalities. Thus, taking inspiration from previous work on the transformer and VQ-GAN combination for bidirectional image and text generation, we build upon this approach and develop a method for instruction-tuning an LLM pre-trained only on text to gain vision-language capabilities for medical images. Specifically, we leverage a pretrained LLM's existing question-answering and instruction-following abilities to teach it to understand visual inputs by instructing it to answer questions about image inputs and, symmetrically, output both text and image responses appropriate to a given query by tuning the LLM with diverse tasks that encompass image-based text-generation and text-based image-generation. We show that our model, LLM-CXR, trained in this approach shows better image-text alignment in both CXR understanding and generation tasks while being smaller in size compared to previously developed models that perform a narrower range of tasks. The code is at https://github.com/hyn2028/llm-cxr.

Representation learning of pathology whole-slide images (WSIs) has been has primarily relied on weak supervision with Multiple Instance Learning (MIL). However, the slide representations resulting from this approach are highly tailored to specific clinical tasks, which limits their expressivity and generalization, particularly in scenarios with limited data. Instead, we hypothesize that morphological redundancy in tissue can be leveraged to build a task-agnostic slide representation in an unsupervised fashion. To this end, we introduce PANTHER, a prototype-based approach rooted in the Gaussian mixture model that summarizes the set of WSI patches into a much smaller set of morphological prototypes. Specifically, each patch is assumed to have been generated from a mixture distribution, where each mixture component represents a morphological exemplar. Utilizing the estimated mixture parameters, we then construct a compact slide representation that can be readily used for a wide range of downstream tasks. By performing an extensive evaluation of PANTHER on subtyping and survival tasks using 13 datasets, we show that 1) PANTHER outperforms or is on par with supervised MIL baselines and 2) the analysis of morphological prototypes brings new qualitative and quantitative insights into model interpretability.

Earlier diagnosis of Leukemia can save thousands of lives annually. The prognosis of leukemia is challenging without the morphological information of White Blood Cells (WBC) and relies on the accessibility of expensive microscopes and the availability of hematologists to analyze Peripheral Blood Samples (PBS). Deep Learning based methods can be employed to assist hematologists. However, these algorithms require a large amount of labeled data, which is not readily available. To overcome this limitation, we have acquired a realistic, generalized, and large dataset. To collect this comprehensive dataset for real-world applications, two microscopes from two different cost spectrums (high-cost HCM and low-cost LCM) are used for dataset capturing at three magnifications (100x, 40x, 10x) through different sensors (high-end camera for HCM, middle-level camera for LCM and mobile-phone camera for both). The high-sensor camera is 47 times more expensive than the middle-level camera and HCM is 17 times more expensive than LCM. In this collection, using HCM at high resolution (100x), experienced hematologists annotated 10.3k WBC types (14) and artifacts, having 55k morphological labels (Cell Size, Nuclear Chromatin, Nuclear Shape, etc.) from 2.4k images of several PBS leukemia patients. Later on, these annotations are transferred to other 2 magnifications of HCM, and 3 magnifications of LCM, and on each camera captured images. Along with the LeukemiaAttri dataset, we provide baselines over multiple object detectors and Unsupervised Domain Adaptation (UDA) strategies, along with morphological information-based attribute prediction. The dataset will be publicly available after publication to facilitate the research in this direction.

Whole Slide Image (WSI) analysis is a powerful method to facilitate the diagnosis of cancer in tissue samples. Automating this diagnosis poses various issues, most notably caused by the immense image resolution and limited annotations. WSIs commonly exhibit resolutions of 100Kx100K pixels. Annotating cancerous areas in WSIs on the pixel level is prohibitively labor-intensive and requires a high level of expert knowledge. Multiple instance learning (MIL) alleviates the need for expensive pixel-level annotations. In MIL, learning is performed on slide-level labels, in which a pathologist provides information about whether a slide includes cancerous tissue. Here, we propose Self-ViT-MIL, a novel approach for classifying and localizing cancerous areas based on slide-level annotations, eliminating the need for pixel-wise annotated training data. Self-ViT- MIL is pre-trained in a self-supervised setting to learn rich feature representation without relying on any labels. The recent Vision Transformer (ViT) architecture builds the feature extractor of Self-ViT-MIL. For localizing cancerous regions, a MIL aggregator with global attention is utilized. To the best of our knowledge, Self-ViT- MIL is the first approach to introduce self-supervised ViTs in MIL-based WSI analysis tasks. We showcase the effectiveness of our approach on the common Camelyon16 dataset. Self-ViT-MIL surpasses existing state-of-the-art MIL-based approaches in terms of accuracy and area under the curve (AUC).

Medical imaging analysis plays a critical role in the diagnosis and treatment of various medical conditions. This paper focuses on chest X-ray images and their corresponding radiological reports. It presents a new model that learns a joint X-ray image & report representation. The model is based on a novel alignment scheme between the visual data and the text, which takes into account both local and global information. Furthermore, the model integrates domain-specific information of two types -- lateral images and the consistent visual structure of chest images. Our representation is shown to benefit three types of retrieval tasks: text-image retrieval, class-based retrieval, and phrase-grounding.

The gigapixel scale of whole slide images (WSIs) poses a challenge for histopathology multi-modal chatbots, requiring a global WSI analysis for diagnosis, compounding evidence from different WSI patches. Current visual instruction datasets, generated through large language models, focus on creating question/answer pairs for individual image patches, which may lack diagnostic capacity on their own in histopathology, further complicated by the absence of spatial grounding in histopathology image captions. To bridge this gap, we introduce Quilt-Instruct, a large-scale dataset of 107,131 histopathology-specific instruction question/answer pairs, that is collected by leveraging educational histopathology videos from YouTube, which provides spatial localization of captions by automatically extracting narrators' cursor movements. In addition, we provide contextual reasoning by extracting diagnosis and supporting facts from the entire video content to guide the extrapolative reasoning of GPT-4. Using Quilt-Instruct, we train Quilt-LLaVA, which can reason beyond the given single image patch, enabling diagnostic reasoning and the capability of spatial awareness. To evaluate Quilt-LLaVA, we propose a comprehensive evaluation dataset created from 985 images and 1283 human-generated question-answers. We also thoroughly evaluate Quilt-LLaVA using public histopathology datasets, where Quilt-LLaVA significantly outperforms SOTA by over 10% on relative GPT-4 score and 4% and 9% on open and closed set VQA. Our code, data, and model are publicly available at quilt-llava.github.io.

Low-Light Image Enhancement (LLIE) is a crucial computer vision task that aims to restore detailed visual information from corrupted low-light images. Many existing LLIE methods are based on standard RGB (sRGB) space, which often produce color bias and brightness artifacts due to inherent high color sensitivity in sRGB. While converting the images using Hue, Saturation and Value (HSV) color space helps resolve the brightness issue, it introduces significant red and black noise artifacts. To address this issue, we propose a new color space for LLIE, namely Horizontal/Vertical-Intensity (HVI), defined by polarized HS maps and learnable intensity. The former enforces small distances for red coordinates to remove the red artifacts, while the latter compresses the low-light regions to remove the black artifacts. To fully leverage the chromatic and intensity information, a novel Color and Intensity Decoupling Network (CIDNet) is further introduced to learn accurate photometric mapping function under different lighting conditions in the HVI space. Comprehensive results from benchmark and ablation experiments show that the proposed HVI color space with CIDNet outperforms the state-of-the-art methods on 10 datasets. The code is available at https://github.com/Fediory/HVI-CIDNet.

Featurizing microscopy images for use in biological research remains a significant challenge, especially for large-scale experiments spanning millions of images. This work explores the scaling properties of weakly supervised classifiers and self-supervised masked autoencoders (MAEs) when training with increasingly larger model backbones and microscopy datasets. Our results show that ViT-based MAEs outperform weakly supervised classifiers on a variety of tasks, achieving as much as a 11.5% relative improvement when recalling known biological relationships curated from public databases. Additionally, we develop a new channel-agnostic MAE architecture (CA-MAE) that allows for inputting images of different numbers and orders of channels at inference time. We demonstrate that CA-MAEs effectively generalize by inferring and evaluating on a microscopy image dataset (JUMP-CP) generated under different experimental conditions with a different channel structure than our pretraining data (RPI-93M). Our findings motivate continued research into scaling self-supervised learning on microscopy data in order to create powerful foundation models of cellular biology that have the potential to catalyze advancements in drug discovery and beyond.

High-resolution (HR) medical videos are vital for accurate diagnosis, yet are hard to acquire due to hardware limitations and physiological constraints. Clinically, the collected low-resolution (LR) medical videos present unique challenges for video super-resolution (VSR) models, including camera shake, noise, and abrupt frame transitions, which result in significant optical flow errors and alignment difficulties. Additionally, tissues and organs exhibit continuous and nuanced structures, but current VSR models are prone to introducing artifacts and distorted features that can mislead doctors. To this end, we propose MedVSR, a tailored framework for medical VSR. It first employs Cross State-Space Propagation (CSSP) to address the imprecise alignment by projecting distant frames as control matrices within state-space models, enabling the selective propagation of consistent and informative features to neighboring frames for effective alignment. Moreover, we design an Inner State-Space Reconstruction (ISSR) module that enhances tissue structures and reduces artifacts with joint long-range spatial feature learning and large-kernel short-range information aggregation. Experiments across four datasets in diverse medical scenarios, including endoscopy and cataract surgeries, show that MedVSR significantly outperforms existing VSR models in reconstruction performance and efficiency. Code released at https://github.com/CUHK-AIM-Group/MedVSR.

Accurate detection and segmentation of cell nuclei in volumetric (3D) fluorescence microscopy datasets is an important step in many biomedical research projects. Although many automated methods for these tasks exist, they often struggle for images with low signal-to-noise ratios and/or dense packing of nuclei. It was recently shown for 2D microscopy images that these issues can be alleviated by training a neural network to directly predict a suitable shape representation (star-convex polygon) for cell nuclei. In this paper, we adopt and extend this approach to 3D volumes by using star-convex polyhedra to represent cell nuclei and similar shapes. To that end, we overcome the challenges of 1) finding parameter-efficient star-convex polyhedra representations that can faithfully describe cell nuclei shapes, 2) adapting to anisotropic voxel sizes often found in fluorescence microscopy datasets, and 3) efficiently computing intersections between pairs of star-convex polyhedra (required for non-maximum suppression). Although our approach is quite general, since star-convex polyhedra include common shapes like bounding boxes and spheres as special cases, our focus is on accurate detection and segmentation of cell nuclei. Finally, we demonstrate on two challenging datasets that our approach (StarDist-3D) leads to superior results when compared to classical and deep learning based methods.

We investigate fine-tuning Vision-Language Models (VLMs) for multi-task medical image understanding, focusing on detection, localization, and counting of findings in medical images. Our objective is to evaluate whether instruction-tuned VLMs can simultaneously improve these tasks, with the goal of enhancing diagnostic accuracy and efficiency. Using MedMultiPoints, a multimodal dataset with annotations from endoscopy (polyps and instruments) and microscopy (sperm cells), we reformulate each task into instruction-based prompts suitable for vision-language reasoning. We fine-tune Qwen2.5-VL-7B-Instruct using Low-Rank Adaptation (LoRA) across multiple task combinations. Results show that multi-task training improves robustness and accuracy. For example, it reduces the Count Mean Absolute Error (MAE) and increases Matching Accuracy in the Counting + Pointing task. However, trade-offs emerge, such as more zero-case point predictions, indicating reduced reliability in edge cases despite overall performance gains. Our study highlights the potential of adapting general-purpose VLMs to specialized medical tasks via prompt-driven fine-tuning. This approach mirrors clinical workflows, where radiologists simultaneously localize, count, and describe findings - demonstrating how VLMs can learn composite diagnostic reasoning patterns. The model produces interpretable, structured outputs, offering a promising step toward explainable and versatile medical AI. Code, model weights, and scripts will be released for reproducibility at https://github.com/simula/PointDetectCount.

A key requirement for the success of supervised deep learning is a large labeled dataset - a condition that is difficult to meet in medical image analysis. Self-supervised learning (SSL) can help in this regard by providing a strategy to pre-train a neural network with unlabeled data, followed by fine-tuning for a downstream task with limited annotations. Contrastive learning, a particular variant of SSL, is a powerful technique for learning image-level representations. In this work, we propose strategies for extending the contrastive learning framework for segmentation of volumetric medical images in the semi-supervised setting with limited annotations, by leveraging domain-specific and problem-specific cues. Specifically, we propose (1) novel contrasting strategies that leverage structural similarity across volumetric medical images (domain-specific cue) and (2) a local version of the contrastive loss to learn distinctive representations of local regions that are useful for per-pixel segmentation (problem-specific cue). We carry out an extensive evaluation on three Magnetic Resonance Imaging (MRI) datasets. In the limited annotation setting, the proposed method yields substantial improvements compared to other self-supervision and semi-supervised learning techniques. When combined with a simple data augmentation technique, the proposed method reaches within 8% of benchmark performance using only two labeled MRI volumes for training, corresponding to only 4% (for ACDC) of the training data used to train the benchmark. The code is made public at https://github.com/krishnabits001/domain_specific_cl.

Traditional fluorescence staining is phototoxic to live cells, slow, and expensive; thus, the subcellular structure prediction (SSP) from transmitted light (TL) images is emerging as a label-free, faster, low-cost alternative. However, existing approaches utilize 3D networks for one-to-one voxel level dense prediction, which necessitates a frequent and time-consuming Z-axis imaging process. Moreover, 3D convolutions inevitably lead to significant computation and GPU memory overhead. Therefore, we propose an efficient framework, SparseSSP, predicting fluorescent intensities within the target voxel grid in an efficient paradigm instead of relying entirely on 3D topologies. In particular, SparseSSP makes two pivotal improvements to prior works. First, SparseSSP introduces a one-to-many voxel mapping paradigm, which permits the sparse TL slices to reconstruct the subcellular structure. Secondly, we propose a hybrid dimensions topology, which folds the Z-axis information into channel features, enabling the 2D network layers to tackle SSP under low computational cost. We conduct extensive experiments to validate the effectiveness and advantages of SparseSSP on diverse sparse imaging ratios, and our approach achieves a leading performance compared to pure 3D topologies. SparseSSP reduces imaging frequencies compared to previous dense-view SSP (i.e., the number of imaging is reduced up to 87.5% at most), which is significant in visualizing rapid biological dynamics on low-cost devices and samples.

Microscopic assessment of histopathology images is vital for accurate cancer diagnosis and treatment. Whole Slide Image (WSI) classification and captioning have become crucial tasks in computer-aided pathology. However, microscopic WSI face challenges such as redundant patches and unknown patch positions due to subjective pathologist captures. Moreover, generating automatic pathology captions remains a significant challenge. To address these issues, we introduce a novel GNN-ViTCap framework for classification and caption generation from histopathological microscopic images. First, a visual feature extractor generates patch embeddings. Redundant patches are then removed by dynamically clustering these embeddings using deep embedded clustering and selecting representative patches via a scalar dot attention mechanism. We build a graph by connecting each node to its nearest neighbors in the similarity matrix and apply a graph neural network to capture both local and global context. The aggregated image embeddings are projected into the language model's input space through a linear layer and combined with caption tokens to fine-tune a large language model. We validate our method on the BreakHis and PatchGastric datasets. GNN-ViTCap achieves an F1 score of 0.934 and an AUC of 0.963 for classification, along with a BLEU-4 score of 0.811 and a METEOR score of 0.569 for captioning. Experimental results demonstrate that GNN-ViTCap outperforms state of the art approaches, offering a reliable and efficient solution for microscopy based patient diagnosis.

Deep convolutional neural networks (CNNs) are the current state-of-the-art for digital analysis of histopathological images. The large size of whole-slide microscopy images (WSIs) requires advanced memory handling to read, display and process these images. There are several open-source platforms for working with WSIs, but few support deployment of CNN models. These applications use third-party solutions for inference, making them less user-friendly and unsuitable for high-performance image analysis. To make deployment of CNNs user-friendly and feasible on low-end machines, we have developed a new platform, FastPathology, using the FAST framework and C++. It minimizes memory usage for reading and processing WSIs, deployment of CNN models, and real-time interactive visualization of results. Runtime experiments were conducted on four different use cases, using different architectures, inference engines, hardware configurations and operating systems. Memory usage for reading, visualizing, zooming and panning a WSI were measured, using FastPathology and three existing platforms. FastPathology performed similarly in terms of memory to the other C++ based application, while using considerably less than the two Java-based platforms. The choice of neural network model, inference engine, hardware and processors influenced runtime considerably. Thus, FastPathology includes all steps needed for efficient visualization and processing of WSIs in a single application, including inference of CNNs with real-time display of the results. Source code, binary releases and test data can be found online on GitHub at https://github.com/SINTEFMedtek/FAST-Pathology/.

Confocal fluorescence microscopy is one of the most accessible and widely used imaging techniques for the study of biological processes. Scanning confocal microscopy allows the capture of high-quality images from 3D samples, yet suffers from well-known limitations such as photobleaching and phototoxicity of specimens caused by intense light exposure, which limits its use in some applications, especially for living cells. Cellular damage can be alleviated by changing imaging parameters to reduce light exposure, often at the expense of image quality. Machine/deep learning methods for single-image super-resolution (SISR) can be applied to restore image quality by upscaling lower-resolution (LR) images to produce high-resolution images (HR). These SISR methods have been successfully applied to photo-realistic images due partly to the abundance of publicly available data. In contrast, the lack of publicly available data partly limits their application and success in scanning confocal microscopy. In this paper, we introduce a large scanning confocal microscopy dataset named SR-CACO-2 that is comprised of low- and high-resolution image pairs marked for three different fluorescent markers. It allows the evaluation of performance of SISR methods on three different upscaling levels (X2, X4, X8). SR-CACO-2 contains the human epithelial cell line Caco-2 (ATCC HTB-37), and it is composed of 22 tiles that have been translated in the form of 9,937 image patches for experiments with SISR methods. Given the new SR-CACO-2 dataset, we also provide benchmarking results for 15 state-of-the-art methods that are representative of the main SISR families. Results show that these methods have limited success in producing high-resolution textures, indicating that SR-CACO-2 represents a challenging problem. Our dataset, code and pretrained weights are available: https://github.com/sbelharbi/sr-caco-2.

Instance segmentation of neurons in volumetric light microscopy images of nervous systems enables groundbreaking research in neuroscience by facilitating joint functional and morphological analyses of neural circuits at cellular resolution. Yet said multi-neuron light microscopy data exhibits extremely challenging properties for the task of instance segmentation: Individual neurons have long-ranging, thin filamentous and widely branching morphologies, multiple neurons are tightly inter-weaved, and partial volume effects, uneven illumination and noise inherent to light microscopy severely impede local disentangling as well as long-range tracing of individual neurons. These properties reflect a current key challenge in machine learning research, namely to effectively capture long-range dependencies in the data. While respective methodological research is buzzing, to date methods are typically benchmarked on synthetic datasets. To address this gap, we release the FlyLight Instance Segmentation Benchmark (FISBe) dataset, the first publicly available multi-neuron light microscopy dataset with pixel-wise annotations. In addition, we define a set of instance segmentation metrics for benchmarking that we designed to be meaningful with regard to downstream analyses. Lastly, we provide three baselines to kick off a competition that we envision to both advance the field of machine learning regarding methodology for capturing long-range data dependencies, and facilitate scientific discovery in basic neuroscience.

Segmenting cells and tracking their motion over time is a common task in biomedical applications. However, predicting accurate instance-wise segmentation and cell motions from microscopy imagery remains a challenging task. Using microstructured environments for analyzing single cells in a constant flow of media adds additional complexity. While large-scale labeled microscopy datasets are available, we are not aware of any large-scale dataset, including both cells and microstructures. In this paper, we introduce the trapped yeast cell (TYC) dataset, a novel dataset for understanding instance-level semantics and motions of cells in microstructures. We release 105 dense annotated high-resolution brightfield microscopy images, including about 19k instance masks. We also release 261 curated video clips composed of 1293 high-resolution microscopy images to facilitate unsupervised understanding of cell motions and morphology. TYC offers ten times more instance annotations than the previously largest dataset, including cells and microstructures. Our effort also exceeds previous attempts in terms of microstructure variability, resolution, complexity, and capturing device (microscopy) variability. We facilitate a unified comparison on our novel dataset by introducing a standardized evaluation strategy. TYC and evaluation code are publicly available under CC BY 4.0 license.

Image outpainting is a very intriguing problem as the outside of a given image can be continuously filled by considering as the context of the image. This task has two main challenges. The first is to maintain the spatial consistency in contents of generated regions and the original input. The second is to generate a high-quality large image with a small amount of adjacent information. Conventional image outpainting methods generate inconsistent, blurry, and repeated pixels. To alleviate the difficulty of an outpainting problem, we propose a novel image outpainting method using bidirectional boundary region rearrangement. We rearrange the image to benefit from the image inpainting task by reflecting more directional information. The bidirectional boundary region rearrangement enables the generation of the missing region using bidirectional information similar to that of the image inpainting task, thereby generating the higher quality than the conventional methods using unidirectional information. Moreover, we use the edge map generator that considers images as original input with structural information and hallucinates the edges of unknown regions to generate the image. Our proposed method is compared with other state-of-the-art outpainting and inpainting methods both qualitatively and quantitatively. We further compared and evaluated them using BRISQUE, one of the No-Reference image quality assessment (IQA) metrics, to evaluate the naturalness of the output. The experimental results demonstrate that our method outperforms other methods and generates new images with 360{\deg}panoramic characteristics.

Diffusion-weighted magnetic resonance imaging (DW-MRI) can be used to characterise the microstructure of the nervous tissue, e.g. to delineate brain white matter connections in a non-invasive manner via fibre tracking. Magnetic Resonance Imaging (MRI) in high spatial resolution would play an important role in visualising such fibre tracts in a superior manner. However, obtaining an image of such resolution comes at the expense of longer scan time. Longer scan time can be associated with the increase of motion artefacts, due to the patient's psychological and physical conditions. Single Image Super-Resolution (SISR), a technique aimed to obtain high-resolution (HR) details from one single low-resolution (LR) input image, achieved with Deep Learning, is the focus of this study. Compared to interpolation techniques or sparse-coding algorithms, deep learning extracts prior knowledge from big datasets and produces superior MRI images from the low-resolution counterparts. In this research, a deep learning based super-resolution technique is proposed and has been applied for DW-MRI. Images from the IXI dataset have been used as the ground-truth and were artificially downsampled to simulate the low-resolution images. The proposed method has shown statistically significant improvement over the baselines and achieved an SSIM of 0.913pm0.045.

Cytology is essential for cancer diagnostics and screening due to its minimally invasive nature. However, the development of robust deep learning models for digital cytology is challenging due to the heterogeneity in staining and preparation methods of samples, differences across organs, and the limited availability of large, diverse, annotated datasets. Developing a task-specific model for every cytology application is impractical and non-cytology-specific foundation models struggle to generalize to tasks in this domain where the emphasis is on cell morphology. To address these challenges, we introduce CytoFM, the first cytology self-supervised foundation model. Using iBOT, a self-supervised Vision Transformer (ViT) training framework incorporating masked image modeling and self-distillation, we pretrain CytoFM on a diverse collection of cytology datasets to learn robust, transferable representations. We evaluate CytoFM on multiple downstream cytology tasks, including breast cancer classification and cell type identification, using an attention-based multiple instance learning framework. Our results demonstrate that CytoFM performs better on two out of three downstream tasks than existing foundation models pretrained on histopathology (UNI) or natural images (iBOT-Imagenet). Visualizations of learned representations demonstrate our model is able to attend to cytologically relevant features. Despite a small pre-training dataset, CytoFM's promising results highlight the ability of task-agnostic pre-training approaches to learn robust and generalizable features from cytology data.

Visual instruction tuning has made considerable strides in enhancing the capabilities of Large Multimodal Models (LMMs). However, existing open LMMs largely focus on single-image tasks, their applications to multi-image scenarios remains less explored. Additionally, prior LMM research separately tackles different scenarios, leaving it impossible to generalize cross scenarios with new emerging capabilities. To this end, we introduce LLaVA-NeXT-Interleave, which simultaneously tackles Multi-image, Multi-frame (video), Multi-view (3D), and Multi-patch (single-image) scenarios in LMMs. To enable these capabilities, we regard the interleaved data format as a general template and compile the M4-Instruct dataset with 1,177.6k samples, spanning 4 primary domains with 14 tasks and 41 datasets. We also curate the LLaVA-Interleave Bench to comprehensively evaluate the multi-image performance of LMMs. Through extensive experiments, LLaVA-NeXT-Interleave achieves leading results in multi-image, video, and 3D benchmarks, while maintaining the performance of single-image tasks. Besides, our model also exhibits several emerging capabilities, e.g., transferring tasks across different settings and modalities. Code is available at https://github.com/LLaVA-VL/LLaVA-NeXT

Automated diagnostic systems (ADS) have shown significant potential in the early detection of polyps during endoscopic examinations, thereby reducing the incidence of colorectal cancer. However, due to high annotation costs and strict privacy concerns, acquiring high-quality endoscopic images poses a considerable challenge in the development of ADS. Despite recent advancements in generating synthetic images for dataset expansion, existing endoscopic image generation algorithms failed to accurately generate the details of polyp boundary regions and typically required medical priors to specify plausible locations and shapes of polyps, which limited the realism and diversity of the generated images. To address these limitations, we present Polyp-Gen, the first full-automatic diffusion-based endoscopic image generation framework. Specifically, we devise a spatial-aware diffusion training scheme with a lesion-guided loss to enhance the structural context of polyp boundary regions. Moreover, to capture medical priors for the localization of potential polyp areas, we introduce a hierarchical retrieval-based sampling strategy to match similar fine-grained spatial features. In this way, our Polyp-Gen can generate realistic and diverse endoscopic images for building reliable ADS. Extensive experiments demonstrate the state-of-the-art generation quality, and the synthetic images can improve the downstream polyp detection task. Additionally, our Polyp-Gen has shown remarkable zero-shot generalizability on other datasets. The source code is available at https://github.com/CUHK-AIM-Group/Polyp-Gen.

Recent accelerations in multi-modal applications have been made possible with the plethora of image and text data available online. However, the scarcity of analogous data in the medical field, specifically in histopathology, has halted comparable progress. To enable similar representation learning for histopathology, we turn to YouTube, an untapped resource of videos, offering 1,087 hours of valuable educational histopathology videos from expert clinicians. From YouTube, we curate Quilt: a large-scale vision-language dataset consisting of 768,826 image and text pairs. Quilt was automatically curated using a mixture of models, including large language models, handcrafted algorithms, human knowledge databases, and automatic speech recognition. In comparison, the most comprehensive datasets curated for histopathology amass only around 200K samples. We combine Quilt with datasets from other sources, including Twitter, research papers, and the internet in general, to create an even larger dataset: Quilt-1M, with 1M paired image-text samples, marking it as the largest vision-language histopathology dataset to date. We demonstrate the value of Quilt-1M by fine-tuning a pre-trained CLIP model. Our model outperforms state-of-the-art models on both zero-shot and linear probing tasks for classifying new histopathology images across 13 diverse patch-level datasets of 8 different sub-pathologies and cross-modal retrieval tasks.

Star-convex shapes arise across bio-microscopy and radiology in the form of nuclei, nodules, metastases, and other units. Existing instance segmentation networks for such structures train on densely labeled instances for each dataset, which requires substantial and often impractical manual annotation effort. Further, significant reengineering or finetuning is needed when presented with new datasets and imaging modalities due to changes in contrast, shape, orientation, resolution, and density. We present AnyStar, a domain-randomized generative model that simulates synthetic training data of blob-like objects with randomized appearance, environments, and imaging physics to train general-purpose star-convex instance segmentation networks. As a result, networks trained using our generative model do not require annotated images from unseen datasets. A single network trained on our synthesized data accurately 3D segments C. elegans and P. dumerilii nuclei in fluorescence microscopy, mouse cortical nuclei in micro-CT, zebrafish brain nuclei in EM, and placental cotyledons in human fetal MRI, all without any retraining, finetuning, transfer learning, or domain adaptation. Code is available at https://github.com/neel-dey/AnyStar.

We introduce Vision as LoRA (VoRA), a novel paradigm for transforming an LLM into an MLLM. Unlike prevalent MLLM architectures that rely on external vision modules for vision encoding, VoRA internalizes visual capabilities by integrating vision-specific LoRA layers directly into the LLM. This design allows the added parameters to be seamlessly merged into the LLM during inference, eliminating structural complexity and minimizing computational overhead. Moreover, inheriting the LLM's ability of handling flexible context, VoRA can process inputs at arbitrary resolutions. To further strengthen VoRA's visual capabilities, we introduce a block-wise distillation method that transfers visual priors from a pre-trained ViT into the LoRA layers, effectively accelerating training by injecting visual knowledge. Additionally, we apply bi-directional attention masks to better capture the context information of an image. We successfully demonstrate that with additional pre-training data, VoRA can perform comparably with conventional encode-based MLLMs. All training data, codes, and model weights will be released at https://github.com/Hon-Wong/VoRA.

Most existing learning-based methods for solving imaging inverse problems can be roughly divided into two classes: iterative algorithms, such as plug-and-play and diffusion methods, that leverage pretrained denoisers, and unrolled architectures that are trained end-to-end for specific imaging problems. Iterative methods in the first class are computationally costly and often provide suboptimal reconstruction performance, whereas unrolled architectures are generally specific to a single inverse problem and require expensive training. In this work, we propose a novel non-iterative, lightweight architecture that incorporates knowledge about the forward operator (acquisition physics and noise parameters) without relying on unrolling. Our model is trained to solve a wide range of inverse problems beyond denoising, including deblurring, magnetic resonance imaging, computed tomography, inpainting, and super-resolution. The proposed model can be easily adapted to unseen inverse problems or datasets with a few fine-tuning steps (up to a few images) in a self-supervised way, without ground-truth references. Throughout a series of experiments, we demonstrate state-of-the-art performance from medical imaging to low-photon imaging and microscopy.

The translation of thermal infrared (TIR) images to visible light (VI) images presents a challenging task with potential applications spanning various domains such as TIR-VI image registration and fusion. Leveraging supplementary information derived from TIR image conversions can significantly enhance model performance and generalization across these applications. However, prevailing issues within this field include suboptimal image fidelity and limited model scalability. In this paper, we introduce an algorithm, LadleNet, based on the U-Net architecture. LadleNet employs a two-stage U-Net concatenation structure, augmented with skip connections and refined feature aggregation techniques, resulting in a substantial enhancement in model performance. Comprising 'Handle' and 'Bowl' modules, LadleNet's Handle module facilitates the construction of an abstract semantic space, while the Bowl module decodes this semantic space to yield mapped VI images. The Handle module exhibits extensibility by allowing the substitution of its network architecture with semantic segmentation networks, thereby establishing more abstract semantic spaces to bolster model performance. Consequently, we propose LadleNet+, which replaces LadleNet's Handle module with the pre-trained DeepLabv3+ network, thereby endowing the model with enhanced semantic space construction capabilities. The proposed method is evaluated and tested on the KAIST dataset, accompanied by quantitative and qualitative analyses. Compared to existing methodologies, our approach achieves state-of-the-art performance in terms of image clarity and perceptual quality. The source code will be made available at https://github.com/Ach-1914/LadleNet/tree/main/.

Although recent inpainting approaches have demonstrated significant improvements with deep neural networks, they still suffer from artifacts such as blunt structures and abrupt colors when filling in the missing regions. To address these issues, we propose an external-internal inpainting scheme with a monochromic bottleneck that helps image inpainting models remove these artifacts. In the external learning stage, we reconstruct missing structures and details in the monochromic space to reduce the learning dimension. In the internal learning stage, we propose a novel internal color propagation method with progressive learning strategies for consistent color restoration. Extensive experiments demonstrate that our proposed scheme helps image inpainting models produce more structure-preserved and visually compelling results.

Medical image segmentation methods downsample images for feature extraction and then upsample them to restore resolution for pixel-level predictions. In such a schema, upsample technique is vital in restoring information for better performance. However, existing upsample techniques leverage little information from downsampling paths. The local and detailed feature from the shallower layer such as boundary and tissue texture is particularly more important in medical segmentation compared with natural image segmentation. To this end, we propose a novel upsample approach for medical image segmentation, Window Attention Upsample (WAU), which upsamples features conditioned on local and detailed features from downsampling path in local windows by introducing attention decoders of Transformer. WAU could serve as a general upsample method and be incorporated into any segmentation model that possesses lateral connections. We first propose the Attention Upsample which consists of Attention Decoder (AD) and bilinear upsample. AD leverages pixel-level attention to model long-range dependency and global information for a better upsample. Bilinear upsample is introduced as the residual connection to complement the upsampled features. Moreover, considering the extensive memory and computation cost of pixel-level attention, we further design a window attention scheme to restrict attention computation in local windows instead of the global range. We evaluate our method (WAU) on classic U-Net structure with lateral connections and achieve state-of-the-art performance on Synapse multi-organ segmentation, Medical Segmentation Decathlon (MSD) Brain, and Automatic Cardiac Diagnosis Challenge (ACDC) datasets. We also validate the effectiveness of our method on multiple classic architectures and achieve consistent improvement.

There is large consent that successful training of deep networks requires many thousand annotated training samples. In this paper, we present a network and training strategy that relies on the strong use of data augmentation to use the available annotated samples more efficiently. The architecture consists of a contracting path to capture context and a symmetric expanding path that enables precise localization. We show that such a network can be trained end-to-end from very few images and outperforms the prior best method (a sliding-window convolutional network) on the ISBI challenge for segmentation of neuronal structures in electron microscopic stacks. Using the same network trained on transmitted light microscopy images (phase contrast and DIC) we won the ISBI cell tracking challenge 2015 in these categories by a large margin. Moreover, the network is fast. Segmentation of a 512x512 image takes less than a second on a recent GPU. The full implementation (based on Caffe) and the trained networks are available at http://lmb.informatik.uni-freiburg.de/people/ronneber/u-net .

Clinical routine and retrospective cohorts commonly include multi-parametric Magnetic Resonance Imaging; however, they are mostly acquired in different anisotropic 2D views due to signal-to-noise-ratio and scan-time constraints. Thus acquired views suffer from poor out-of-plane resolution and affect downstream volumetric image analysis that typically requires isotropic 3D scans. Combining different views of multi-contrast scans into high-resolution isotropic 3D scans is challenging due to the lack of a large training cohort, which calls for a subject-specific framework. This work proposes a novel solution to this problem leveraging Implicit Neural Representations (INR). Our proposed INR jointly learns two different contrasts of complementary views in a continuous spatial function and benefits from exchanging anatomical information between them. Trained within minutes on a single commodity GPU, our model provides realistic super-resolution across different pairs of contrasts in our experiments with three datasets. Using Mutual Information (MI) as a metric, we find that our model converges to an optimum MI amongst sequences, achieving anatomically faithful reconstruction. Code is available at: https://github.com/jqmcginnis/multi_contrast_inr/

Vision foundation models (FMs) are accelerating the development of digital pathology algorithms and transforming biomedical research. These models learn, in a self-supervised manner, to represent histological features in highly heterogeneous tiles extracted from whole-slide images (WSIs) of real-world patient samples. The performance of these FMs is significantly influenced by the size, diversity, and balance of the pre-training data. However, data selection has been primarily guided by expert knowledge at the WSI level, focusing on factors such as disease classification and tissue types, while largely overlooking the granular details available at the tile level. In this paper, we investigate the potential of unsupervised automatic data curation at the tile-level, taking into account 350 million tiles. Specifically, we apply hierarchical clustering trees to pre-extracted tile embeddings, allowing us to sample balanced datasets uniformly across the embedding space of the pretrained FM. We further identify these datasets are subject to a trade-off between size and balance, potentially compromising the quality of representations learned by FMs, and propose tailored batch sampling strategies to mitigate this effect. We demonstrate the effectiveness of our method through improved performance on a diverse range of clinically relevant downstream tasks.

An image, especially with high-resolution, typically consists of numerous visual elements, ranging from dominant large objects to fine-grained detailed objects. When perceiving such images, multimodal large language models~(MLLMs) face limitations due to the restricted input resolution of the pretrained vision encoder and the cluttered, dense context of the image, resulting in a focus on primary objects while easily overlooking detailed ones. In this paper, we propose Zoom Eye, a tree search algorithm designed to navigate the hierarchical and visual nature of images to capture relevant information. Zoom Eye conceptualizes an image as a tree, with each children node representing a zoomed sub-patch of the parent node and the root represents the overall image. Moreover, Zoom Eye is model-agnostic and training-free, so it enables any MLLMs to simulate human zooming actions by searching along the image tree from root to leaf nodes, seeking out pertinent information, and accurately responding to related queries. We experiment on a series of elaborate high-resolution benchmarks and the results demonstrate that Zoom Eye not only consistently improves the performance of a series base MLLMs with large margin~(e.g., LLaVA-v1.5-7B increases by 34.57\% on V^* Bench and 17.88\% on HR-Bench), but also enables small 7B MLLMs to outperform strong large models such as GPT-4o. Our code is available at https://github.com/om-ai-lab/ZoomEye{https://github.com/om-ai-lab/ZoomEye}.

Mitotic figure (MF) detection in histopathology images is challenging due to large variations in slide scanners, staining protocols, tissue types, and the presence of artifacts. This paper presents a collection of training techniques - a bag of tricks - that enable robust, real-time MF detection across diverse domains. We build on the efficient RTMDet single stage object detector to achieve high inference speed suitable for clinical deployment. Our method addresses scanner variability and tumor heterogeneity via extensive multi-domain training data, balanced sampling, and careful augmentation. Additionally, we employ targeted, hard negative mining on necrotic and debris tissue to reduce false positives. In a grouped 5-fold cross-validation across multiple MF datasets, our model achieves an F1 score between 0.78 and 0.84. On the preliminary test set of the MItosis DOmain Generalization (MIDOG) 2025 challenge, our single-stage RTMDet-S based approach reaches an F1 of 0.81, outperforming larger models and demonstrating adaptability to new, unfamiliar domains. The proposed solution offers a practical trade-off between accuracy and speed, making it attractive for real-world clinical adoption.

Medical image segmentation allows quantifying target structure size and shape, aiding in disease diagnosis, prognosis, surgery planning, and comprehension.Building upon recent advancements in foundation Vision-Language Models (VLMs) from natural image-text pairs, several studies have proposed adapting them to Vision-Language Segmentation Models (VLSMs) that allow using language text as an additional input to segmentation models. Introducing auxiliary information via text with human-in-the-loop prompting during inference opens up unique opportunities, such as open vocabulary segmentation and potentially more robust segmentation models against out-of-distribution data. Although transfer learning from natural to medical images has been explored for image-only segmentation models, the joint representation of vision-language in segmentation problems remains underexplored. This study introduces the first systematic study on transferring VLSMs to 2D medical images, using carefully curated 11 datasets encompassing diverse modalities and insightful language prompts and experiments. Our findings demonstrate that although VLSMs show competitive performance compared to image-only models for segmentation after finetuning in limited medical image datasets, not all VLSMs utilize the additional information from language prompts, with image features playing a dominant role. While VLSMs exhibit enhanced performance in handling pooled datasets with diverse modalities and show potential robustness to domain shifts compared to conventional segmentation models, our results suggest that novel approaches are required to enable VLSMs to leverage the various auxiliary information available through language prompts. The code and datasets are available at https://github.com/naamiinepal/medvlsm.

Recent advancements in Digital Pathology (DP), particularly through artificial intelligence and Foundation Models, have underscored the importance of large-scale, diverse, and richly annotated datasets. Despite their critical role, publicly available Whole Slide Image (WSI) datasets often lack sufficient scale, tissue diversity, and comprehensive clinical metadata, limiting the robustness and generalizability of AI models. In response, we introduce the HISTAI dataset, a large, multimodal, open-access WSI collection comprising over 60,000 slides from various tissue types. Each case in the HISTAI dataset is accompanied by extensive clinical metadata, including diagnosis, demographic information, detailed pathological annotations, and standardized diagnostic coding. The dataset aims to fill gaps identified in existing resources, promoting innovation, reproducibility, and the development of clinically relevant computational pathology solutions. The dataset can be accessed at https://github.com/HistAI/HISTAI.

Recent advancements in Large Vision-Language Models built upon Large Language Models have established aligning visual features with LLM representations as the dominant paradigm. However, inherited LLM architectural designs introduce suboptimal characteristics for multimodal processing. First, LVLMs exhibit a bimodal distribution in attention allocation, leading to the progressive neglect of middle visual content as context expands. Second, conventional positional encoding schemes fail to preserve vital 2D structural relationships when processing dynamic high-resolution images. To address these limitations, we propose CoMemo - a dual-path architecture that combines a Context image path with an image Memory path for visual processing, effectively alleviating visual information neglect. Additionally, we introduce RoPE-DHR, a novel positional encoding mechanism that employs thumbnail-based positional aggregation to maintain 2D spatial awareness while mitigating remote decay in extended sequences. Evaluations across seven benchmarks,including long-context comprehension, multi-image reasoning, and visual question answering, demonstrate CoMemo's superior performance compared to conventional LVLM architectures. Project page is available at https://lalbj.github.io/projects/CoMemo/.

Tissue phenotyping is a fundamental task in learning objective characterizations of histopathologic biomarkers within the tumor-immune microenvironment in cancer pathology. However, whole-slide imaging (WSI) is a complex computer vision in which: 1) WSIs have enormous image resolutions with precludes large-scale pixel-level efforts in data curation, and 2) diversity of morphological phenotypes results in inter- and intra-observer variability in tissue labeling. To address these limitations, current efforts have proposed using pretrained image encoders (transfer learning from ImageNet, self-supervised pretraining) in extracting morphological features from pathology, but have not been extensively validated. In this work, we conduct a search for good representations in pathology by training a variety of self-supervised models with validation on a variety of weakly-supervised and patch-level tasks. Our key finding is in discovering that Vision Transformers using DINO-based knowledge distillation are able to learn data-efficient and interpretable features in histology images wherein the different attention heads learn distinct morphological phenotypes. We make evaluation code and pretrained weights publicly-available at: https://github.com/Richarizardd/Self-Supervised-ViT-Path.

High-content screening (HCS) assays based on high-throughput microscopy techniques such as Cell Painting have enabled the interrogation of cells' morphological responses to perturbations at an unprecedented scale. The collection of such data promises to facilitate a better understanding of the relationships between different perturbations and their effects on cellular state. Towards achieving this goal, recent advances in cross-modal contrastive learning could, in theory, be leveraged to learn a unified latent space that aligns perturbations with their corresponding morphological effects. However, the application of such methods to HCS data is not straightforward due to substantial differences in the semantics of Cell Painting images compared to natural images, and the difficulty of representing different classes of perturbations (e.g., small molecule vs CRISPR gene knockout) in a single latent space. In response to these challenges, here we introduce CellCLIP, a cross-modal contrastive learning framework for HCS data. CellCLIP leverages pre-trained image encoders coupled with a novel channel encoding scheme to better capture relationships between different microscopy channels in image embeddings, along with natural language encoders for representing perturbations. Our framework outperforms current open-source models, demonstrating the best performance in both cross-modal retrieval and biologically meaningful downstream tasks while also achieving significant reductions in computation time.

Medical images and radiology reports are crucial for diagnosing medical conditions, highlighting the importance of quantitative analysis for clinical decision-making. However, the diversity and cross-source heterogeneity of these data challenge the generalizability of current data-mining methods. Multimodal large language models (MLLMs) have recently transformed many domains, significantly affecting the medical field. Notably, Gemini-Vision-series (Gemini) and GPT-4-series (GPT-4) models have epitomized a paradigm shift in Artificial General Intelligence (AGI) for computer vision, showcasing their potential in the biomedical domain. In this study, we evaluated the performance of the Gemini, GPT-4, and 4 popular large models for an exhaustive evaluation across 14 medical imaging datasets, including 5 medical imaging categories (dermatology, radiology, dentistry, ophthalmology, and endoscopy), and 3 radiology report datasets. The investigated tasks encompass disease classification, lesion segmentation, anatomical localization, disease diagnosis, report generation, and lesion detection. Our experimental results demonstrated that Gemini-series models excelled in report generation and lesion detection but faces challenges in disease classification and anatomical localization. Conversely, GPT-series models exhibited proficiency in lesion segmentation and anatomical localization but encountered difficulties in disease diagnosis and lesion detection. Additionally, both the Gemini series and GPT series contain models that have demonstrated commendable generation efficiency. While both models hold promise in reducing physician workload, alleviating pressure on limited healthcare resources, and fostering collaboration between clinical practitioners and artificial intelligence technologies, substantial enhancements and comprehensive validations remain imperative before clinical deployment.

Several medical Multimodal Large Languange Models (MLLMs) have been developed to address tasks involving visual images with textual instructions across various medical modalities, achieving impressive results. Most current medical generalist models are region-agnostic, treating the entire image as a holistic representation. However, they struggle to identify which specific regions they are focusing on when generating a sentence. To mimic the behavior of doctors, who typically begin by reviewing the entire image before concentrating on specific regions for a thorough evaluation, we aim to enhance the capability of medical MLLMs in understanding anatomical regions within entire medical scans. To achieve it, we first formulate Region-Centric tasks and construct a large-scale dataset, MedRegInstruct, to incorporate regional information into training. Combining our collected dataset with other medical multimodal corpora for training, we propose a Region-Aware medical MLLM, MedRegA, which is the first bilingual generalist medical AI system to simultaneously handle image-level and region-level medical vision-language tasks across a broad range of modalities. Our MedRegA not only enables three region-centric tasks, but also achieves the best performance for visual question answering, report generation and medical image classification over 8 modalities, showcasing significant versatility. Experiments demonstrate that our model can not only accomplish powerful performance across various medical vision-language tasks in bilingual settings, but also recognize and detect structures in multimodal medical scans, boosting the interpretability and user interactivity of medical MLLMs. Our project page is https://medrega.github.io.

Once deployed, medical image analysis methods are often faced with unexpected image corruptions and noise perturbations. These unknown covariate shifts present significant challenges to deep learning based methods trained on "clean" images. This often results in unreliable predictions and poorly calibrated confidence, hence hindering clinical applicability. While recent methods have been developed to address specific issues such as confidence calibration or adversarial robustness, no single framework effectively tackles all these challenges simultaneously. To bridge this gap, we propose LaDiNE, a novel ensemble learning method combining the robustness of Vision Transformers with diffusion-based generative models for improved reliability in medical image classification. Specifically, transformer encoder blocks are used as hierarchical feature extractors that learn invariant features from images for each ensemble member, resulting in features that are robust to input perturbations. In addition, diffusion models are used as flexible density estimators to estimate member densities conditioned on the invariant features, leading to improved modeling of complex data distributions while retaining properly calibrated confidence. Extensive experiments on tuberculosis chest X-rays and melanoma skin cancer datasets demonstrate that LaDiNE achieves superior performance compared to a wide range of state-of-the-art methods by simultaneously improving prediction accuracy and confidence calibration under unseen noise, adversarial perturbations, and resolution degradation.

The field of computational pathology has recently seen rapid advances driven by the development of modern vision foundation models (FMs), typically trained on vast collections of pathology images. Recent studies demonstrate that increasing the training data set and model size and integrating domain-specific image processing techniques can significantly enhance the model's performance on downstream tasks. Building on these insights, our work incorporates several recent modifications to the standard DINOv2 framework from the literature to optimize the training of pathology FMs. We also apply a post-training procedure for fine-tuning models on higher-resolution images to further enrich the information encoded in the embeddings. We present three novel pathology FMs trained on up to two orders of magnitude fewer WSIs than those used to train other state-of-the-art FMs while demonstrating a comparable or superior performance on downstream tasks. Even the model trained on TCGA alone (12k WSIs) outperforms most existing FMs and, on average, matches Virchow2, the second-best FM published to date. This suggests that there still remains a significant potential for further improving the models and algorithms used to train pathology FMs to take full advantage of the vast data collections.

Recent advances in multi-modal algorithms have driven and been driven by the increasing availability of large image-text datasets, leading to significant strides in various fields, including computational pathology. However, in most existing medical image-text datasets, the text typically provides high-level summaries that may not sufficiently describe sub-tile regions within a large pathology image. For example, an image might cover an extensive tissue area containing cancerous and healthy regions, but the accompanying text might only specify that this image is a cancer slide, lacking the nuanced details needed for in-depth analysis. In this study, we introduce STimage-1K4M, a novel dataset designed to bridge this gap by providing genomic features for sub-tile images. STimage-1K4M contains 1,149 images derived from spatial transcriptomics data, which captures gene expression information at the level of individual spatial spots within a pathology image. Specifically, each image in the dataset is broken down into smaller sub-image tiles, with each tile paired with 15,000-30,000 dimensional gene expressions. With 4,293,195 pairs of sub-tile images and gene expressions, STimage-1K4M offers unprecedented granularity, paving the way for a wide range of advanced research in multi-modal data analysis an innovative applications in computational pathology, and beyond.

Medical image analysis is essential to clinical diagnosis and treatment, which is increasingly supported by multi-modal large language models (MLLMs). However, previous research has primarily focused on 2D medical images, leaving 3D images under-explored, despite their richer spatial information. This paper aims to advance 3D medical image analysis with MLLMs. To this end, we present a large-scale 3D multi-modal medical dataset, M3D-Data, comprising 120K image-text pairs and 662K instruction-response pairs specifically tailored for various 3D medical tasks, such as image-text retrieval, report generation, visual question answering, positioning, and segmentation. Additionally, we propose M3D-LaMed, a versatile multi-modal large language model for 3D medical image analysis. Furthermore, we introduce a new 3D multi-modal medical benchmark, M3D-Bench, which facilitates automatic evaluation across eight tasks. Through comprehensive evaluation, our method proves to be a robust model for 3D medical image analysis, outperforming existing solutions. All code, data, and models are publicly available at: https://github.com/BAAI-DCAI/M3D.

The rapid identification and accurate diagnosis of breast cancer, known as the killer of women, have become greatly significant for those patients. Numerous breast cancer histopathological image classification methods have been proposed. But they still suffer from two problems. (1) These methods can only hand high-resolution (HR) images. However, the low-resolution (LR) images are often collected by the digital slide scanner with limited hardware conditions. Compared with HR images, LR images often lose some key features like texture, which deeply affects the accuracy of diagnosis. (2) The existing methods have fixed receptive fields, so they can not extract and fuse multi-scale features well for images with different magnification factors. To fill these gaps, we present a Single Histopathological Image Super-Resolution Classification network (SHISRCNet), which consists of two modules: Super-Resolution (SR) and Classification (CF) modules. SR module reconstructs LR images into SR ones. CF module extracts and fuses the multi-scale features of SR images for classification. In the training stage, we introduce HR images into the CF module to enhance SHISRCNet's performance. Finally, through the joint training of these two modules, super-resolution and classified of LR images are integrated into our model. The experimental results demonstrate that the effects of our method are close to the SOTA methods with taking HR images as inputs.

Vision-language pre-training (VLP) models have shown significant advancements in the medical domain. Yet, most VLP models align raw reports to images at a very coarse level, without modeling fine-grained relationships between anatomical and pathological concepts outlined in reports and the corresponding semantic counterparts in images. To address this problem, we propose a Medical Dual-Stream Language-Image Pre-training (MeDSLIP) framework. Specifically, MeDSLIP establishes vision-language fine-grained alignments via disentangling visual and textual representations into anatomy-relevant and pathology-relevant streams. Moreover, a novel vision-language Prototypical Contr-astive Learning (ProtoCL) method is adopted in MeDSLIP to enhance the alignment within the anatomical and pathological streams. MeDSLIP further employs cross-stream Intra-image Contrastive Learning (ICL) to ensure the consistent coexistence of paired anatomical and pathological concepts within the same image. Such a cross-stream regularization encourages the model to exploit the synchrony between two streams for a more comprehensive representation learning. MeDSLIP is evaluated under zero-shot and supervised fine-tuning settings on three public datasets: NIH CXR14, RSNA Pneumonia, and SIIM-ACR Pneumothorax. Under these settings, MeDSLIP outperforms six leading CNN-based models on classification, grounding, and segmentation tasks.

Task-specific deep learning models in histopathology offer promising opportunities for improving diagnosis, clinical research, and precision medicine. However, development of such models is often limited by availability of high-quality data. Foundation models in histopathology that learn general representations across a wide range of tissue types, diagnoses, and magnifications offer the potential to reduce the data, compute, and technical expertise necessary to develop task-specific deep learning models with the required level of model performance. In this work, we describe the development and evaluation of foundation models for histopathology via self-supervised learning (SSL). We first establish a diverse set of benchmark tasks involving 17 unique tissue types and 12 unique cancer types and spanning different optimal magnifications and task types. Next, we use this benchmark to explore and evaluate histopathology-specific SSL methods followed by further evaluation on held out patch-level and weakly supervised tasks. We found that standard SSL methods thoughtfully applied to histopathology images are performant across our benchmark tasks and that domain-specific methodological improvements can further increase performance. Our findings reinforce the value of using domain-specific SSL methods in pathology, and establish a set of high quality foundation models to enable further research across diverse applications.

This paper presents an annotated dataset of brain MRI images designed to advance the field of brain symmetry study. Magnetic resonance imaging (MRI) has gained interest in analyzing brain symmetry in neonatal infants, and challenges remain due to the vast size differences between fetal and adult brains. Classification methods for brain structural MRI use scales and visual cues to assess hemisphere symmetry, which can help diagnose neonatal patients by comparing hemispheres and anatomical regions of interest in the brain. Using the Developing Human Connectome Project dataset, this work presents a dataset comprising cerebral images extracted as slices across selected portions of interest for clinical evaluation . All the extracted images are annotated with the brain's midline. All the extracted images are annotated with the brain's midline. From the assumption that a decrease in symmetry is directly related to possible clinical pathologies, the dataset can contribute to a more precise diagnosis because it can be used to train deep learning model application in neonatal cerebral MRI anomaly detection from postnatal infant scans thanks to computer vision. Such models learn to identify and classify anomalies by identifying potential asymmetrical patterns in medical MRI images. Furthermore, this dataset can contribute to the research and development of methods using the relative symmetry of the two brain hemispheres for crucial diagnosis and treatment planning.

The chest X-ray is one of the most commonly accessible radiological examinations for screening and diagnosis of many lung diseases. A tremendous number of X-ray imaging studies accompanied by radiological reports are accumulated and stored in many modern hospitals' Picture Archiving and Communication Systems (PACS). On the other side, it is still an open question how this type of hospital-size knowledge database containing invaluable imaging informatics (i.e., loosely labeled) can be used to facilitate the data-hungry deep learning paradigms in building truly large-scale high precision computer-aided diagnosis (CAD) systems. In this paper, we present a new chest X-ray database, namely "ChestX-ray8", which comprises 108,948 frontal-view X-ray images of 32,717 unique patients with the text-mined eight disease image labels (where each image can have multi-labels), from the associated radiological reports using natural language processing. Importantly, we demonstrate that these commonly occurring thoracic diseases can be detected and even spatially-located via a unified weakly-supervised multi-label image classification and disease localization framework, which is validated using our proposed dataset. Although the initial quantitative results are promising as reported, deep convolutional neural network based "reading chest X-rays" (i.e., recognizing and locating the common disease patterns trained with only image-level labels) remains a strenuous task for fully-automated high precision CAD systems. Data download link: https://nihcc.app.box.com/v/ChestXray-NIHCC

Histopathological cancer diagnostics has become more complex, and the increasing number of biopsies is a challenge for most pathology laboratories. Thus, development of automatic methods for evaluation of histopathological cancer sections would be of value. In this study, we used 624 whole slide images (WSIs) of breast cancer from a Norwegian cohort. We propose a cascaded convolutional neural network design, called H2G-Net, for semantic segmentation of gigapixel histopathological images. The design involves a detection stage using a patch-wise method, and a refinement stage using a convolutional autoencoder. To validate the design, we conducted an ablation study to assess the impact of selected components in the pipeline on tumour segmentation. Guiding segmentation, using hierarchical sampling and deep heatmap refinement, proved to be beneficial when segmenting the histopathological images. We found a significant improvement when using a refinement network for postprocessing the generated tumour segmentation heatmaps. The overall best design achieved a Dice score of 0.933 on an independent test set of 90 WSIs. The design outperformed single-resolution approaches, such as cluster-guided, patch-wise high-resolution classification using MobileNetV2 (0.872) and a low-resolution U-Net (0.874). In addition, segmentation on a representative x400 WSI took ~58 seconds, using only the CPU. The findings demonstrate the potential of utilizing a refinement network to improve patch-wise predictions. The solution is efficient and does not require overlapping patch inference or ensembling. Furthermore, we showed that deep neural networks can be trained using a random sampling scheme that balances on multiple different labels simultaneously, without the need of storing patches on disk. Future work should involve more efficient patch generation and sampling, as well as improved clustering.

Self-supervised learning (SSL) has recently achieved promising performance for 3D medical image analysis tasks. Most current methods follow existing SSL paradigm originally designed for photographic or natural images, which cannot explicitly and thoroughly exploit the intrinsic similar anatomical structures across varying medical images. This may in fact degrade the quality of learned deep representations by maximizing the similarity among features containing spatial misalignment information and different anatomical semantics. In this work, we propose a new self-supervised learning framework, namely Alice, that explicitly fulfills Anatomical invariance modeling and semantic alignment via elaborately combining discriminative and generative objectives. Alice introduces a new contrastive learning strategy which encourages the similarity between views that are diversely mined but with consistent high-level semantics, in order to learn invariant anatomical features. Moreover, we design a conditional anatomical feature alignment module to complement corrupted embeddings with globally matched semantics and inter-patch topology information, conditioned by the distribution of local image content, which permits to create better contrastive pairs. Our extensive quantitative experiments on three 3D medical image analysis tasks demonstrate and validate the performance superiority of Alice, surpassing the previous best SSL counterpart methods and showing promising ability for united representation learning. Codes are available at https://github.com/alibaba-damo-academy/alice.

Sparse autoencoders have recently produced dictionaries of high-dimensional vectors corresponding to the universe of concepts represented by large language models. We find that this concept universe has interesting structure at three levels: 1) The "atomic" small-scale structure contains "crystals" whose faces are parallelograms or trapezoids, generalizing well-known examples such as (man-woman-king-queen). We find that the quality of such parallelograms and associated function vectors improves greatly when projecting out global distractor directions such as word length, which is efficiently done with linear discriminant analysis. 2) The "brain" intermediate-scale structure has significant spatial modularity; for example, math and code features form a "lobe" akin to functional lobes seen in neural fMRI images. We quantify the spatial locality of these lobes with multiple metrics and find that clusters of co-occurring features, at coarse enough scale, also cluster together spatially far more than one would expect if feature geometry were random. 3) The "galaxy" scale large-scale structure of the feature point cloud is not isotropic, but instead has a power law of eigenvalues with steepest slope in middle layers. We also quantify how the clustering entropy depends on the layer.

Exploiting spatial-angular correlation is crucial to light field (LF) image super-resolution (SR), but is highly challenging due to its non-local property caused by the disparities among LF images. Although many deep neural networks (DNNs) have been developed for LF image SR and achieved continuously improved performance, existing methods cannot well leverage the long-range spatial-angular correlation and thus suffer a significant performance drop when handling scenes with large disparity variations. In this paper, we propose a simple yet effective method to learn the non-local spatial-angular correlation for LF image SR. In our method, we adopt the epipolar plane image (EPI) representation to project the 4D spatial-angular correlation onto multiple 2D EPI planes, and then develop a Transformer network with repetitive self-attention operations to learn the spatial-angular correlation by modeling the dependencies between each pair of EPI pixels. Our method can fully incorporate the information from all angular views while achieving a global receptive field along the epipolar line. We conduct extensive experiments with insightful visualizations to validate the effectiveness of our method. Comparative results on five public datasets show that our method not only achieves state-of-the-art SR performance, but also performs robust to disparity variations. Code is publicly available at https://github.com/ZhengyuLiang24/EPIT.

The science of fractography revolves around the correlation between topographic characteristics of the fracture surface and the mechanisms and external conditions leading to their creation. While being a topic of investigation for centuries, it has remained mostly qualitative to date. A quantitative analysis of fracture surfaces is of prime interest for both the scientific community and the industrial sector, bearing the potential for improved understanding on the mechanisms controlling the fracture process and at the same time assessing the reliability of computational models currently being used for material design. With new advances in the field of image analysis, and specifically with machine learning tools becoming more accessible and reliable, it is now feasible to automate the process of extracting meaningful information from fracture surface images. Here, we propose a method of identifying and quantifying the relative appearance of intergranular and transgranular fracture events from scanning electron microscope images. The newly proposed method is based on a convolutional neural network algorithm for semantic segmentation. The proposed method is extensively tested and evaluated against two ceramic material systems (Al_2O_3,MgAl_2O_4) and shows high prediction accuracy, despite being trained on only one material system (MgAl_2O_4). While here attention is focused on brittle fracture characteristics, the method can be easily extended to account for other fracture morphologies, such as dimples, fatigue striations, etc.

Breast-conserving surgery (BCS) aims to completely remove malignant lesions while maximizing healthy tissue preservation. Intraoperative margin assessment is essential to achieve a balance between thorough cancer resection and tissue conservation. A deep ultraviolet fluorescence scanning microscope (DUV-FSM) enables rapid acquisition of whole surface images (WSIs) for excised tissue, providing contrast between malignant and normal tissues. However, breast cancer classification with DUV WSIs is challenged by high resolutions and complex histopathological features. This study introduces a DUV WSI classification framework using a patch-level vision transformer (ViT) model, capturing local and global features. Grad-CAM++ saliency weighting highlights relevant spatial regions, enhances result interpretability, and improves diagnostic accuracy for benign and malignant tissue classification. A comprehensive 5-fold cross-validation demonstrates the proposed approach significantly outperforms conventional deep learning methods, achieving a classification accuracy of 98.33%.

The field of Machine Learning, a subset of Artificial Intelligence, has led to remarkable advancements in many areas, including medicine. Machine Learning algorithms require large datasets to train computer models successfully. Although there are medical image datasets available, more image datasets are needed from a variety of medical entities, especially cancer pathology. Even more scarce are ML-ready image datasets. To address this need, we created an image dataset (LC25000) with 25,000 color images in 5 classes. Each class contains 5,000 images of the following histologic entities: colon adenocarcinoma, benign colonic tissue, lung adenocarcinoma, lung squamous cell carcinoma, and benign lung tissue. All images are de-identified, HIPAA compliant, validated, and freely available for download to AI researchers.

Despite the progress made by multimodal large language models (MLLMs) in computational pathology, they remain limited by a predominant focus on patch-level analysis, missing essential contextual information at the whole-slide level. The lack of large-scale instruction datasets and the gigapixel scale of whole slide images (WSIs) pose significant developmental challenges. In this paper, we present SlideChat, the first vision-language assistant capable of understanding gigapixel whole-slide images, exhibiting excellent multimodal conversational capability and response complex instruction across diverse pathology scenarios. To support its development, we created SlideInstruction, the largest instruction-following dataset for WSIs consisting of 4.2K WSI captions and 176K VQA pairs with multiple categories. Furthermore, we propose SlideBench, a multimodal benchmark that incorporates captioning and VQA tasks to assess SlideChat's capabilities in varied clinical settings such as microscopy, diagnosis. Compared to both general and specialized MLLMs, SlideChat exhibits exceptional capabilities achieving state-of-the-art performance on 18 of 22 tasks. For example, it achieved an overall accuracy of 81.17% on SlideBench-VQA (TCGA), and 54.15% on SlideBench-VQA (BCNB). We will fully release SlideChat, SlideInstruction and SlideBench as open-source resources to facilitate research and development in computational pathology.

Single-view depth estimation can be remarkably effective if there is enough ground-truth depth data for supervised training. However, there are scenarios, especially in medicine in the case of endoscopies, where such data cannot be obtained. In such cases, multi-view self-supervision and synthetic-to-real transfer serve as alternative approaches, however, with a considerable performance reduction in comparison to supervised case. Instead, we propose a single-view self-supervised method that achieves a performance similar to the supervised case. In some medical devices, such as endoscopes, the camera and light sources are co-located at a small distance from the target surfaces. Thus, we can exploit that, for any given albedo and surface orientation, pixel brightness is inversely proportional to the square of the distance to the surface, providing a strong single-view self-supervisory signal. In our experiments, our self-supervised models deliver accuracies comparable to those of fully supervised ones, while being applicable without depth ground-truth data.

Transforming two-dimensional (2D) images into three-dimensional (3D) volumes is a well-known yet challenging problem for the computer vision community. In the medical domain, a few previous studies attempted to convert two or more input radiographs into computed tomography (CT) volumes. Following their effort, we introduce a diffusion model-based technology that can rotate the anatomical content of any input radiograph in 3D space, potentially enabling the visualization of the entire anatomical content of the radiograph from any viewpoint in 3D. Similar to previous studies, we used CT volumes to create Digitally Reconstructed Radiographs (DRRs) as the training data for our model. However, we addressed two significant limitations encountered in previous studies: 1. We utilized conditional diffusion models with classifier-free guidance instead of Generative Adversarial Networks (GANs) to achieve higher mode coverage and improved output image quality, with the only trade-off being slower inference time, which is often less critical in medical applications; and 2. We demonstrated that the unreliable output of style transfer deep learning (DL) models, such as Cycle-GAN, to transfer the style of actual radiographs to DRRs could be replaced with a simple yet effective training transformation that randomly changes the pixel intensity histograms of the input and ground-truth imaging data during training. This transformation makes the diffusion model agnostic to any distribution variations of the input data pixel intensity, enabling the reliable training of a DL model on input DRRs and applying the exact same model to conventional radiographs (or DRRs) during inference.

We propose to restore old photos that suffer from severe degradation through a deep learning approach. Unlike conventional restoration tasks that can be solved through supervised learning, the degradation in real photos is complex and the domain gap between synthetic images and real old photos makes the network fail to generalize. Therefore, we propose a novel triplet domain translation network by leveraging real photos along with massive synthetic image pairs. Specifically, we train two variational autoencoders (VAEs) to respectively transform old photos and clean photos into two latent spaces. And the translation between these two latent spaces is learned with synthetic paired data. This translation generalizes well to real photos because the domain gap is closed in the compact latent space. Besides, to address multiple degradations mixed in one old photo, we design a global branch with apartial nonlocal block targeting to the structured defects, such as scratches and dust spots, and a local branch targeting to the unstructured defects, such as noises and blurriness. Two branches are fused in the latent space, leading to improved capability to restore old photos from multiple defects. Furthermore, we apply another face refinement network to recover fine details of faces in the old photos, thus ultimately generating photos with enhanced perceptual quality. With comprehensive experiments, the proposed pipeline demonstrates superior performance over state-of-the-art methods as well as existing commercial tools in terms of visual quality for old photos restoration.

Humans can develop internal world models that encode common sense knowledge, telling them how the world works and predicting the consequences of their actions. This concept has emerged as a promising direction for establishing general-purpose machine-learning models in recent preliminary works, e.g., for visual representation learning. In this paper, we present CheXWorld, the first effort towards a self-supervised world model for radiographic images. Specifically, our work develops a unified framework that simultaneously models three aspects of medical knowledge essential for qualified radiologists, including 1) local anatomical structures describing the fine-grained characteristics of local tissues (e.g., architectures, shapes, and textures); 2) global anatomical layouts describing the global organization of the human body (e.g., layouts of organs and skeletons); and 3) domain variations that encourage CheXWorld to model the transitions across different appearance domains of radiographs (e.g., varying clarity, contrast, and exposure caused by collecting radiographs from different hospitals, devices, or patients). Empirically, we design tailored qualitative and quantitative analyses, revealing that CheXWorld successfully captures these three dimensions of medical knowledge. Furthermore, transfer learning experiments across eight medical image classification and segmentation benchmarks showcase that CheXWorld significantly outperforms existing SSL methods and large-scale medical foundation models. Code & pre-trained models are available at https://github.com/LeapLabTHU/CheXWorld.

Due to the necessity for precise treatment planning, the use of panoramic X-rays to identify different dental diseases has tremendously increased. Although numerous ML models have been developed for the interpretation of panoramic X-rays, there has not been an end-to-end model developed that can identify problematic teeth with dental enumeration and associated diagnoses at the same time. To develop such a model, we structure the three distinct types of annotated data hierarchically following the FDI system, the first labeled with only quadrant, the second labeled with quadrant-enumeration, and the third fully labeled with quadrant-enumeration-diagnosis. To learn from all three hierarchies jointly, we introduce a novel diffusion-based hierarchical multi-label object detection framework by adapting a diffusion-based method that formulates object detection as a denoising diffusion process from noisy boxes to object boxes. Specifically, to take advantage of the hierarchically annotated data, our method utilizes a novel noisy box manipulation technique by adapting the denoising process in the diffusion network with the inference from the previously trained model in hierarchical order. We also utilize a multi-label object detection method to learn efficiently from partial annotations and to give all the needed information about each abnormal tooth for treatment planning. Experimental results show that our method significantly outperforms state-of-the-art object detection methods, including RetinaNet, Faster R-CNN, DETR, and DiffusionDet for the analysis of panoramic X-rays, demonstrating the great potential of our method for hierarchically and partially annotated datasets. The code and the data are available at: https://github.com/ibrahimethemhamamci/HierarchicalDet.

Medical image analysis is a fundamental component. As deep learning progresses, the focus has shifted from single-task applications, such as classification and segmentation, to more complex multimodal tasks, including medical visual question answering and report generation. Traditional shallow and task-specific models are increasingly limited in addressing the complexity and scalability required in clinical practice. The emergence of large language models (LLMs) has driven the development of medical Large Vision-Language Models (LVLMs), offering a unified solution for diverse vision-language tasks. In this study, we investigate various architectural designs for medical LVLMs based on the widely adopted LLaVA framework, which follows an encoder-connector-LLM paradigm. We construct two distinct models targeting 2D and 3D modalities, respectively. These models are designed to support both general-purpose medical tasks and domain-specific fine-tuning, thereby serving as effective foundation models. To facilitate reproducibility and further research, we develop a modular and extensible codebase, MedM-VL, and release two LVLM variants: MedM-VL-2D for 2D medical image analysis and MedM-VL-CT-Chest for 3D CT-based applications. The code and models are available at: https://github.com/MSIIP/MedM-VL

Feature vectors provided by pre-trained deep artificial neural networks have become a dominant source for image representation in recent literature. Their contribution to the performance of image analysis can be improved through finetuning. As an ultimate solution, one might even train a deep network from scratch with the domain-relevant images, a highly desirable option which is generally impeded in pathology by lack of labeled images and the computational expense. In this study, we propose a new network, namely KimiaNet, that employs the topology of the DenseNet with four dense blocks, fine-tuned and trained with histopathology images in different configurations. We used more than 240,000 image patches with 1000x1000 pixels acquired at 20x magnification through our proposed "highcellularity mosaic" approach to enable the usage of weak labels of 7,126 whole slide images of formalin-fixed paraffin-embedded human pathology samples publicly available through the The Cancer Genome Atlas (TCGA) repository. We tested KimiaNet using three public datasets, namely TCGA, endometrial cancer images, and colorectal cancer images by evaluating the performance of search and classification when corresponding features of different networks are used for image representation. As well, we designed and trained multiple convolutional batch-normalized ReLU (CBR) networks. The results show that KimiaNet provides superior results compared to the original DenseNet and smaller CBR networks when used as feature extractor to represent histopathology images.

Dictionary learning (DL) has emerged as a powerful interpretability tool for large language models. By extracting known concepts (e.g., Golden-Gate Bridge) from human-interpretable data (e.g., text), sparse DL can elucidate a model's inner workings. In this work, we ask if DL can also be used to discover unknown concepts from less human-interpretable scientific data (e.g., cell images), ultimately enabling modern approaches to scientific discovery. As a first step, we use DL algorithms to study microscopy foundation models trained on multi-cell image data, where little prior knowledge exists regarding which high-level concepts should arise. We show that sparse dictionaries indeed extract biologically-meaningful concepts such as cell type and genetic perturbation type. We also propose a new DL algorithm, Iterative Codebook Feature Learning~(ICFL), and combine it with a pre-processing step that uses PCA whitening from a control dataset. In our experiments, we demonstrate that both ICFL and PCA improve the selectivity of extracted features compared to TopK sparse autoencoders.

Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer vision, for extracting biologically relevant information from images for science and conservation. Yet most of these are bespoke approaches designed for a specific task and are not easily adaptable or extendable to new questions, contexts, and datasets. A vision model for general organismal biology questions on images is of timely need. To approach this, we curate and release TreeOfLife-10M, the largest and most diverse ML-ready dataset of biology images. We then develop BioCLIP, a foundation model for the tree of life, leveraging the unique properties of biology captured by TreeOfLife-10M, namely the abundance and variety of images of plants, animals, and fungi, together with the availability of rich structured biological knowledge. We rigorously benchmark our approach on diverse fine-grained biology classification tasks, and find that BioCLIP consistently and substantially outperforms existing baselines (by 17% to 20% absolute). Intrinsic evaluation reveals that BioCLIP has learned a hierarchical representation conforming to the tree of life, shedding light on its strong generalizability. Our code, models and data will be made available at https://github.com/Imageomics/bioclip.

Recently, State Space Models (SSMs), with Mamba as a prime example, have shown great promise for long-range dependency modeling with linear complexity. Then, Vision Mamba and the subsequent architectures are presented successively, and they perform well on visual tasks. The crucial step of applying Mamba to visual tasks is to construct 2D visual features in sequential manners. To effectively organize and construct visual features within the 2D image space through 1D selective scan, we propose a novel Multi-Head Scan (MHS) module. The embeddings extracted from the preceding layer are projected into multiple lower-dimensional subspaces. Subsequently, within each subspace, the selective scan is performed along distinct scan routes. The resulting sub-embeddings, obtained from the multi-head scan process, are then integrated and ultimately projected back into the high-dimensional space. Moreover, we incorporate a Scan Route Attention (SRA) mechanism to enhance the module's capability to discern complex structures. To validate the efficacy of our module, we exclusively substitute the 2D-Selective-Scan (SS2D) block in VM-UNet with our proposed module, and we train our models from scratch without using any pre-trained weights. The results indicate a significant improvement in performance while reducing the parameters of the original VM-UNet. The code for this study is publicly available at https://github.com/PixDeep/MHS-VM.

Vision Language Models (VLMs) like CLIP have attracted substantial attention in pathology, serving as backbones for applications such as zero-shot image classification and Whole Slide Image (WSI) analysis. Additionally, they can function as vision encoders when combined with large language models (LLMs) to support broader capabilities. Current efforts to train pathology VLMs rely on pathology image-text pairs from platforms like PubMed, YouTube, and Twitter, which provide limited, unscalable data with generally suboptimal image quality. In this work, we leverage large-scale WSI datasets like TCGA to extract numerous high-quality image patches. We then train a large multimodal model to generate captions for these images, creating PathGen-1.6M, a dataset containing 1.6 million high-quality image-caption pairs. Our approach involves multiple agent models collaborating to extract representative WSI patches, generating and refining captions to obtain high-quality image-text pairs. Extensive experiments show that integrating these generated pairs with existing datasets to train a pathology-specific CLIP model, PathGen-CLIP, significantly enhances its ability to analyze pathological images, with substantial improvements across nine pathology-related zero-shot image classification tasks and three whole-slide image tasks. Furthermore, we construct 200K instruction-tuning data based on PathGen-1.6M and integrate PathGen-CLIP with the Vicuna LLM to create more powerful multimodal models through instruction tuning. Overall, we provide a scalable pathway for high-quality data generation in pathology, paving the way for next-generation general pathology models.

Tissue phenotyping is a fundamental computational pathology (CPath) task in learning objective characterizations of histopathologic biomarkers in anatomic pathology. However, whole-slide imaging (WSI) poses a complex computer vision problem in which the large-scale image resolutions of WSIs and the enormous diversity of morphological phenotypes preclude large-scale data annotation. Current efforts have proposed using pretrained image encoders with either transfer learning from natural image datasets or self-supervised pretraining on publicly-available histopathology datasets, but have not been extensively developed and evaluated across diverse tissue types at scale. We introduce UNI, a general-purpose self-supervised model for pathology, pretrained using over 100 million tissue patches from over 100,000 diagnostic haematoxylin and eosin-stained WSIs across 20 major tissue types, and evaluated on 33 representative CPath clinical tasks in CPath of varying diagnostic difficulties. In addition to outperforming previous state-of-the-art models, we demonstrate new modeling capabilities in CPath such as resolution-agnostic tissue classification, slide classification using few-shot class prototypes, and disease subtyping generalization in classifying up to 108 cancer types in the OncoTree code classification system. UNI advances unsupervised representation learning at scale in CPath in terms of both pretraining data and downstream evaluation, enabling data-efficient AI models that can generalize and transfer to a gamut of diagnostically-challenging tasks and clinical workflows in anatomic pathology.

With applications ranging from metabolomics to histopathology, quantitative phase microscopy (QPM) is a powerful label-free imaging modality. Despite significant advances in fast multiplexed imaging sensors and deep-learning-based inverse solvers, the throughput of QPM is currently limited by the speed of electronic hardware. Complementarily, to improve throughput further, here we propose to acquire images in a compressed form such that more information can be transferred beyond the existing electronic hardware bottleneck. To this end, we present a learnable optical compression-decompression framework that learns content-specific features. The proposed differentiable quantitative phase microscopy (partial mu) first uses learnable optical feature extractors as image compressors. The intensity representation produced by these networks is then captured by the imaging sensor. Finally, a reconstruction network running on electronic hardware decompresses the QPM images. In numerical experiments, the proposed system achieves compression of times 64 while maintaining the SSIM of sim 0.90 and PSNR of sim 30 dB on cells. The results demonstrated by our experiments open up a new pathway for achieving end-to-end optimized (i.e., optics and electronic) compact QPM systems that may provide unprecedented throughput improvements.

Multimodal Large Language Models (MLLMs) have shown significant potential in medical image analysis. However, their capabilities in interpreting fundus images, a critical skill for ophthalmology, remain under-evaluated. Existing benchmarks lack fine-grained task divisions and fail to provide modular analysis of its two key modules, i.e., large language model (LLM) and vision encoder (VE). This paper introduces FunBench, a novel visual question answering (VQA) benchmark designed to comprehensively evaluate MLLMs' fundus reading skills. FunBench features a hierarchical task organization across four levels (modality perception, anatomy perception, lesion analysis, and disease diagnosis). It also offers three targeted evaluation modes: linear-probe based VE evaluation, knowledge-prompted LLM evaluation, and holistic evaluation. Experiments on nine open-source MLLMs plus GPT-4o reveal significant deficiencies in fundus reading skills, particularly in basic tasks such as laterality recognition. The results highlight the limitations of current MLLMs and emphasize the need for domain-specific training and improved LLMs and VEs.

Developing advanced medical imaging retrieval systems is challenging due to the varying definitions of `similar images' across different medical contexts. This challenge is compounded by the lack of large-scale, high-quality medical imaging retrieval datasets and benchmarks. In this paper, we propose a novel methodology that leverages dense radiology reports to define image-wise similarity ordering at multiple granularities in a scalable and fully automatic manner. Using this approach, we construct two comprehensive medical imaging retrieval datasets: MIMIC-IR for Chest X-rays and CTRATE-IR for CT scans, providing detailed image-image ranking annotations conditioned on diverse anatomical structures. Furthermore, we develop two retrieval systems, RadIR-CXR and model-ChestCT, which demonstrate superior performance in traditional image-image and image-report retrieval tasks. These systems also enable flexible, effective image retrieval conditioned on specific anatomical structures described in text, achieving state-of-the-art results on 77 out of 78 metrics.

Prior work using Masked Autoencoders (MAEs) typically relies on random patch masking based on the assumption that images have significant redundancies across different channels, allowing for the reconstruction of masked content using cross-channel correlations. However, this assumption does not hold in Multi-Channel Imaging (MCI), where channels may provide complementary information with minimal feature overlap. Thus, these MAEs primarily learn local structures within individual channels from patch reconstruction, failing to fully leverage cross-channel interactions and limiting their MCI effectiveness. In this paper, we present ChA-MAEViT, an MAE-based method that enhances feature learning across MCI channels via four key strategies: (1) dynamic channel-patch masking, which compels the model to reconstruct missing channels in addition to masked patches, thereby enhancing cross-channel dependencies and improving robustness to varying channel configurations; (2) memory tokens, which serve as long-term memory aids to promote information sharing across channels, addressing the challenges of reconstructing structurally diverse channels; (3) hybrid token fusion module, which merges fine-grained patch tokens with a global class token to capture richer representations; and (4) Channel-Aware Decoder, a lightweight decoder utilizes channel tokens to effectively reconstruct image patches. Experiments on satellite and microscopy datasets, CHAMMI, JUMP-CP, and So2Sat, show that ChA-MAEViT significantly outperforms state-of-the-art MCI-ViTs by 3.0-21.5%, highlighting the importance of cross-channel interactions in MCI. Our code is publicly available at https://github.com/chaudatascience/cha_mae_vit.

Deep learning (DL), a pivotal technology in artificial intelligence, has recently gained substantial traction in the domain of dental auxiliary diagnosis. However, its application has predominantly been confined to imaging modalities such as panoramic radiographs and Cone Beam Computed Tomography, with limited focus on auxiliary analysis specifically targeting Periapical Radiographs (PR). PR are the most extensively utilized imaging modality in endodontics and periodontics due to their capability to capture detailed local lesions at a low cost. Nevertheless, challenges such as resolution limitations and artifacts complicate the annotation and recognition of PR, leading to a scarcity of publicly available, large-scale, high-quality PR analysis datasets. This scarcity has somewhat impeded the advancement of DL applications in PR analysis. In this paper, we present PRAD-10K, a dataset for PR analysis. PRAD-10K comprises 10,000 clinical periapical radiograph images, with pixel-level annotations provided by professional dentists for nine distinct anatomical structures, lesions, and artificial restorations or medical devices, We also include classification labels for images with typical conditions or lesions. Furthermore, we introduce a DL network named PRNet to establish benchmarks for PR segmentation tasks. Experimental results demonstrate that PRNet surpasses previous state-of-the-art medical image segmentation models on the PRAD-10K dataset. The codes and dataset will be made publicly available.

Background: AI-based classification models are essential for improving lung cancer diagnosis. However, the relative performance of lesion-level versus chest-region models in internal and external datasets remains unclear. Purpose: This study evaluates the performance of lesion-level and chest-region models for lung cancer classification, comparing their effectiveness across internal Duke Lung Nodule Dataset 2024 (DLND24) and external (LUNA16, NLST) datasets, with a focus on subgroup analyses by demographics, histology, and imaging characteristics. Materials and Methods: Two AI models were trained: one using lesion-centric patches (64,64,64) and the other using chest-region patches (512,512,8). Internal validation was conducted on DLND24, while external validation utilized LUNA16 and NLST datasets. The models performances were assessed using AUC-ROC, with subgroup analyses for demographic, clinical, and imaging factors. Statistical comparisons were performed using DeLongs test. Gradient-based visualizations and probability distribution were further used for analysis. Results: The lesion-level model consistently outperformed the chest-region model across datasets. In internal validation, the lesion-level model achieved an AUC of 0.71(CI: 0.61-0.81), compared to 0.68(0.57-0.77) for the chest-region model. External validation showed similar trends, with AUCs of 0.90(0.87-0.92) and 0.81(0.79-0.82) on LUNA16 and NLST, respectively. Subgroup analyses revealed significant advantages for lesion-level models in certain histological subtypes (adenocarcinoma) and imaging conditions (CT manufacturers). Conclusion: Lesion-level models demonstrate superior classification performance, especially for external datasets and challenging subgroups, suggesting their clinical utility for precision lung cancer diagnostics.

The analysis of 3D medical images is crucial for modern healthcare, yet traditional task-specific models are becoming increasingly inadequate due to limited generalizability across diverse clinical scenarios. Multimodal large language models (MLLMs) offer a promising solution to these challenges. However, existing MLLMs have limitations in fully leveraging the rich, hierarchical information embedded in 3D medical images. Inspired by clinical practice, where radiologists focus on both 3D spatial structure and 2D planar content, we propose Med-2E3, a novel MLLM for 3D medical image analysis that integrates 3D and 2D encoders. To aggregate 2D features more effectively, we design a Text-Guided Inter-Slice (TG-IS) scoring module, which scores the attention of each 2D slice based on slice contents and task instructions. To the best of our knowledge, Med-2E3 is the first MLLM to integrate both 3D and 2D features for 3D medical image analysis. Experiments on a large-scale, open-source 3D medical multimodal benchmark demonstrate that Med-2E3 exhibits task-specific attention distribution and significantly outperforms current state-of-the-art models, with a 14% improvement in report generation and a 5% gain in medical visual question answering (VQA), highlighting the model's potential in addressing complex multimodal clinical tasks. The code will be released upon acceptance.

A brain tumour is a mass or cluster of abnormal cells in the brain, which has the possibility of becoming life-threatening because of its ability to invade neighbouring tissues and also form metastases. An accurate diagnosis is essential for successful treatment planning and magnetic resonance imaging is the principal imaging modality for diagnostic of brain tumours and their extent. Deep Learning methods in computer vision applications have shown significant improvement in recent years, most of which can be credited to the fact that a sizeable amount of data is available to train models on, and the improvements in the model architectures yielding better approximations in a supervised setting. Classifying tumours using such deep learning methods has made significant progress with the availability of open datasets with reliable annotations. Typically those methods are either 3D models, which use 3D volumetric MRIs or even 2D models considering each slice separately. However, by treating the slice spatial dimension separately, spatiotemporal models can be employed as spatiospatial models for this task. These models have the capabilities of learning specific spatial and temporal relationship, while reducing computational costs. This paper uses two spatiotemporal models, ResNet (2+1)D and ResNet Mixed Convolution, to classify different types of brain tumours. It was observed that both these models performed superior to the pure 3D convolutional model, ResNet18. Furthermore, it was also observed that pre-training the models on a different, even unrelated dataset before training them for the task of tumour classification improves the performance. Finally, Pre-trained ResNet Mixed Convolution was observed to be the best model in these experiments, achieving a macro F1-score of 0.93 and a test accuracy of 96.98\%, while at the same time being the model with the least computational cost.

We show how perceptual embeddings of the visual system can be constructed at inference-time with no training data or deep neural network features. Our perceptual embeddings are solutions to a weighted least squares (WLS) problem, defined at the pixel-level, and solved at inference-time, that can capture global and local image characteristics. The distance in embedding space is used to define a perceptual similarity metric which we call LASI: Linear Autoregressive Similarity Index. Experiments on full-reference image quality assessment datasets show LASI performs competitively with learned deep feature based methods like LPIPS (Zhang et al., 2018) and PIM (Bhardwaj et al., 2020), at a similar computational cost to hand-crafted methods such as MS-SSIM (Wang et al., 2003). We found that increasing the dimensionality of the embedding space consistently reduces the WLS loss while increasing performance on perceptual tasks, at the cost of increasing the computational complexity. LASI is fully differentiable, scales cubically with the number of embedding dimensions, and can be parallelized at the pixel-level. A Maximum Differentiation (MAD) competition (Wang & Simoncelli, 2008) between LASI and LPIPS shows that both methods are capable of finding failure points for the other, suggesting these metrics can be combined.

Conditional normalizing flows can generate diverse image samples for solving inverse problems. Most normalizing flows for inverse problems in imaging employ the conditional affine coupling layer that can generate diverse images quickly. However, unintended severe artifacts are occasionally observed in the output of them. In this work, we address this critical issue by investigating the origins of these artifacts and proposing the conditions to avoid them. First of all, we empirically and theoretically reveal that these problems are caused by "exploding inverse" in the conditional affine coupling layer for certain out-of-distribution (OOD) conditional inputs. Then, we further validated that the probability of causing erroneous artifacts in pixels is highly correlated with a Mahalanobis distance-based OOD score for inverse problems in imaging. Lastly, based on our investigations, we propose a remark to avoid exploding inverse and then based on it, we suggest a simple remedy that substitutes the affine coupling layers with the modified rational quadratic spline coupling layers in normalizing flows, to encourage the robustness of generated image samples. Our experimental results demonstrated that our suggested methods effectively suppressed critical artifacts occurring in normalizing flows for super-resolution space generation and low-light image enhancement.

Lung diseases represent a significant global health challenge, with Chest X-Ray (CXR) being a key diagnostic tool due to their accessibility and affordability. Nonetheless, the detection of pulmonary lesions is often hindered by overlapping bone structures in CXR images, leading to potential misdiagnoses. To address this issue, we developed an end-to-end framework called BS-LDM, designed to effectively suppress bone in high-resolution CXR images. This framework is based on conditional latent diffusion models and incorporates a multi-level hybrid loss-constrained vector-quantized generative adversarial network which is crafted for perceptual compression, ensuring the preservation of details. To further enhance the framework's performance, we introduce offset noise and a temporal adaptive thresholding strategy. These additions help minimize discrepancies in generating low-frequency information, thereby improving the clarity of the generated soft tissue images. Additionally, we have compiled a high-quality bone suppression dataset named SZCH-X-Rays. This dataset includes 818 pairs of high-resolution CXR and dual-energy subtraction soft tissue images collected from a partner hospital. Moreover, we processed 241 data pairs from the JSRT dataset into negative images, which are more commonly used in clinical practice. Our comprehensive experimental and clinical evaluations reveal that BS-LDM excels in bone suppression, underscoring its significant clinical value.

In healthcare, medical image segmentation is crucial for accurate disease diagnosis and the development of effective treatment strategies. Early detection can significantly aid in managing diseases and potentially prevent their progression. Machine learning, particularly deep convolutional neural networks, has emerged as a promising approach to addressing segmentation challenges. Traditional methods like U-Net use encoding blocks for local representation modeling and decoding blocks to uncover semantic relationships. However, these models often struggle with multi-scale objects exhibiting significant variations in texture and shape, and they frequently fail to capture long-range dependencies in the input data. Transformers designed for sequence-to-sequence predictions have been proposed as alternatives, utilizing global self-attention mechanisms. Yet, they can sometimes lack precise localization due to insufficient granular details. To overcome these limitations, we introduce TransDAE: a novel approach that reimagines the self-attention mechanism to include both spatial and channel-wise associations across the entire feature space, while maintaining computational efficiency. Additionally, TransDAE enhances the skip connection pathway with an inter-scale interaction module, promoting feature reuse and improving localization accuracy. Remarkably, TransDAE outperforms existing state-of-the-art methods on the Synaps multi-organ dataset, even without relying on pre-trained weights.

It has been shown that traditional deep learning methods for electronic microscopy segmentation usually suffer from low transferability when samples and annotations are limited, while large-scale vision foundation models are more robust when transferring between different domains but facing sub-optimal improvement under fine-tuning. In this work, we present a new few-shot domain adaptation framework SAMDA, which combines the Segment Anything Model(SAM) with nnUNet in the embedding space to achieve high transferability and accuracy. Specifically, we choose the Unet-based network as the "expert" component to learn segmentation features efficiently and design a SAM-based adaptation module as the "generic" component for domain transfer. By amalgamating the "generic" and "expert" components, we mitigate the modality imbalance in the complex pre-training knowledge inherent to large-scale Vision Foundation models and the challenge of transferability inherent to traditional neural networks. The effectiveness of our model is evaluated on two electron microscopic image datasets with different modalities for mitochondria segmentation, which improves the dice coefficient on the target domain by 6.7%. Also, the SAM-based adaptor performs significantly better with only a single annotated image than the 10-shot domain adaptation on nnUNet. We further verify our model on four MRI datasets from different sources to prove its generalization ability.

This paper introduces an innovative methodology for producing high-quality 3D lung CT images guided by textual information. While diffusion-based generative models are increasingly used in medical imaging, current state-of-the-art approaches are limited to low-resolution outputs and underutilize radiology reports' abundant information. The radiology reports can enhance the generation process by providing additional guidance and offering fine-grained control over the synthesis of images. Nevertheless, expanding text-guided generation to high-resolution 3D images poses significant memory and anatomical detail-preserving challenges. Addressing the memory issue, we introduce a hierarchical scheme that uses a modified UNet architecture. We start by synthesizing low-resolution images conditioned on the text, serving as a foundation for subsequent generators for complete volumetric data. To ensure the anatomical plausibility of the generated samples, we provide further guidance by generating vascular, airway, and lobular segmentation masks in conjunction with the CT images. The model demonstrates the capability to use textual input and segmentation tasks to generate synthesized images. The results of comparative assessments indicate that our approach exhibits superior performance compared to the most advanced models based on GAN and diffusion techniques, especially in accurately retaining crucial anatomical features such as fissure lines, airways, and vascular structures. This innovation introduces novel possibilities. This study focuses on two main objectives: (1) the development of a method for creating images based on textual prompts and anatomical components, and (2) the capability to generate new images conditioning on anatomical elements. The advancements in image generation can be applied to enhance numerous downstream tasks.

Image copy detection (ICD) aims to determine whether a query image is an edited copy of any image from a reference set. Currently, there are very limited public benchmarks for ICD, while all overlook a critical challenge in real-world applications, i.e., the distraction from hard negative queries. Specifically, some queries are not edited copies but are inherently similar to some reference images. These hard negative queries are easily false recognized as edited copies, significantly compromising the ICD accuracy. This observation motivates us to build the first ICD benchmark featuring this characteristic. Based on existing ICD datasets, this paper constructs a new dataset by additionally adding 100, 000 and 24, 252 hard negative pairs into the training and test set, respectively. Moreover, this paper further reveals a unique difficulty for solving the hard negative problem in ICD, i.e., there is a fundamental conflict between current metric learning and ICD. This conflict is: the metric learning adopts symmetric distance while the edited copy is an asymmetric (unidirectional) process, e.g., a partial crop is close to its holistic reference image and is an edited copy, while the latter cannot be the edited copy of the former (in spite the distance is equally small). This insight results in an Asymmetrical-Similarity Learning (ASL) method, which allows the similarity in two directions (the query <-> the reference image) to be different from each other. Experimental results show that ASL outperforms state-of-the-art methods by a clear margin, confirming that solving the symmetric-asymmetric conflict is critical for ICD. The NDEC dataset and code are available at https://github.com/WangWenhao0716/ASL.

Recent advancements in multimodal large language models (MLLMs) have been noteworthy, yet, these general-domain MLLMs often fall short in their ability to comprehend and interact effectively with user interface (UI) screens. In this paper, we present Ferret-UI, a new MLLM tailored for enhanced understanding of mobile UI screens, equipped with referring, grounding, and reasoning capabilities. Given that UI screens typically exhibit a more elongated aspect ratio and contain smaller objects of interest (e.g., icons, texts) than natural images, we incorporate "any resolution" on top of Ferret to magnify details and leverage enhanced visual features. Specifically, each screen is divided into 2 sub-images based on the original aspect ratio (i.e., horizontal division for portrait screens and vertical division for landscape screens). Both sub-images are encoded separately before being sent to LLMs. We meticulously gather training samples from an extensive range of elementary UI tasks, such as icon recognition, find text, and widget listing. These samples are formatted for instruction-following with region annotations to facilitate precise referring and grounding. To augment the model's reasoning ability, we further compile a dataset for advanced tasks, including detailed description, perception/interaction conversations, and function inference. After training on the curated datasets, Ferret-UI exhibits outstanding comprehension of UI screens and the capability to execute open-ended instructions. For model evaluation, we establish a comprehensive benchmark encompassing all the aforementioned tasks. Ferret-UI excels not only beyond most open-source UI MLLMs, but also surpasses GPT-4V on all the elementary UI tasks.

Self-supervised learning (SSL) approaches have recently shown substantial success in learning visual representations from unannotated images. Compared with photographic images, medical images acquired with the same imaging protocol exhibit high consistency in anatomy. To exploit this anatomical consistency, this paper introduces a novel SSL approach, called PEAC (patch embedding of anatomical consistency), for medical image analysis. Specifically, in this paper, we propose to learn global and local consistencies via stable grid-based matching, transfer pre-trained PEAC models to diverse downstream tasks, and extensively demonstrate that (1) PEAC achieves significantly better performance than the existing state-of-the-art fully/self-supervised methods, and (2) PEAC captures the anatomical structure consistency across views of the same patient and across patients of different genders, weights, and healthy statuses, which enhances the interpretability of our method for medical image analysis.

Single cell analysis of human skeletal muscle (SM) tissue cross-sections is a fundamental tool for understanding many neuromuscular disorders. For this analysis to be reliable and reproducible, identification of individual fibres within microscopy images (segmentation) of SM tissue should be automatic and precise. Biomedical scientists in this field currently rely on custom tools and general machine learning (ML) models, both followed by labour intensive and subjective manual interventions to fine-tune segmentation. We believe that fully automated, precise, reproducible segmentation is possible by training ML models. However, in this important biomedical domain, there are currently no good quality, publicly available annotated imaging datasets available for ML model training. In this paper we release NCL-SM: a high quality bioimaging dataset of 46 human SM tissue cross-sections from both healthy control subjects and from patients with genetically diagnosed muscle pathology. These images include > 50k manually segmented muscle fibres (myofibres). In addition we also curated high quality myofibre segmentations, annotating reasons for rejecting low quality myofibres and low quality regions in SM tissue images, making these annotations completely ready for downstream analysis. This, we believe, will pave the way for development of a fully automatic pipeline that identifies individual myofibres within images of tissue sections and, in particular, also classifies individual myofibres that are fit for further analysis.

The advent of large-scale vision foundation models, pre-trained on diverse natural images, has marked a paradigm shift in computer vision. However, how the frontier vision foundation models' efficacies transfer to specialized domains remains such as medical imaging remains an open question. This report investigates whether DINOv3, a state-of-the-art self-supervised vision transformer (ViT) that features strong capability in dense prediction tasks, can directly serve as a powerful, unified encoder for medical vision tasks without domain-specific pre-training. To answer this, we benchmark DINOv3 across common medical vision tasks, including 2D/3D classification and segmentation on a wide range of medical imaging modalities. We systematically analyze its scalability by varying model sizes and input image resolutions. Our findings reveal that DINOv3 shows impressive performance and establishes a formidable new baseline. Remarkably, it can even outperform medical-specific foundation models like BiomedCLIP and CT-Net on several tasks, despite being trained solely on natural images. However, we identify clear limitations: The model's features degrade in scenarios requiring deep domain specialization, such as in Whole-Slide Pathological Images (WSIs), Electron Microscopy (EM), and Positron Emission Tomography (PET). Furthermore, we observe that DINOv3 does not consistently obey scaling law in the medical domain; performance does not reliably increase with larger models or finer feature resolutions, showing diverse scaling behaviors across tasks. Ultimately, our work establishes DINOv3 as a strong baseline, whose powerful visual features can serve as a robust prior for multiple complex medical tasks. This opens promising future directions, such as leveraging its features to enforce multiview consistency in 3D reconstruction.

In Multimodal Large Language Models (MLLMs), a visual projector plays a crucial role in bridging pre-trained vision encoders with LLMs, enabling profound visual understanding while harnessing the LLMs' robust capabilities. Despite the importance of the visual projector, it has been relatively less explored. In this study, we first identify two essential projector properties: (i) flexibility in managing the number of visual tokens, crucial for MLLMs' overall efficiency, and (ii) preservation of local context from visual features, vital for spatial understanding. Based on these findings, we propose a novel projector design that is both flexible and locality-enhanced, effectively satisfying the two desirable properties. Additionally, we present comprehensive strategies to effectively utilize multiple and multifaceted instruction datasets. Through extensive experiments, we examine the impact of individual design choices. Finally, our proposed MLLM, Honeybee, remarkably outperforms previous state-of-the-art methods across various benchmarks, including MME, MMBench, SEED-Bench, and LLaVA-Bench, achieving significantly higher efficiency. Code and models are available at https://github.com/kakaobrain/honeybee.

Few-shot image classification(FSIC) aims to recognize novel classes given few labeled images from base classes. Recent works have achieved promising classification performance, especially for metric-learning methods, where a measure at only image feature level is usually used. In this paper, we argue that measure at such a level may not be effective enough to generalize from base to novel classes when using only a few images. Instead, a multi-level descriptor of an image is taken for consideration in this paper. We propose a multi-level correlation network (MLCN) for FSIC to tackle this problem by effectively capturing local information. Concretely, we present the self-correlation module and cross-correlation module to learn the semantic correspondence relation of local information based on learned representations. Moreover, we propose a pattern-correlation module to capture the pattern of fine-grained images and find relevant structural patterns between base classes and novel classes. Extensive experiments and analysis show the effectiveness of our proposed method on four widely-used FSIC benchmarks. The code for our approach is available at: https://github.com/Yunkai696/MLCN.

MIDOG 2025 Track 1 requires mitosis detection in whole-slideimages (WSIs) containing non-tumor, inflamed, and necrotic re-gions. Due to the complicated and heterogeneous context, aswell as possible artifacts, there are often false positives and falsenegatives, thus degrading the detection F1-score. To addressthis problem, we propose a two-stage framework. Firstly, an im-proved YOLO11x, integrated with EMA attention and LSConv,is employed to generate mitosis candidates. We use a low confi-dence threshold to generate as many proposals as possible, en-suring the detection recall. Then, a ConvNeXt-Tiny classifieris employed to filter out the false positives, ensuring the detec-tion precision. Consequently, the proposed two-stage frame-work can generate a high detection F1-score. Evaluated on afused dataset comprising MIDOG++, MITOS_WSI_CCMCT,and MITOS_WSI_CMC, our framework achieves an F1-scoreof 0.882, which is 0.035 higher than the single-stage YOLO11xbaseline. This performance gain is produced by a significantprecision improvement, from 0.762 to 0.839, and a comparablerecall. On the MIDOG 2025 Track 1 preliminary test set, thealgorithm scores an F1 score of 0.7587. The code is available athttps://github.com/xxiao0304/MIDOG-2025-Track-1-of-SZTU.

Medical image arbitrary-scale super-resolution (MIASSR) has recently gained widespread attention, aiming to super sample medical volumes at arbitrary scales via a single model. However, existing MIASSR methods face two major limitations: (i) reliance on high-resolution (HR) volumes and (ii) limited generalization ability, which restricts their application in various scenarios. To overcome these limitations, we propose Cube-based Neural Radiance Field (CuNeRF), a zero-shot MIASSR framework that can yield medical images at arbitrary scales and viewpoints in a continuous domain. Unlike existing MIASSR methods that fit the mapping between low-resolution (LR) and HR volumes, CuNeRF focuses on building a coordinate-intensity continuous representation from LR volumes without the need for HR references. This is achieved by the proposed differentiable modules: including cube-based sampling, isotropic volume rendering, and cube-based hierarchical rendering. Through extensive experiments on magnetic resource imaging (MRI) and computed tomography (CT) modalities, we demonstrate that CuNeRF outperforms state-of-the-art MIASSR methods. CuNeRF yields better visual verisimilitude and reduces aliasing artifacts at various upsampling factors. Moreover, our CuNeRF does not need any LR-HR training pairs, which is more flexible and easier to be used than others. Our code will be publicly available soon.

Multimodal large language models (MLLMs) have recently achieved remarkable progress in radiology by integrating visual perception with natural language understanding. However, they often generate clinically unsupported descriptions, known as medical hallucinations, which pose serious risks in medical applications that demand accuracy and image-grounded outputs. Through empirical analysis, we find that prompt-induced hallucinations remain prevalent in radiology MLLMs, largely due to over-sensitivity to clinical sections. To address this, we introduce Clinical Contrastive Cecoding (CCD), a training-free and retrieval-free inference framework that integrates structured clinical signals from task-specific radiology expert models. CCD introduces a dual-stage contrastive mechanism to refine token-level logits during generation, thereby enhancing clinical fidelity without modifying the base MLLM. Experiments on three datasets and multiple models demonstrate that CCD consistently improves overall performance on radiology report generation (RRG). On the MIMIC-CXR dataset, it yields up to a 17% improvement in RadGraph-F1 when applied to state-of-the-art RRG models. Our approach provides a lightweight and generalisable solution for mitigating medical hallucinations, effectively bridging expert models and MLLMs in radiology.

Due to the three-dimensional nature of CT- or MR-scans, generative modeling of medical images is a particularly challenging task. Existing approaches mostly apply patch-wise, slice-wise, or cascaded generation techniques to fit the high-dimensional data into the limited GPU memory. However, these approaches may introduce artifacts and potentially restrict the model's applicability for certain downstream tasks. This work presents WDM, a wavelet-based medical image synthesis framework that applies a diffusion model on wavelet decomposed images. The presented approach is a simple yet effective way of scaling diffusion models to high resolutions and can be trained on a single 40 GB GPU. Experimental results on BraTS and LIDC-IDRI unconditional image generation at a resolution of 128 times 128 times 128 show state-of-the-art image fidelity (FID) and sample diversity (MS-SSIM) scores compared to GANs, Diffusion Models, and Latent Diffusion Models. Our proposed method is the only one capable of generating high-quality images at a resolution of 256 times 256 times 256.

The recent years have witnessed a great array of large multimodal models (LMMs) to effectively solve single-image vision language tasks. However, their abilities to solve multi-image visual language tasks is yet to be improved. The existing multi-image LMMs (e.g. OpenFlamingo, Emu, Idefics, etc) mostly gain their multi-image ability through pre-training on hundreds of millions of noisy interleaved image-text data from web, which is neither efficient nor effective. In this paper, we aim at building strong multi-image LMMs via instruction tuning with academic-level resources. Therefore, we meticulously construct Mantis-Instruct containing 721K instances from 14 multi-image datasets. We design Mantis-Instruct to cover different multi-image skills like co-reference, reasoning, comparing, temporal understanding. We combine Mantis-Instruct with several single-image visual-language datasets to train our model Mantis to handle any interleaved image-text inputs. We evaluate the trained Mantis on five multi-image benchmarks and eight single-image benchmarks. Though only requiring academic-level resources (i.e. 36 hours on 16xA100-40G), Mantis-8B can achieve state-of-the-art performance on all the multi-image benchmarks and beats the existing best multi-image LMM Idefics2-8B by an average of 9 absolute points. We observe that Mantis performs equivalently well on the held-in and held-out evaluation benchmarks. We further evaluate Mantis on single-image benchmarks and demonstrate that Mantis can maintain a strong single-image performance on par with CogVLM and Emu2. Our results are particularly encouraging as it shows that low-cost instruction tuning is indeed much more effective than intensive pre-training in terms of building multi-image LMMs.

In recent years, the increasing popularity of Hi-DPI screens has driven a rising demand for high-resolution images. However, the limited computational power of edge devices poses a challenge in deploying complex super-resolution neural networks, highlighting the need for efficient methods. While prior works have made significant progress, they have not fully exploited pixel-level information. Moreover, their reliance on fixed sampling patterns limits both accuracy and the ability to capture fine details in low-resolution images. To address these challenges, we introduce two plug-and-play modules designed to capture and leverage pixel information effectively in Look-Up Table (LUT) based super-resolution networks. Our method introduces Automatic Sampling (AutoSample), a flexible LUT sampling approach where sampling weights are automatically learned during training to adapt to pixel variations and expand the receptive field without added inference cost. We also incorporate Adaptive Residual Learning (AdaRL) to enhance inter-layer connections, enabling detailed information flow and improving the network's ability to reconstruct fine details. Our method achieves significant performance improvements on both MuLUT and SPF-LUT while maintaining similar storage sizes. Specifically, for MuLUT, we achieve a PSNR improvement of approximately +0.20 dB improvement on average across five datasets. For SPF-LUT, with more than a 50% reduction in storage space and about a 2/3 reduction in inference time, our method still maintains performance comparable to the original. The code is available at https://github.com/SuperKenVery/AutoLUT.

Whole slide image (WSI) analysis has become increasingly important in the medical imaging community, enabling automated and objective diagnosis, prognosis, and therapeutic-response prediction. However, in clinical practice, the ever-evolving environment hamper the utility of WSI analysis models. In this paper, we propose the FIRST continual learning framework for WSI analysis, named ConSlide, to tackle the challenges of enormous image size, utilization of hierarchical structure, and catastrophic forgetting by progressive model updating on multiple sequential datasets. Our framework contains three key components. The Hierarchical Interaction Transformer (HIT) is proposed to model and utilize the hierarchical structural knowledge of WSI. The Breakup-Reorganize (BuRo) rehearsal method is developed for WSI data replay with efficient region storing buffer and WSI reorganizing operation. The asynchronous updating mechanism is devised to encourage the network to learn generic and specific knowledge respectively during the replay stage, based on a nested cross-scale similarity learning (CSSL) module. We evaluated the proposed ConSlide on four public WSI datasets from TCGA projects. It performs best over other state-of-the-art methods with a fair WSI-based continual learning setting and achieves a better trade-off of the overall performance and forgetting on previous task

Latent diffusion models (LDMs) exhibit an impressive ability to produce realistic images, yet the inner workings of these models remain mysterious. Even when trained purely on images without explicit depth information, they typically output coherent pictures of 3D scenes. In this work, we investigate a basic interpretability question: does an LDM create and use an internal representation of simple scene geometry? Using linear probes, we find evidence that the internal activations of the LDM encode linear representations of both 3D depth data and a salient-object / background distinction. These representations appear surprisingly early in the denoising process-well before a human can easily make sense of the noisy images. Intervention experiments further indicate these representations play a causal role in image synthesis, and may be used for simple high-level editing of an LDM's output. Project page: https://yc015.github.io/scene-representation-diffusion-model/

Deep learning (DL) has proven highly effective for ultrasound-based computer-aided diagnosis (CAD) of breast cancers. In an automaticCAD system, lesion detection is critical for the following diagnosis. However, existing DL-based methods generally require voluminous manually-annotated region of interest (ROI) labels and class labels to train both the lesion detection and diagnosis models. In clinical practice, the ROI labels, i.e. ground truths, may not always be optimal for the classification task due to individual experience of sonologists, resulting in the issue of coarse annotation that limits the diagnosis performance of a CAD model. To address this issue, a novel Two-Stage Detection and Diagnosis Network (TSDDNet) is proposed based on weakly supervised learning to enhance diagnostic accuracy of the ultrasound-based CAD for breast cancers. In particular, all the ROI-level labels are considered as coarse labels in the first training stage, and then a candidate selection mechanism is designed to identify optimallesion areas for both the fully and partially annotated samples. It refines the current ROI-level labels in the fully annotated images and the detected ROIs in the partially annotated samples with a weakly supervised manner under the guidance of class labels. In the second training stage, a self-distillation strategy further is further proposed to integrate the detection network and classification network into a unified framework as the final CAD model for joint optimization, which then further improves the diagnosis performance. The proposed TSDDNet is evaluated on a B-mode ultrasound dataset, and the experimental results show that it achieves the best performance on both lesion detection and diagnosis tasks, suggesting promising application potential.

The previous advancements in pathology image understanding primarily involved developing models tailored to specific tasks. Recent studies has demonstrated that the large vision-language model can enhance the performance of various downstream tasks in medical image understanding. In this study, we developed a domain-specific large language-vision assistant (PA-LLaVA) for pathology image understanding. Specifically, (1) we first construct a human pathology image-text dataset by cleaning the public medical image-text data for domain-specific alignment; (2) Using the proposed image-text data, we first train a pathology language-image pretraining (PLIP) model as the specialized visual encoder for pathology image, and then we developed scale-invariant connector to avoid the information loss caused by image scaling; (3) We adopt two-stage learning to train PA-LLaVA, first stage for domain alignment, and second stage for end to end visual question \& answering (VQA) task. In experiments, we evaluate our PA-LLaVA on both supervised and zero-shot VQA datasets, our model achieved the best overall performance among multimodal models of similar scale. The ablation experiments also confirmed the effectiveness of our design. We posit that our PA-LLaVA model and the datasets presented in this work can promote research in field of computational pathology. All codes are available at: https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA}{https://github.com/ddw2AIGROUP2CQUPT/PA-LLaVA

Inferring biological relationships from cellular phenotypes in high-content microscopy screens provides significant opportunity and challenge in biological research. Prior results have shown that deep vision models can capture biological signal better than hand-crafted features. This work explores how self-supervised deep learning approaches scale when training larger models on larger microscopy datasets. Our results show that both CNN- and ViT-based masked autoencoders significantly outperform weakly supervised baselines. At the high-end of our scale, a ViT-L/8 trained on over 3.5-billion unique crops sampled from 93-million microscopy images achieves relative improvements as high as 28% over our best weakly supervised baseline at inferring known biological relationships curated from public databases. Relevant code and select models released with this work can be found at: https://github.com/recursionpharma/maes_microscopy.

Visual Language Models (VLMs) have demonstrated impressive capabilities in visual grounding tasks. However, their effectiveness in the medical domain, particularly for abnormality detection and localization within medical images, remains underexplored. A major challenge is the complex and abstract nature of medical terminology, which makes it difficult to directly associate pathological anomaly terms with their corresponding visual features. In this work, we introduce a novel approach to enhance VLM performance in medical abnormality detection and localization by leveraging decomposed medical knowledge. Instead of directly prompting models to recognize specific abnormalities, we focus on breaking down medical concepts into fundamental attributes and common visual patterns. This strategy promotes a stronger alignment between textual descriptions and visual features, improving both the recognition and localization of abnormalities in medical images.We evaluate our method on the 0.23B Florence-2 base model and demonstrate that it achieves comparable performance in abnormality grounding to significantly larger 7B LLaVA-based medical VLMs, despite being trained on only 1.5% of the data used for such models. Experimental results also demonstrate the effectiveness of our approach in both known and previously unseen abnormalities, suggesting its strong generalization capabilities.

Medical image retrieval is essential for clinical decision-making and translational research, relying on discriminative visual representations. Yet, current methods remain fragmented, relying on separate architectures and training strategies for 2D, 3D, and video-based medical data. This modality-specific design hampers scalability and inhibits the development of unified representations. To enable unified learning, we curate a large-scale hybrid-modality dataset comprising 867,653 medical imaging samples, including 2D X-rays and ultrasounds, RGB endoscopy videos, and 3D CT scans. Leveraging this dataset, we train M3Ret, a unified visual encoder without any modality-specific customization. It successfully learns transferable representations using both generative (MAE) and contrastive (SimDINO) self-supervised learning (SSL) paradigms. Our approach sets a new state-of-the-art in zero-shot image-to-image retrieval across all individual modalities, surpassing strong baselines such as DINOv3 and the text-supervised BMC-CLIP. More remarkably, strong cross-modal alignment emerges without paired data, and the model generalizes to unseen MRI tasks, despite never observing MRI during pretraining, demonstrating the generalizability of purely visual self-supervision to unseen modalities. Comprehensive analyses further validate the scalability of our framework across model and data sizes. These findings deliver a promising signal to the medical imaging community, positioning M3Ret as a step toward foundation models for visual SSL in multimodal medical image understanding.

In this paper, we introduce a novel 3D-aware image generation method that leverages 2D diffusion models. We formulate the 3D-aware image generation task as multiview 2D image set generation, and further to a sequential unconditional-conditional multiview image generation process. This allows us to utilize 2D diffusion models to boost the generative modeling power of the method. Additionally, we incorporate depth information from monocular depth estimators to construct the training data for the conditional diffusion model using only still images. We train our method on a large-scale dataset, i.e., ImageNet, which is not addressed by previous methods. It produces high-quality images that significantly outperform prior methods. Furthermore, our approach showcases its capability to generate instances with large view angles, even though the training images are diverse and unaligned, gathered from "in-the-wild" real-world environments.

With advancements in data availability and computing resources, Multimodal Large Language Models (MLLMs) have showcased capabilities across various fields. However, the quadratic complexity of the vision encoder in MLLMs constrains the resolution of input images. Most current approaches mitigate this issue by cropping high-resolution images into smaller sub-images, which are then processed independently by the vision encoder. Despite capturing sufficient local details, these sub-images lack global context and fail to interact with one another. To address this limitation, we propose a novel MLLM, INF-LLaVA, designed for effective high-resolution image perception. INF-LLaVA incorporates two innovative components. First, we introduce a Dual-perspective Cropping Module (DCM), which ensures that each sub-image contains continuous details from a local perspective and comprehensive information from a global perspective. Second, we introduce Dual-perspective Enhancement Module (DEM) to enable the mutual enhancement of global and local features, allowing INF-LLaVA to effectively process high-resolution images by simultaneously capturing detailed local information and comprehensive global context. Extensive ablation studies validate the effectiveness of these components, and experiments on a diverse set of benchmarks demonstrate that INF-LLaVA outperforms existing MLLMs. Code and pretrained model are available at https://github.com/WeihuangLin/INF-LLaVA.

Wood species identification plays a crucial role in various industries, from ensuring the legality of timber products to advancing ecological conservation efforts. This paper introduces WoodYOLO, a novel object detection algorithm specifically designed for microscopic wood fiber analysis. Our approach adapts the YOLO architecture to address the challenges posed by large, high-resolution microscopy images and the need for high recall in localization of the cell type of interest (vessel elements). Our results show that WoodYOLO significantly outperforms state-of-the-art models, achieving performance gains of 12.9% and 6.5% in F2 score over YOLOv10 and YOLOv7, respectively. This improvement in automated wood cell type localization capabilities contributes to enhancing regulatory compliance, supporting sustainable forestry practices, and promoting biodiversity conservation efforts globally.

Recent advancements in Mamba have shown promising results in image restoration. These methods typically flatten 2D images into multiple distinct 1D sequences along rows and columns, process each sequence independently using selective scan operation, and recombine them to form the outputs. However, such a paradigm overlooks two vital aspects: i) the local relationships and spatial continuity inherent in natural images, and ii) the discrepancies among sequences unfolded through totally different ways. To overcome the drawbacks, we explore two problems in Mamba-based restoration methods: i) how to design a scanning strategy preserving both locality and continuity while facilitating restoration, and ii) how to aggregate the distinct sequences unfolded in totally different ways. To address these problems, we propose a novel Mamba-based Image Restoration model (MaIR), which consists of Nested S-shaped Scanning strategy (NSS) and Sequence Shuffle Attention block (SSA). Specifically, NSS preserves locality and continuity of the input images through the stripe-based scanning region and the S-shaped scanning path, respectively. SSA aggregates sequences through calculating attention weights within the corresponding channels of different sequences. Thanks to NSS and SSA, MaIR surpasses 40 baselines across 14 challenging datasets, achieving state-of-the-art performance on the tasks of image super-resolution, denoising, deblurring and dehazing. The code is available at https://github.com/XLearning-SCU/2025-CVPR-MaIR.

3D super-resolution aims to reconstruct high-fidelity 3D models from low-resolution (LR) multi-view images. Early studies primarily focused on single-image super-resolution (SISR) models to upsample LR images into high-resolution images. However, these methods often lack view consistency because they operate independently on each image. Although various post-processing techniques have been extensively explored to mitigate these inconsistencies, they have yet to fully resolve the issues. In this paper, we perform a comprehensive study of 3D super-resolution by leveraging video super-resolution (VSR) models. By utilizing VSR models, we ensure a higher degree of spatial consistency and can reference surrounding spatial information, leading to more accurate and detailed reconstructions. Our findings reveal that VSR models can perform remarkably well even on sequences that lack precise spatial alignment. Given this observation, we propose a simple yet practical approach to align LR images without involving fine-tuning or generating 'smooth' trajectory from the trained 3D models over LR images. The experimental results show that the surprisingly simple algorithms can achieve the state-of-the-art results of 3D super-resolution tasks on standard benchmark datasets, such as the NeRF-synthetic and MipNeRF-360 datasets. Project page: https://ko-lani.github.io/Sequence-Matters

We present an ultra-fast, precise, parameter-free method, which we term Deep-STORM, for obtaining super-resolution images from stochastically-blinking emitters, such as fluorescent molecules used for localization microscopy. Deep-STORM uses a deep convolutional neural network that can be trained on simulated data or experimental measurements, both of which are demonstrated. The method achieves state-of-the-art resolution under challenging signal-to-noise conditions and high emitter densities, and is significantly faster than existing approaches. Additionally, no prior information on the shape of the underlying structure is required, making the method applicable to any blinking data-set. We validate our approach by super-resolution image reconstruction of simulated and experimentally obtained data.

Whole slide image (WSI) analysis in digital pathology presents unique challenges due to the gigapixel resolution of WSIs and the scarcity of dense supervision signals. While Multiple Instance Learning (MIL) is a natural fit for slide-level tasks, training robust models requires large and diverse datasets. Even though image augmentation techniques could be utilized to increase data variability and reduce overfitting, implementing them effectively is not a trivial task. Traditional patch-level augmentation is prohibitively expensive due to the large number of patches extracted from each WSI, and existing feature-level augmentation methods lack control over transformation semantics. We introduce HistAug, a fast and efficient generative model for controllable augmentations in the latent space for digital pathology. By conditioning on explicit patch-level transformations (e.g., hue, erosion), HistAug generates realistic augmented embeddings while preserving initial semantic information. Our method allows the processing of a large number of patches in a single forward pass efficiently, while at the same time consistently improving MIL model performance. Experiments across multiple slide-level tasks and diverse organs show that HistAug outperforms existing methods, particularly in low-data regimes. Ablation studies confirm the benefits of learned transformations over noise-based perturbations and highlight the importance of uniform WSI-wise augmentation. Code is available at https://github.com/MICS-Lab/HistAug.

Diffusion models (DMs) have recently gained attention with state-of-the-art performance in text-to-image synthesis. Abiding by the tradition in deep learning, DMs are trained and evaluated on the images with fixed sizes. However, users are demanding for various images with specific sizes and various aspect ratio. This paper focuses on adapting text-to-image diffusion models to handle such variety while maintaining visual fidelity. First we observe that, during the synthesis, lower resolution images suffer from incomplete object portrayal, while higher resolution images exhibit repetitively disordered presentation. Next, we establish a statistical relationship indicating that attention entropy changes with token quantity, suggesting that models aggregate spatial information in proportion to image resolution. The subsequent interpretation on our observations is that objects are incompletely depicted due to limited spatial information for low resolutions, while repetitively disorganized presentation arises from redundant spatial information for high resolutions. From this perspective, we propose a scaling factor to alleviate the change of attention entropy and mitigate the defective pattern observed. Extensive experimental results validate the efficacy of the proposed scaling factor, enabling models to achieve better visual effects, image quality, and text alignment. Notably, these improvements are achieved without additional training or fine-tuning techniques.

Object segmentation is an important step in the workflow of computational pathology. Deep learning based models generally require large amount of labeled data for precise and reliable prediction. However, collecting labeled data is expensive because it often requires expert knowledge, particularly in medical imaging domain where labels are the result of a time-consuming analysis made by one or more human experts. As nuclei, cells and glands are fundamental objects for downstream analysis in computational pathology/cytology, in this paper we propose a simple CNN-based approach to speed up collecting annotations for these objects which requires minimum interaction from the annotator. We show that for nuclei and cells in histology and cytology images, one click inside each object is enough for NuClick to yield a precise annotation. For multicellular structures such as glands, we propose a novel approach to provide the NuClick with a squiggle as a guiding signal, enabling it to segment the glandular boundaries. These supervisory signals are fed to the network as auxiliary inputs along with RGB channels. With detailed experiments, we show that NuClick is adaptable to the object scale, robust against variations in the user input, adaptable to new domains, and delivers reliable annotations. An instance segmentation model trained on masks generated by NuClick achieved the first rank in LYON19 challenge. As exemplar outputs of our framework, we are releasing two datasets: 1) a dataset of lymphocyte annotations within IHC images, and 2) a dataset of segmented WBCs in blood smear images.

Multiple Instance learning (MIL) models have been extensively used in pathology to predict biomarkers and risk-stratify patients from gigapixel-sized images. Machine learning problems in medical imaging often deal with rare diseases, making it important for these models to work in a label-imbalanced setting. In pathology images, there is another level of imbalance, where given a positively labeled Whole Slide Image (WSI), only a fraction of pixels within it contribute to the positive label. This compounds the severity of imbalance and makes imbalanced classification in pathology challenging. Furthermore, these imbalances can occur in out-of-distribution (OOD) datasets when the models are deployed in the real-world. We leverage the idea that decoupling feature and classifier learning can lead to improved decision boundaries for label imbalanced datasets. To this end, we investigate the integration of supervised contrastive learning with multiple instance learning (SC-MIL). Specifically, we propose a joint-training MIL framework in the presence of label imbalance that progressively transitions from learning bag-level representations to optimal classifier learning. We perform experiments with different imbalance settings for two well-studied problems in cancer pathology: subtyping of non-small cell lung cancer and subtyping of renal cell carcinoma. SC-MIL provides large and consistent improvements over other techniques on both in-distribution (ID) and OOD held-out sets across multiple imbalanced settings.

The raster-ordered image token sequence exhibits a significant Euclidean distance between index-adjacent tokens at line breaks, making it unsuitable for autoregressive generation. To address this issue, this paper proposes Direction-Aware Diagonal Autoregressive Image Generation (DAR) method, which generates image tokens following a diagonal scanning order. The proposed diagonal scanning order ensures that tokens with adjacent indices remain in close proximity while enabling causal attention to gather information from a broader range of directions. Additionally, two direction-aware modules: 4D-RoPE and direction embeddings are introduced, enhancing the model's capability to handle frequent changes in generation direction. To leverage the representational capacity of the image tokenizer, we use its codebook as the image token embeddings. We propose models of varying scales, ranging from 485M to 2.0B. On the 256times256 ImageNet benchmark, our DAR-XL (2.0B) outperforms all previous autoregressive image generators, achieving a state-of-the-art FID score of 1.37.

Identification of vessel structures of different sizes in biomedical images is crucial in the diagnosis of many neurodegenerative diseases. However, the sparsity of good-quality annotations of such images makes the task of vessel segmentation challenging. Deep learning offers an efficient way to segment vessels of different sizes by learning their high-level feature representations and the spatial continuity of such features across dimensions. Semi-supervised patch-based approaches have been effective in identifying small vessels of one to two voxels in diameter. This study focuses on improving the segmentation quality by considering the spatial correlation of the features using the Maximum Intensity Projection~(MIP) as an additional loss criterion. Two methods are proposed with the incorporation of MIPs of label segmentation on the single~(z-axis) and multiple perceivable axes of the 3D volume. The proposed MIP-based methods produce segmentations with improved vessel continuity, which is evident in visual examinations of ROIs. Patch-based training is improved by introducing an additional loss term, MIP loss, to penalise the predicted discontinuity of vessels. A training set of 14 volumes is selected from the StudyForrest dataset comprising of 18 7-Tesla 3D Time-of-Flight~(ToF) Magnetic Resonance Angiography (MRA) images. The generalisation performance of the method is evaluated using the other unseen volumes in the dataset. It is observed that the proposed method with multi-axes MIP loss produces better quality segmentations with a median Dice of 80.245 pm 0.129. Also, the method with single-axis MIP loss produces segmentations with a median Dice of 79.749 pm 0.109. Furthermore, a visual comparison of the ROIs in the predicted segmentation reveals a significant improvement in the continuity of the vessels when MIP loss is incorporated into training.

Chest X-Ray (CXR) imaging for pulmonary diagnosis raises significant challenges, primarily because bone structures can obscure critical details necessary for accurate diagnosis. Recent advances in deep learning, particularly with diffusion models, offer significant promise for effectively minimizing the visibility of bone structures in CXR images, thereby improving clarity and diagnostic accuracy. Nevertheless, existing diffusion-based methods for bone suppression in CXR imaging struggle to balance the complete suppression of bones with preserving local texture details. Additionally, their high computational demand and extended processing time hinder their practical use in clinical settings. To address these limitations, we introduce a Global-Local Latent Consistency Model (GL-LCM) architecture. This model combines lung segmentation, dual-path sampling, and global-local fusion, enabling fast high-resolution bone suppression in CXR images. To tackle potential boundary artifacts and detail blurring in local-path sampling, we further propose Local-Enhanced Guidance, which addresses these issues without additional training. Comprehensive experiments on a self-collected dataset SZCH-X-Rays, and the public dataset JSRT, reveal that our GL-LCM delivers superior bone suppression and remarkable computational efficiency, significantly outperforming several competitive methods. Our code is available at https://github.com/diaoquesang/GL-LCM.

This study introduces a modular framework for spatial image processing, integrating grayscale quantization, color and brightness enhancement, image sharpening, bidirectional transformation pipelines, and geometric feature extraction. A stepwise intensity transformation quantizes grayscale images into eight discrete levels, producing a posterization effect that simplifies representation while preserving structural detail. Color enhancement is achieved via histogram equalization in both RGB and YCrCb color spaces, with the latter improving contrast while maintaining chrominance fidelity. Brightness adjustment is implemented through HSV value-channel manipulation, and image sharpening is performed using a 3 * 3 convolution kernel to enhance high-frequency details. A bidirectional transformation pipeline that integrates unsharp masking, gamma correction, and noise amplification achieved accuracy levels of 76.10% and 74.80% for the forward and reverse processes, respectively. Geometric feature extraction employed Canny edge detection, Hough-based line estimation (e.g., 51.50{\deg} for billiard cue alignment), Harris corner detection, and morphological window localization. Cue isolation further yielded 81.87\% similarity against ground truth images. Experimental evaluation across diverse datasets demonstrates robust and deterministic performance, highlighting its potential for real-time image analysis and computer vision.

Domain generalization is critical for real-world applications of machine learning to microscopy images, including histopathology and fluorescence imaging. Artifacts in these modalities arise through a complex combination of factors relating to tissue collection and laboratory processing, as well as factors intrinsic to patient samples. In fluorescence imaging, these artifacts stem from variations across experimental batches. The complexity and subtlety of these artifacts make the enumeration of data domains intractable. Therefore, augmentation-based methods of domain generalization that require domain identifiers and manual fine-tuning are inadequate in this setting. To overcome this challenge, we introduce ContriMix, a domain generalization technique that learns to generate synthetic images by disentangling and permuting the biological content ("content") and technical variations ("attributes") in microscopy images. ContriMix does not rely on domain identifiers or handcrafted augmentations and makes no assumptions about the input characteristics of images. We assess the performance of ContriMix on two pathology datasets dealing with patch classification and Whole Slide Image label prediction tasks respectively (Camelyon17-WILDS and RCC subtyping), and one fluorescence microscopy dataset (RxRx1-WILDS). Without any access to domain identifiers at train or test time, ContriMix performs similar or better than current state-of-the-art methods in all these datasets, motivating its usage for microscopy image analysis in real-world settings where domain information is hard to come by. The code for ContriMix can be found at https://gitlab.com/huutan86/contrimix

Time-lapse fluorescent microscopy (TLFM) combined with predictive mathematical modelling is a powerful tool to study the inherently dynamic processes of life on the single-cell level. Such experiments are costly, complex and labour intensive. A complimentary approach and a step towards in silico experimentation, is to synthesise the imagery itself. Here, we propose Multi-StyleGAN as a descriptive approach to simulate time-lapse fluorescence microscopy imagery of living cells, based on a past experiment. This novel generative adversarial network synthesises a multi-domain sequence of consecutive timesteps. We showcase Multi-StyleGAN on imagery of multiple live yeast cells in microstructured environments and train on a dataset recorded in our laboratory. The simulation captures underlying biophysical factors and time dependencies, such as cell morphology, growth, physical interactions, as well as the intensity of a fluorescent reporter protein. An immediate application is to generate additional training and validation data for feature extraction algorithms or to aid and expedite development of advanced experimental techniques such as online monitoring or control of cells. Code and dataset is available at https://git.rwth-aachen.de/bcs/projects/tp/multi-stylegan.

Nucleus instance segmentation in histology images is crucial for a broad spectrum of clinical applications. Current dominant algorithms rely on regression of nuclear proxy maps. Distinguishing nucleus instances from the estimated maps requires carefully curated post-processing, which is error-prone and parameter-sensitive. Recently, the Segment Anything Model (SAM) has earned huge attention in medical image segmentation, owing to its impressive generalization ability and promptable property. Nevertheless, its potential on nucleus instance segmentation remains largely underexplored. In this paper, we present a novel prompt-driven framework that consists of a nucleus prompter and SAM for automatic nucleus instance segmentation. Specifically, the prompter learns to generate a unique point prompt for each nucleus while the SAM is fine-tuned to output the corresponding mask for the prompted nucleus. Furthermore, we propose the inclusion of adjacent nuclei as negative prompts to enhance the model's capability to identify overlapping nuclei. Without complicated post-processing, our proposed method sets a new state-of-the-art performance on three challenging benchmarks. Code is available at github.com/windygoo/PromptNucSeg

We propose to restore old photos that suffer from severe degradation through a deep learning approach. Unlike conventional restoration tasks that can be solved through supervised learning, the degradation in real photos is complex and the domain gap between synthetic images and real old photos makes the network fail to generalize. Therefore, we propose a novel triplet domain translation network by leveraging real photos along with massive synthetic image pairs. Specifically, we train two variational autoencoders (VAEs) to respectively transform old photos and clean photos into two latent spaces. And the translation between these two latent spaces is learned with synthetic paired data. This translation generalizes well to real photos because the domain gap is closed in the compact latent space. Besides, to address multiple degradations mixed in one old photo, we design a global branch with a partial nonlocal block targeting to the structured defects, such as scratches and dust spots, and a local branch targeting to the unstructured defects, such as noises and blurriness. Two branches are fused in the latent space, leading to improved capability to restore old photos from multiple defects. The proposed method outperforms state-of-the-art methods in terms of visual quality for old photos restoration.

This paper contributes to the "BraTS 2024 Brain MR Image Synthesis Challenge" and presents a conditional Wavelet Diffusion Model (cWDM) for directly solving a paired image-to-image translation task on high-resolution volumes. While deep learning-based brain tumor segmentation models have demonstrated clear clinical utility, they typically require MR scans from various modalities (T1, T1ce, T2, FLAIR) as input. However, due to time constraints or imaging artifacts, some of these modalities may be missing, hindering the application of well-performing segmentation algorithms in clinical routine. To address this issue, we propose a method that synthesizes one missing modality image conditioned on three available images, enabling the application of downstream segmentation models. We treat this paired image-to-image translation task as a conditional generation problem and solve it by combining a Wavelet Diffusion Model for high-resolution 3D image synthesis with a simple conditioning strategy. This approach allows us to directly apply our model to full-resolution volumes, avoiding artifacts caused by slice- or patch-wise data processing. While this work focuses on a specific application, the presented method can be applied to all kinds of paired image-to-image translation problems, such as CT leftrightarrow MR and MR leftrightarrow PET translation, or mask-conditioned anatomically guided image generation.

In clinical radiology reports, doctors capture important information about the patient's health status. They convey their observations from raw medical imaging data about the inner structures of a patient. As such, formulating reports requires medical experts to possess wide-ranging knowledge about anatomical regions with their normal, healthy appearance as well as the ability to recognize abnormalities. This explicit grasp on both the patient's anatomy and their appearance is missing in current medical image-processing systems as annotations are especially difficult to gather. This renders the models to be narrow experts e.g. for identifying specific diseases. In this work, we recover this missing link by adding human anatomy into the mix and enable the association of content in medical reports to their occurrence in associated imagery (medical phrase grounding). To exploit anatomical structures in this scenario, we present a sophisticated automatic pipeline to gather and integrate human bodily structures from computed tomography datasets, which we incorporate in our PAXRay: A Projected dataset for the segmentation of Anatomical structures in X-Ray data. Our evaluation shows that methods that take advantage of anatomical information benefit heavily in visually grounding radiologists' findings, as our anatomical segmentations allow for up to absolute 50% better grounding results on the OpenI dataset as compared to commonly used region proposals. The PAXRay dataset is available at https://constantinseibold.github.io/paxray/.

Immunohistochemical (IHC) staining highlights the molecular information critical to diagnostics in tissue samples. However, compared to H&E staining, IHC staining can be much more expensive in terms of both labor and the laboratory equipment required. This motivates recent research that demonstrates that the correlations between the morphological information present in the H&E-stained slides and the molecular information in the IHC-stained slides can be used for H&E-to-IHC stain translation. However, due to a lack of pixel-perfect H&E-IHC groundtruth pairs, most existing methods have resorted to relying on expert annotations. To remedy this situation, we present a new loss function, Adaptive Supervised PatchNCE (ASP), to directly deal with the input to target inconsistencies in a proposed H&E-to-IHC image-to-image translation framework. The ASP loss is built upon a patch-based contrastive learning criterion, named Supervised PatchNCE (SP), and augments it further with weight scheduling to mitigate the negative impact of noisy supervision. Lastly, we introduce the Multi-IHC Stain Translation (MIST) dataset, which contains aligned H&E-IHC patches for 4 different IHC stains critical to breast cancer diagnosis. In our experiment, we demonstrate that our proposed method outperforms existing image-to-image translation methods for stain translation to multiple IHC stains. All of our code and datasets are available at https://github.com/lifangda01/AdaptiveSupervisedPatchNCE.

Growing evidence indicates that only a sparse subset from a pool of sensory neurons is active for the encoding of visual stimuli at any instant in time. Traditionally, to replicate such biological sparsity, generative models have been using the ell_1 norm as a penalty due to its convexity, which makes it amenable to fast and simple algorithmic solvers. In this work, we use biological vision as a test-bed and show that the soft thresholding operation associated to the use of the ell_1 norm is highly suboptimal compared to other functions suited to approximating ell_q with 0 leq q < 1 (including recently proposed Continuous Exact relaxations), both in terms of performance and in the production of features that are akin to signatures of the primary visual cortex. We show that ell_1 sparsity produces a denser code or employs a pool with more neurons, i.e. has a higher degree of overcompleteness, in order to maintain the same reconstruction error as the other methods considered. For all the penalty functions tested, a subset of the neurons develop orientation selectivity similarly to V1 neurons. When their code is sparse enough, the methods also develop receptive fields with varying functionalities, another signature of V1. Compared to other methods, soft thresholding achieves this level of sparsity at the expense of much degraded reconstruction performance, that more likely than not is not acceptable in biological vision. Our results indicate that V1 uses a sparsity inducing regularization that is closer to the ell_0 pseudo-norm rather than to the ell_1 norm.

We use images of cars of a wide range of varieties to compose an image of an animal such as a bird or a lion for the theme of environmental protection to maximize the information about cars in a single composed image and to raise the awareness about environmental challenges. We present a novel way of image interaction with an artistically-composed photomosaic image, in which a simple operation of "click and display" is used to demonstrate the interactive switch between a tile image in a photomosaic image and the corresponding original car image, which will be automatically saved on the Desktop. We build a multimodal custom GPT named TalkMosaic by incorporating car images information and the related knowledge to ChatGPT. By uploading the original car image to TalkMosaic, we can ask questions about the given car image and get the corresponding answers efficiently and effectively such as where to buy the tire in the car image that satisfies high environmental standards. We give an in-depth analysis on how to speed up the inference of multimodal LLM using sparse attention and quantization techniques with presented probabilistic FlashAttention (PrFlashAttention) and Staircase Adaptive Quantization (SAQ) methods. The implemented prototype demonstrates the feasibility and effectiveness of the presented approach.

The proliferation of digital microscopy images, driven by advances in automated whole slide scanning, presents significant opportunities for biomedical research and clinical diagnostics. However, accurately annotating densely packed information in these images remains a major challenge. To address this, we introduce DiffKillR, a novel framework that reframes cell annotation as the combination of archetype matching and image registration tasks. DiffKillR employs two complementary neural networks: one that learns a diffeomorphism-invariant feature space for robust cell matching and another that computes the precise warping field between cells for annotation mapping. Using a small set of annotated archetypes, DiffKillR efficiently propagates annotations across large microscopy images, reducing the need for extensive manual labeling. More importantly, it is suitable for any type of pixel-level annotation. We will discuss the theoretical properties of DiffKillR and validate it on three microscopy tasks, demonstrating its advantages over existing supervised, semi-supervised, and unsupervised methods. The code is available at https://github.com/KrishnaswamyLab/DiffKillR.

Active learning promises to improve annotation efficiency by iteratively selecting the most important data to be annotated first. However, we uncover a striking contradiction to this promise: active learning fails to select data as efficiently as random selection at the first few choices. We identify this as the cold start problem in vision active learning, caused by a biased and outlier initial query. This paper seeks to address the cold start problem by exploiting the three advantages of contrastive learning: (1) no annotation is required; (2) label diversity is ensured by pseudo-labels to mitigate bias; (3) typical data is determined by contrastive features to reduce outliers. Experiments are conducted on CIFAR-10-LT and three medical imaging datasets (i.e. Colon Pathology, Abdominal CT, and Blood Cell Microscope). Our initial query not only significantly outperforms existing active querying strategies but also surpasses random selection by a large margin. We foresee our solution to the cold start problem as a simple yet strong baseline to choose the initial query for vision active learning. Code is available: https://github.com/c-liangyu/CSVAL

Large Vision-Language Models (LVLMs) typically learn visual capacity through visual instruction tuning, involving updates to both a projector and their LLM backbones. Drawing inspiration from the concept of visual region in the human brain, we investigate the existence of an analogous visual region within LLMs that functions as a cognitive core, and explore the possibility of efficient training of LVLMs via selective layers tuning. We use Bunny-Llama-3-8B-V for detailed experiments and LLaVA-1.5-7B and LLaVA-1.5-13B for validation across a range of visual and textual tasks. Our findings reveal that selectively updating 25\% of LLMs layers, when sparsely and uniformly distributed, can preserve nearly 99\% of visual performance while maintaining or enhancing textual task results, and also effectively reducing training time. Based on this targeted training approach, we further propose a novel visual region-based pruning paradigm, removing non-critical layers outside the visual region, which can achieve minimal performance loss. This study offers an effective and efficient strategy for LVLM training and inference by activating a layer-wise visual region within LLMs, which is consistently effective across different models and parameter scales.

Recent work has investigated the distributions of learned convolution filters through a large-scale study containing hundreds of heterogeneous image models. Surprisingly, on average, the distributions only show minor drifts in comparisons of various studied dimensions including the learned task, image domain, or dataset. However, among the studied image domains, medical imaging models appeared to show significant outliers through "spikey" distributions, and, therefore, learn clusters of highly specific filters different from other domains. Following this observation, we study the collected medical imaging models in more detail. We show that instead of fundamental differences, the outliers are due to specific processing in some architectures. Quite the contrary, for standardized architectures, we find that models trained on medical data do not significantly differ in their filter distributions from similar architectures trained on data from other domains. Our conclusions reinforce previous hypotheses stating that pre-training of imaging models can be done with any kind of diverse image data.

Self-supervised learning in vision-language processing exploits semantic alignment between imaging and text modalities. Prior work in biomedical VLP has mostly relied on the alignment of single image and report pairs even though clinical notes commonly refer to prior images. This does not only introduce poor alignment between the modalities but also a missed opportunity to exploit rich self-supervision through existing temporal content in the data. In this work, we explicitly account for prior images and reports when available during both training and fine-tuning. Our approach, named BioViL-T, uses a CNN-Transformer hybrid multi-image encoder trained jointly with a text model. It is designed to be versatile to arising challenges such as pose variations and missing input images across time. The resulting model excels on downstream tasks both in single- and multi-image setups, achieving state-of-the-art performance on (I) progression classification, (II) phrase grounding, and (III) report generation, whilst offering consistent improvements on disease classification and sentence-similarity tasks. We release a novel multi-modal temporal benchmark dataset, MS-CXR-T, to quantify the quality of vision-language representations in terms of temporal semantics. Our experimental results show the advantages of incorporating prior images and reports to make most use of the data.

Ultrasound Localization Microscopy (ULM) enables imaging of vascular structures in the micrometer range by accumulating contrast agent particle locations over time. Precise and efficient target localization accuracy remains an active research topic in the ULM field to further push the boundaries of this promising medical imaging technology. Existing work incorporates Delay-And-Sum (DAS) beamforming into particle localization pipelines, which ultimately determines the ULM image resolution capability. In this paper we propose to feed unprocessed Radio-Frequency (RF) data into a super-resolution network while bypassing DAS beamforming and its limitations. To facilitate this, we demonstrate label projection and inverse point transformation between B-mode and RF coordinate space as required by our approach. We assess our method against state-of-the-art techniques based on a public dataset featuring in silico and in vivo data. Results from our RF-trained network suggest that excluding DAS beamforming offers a great potential to optimize on the ULM resolution performance.

We introduce DLSIA (Deep Learning for Scientific Image Analysis), a Python-based machine learning library that empowers scientists and researchers across diverse scientific domains with a range of customizable convolutional neural network (CNN) architectures for a wide variety of tasks in image analysis to be used in downstream data processing, or for experiment-in-the-loop computing scenarios. DLSIA features easy-to-use architectures such as autoencoders, tunable U-Nets, and parameter-lean mixed-scale dense networks (MSDNets). Additionally, we introduce sparse mixed-scale networks (SMSNets), generated using random graphs and sparse connections. As experimental data continues to grow in scale and complexity, DLSIA provides accessible CNN construction and abstracts CNN complexities, allowing scientists to tailor their machine learning approaches, accelerate discoveries, foster interdisciplinary collaboration, and advance research in scientific image analysis.

We introduce a radiology-focused visual language model designed to generate radiology reports from chest X-rays. Building on previous findings that large language models (LLMs) can acquire multimodal capabilities when aligned with pretrained vision encoders, we demonstrate similar potential with chest X-ray images. This integration enhances the ability of model to understand and describe chest X-ray images. Our model combines an image encoder with a fine-tuned LLM based on the Vicuna-7B architecture, enabling it to generate different sections of a radiology report with notable accuracy. The training process involves a two-stage approach: (i) initial alignment of chest X-ray features with the LLM (ii) followed by fine-tuning for radiology report generation.

Foundation models, often pre-trained with large-scale data, have achieved paramount success in jump-starting various vision and language applications. Recent advances further enable adapting foundation models in downstream tasks efficiently using only a few training samples, e.g., in-context learning. Yet, the application of such learning paradigms in medical image analysis remains scarce due to the shortage of publicly accessible data and benchmarks. In this paper, we aim at approaches adapting the foundation models for medical image classification and present a novel dataset and benchmark for the evaluation, i.e., examining the overall performance of accommodating the large-scale foundation models downstream on a set of diverse real-world clinical tasks. We collect five sets of medical imaging data from multiple institutes targeting a variety of real-world clinical tasks (22,349 images in total), i.e., thoracic diseases screening in X-rays, pathological lesion tissue screening, lesion detection in endoscopy images, neonatal jaundice evaluation, and diabetic retinopathy grading. Results of multiple baseline methods are demonstrated using the proposed dataset from both accuracy and cost-effective perspectives.

Endoscopic procedures are essential for diagnosing and treating internal diseases, and multi-modal large language models (MLLMs) are increasingly applied to assist in endoscopy analysis. However, current benchmarks are limited, as they typically cover specific endoscopic scenarios and a small set of clinical tasks, failing to capture the real-world diversity of endoscopic scenarios and the full range of skills needed in clinical workflows. To address these issues, we introduce EndoBench, the first comprehensive benchmark specifically designed to assess MLLMs across the full spectrum of endoscopic practice with multi-dimensional capacities. EndoBench encompasses 4 distinct endoscopic scenarios, 12 specialized clinical tasks with 12 secondary subtasks, and 5 levels of visual prompting granularities, resulting in 6,832 rigorously validated VQA pairs from 21 diverse datasets. Our multi-dimensional evaluation framework mirrors the clinical workflow--spanning anatomical recognition, lesion analysis, spatial localization, and surgical operations--to holistically gauge the perceptual and diagnostic abilities of MLLMs in realistic scenarios. We benchmark 23 state-of-the-art models, including general-purpose, medical-specialized, and proprietary MLLMs, and establish human clinician performance as a reference standard. Our extensive experiments reveal: (1) proprietary MLLMs outperform open-source and medical-specialized models overall, but still trail human experts; (2) medical-domain supervised fine-tuning substantially boosts task-specific accuracy; and (3) model performance remains sensitive to prompt format and clinical task complexity. EndoBench establishes a new standard for evaluating and advancing MLLMs in endoscopy, highlighting both progress and persistent gaps between current models and expert clinical reasoning. We publicly release our benchmark and code.

The most widely used method for obtaining high-quality two-dimensional materials is through mechanical exfoliation of bulk crystals. Manual identification of suitable flakes from the resulting random distribution of crystal thicknesses and sizes on a substrate is a time-consuming, tedious task. Here, we present a platform for fully automated scanning, detection, and classification of two-dimensional materials, the source code of which we make openly available. Our platform is designed to be accurate, reliable, fast, and versatile in integrating new materials, making it suitable for everyday laboratory work. The implementation allows fully automated scanning and analysis of wafers with an average inference time of 100 ms for images of 2.3 Mpixels. The developed detection algorithm is based on a combination of the flakes' optical contrast toward the substrate and their geometric shape. We demonstrate that it is able to detect the majority of exfoliated flakes of various materials, with an average recall (AR50) between 67% and 89%. We also show that the algorithm can be trained with as few as five flakes of a given material, which we demonstrate for the examples of few-layer graphene, WSe_2, MoSe_2, CrI_3, 1T-TaS_2 and hexagonal BN. Our platform has been tested over a two-year period, during which more than 10^6 images of multiple different materials were acquired by over 30 individual researchers.

Built on the power of LLMs, numerous multimodal large language models (MLLMs) have recently achieved remarkable performance on various vision-language tasks across multiple benchmarks. However, most existing MLLMs and benchmarks primarily focus on single-image input scenarios, leaving the performance of MLLMs when handling realistic multiple images remain underexplored. Although a few benchmarks consider multiple images, their evaluation dimensions and samples are very limited. Therefore, in this paper, we propose a new benchmark MIBench, to comprehensively evaluate fine-grained abilities of MLLMs in multi-image scenarios. Specifically, MIBench categorizes the multi-image abilities into three scenarios: multi-image instruction (MII), multimodal knowledge-seeking (MKS) and multimodal in-context learning (MIC), and constructs 13 tasks with a total of 13K annotated samples. During data construction, for MII and MKS, we extract correct options from manual annotations and create challenging distractors to obtain multiple-choice questions. For MIC, to enable an in-depth evaluation, we set four sub-tasks and transform the original datasets into in-context learning formats. We evaluate several open-source MLLMs and close-source MLLMs on the proposed MIBench. The results reveal that although current models excel in single-image tasks, they exhibit significant shortcomings when faced with multi-image inputs, such as confused fine-grained perception, limited multi-image reasoning, and unstable in-context learning. The annotated data in MIBench is available at https://huggingface.co/datasets/StarBottle/MIBench.

We introduce a novel bilateral reference framework (BiRefNet) for high-resolution dichotomous image segmentation (DIS). It comprises two essential components: the localization module (LM) and the reconstruction module (RM) with our proposed bilateral reference (BiRef). The LM aids in object localization using global semantic information. Within the RM, we utilize BiRef for the reconstruction process, where hierarchical patches of images provide the source reference and gradient maps serve as the target reference. These components collaborate to generate the final predicted maps. We also introduce auxiliary gradient supervision to enhance focus on regions with finer details. Furthermore, we outline practical training strategies tailored for DIS to improve map quality and training process. To validate the general applicability of our approach, we conduct extensive experiments on four tasks to evince that BiRefNet exhibits remarkable performance, outperforming task-specific cutting-edge methods across all benchmarks. Our codes are available at https://github.com/ZhengPeng7/BiRefNet.

Vision-language models in pathology enable multimodal case retrieval and automated report generation. Many of the models developed so far, however, have been trained on pathology reports that include information which cannot be inferred from paired whole slide images (e.g., patient history), potentially leading to hallucinated sentences in generated reports. To this end, we investigate how the selection of information from pathology reports for vision-language modeling affects the quality of the multimodal representations and generated reports. More concretely, we compare a model trained on full reports against a model trained on preprocessed reports that only include sentences describing the cell and tissue appearances based on the H&E-stained slides. For the experiments, we built upon the BLIP-2 framework and used a cutaneous melanocytic lesion dataset of 42,433 H&E-stained whole slide images and 19,636 corresponding pathology reports. Model performance was assessed using image-to-text and text-to-image retrieval, as well as qualitative evaluation of the generated reports by an expert pathologist. Our results demonstrate that text preprocessing prevents hallucination in report generation. Despite the improvement in the quality of the generated reports, training the vision-language model on full reports showed better cross-modal retrieval performance.

Despite the progress in automatic detection of radiologic findings from chest X-ray (CXR) images in recent years, a quantitative evaluation of the explainability of these models is hampered by the lack of locally labeled datasets for different findings. With the exception of a few expert-labeled small-scale datasets for specific findings, such as pneumonia and pneumothorax, most of the CXR deep learning models to date are trained on global "weak" labels extracted from text reports, or trained via a joint image and unstructured text learning strategy. Inspired by the Visual Genome effort in the computer vision community, we constructed the first Chest ImaGenome dataset with a scene graph data structure to describe 242,072 images. Local annotations are automatically produced using a joint rule-based natural language processing (NLP) and atlas-based bounding box detection pipeline. Through a radiologist constructed CXR ontology, the annotations for each CXR are connected as an anatomy-centered scene graph, useful for image-level reasoning and multimodal fusion applications. Overall, we provide: i) 1,256 combinations of relation annotations between 29 CXR anatomical locations (objects with bounding box coordinates) and their attributes, structured as a scene graph per image, ii) over 670,000 localized comparison relations (for improved, worsened, or no change) between the anatomical locations across sequential exams, as well as ii) a manually annotated gold standard scene graph dataset from 500 unique patients.

State Space Models (SSMs), especially Mamba, have shown great promise in medical image segmentation due to their ability to model long-range dependencies with linear computational complexity. However, accurate medical image segmentation requires the effective learning of both multi-scale detailed feature representations and global contextual dependencies. Although existing works have attempted to address this issue by integrating CNNs and SSMs to leverage their respective strengths, they have not designed specialized modules to effectively capture multi-scale feature representations, nor have they adequately addressed the directional sensitivity problem when applying Mamba to 2D image data. To overcome these limitations, we propose a Multi-Scale Vision Mamba UNet model for medical image segmentation, termed MSVM-UNet. Specifically, by introducing multi-scale convolutions in the VSS blocks, we can more effectively capture and aggregate multi-scale feature representations from the hierarchical features of the VMamba encoder and better handle 2D visual data. Additionally, the large kernel patch expanding (LKPE) layers achieve more efficient upsampling of feature maps by simultaneously integrating spatial and channel information. Extensive experiments on the Synapse and ACDC datasets demonstrate that our approach is more effective than some state-of-the-art methods in capturing and aggregating multi-scale feature representations and modeling long-range dependencies between pixels.

This paper presents a comprehensive review of the NTIRE 2025 Challenge on Single-Image Efficient Super-Resolution (ESR). The challenge aimed to advance the development of deep models that optimize key computational metrics, i.e., runtime, parameters, and FLOPs, while achieving a PSNR of at least 26.90 dB on the DIV2K_LSDIR_valid dataset and 26.99 dB on the DIV2K_LSDIR_test dataset. A robust participation saw 244 registered entrants, with 43 teams submitting valid entries. This report meticulously analyzes these methods and results, emphasizing groundbreaking advancements in state-of-the-art single-image ESR techniques. The analysis highlights innovative approaches and establishes benchmarks for future research in the field.

In this work, we focused on deep learning image processing in the context of oral rare diseases, which pose challenges due to limited data availability. A crucial step involves teeth detection, segmentation and numbering in panoramic radiographs. To this end, we used a dataset consisting of 156 panoramic radiographs from individuals with rare oral diseases and labeled by experts. We trained the Detection Transformer (DETR) neural network for teeth detection, segmentation, and numbering the 52 teeth classes. In addition, we used data augmentation techniques, including geometric transformations. Finally, we generated new panoramic images using inpainting techniques with stable diffusion, by removing teeth from a panoramic radiograph and integrating teeth into it. The results showed a mAP exceeding 0,69 for DETR without data augmentation. The mAP was improved to 0,82 when data augmentation techniques are used. Furthermore, we observed promising performances when using new panoramic radiographs generated with inpainting technique, with mAP of 0,76.

Recent advances in large multimodal models (LMMs) suggest that higher image resolution enhances the fine-grained understanding of image details, crucial for tasks such as visual commonsense reasoning and analyzing biomedical images. However, increasing input resolution poses two main challenges: 1) It extends the context length required by the language model, leading to inefficiencies and hitting the model's context limit; 2) It increases the complexity of visual features, necessitating more training data or more complex architecture. We introduce Dragonfly, a new LMM architecture that enhances fine-grained visual understanding and reasoning about image regions to address these challenges. Dragonfly employs two key strategies: multi-resolution visual encoding and zoom-in patch selection. These strategies allow the model to process high-resolution images efficiently while maintaining reasonable context length. Our experiments on eight popular benchmarks demonstrate that Dragonfly achieves competitive or better performance compared to other architectures, highlighting the effectiveness of our design. Additionally, we finetuned Dragonfly on biomedical instructions, achieving state-of-the-art results on multiple biomedical tasks requiring fine-grained visual understanding, including 92.3% accuracy on the Path-VQA dataset (compared to 83.3% for Med-Gemini) and the highest reported results on biomedical image captioning. To support model training, we curated a visual instruction-tuning dataset with 5.5 million image-instruction samples in the general domain and 1.4 million samples in the biomedical domain. We also conducted ablation studies to characterize the impact of various architectural designs and image resolutions, providing insights for future research on visual instruction alignment. The codebase and model are available at https://github.com/togethercomputer/Dragonfly.

We introduce the first publicly available breast MRI dataset with explicit left and right breast segmentation labels, encompassing more than 13,000 annotated cases. Alongside this dataset, we provide a robust deep-learning model trained for left-right breast segmentation. This work addresses a critical gap in breast MRI analysis and offers a valuable resource for the development of advanced tools in women's health. The dataset and trained model are publicly available at: www.github.com/MIC-DKFZ/BreastDivider

We present SAM4EM, a novel approach for 3D segmentation of complex neural structures in electron microscopy (EM) data by leveraging the Segment Anything Model (SAM) alongside advanced fine-tuning strategies. Our contributions include the development of a prompt-free adapter for SAM using two stage mask decoding to automatically generate prompt embeddings, a dual-stage fine-tuning method based on Low-Rank Adaptation (LoRA) for enhancing segmentation with limited annotated data, and a 3D memory attention mechanism to ensure segmentation consistency across 3D stacks. We further release a unique benchmark dataset for the segmentation of astrocytic processes and synapses. We evaluated our method on challenging neuroscience segmentation benchmarks, specifically targeting mitochondria, glia, and synapses, with significant accuracy improvements over state-of-the-art (SOTA) methods, including recent SAM-based adapters developed for the medical domain and other vision transformer-based approaches. Experimental results indicate that our approach outperforms existing solutions in the segmentation of complex processes like glia and post-synaptic densities. Our code and models are available at https://github.com/Uzshah/SAM4EM.

In the radiation therapy of nasopharyngeal carcinoma (NPC), clinicians typically delineate the gross tumor volume (GTV) using non-contrast planning computed tomography to ensure accurate radiation dose delivery. However, the low contrast between tumors and adjacent normal tissues necessitates that radiation oncologists manually delineate the tumors, often relying on diagnostic MRI for guidance. % In this study, we propose a novel approach to directly segment NPC gross tumors on non-contrast planning CT images, circumventing potential registration errors when aligning MRI or MRI-derived tumor masks to planning CT. To address the low contrast issues between tumors and adjacent normal structures in planning CT, we introduce a 3D Semantic Asymmetry Tumor segmentation (SATs) method. Specifically, we posit that a healthy nasopharyngeal region is characteristically bilaterally symmetric, whereas the emergence of nasopharyngeal carcinoma disrupts this symmetry. Then, we propose a Siamese contrastive learning segmentation framework that minimizes the voxel-wise distance between original and flipped areas without tumor and encourages a larger distance between original and flipped areas with tumor. Thus, our approach enhances the sensitivity of features to semantic asymmetries. % Extensive experiments demonstrate that the proposed SATs achieves the leading NPC GTV segmentation performance in both internal and external testing, e.g., with at least 2\% absolute Dice score improvement and 12\% average distance error reduction when compared to other state-of-the-art methods in the external testing.

Identifying cell types and understanding their functional properties is crucial for unraveling the mechanisms underlying perception and cognition. In the retina, functional types can be identified by carefully selected stimuli, but this requires expert domain knowledge and biases the procedure towards previously known cell types. In the visual cortex, it is still unknown what functional types exist and how to identify them. Thus, for unbiased identification of the functional cell types in retina and visual cortex, new approaches are needed. Here we propose an optimization-based clustering approach using deep predictive models to obtain functional clusters of neurons using Most Discriminative Stimuli (MDS). Our approach alternates between stimulus optimization with cluster reassignment akin to an expectation-maximization algorithm. The algorithm recovers functional clusters in mouse retina, marmoset retina and macaque visual area V4. This demonstrates that our approach can successfully find discriminative stimuli across species, stages of the visual system and recording techniques. The resulting most discriminative stimuli can be used to assign functional cell types fast and on the fly, without the need to train complex predictive models or show a large natural scene dataset, paving the way for experiments that were previously limited by experimental time. Crucially, MDS are interpretable: they visualize the distinctive stimulus patterns that most unambiguously identify a specific type of neuron.

The development of vision-language models (VLMs) is driven by large-scale and diverse multimodal datasets. However, progress toward generalist biomedical VLMs is limited by the lack of annotated, publicly accessible datasets across biology and medicine. Existing efforts are restricted to narrow domains, missing the full diversity of biomedical knowledge encoded in scientific literature. To address this gap, we introduce BIOMEDICA, a scalable, open-source framework to extract, annotate, and serialize the entirety of the PubMed Central Open Access subset into an easy-to-use, publicly accessible dataset.Our framework produces a comprehensive archive with over 24 million unique image-text pairs from over 6 million articles. Metadata and expert-guided annotations are also provided. We demonstrate the utility and accessibility of our resource by releasing BMCA-CLIP, a suite of CLIP-style models continuously pre-trained on the BIOMEDICA dataset via streaming, eliminating the need to download 27 TB of data locally.On average, our models achieve state-of-the-art performance across 40 tasks - spanning pathology, radiology, ophthalmology, dermatology, surgery, molecular biology, parasitology, and cell biology - excelling in zero-shot classification with a 6.56% average improvement (as high as 29.8% and 17.5% in dermatology and ophthalmology, respectively), and stronger image-text retrieval, all while using 10x less compute. To foster reproducibility and collaboration, we release our codebase and dataset for the broader research community.

Recently, Neural Radiance Field (NeRF) has shown great success in rendering novel-view images of a given scene by learning an implicit representation with only posed RGB images. NeRF and relevant neural field methods (e.g., neural surface representation) typically optimize a point-wise loss and make point-wise predictions, where one data point corresponds to one pixel. Unfortunately, this line of research failed to use the collective supervision of distant pixels, although it is known that pixels in an image or scene can provide rich structural information. To the best of our knowledge, we are the first to design a nonlocal multiplex training paradigm for NeRF and relevant neural field methods via a novel Stochastic Structural SIMilarity (S3IM) loss that processes multiple data points as a whole set instead of process multiple inputs independently. Our extensive experiments demonstrate the unreasonable effectiveness of S3IM in improving NeRF and neural surface representation for nearly free. The improvements of quality metrics can be particularly significant for those relatively difficult tasks: e.g., the test MSE loss unexpectedly drops by more than 90% for TensoRF and DVGO over eight novel view synthesis tasks; a 198% F-score gain and a 64% Chamfer L_{1} distance reduction for NeuS over eight surface reconstruction tasks. Moreover, S3IM is consistently robust even with sparse inputs, corrupted images, and dynamic scenes.

Most in-the-wild images are stored in Low Dynamic Range (LDR) form, serving as a partial observation of the High Dynamic Range (HDR) visual world. Despite limited dynamic range, these LDR images are often captured with different exposures, implicitly containing information about the underlying HDR image distribution. Inspired by this intuition, in this work we present, to the best of our knowledge, the first method for learning a generative model of HDR images from in-the-wild LDR image collections in a fully unsupervised manner. The key idea is to train a generative adversarial network (GAN) to generate HDR images which, when projected to LDR under various exposures, are indistinguishable from real LDR images. The projection from HDR to LDR is achieved via a camera model that captures the stochasticity in exposure and camera response function. Experiments show that our method GlowGAN can synthesize photorealistic HDR images in many challenging cases such as landscapes, lightning, or windows, where previous supervised generative models produce overexposed images. We further demonstrate the new application of unsupervised inverse tone mapping (ITM) enabled by GlowGAN. Our ITM method does not need HDR images or paired multi-exposure images for training, yet it reconstructs more plausible information for overexposed regions than state-of-the-art supervised learning models trained on such data.

Great successes have been achieved using deep learning techniques for image super-resolution (SR) with fixed scales. To increase its real world applicability, numerous models have also been proposed to restore SR images with arbitrary scale factors, including asymmetric ones where images are resized to different scales along horizontal and vertical directions. Though most models are only optimized for the unidirectional upscaling task while assuming a predefined downscaling kernel for low-resolution (LR) inputs, recent models based on Invertible Neural Networks (INN) are able to increase upscaling accuracy significantly by optimizing the downscaling and upscaling cycle jointly. However, limited by the INN architecture, it is constrained to fixed integer scale factors and requires one model for each scale. Without increasing model complexity, a simple and effective invertible arbitrary rescaling network (IARN) is proposed to achieve arbitrary image rescaling by training only one model in this work. Using innovative components like position-aware scale encoding and preemptive channel splitting, the network is optimized to convert the non-invertible rescaling cycle to an effectively invertible process. It is shown to achieve a state-of-the-art (SOTA) performance in bidirectional arbitrary rescaling without compromising perceptual quality in LR outputs. It is also demonstrated to perform well on tests with asymmetric scales using the same network architecture.

Multimodal large language models (LLMs) have demonstrated impressive capabilities in generating high-quality images from textual instructions. However, their performance in generating scientific images--a critical application for accelerating scientific progress--remains underexplored. In this work, we address this gap by introducing ScImage, a benchmark designed to evaluate the multimodal capabilities of LLMs in generating scientific images from textual descriptions. ScImage assesses three key dimensions of understanding: spatial, numeric, and attribute comprehension, as well as their combinations, focusing on the relationships between scientific objects (e.g., squares, circles). We evaluate five models, GPT-4o, Llama, AutomaTikZ, Dall-E, and StableDiffusion, using two modes of output generation: code-based outputs (Python, TikZ) and direct raster image generation. Additionally, we examine four different input languages: English, German, Farsi, and Chinese. Our evaluation, conducted with 11 scientists across three criteria (correctness, relevance, and scientific accuracy), reveals that while GPT-4o produces outputs of decent quality for simpler prompts involving individual dimensions such as spatial, numeric, or attribute understanding in isolation, all models face challenges in this task, especially for more complex prompts.

We propose a learning-based method to recover normals, specularity, and roughness from a single diffuse image of a material, using microgeometry appearance as our primary cue. Previous methods that work on single images tend to produce over-smooth outputs with artifacts, operate at limited resolution, or train one model per class with little room for generalization. Previous methods that work on single images tend to produce over-smooth outputs with artifacts, operate at limited resolution, or train one model per class with little room for generalization. In contrast, in this work, we propose a novel capture approach that leverages a generative network with attention and a U-Net discriminator, which shows outstanding performance integrating global information at reduced computational complexity. We showcase the performance of our method with a real dataset of digitized textile materials and show that a commodity flatbed scanner can produce the type of diffuse illumination required as input to our method. Additionally, because the problem might be illposed -more than a single diffuse image might be needed to disambiguate the specular reflection- or because the training dataset is not representative enough of the real distribution, we propose a novel framework to quantify the model's confidence about its prediction at test time. Our method is the first one to deal with the problem of modeling uncertainty in material digitization, increasing the trustworthiness of the process and enabling more intelligent strategies for dataset creation, as we demonstrate with an active learning experiment.

The digitization of histology slides has revolutionized pathology, providing massive datasets for cancer diagnosis and research. Contrastive self-supervised and vision-language models have been shown to effectively mine large pathology datasets to learn discriminative representations. On the other hand, generative models, capable of synthesizing realistic and diverse images, present a compelling solution to address unique problems in pathology that involve synthesizing images; overcoming annotated data scarcity, enabling privacy-preserving data sharing, and performing inherently generative tasks, such as virtual staining. We introduce PixCell, the first diffusion-based generative foundation model for histopathology. We train PixCell on PanCan-30M, a vast, diverse dataset derived from 69,184 H\&E-stained whole slide images covering various cancer types. We employ a progressive training strategy and a self-supervision-based conditioning that allows us to scale up training without any annotated data. PixCell generates diverse and high-quality images across multiple cancer types, which we find can be used in place of real data to train a self-supervised discriminative model. Synthetic images shared between institutions are subject to fewer regulatory barriers than would be the case with real clinical images. Furthermore, we showcase the ability to precisely control image generation using a small set of annotated images, which can be used for both data augmentation and educational purposes. Testing on a cell segmentation task, a mask-guided PixCell enables targeted data augmentation, improving downstream performance. Finally, we demonstrate PixCell's ability to use H\&E structural staining to infer results from molecular marker studies; we use this capability to infer IHC staining from H\&E images. Our trained models are publicly released to accelerate research in computational pathology.

Recent efforts on image restoration have focused on developing "all-in-one" models that can handle different degradation types and levels within single model. However, most of mainstream Transformer-based ones confronted with dilemma between model capabilities and computation burdens, since self-attention mechanism quadratically increase in computational complexity with respect to image size, and has inadequacies in capturing long-range dependencies. Most of Mamba-related ones solely scanned feature map in spatial dimension for global modeling, failing to fully utilize information in channel dimension. To address aforementioned problems, this paper has proposed to fully utilize complementary advantages from Mamba and Transformer without sacrificing computation efficiency. Specifically, the selective scanning mechanism of Mamba is employed to focus on spatial modeling, enabling capture long-range spatial dependencies under linear complexity. The self-attention mechanism of Transformer is applied to focus on channel modeling, avoiding high computation burdens that are in quadratic growth with image's spatial dimensions. Moreover, to enrich informative prompts for effective image restoration, multi-dimensional prompt learning modules are proposed to learn prompt-flows from multi-scale encoder/decoder layers, benefiting for revealing underlying characteristic of various degradations from both spatial and channel perspectives, therefore, enhancing the capabilities of "all-in-one" model to solve various restoration tasks. Extensive experiment results on several image restoration benchmark tasks such as image denoising, dehazing, and deraining, have demonstrated that the proposed method can achieve new state-of-the-art performance, compared with many popular mainstream methods. Related source codes and pre-trained parameters will be public on github https://github.com/12138-chr/MTAIR.

In Ultrasound Localization Microscopy (ULM),achieving high-resolution images relies on the precise localization of contrast agent particles across consecutive beam-formed frames. However, our study uncovers an enormous potential: The process of delay-and-sum beamforming leads to an irreversible reduction of Radio-Frequency (RF) data, while its implications for localization remain largely unexplored. The rich contextual information embedded within RF wavefronts, including their hyperbolic shape and phase, offers great promise for guiding Deep Neural Networks (DNNs) in challenging localization scenarios. To fully exploit this data, we propose to directly localize scatterers in RF signals. Our approach involves a custom super-resolution DNN using learned feature channel shuffling and a novel semi-global convolutional sampling block tailored for reliable and accurate wavefront localization. Additionally, we introduce a geometric point transformation that facilitates seamless mapping between RF and B-mode coordinate space. To understand the impact of beamforming on ULM, we validate the effectiveness of our method by conducting an extensive comparison with State-Of-The-Art (SOTA) techniques. We present the inaugural in vivo results from an RF-trained DNN, highlighting its real-world practicality. Our findings show that RF-ULM bridges the domain gap between synthetic and real datasets, offering a considerable advantage in terms of precision and complexity. To enable the broader research community to benefit from our findings, our code and the associated SOTA methods are made available at https://github.com/hahnec/rf-ulm.

Transformer-based methods have demonstrated impressive performance in low-level visual tasks such as Image Super-Resolution (SR). However, its computational complexity grows quadratically with the spatial resolution. A series of works attempt to alleviate this problem by dividing Low-Resolution images into local windows, axial stripes, or dilated windows. SR typically leverages the redundancy of images for reconstruction, and this redundancy appears not only in local regions but also in long-range regions. However, these methods limit attention computation to content-agnostic local regions, limiting directly the ability of attention to capture long-range dependency. To address these issues, we propose a lightweight Content-Aware Token Aggregation Network (CATANet). Specifically, we propose an efficient Content-Aware Token Aggregation module for aggregating long-range content-similar tokens, which shares token centers across all image tokens and updates them only during the training phase. Then we utilize intra-group self-attention to enable long-range information interaction. Moreover, we design an inter-group cross-attention to further enhance global information interaction. The experimental results show that, compared with the state-of-the-art cluster-based method SPIN, our method achieves superior performance, with a maximum PSNR improvement of 0.33dB and nearly double the inference speed.

Digitizing pathological images into gigapixel Whole Slide Images (WSIs) has opened new avenues for Computational Pathology (CPath). As positive tissue comprises only a small fraction of gigapixel WSIs, existing Multiple Instance Learning (MIL) methods typically focus on identifying salient instances via attention mechanisms. However, this leads to a bias towards easy-to-classify instances while neglecting challenging ones. Recent studies have shown that hard examples are crucial for accurately modeling discriminative boundaries. Applying such an idea at the instance level, we elaborate a novel MIL framework with masked hard instance mining (MHIM-MIL), which utilizes a Siamese structure with a consistency constraint to explore the hard instances. Using a class-aware instance probability, MHIM-MIL employs a momentum teacher to mask salient instances and implicitly mine hard instances for training the student model. To obtain diverse, non-redundant hard instances, we adopt large-scale random masking while utilizing a global recycle network to mitigate the risk of losing key features. Furthermore, the student updates the teacher using an exponential moving average, which identifies new hard instances for subsequent training iterations and stabilizes optimization. Experimental results on cancer diagnosis, subtyping, survival analysis tasks, and 12 benchmarks demonstrate that MHIM-MIL outperforms the latest methods in both performance and efficiency. The code is available at: https://github.com/DearCaat/MHIM-MIL.

We study the behavior of deterministic methods for solving inverse problems in imaging. These methods are commonly designed to achieve two goals: (1) attaining high perceptual quality, and (2) generating reconstructions that are consistent with the measurements. We provide a rigorous proof that the better a predictor satisfies these two requirements, the larger its Lipschitz constant must be, regardless of the nature of the degradation involved. In particular, to approach perfect perceptual quality and perfect consistency, the Lipschitz constant of the model must grow to infinity. This implies that such methods are necessarily more susceptible to adversarial attacks. We demonstrate our theory on single image super-resolution algorithms, addressing both noisy and noiseless settings. We also show how this undesired behavior can be leveraged to explore the posterior distribution, thereby allowing the deterministic model to imitate stochastic methods.

We investigate to what extent Multimodal Large Language Models (MLLMs) can accurately identify the orientation of input images rotated 0{\deg}, 90{\deg}, 180{\deg}, and 270{\deg}. This task demands robust visual reasoning capabilities to detect rotational cues and contextualize spatial relationships within images, regardless of their orientation. To evaluate MLLMs on these abilities, we introduce RotBench -- a 350-image manually-filtered benchmark comprising lifestyle, portrait, and landscape images. Despite the relatively simple nature of this task, we show that several state-of-the-art open and proprietary MLLMs, including GPT-5, o3, and Gemini-2.5-Pro, do not reliably identify rotation in input images. Providing models with auxiliary information -- including captions, depth maps, and more -- or using chain-of-thought prompting offers only small and inconsistent improvements. Our results indicate that most models are able to reliably identify right-side-up (0{\deg}) images, while certain models are able to identify upside-down (180{\deg}) images. None can reliably distinguish between 90{\deg} and 270{\deg}. Simultaneously showing the image rotated in different orientations leads to moderate performance gains for reasoning models, while a modified setup using voting improves the performance of weaker models. We further show that fine-tuning does not improve models' ability to distinguish 90{\deg} and 270{\deg} rotations, despite substantially improving the identification of 180{\deg} images. Together, these results reveal a significant gap between MLLMs' spatial reasoning capabilities and human perception in identifying rotation.

This paper introduces a network for volumetric segmentation that learns from sparsely annotated volumetric images. We outline two attractive use cases of this method: (1) In a semi-automated setup, the user annotates some slices in the volume to be segmented. The network learns from these sparse annotations and provides a dense 3D segmentation. (2) In a fully-automated setup, we assume that a representative, sparsely annotated training set exists. Trained on this data set, the network densely segments new volumetric images. The proposed network extends the previous u-net architecture from Ronneberger et al. by replacing all 2D operations with their 3D counterparts. The implementation performs on-the-fly elastic deformations for efficient data augmentation during training. It is trained end-to-end from scratch, i.e., no pre-trained network is required. We test the performance of the proposed method on a complex, highly variable 3D structure, the Xenopus kidney, and achieve good results for both use cases.

This paper introduces a novel one-stage end-to-end detector specifically designed to detect small lesions in medical images. Precise localization of small lesions presents challenges due to their appearance and the diverse contextual backgrounds in which they are found. To address this, our approach introduces a new type of pixel-based anchor that dynamically moves towards the targeted lesion for detection. We refer to this new architecture as GravityNet, and the novel anchors as gravity points since they appear to be "attracted" by the lesions. We conducted experiments on two well-established medical problems involving small lesions to evaluate the performance of the proposed approach: microcalcifications detection in digital mammograms and microaneurysms detection in digital fundus images. Our method demonstrates promising results in effectively detecting small lesions in these medical imaging tasks.

Geometric alignment appears in a variety of applications, ranging from domain adaptation, optimal transport, and normalizing flows in machine learning; optical flow and learned augmentation in computer vision and deformable registration within biomedical imaging. A recurring challenge is the alignment of domains whose topology is not the same; a problem that is routinely ignored, potentially introducing bias in downstream analysis. As a first step towards solving such alignment problems, we propose an unsupervised algorithm for the detection of changes in image topology. The model is based on a conditional variational auto-encoder and detects topological changes between two images during the registration step. We account for both topological changes in the image under spatial variation and unexpected transformations. Our approach is validated on two tasks and datasets: detection of topological changes in microscopy images of cells, and unsupervised anomaly detection brain imaging.