Daily Papers

Plankton recognition provides novel possibilities to study various environmental aspects and an interesting real-world context to develop domain adaptation (DA) methods. Different imaging instruments cause domain shift between datasets hampering the development of general plankton recognition methods. A promising remedy for this is DA allowing to adapt a model trained on one instrument to other instruments. In this paper, we present a new DA dataset called DAPlankton which consists of phytoplankton images obtained with different instruments. Phytoplankton provides a challenging DA problem due to the fine-grained nature of the task and high class imbalance in real-world datasets. DAPlankton consists of two subsets. DAPlankton_LAB contains images of cultured phytoplankton providing a balanced dataset with minimal label uncertainty. DAPlankton_SEA consists of images collected from the Baltic Sea providing challenging real-world data with large intra-class variance and class imbalance. We further present a benchmark comparison of three widely used DA methods.

Planktonic organisms are of fundamental importance to marine ecosystems: they form the basis of the food web, provide the link between the atmosphere and the deep ocean, and influence global-scale biogeochemical cycles. Scientists are increasingly using imaging-based technologies to study these creatures in their natural habit. Images from such systems provide an unique opportunity to model and understand plankton ecosystems, but the collected datasets can be enormous. The Imaging FlowCytobot (IFCB) at Woods Hole Oceanographic Institution, for example, is an in situ system that has been continuously imaging plankton since 2006. To date, it has generated more than 700 million samples. Manual classification of such a vast image collection is impractical due to the size of the data set. In addition, the annotation task is challenging due to the large space of relevant classes, intra-class variability, and inter-class similarity. Methods for automated classification exist, but the accuracy is often below that of human experts. Here we introduce WHOI-Plankton: a large scale, fine-grained visual recognition dataset for plankton classification, which comprises over 3.4 million expert-labeled images across 70 classes. The labeled image set is complied from over 8 years of near continuous data collection with the IFCB at the Martha's Vineyard Coastal Observatory (MVCO). We discuss relevant metrics for evaluation of classification performance and provide results for a traditional method based on hand-engineered features and two methods based on convolutional neural networks.

Plankton recognition is an important computer vision problem due to plankton's essential role in ocean food webs and carbon capture, highlighting the need for species-level monitoring. However, this task is challenging due to its fine-grained nature and dataset shifts caused by different imaging instruments and varying species distributions. As new plankton image datasets are collected at an increasing pace, there is a need for general plankton recognition models that require minimal expert effort for data labeling. In this work, we study large-scale self-supervised pretraining for fine-grained plankton recognition. We first employ masked autoencoding and a large volume of diverse plankton image data to pretrain a general-purpose plankton image encoder. Then we utilize fine-tuning to obtain accurate plankton recognition models for new datasets with a very limited number of labeled training images. Our experiments show that self-supervised pretraining with diverse plankton data clearly increases plankton recognition accuracy compared to standard ImageNet pretraining when the amount of training data is limited. Moreover, the accuracy can be further improved when unlabeled target data is available and utilized during the pretraining.

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.

Synthetic Aperture Radar (SAR) imagery is the primary data type used for sea ice mapping due to its spatio-temporal coverage and the ability to detect sea ice independent of cloud and lighting conditions. Automatic sea ice detection using SAR imagery remains problematic due to the presence of ambiguous signal and noise within the image. Conversely, ice and water are easily distinguishable using multispectral imagery (MSI), but in the polar regions the ocean's surface is often occluded by cloud or the sun may not appear above the horizon for many months. To address some of these limitations, this paper proposes a new tool trained using concurrent multispectral Visible and SAR imagery for sea Ice Detection (ViSual\_IceD). ViSual\_IceD is a convolution neural network (CNN) that builds on the classic U-Net architecture by containing two parallel encoder stages, enabling the fusion and concatenation of MSI and SAR imagery containing different spatial resolutions. The performance of ViSual\_IceD is compared with U-Net models trained using concatenated MSI and SAR imagery as well as models trained exclusively on MSI or SAR imagery. ViSual\_IceD outperforms the other networks, with a F1 score 1.60\% points higher than the next best network, and results indicate that ViSual\_IceD is selective in the image type it uses during image segmentation. Outputs from ViSual\_IceD are compared to sea ice concentration products derived from the AMSR2 Passive Microwave (PMW) sensor. Results highlight how ViSual\_IceD is a useful tool to use in conjunction with PMW data, particularly in coastal regions. As the spatial-temporal coverage of MSI and SAR imagery continues to increase, ViSual\_IceD provides a new opportunity for robust, accurate sea ice coverage detection in polar regions.

Camera-based electronic monitoring (EM) systems are increasingly being deployed onboard commercial fishing vessels to collect essential data for fisheries management and regulation. These systems generate large quantities of video data which must be reviewed on land by human experts. Computer vision can assist this process by automatically detecting and classifying fish species, however the lack of existing public data in this domain has hindered progress. To address this, we present the Fishnet Open Images Database, a large dataset of EM imagery for fish detection and fine-grained categorization onboard commercial fishing vessels. The dataset consists of 86,029 images containing 34 object classes, making it the largest and most diverse public dataset of fisheries EM imagery to-date. It includes many of the characteristic challenges of EM data: visual similarity between species, skewed class distributions, harsh weather conditions, and chaotic crew activity. We evaluate the performance of existing detection and classification algorithms and demonstrate that the dataset can serve as a challenging benchmark for development of computer vision algorithms in fisheries. The dataset is available at https://www.fishnet.ai/.

Ocean scientists have been collecting visual data to study marine organisms for decades. These images and videos are extremely valuable both for basic science and environmental monitoring tasks. There are tools for automatically processing these data, but none that are capable of handling the extreme variability in sample populations, image quality, and habitat characteristics that are common in visual sampling of the ocean. Such distribution shifts can occur over very short physical distances and in narrow time windows. Creating models that are able to recognize when an image or video sequence contains a new organism, an unusual collection of animals, or is otherwise out-of-sample is critical to fully leverage visual data in the ocean. The FathomNet2023 competition dataset presents a realistic scenario where the set of animals in the target data differs from the training data. The challenge is both to identify the organisms in a target image and assess whether it is out-of-sample.

Advances in underwater imaging enable the collection of extensive seafloor image datasets that are necessary for monitoring important benthic ecosystems. The ability to collect seafloor imagery has outpaced our capacity to analyze it, hindering expedient mobilization of this crucial environmental information. Recent machine learning approaches provide opportunities to increase the efficiency with which seafloor image datasets are analyzed, yet large and consistent datasets necessary to support development of such approaches are scarce. Here we present BenthicNet: a global compilation of seafloor imagery designed to support the training and evaluation of large-scale image recognition models. An initial set of over 11.4 million images was collected and curated to represent a diversity of seafloor environments using a representative subset of 1.3 million images. These are accompanied by 2.6 million annotations translated to the CATAMI scheme, which span 190,000 of the images. A large deep learning model was trained on this compilation and preliminary results suggest it has utility for automating large and small-scale image analysis tasks. The compilation and model are made openly available for use by the scientific community at https://doi.org/10.20383/103.0614.

Seagrass meadows serve as critical carbon sinks, but accurately estimating the amount of carbon they store requires knowledge of the seagrass species present. Using underwater and surface vehicles equipped with machine learning algorithms can help to accurately estimate the composition and extent of seagrass meadows at scale. However, previous approaches for seagrass detection and classification have required full supervision from patch-level labels. In this paper, we reframe seagrass classification as a weakly supervised coarse segmentation problem where image-level labels are used during training (25 times fewer labels compared to patch-level labeling) and patch-level outputs are obtained at inference time. To this end, we introduce SeaFeats, an architecture that uses unsupervised contrastive pretraining and feature similarity to separate background and seagrass patches, and SeaCLIP, a model that showcases the effectiveness of large language models as a supervisory signal in domain-specific applications. We demonstrate that an ensemble of SeaFeats and SeaCLIP leads to highly robust performance, with SeaCLIP conservatively predicting the background class to avoid false seagrass misclassifications in blurry or dark patches. Our method outperforms previous approaches that require patch-level labels on the multi-species 'DeepSeagrass' dataset by 6.8% (absolute) for the class-weighted F1 score, and by 12.1% (absolute) F1 score for seagrass presence/absence on the 'Global Wetlands' dataset. We also present two case studies for real-world deployment: outlier detection on the Global Wetlands dataset, and application of our method on imagery collected by FloatyBoat, an autonomous surface vehicle.

In recent years, the underwater image formation model has found extensive use in the generation of synthetic underwater data. Although many approaches focus on scenes primarily affected by discoloration, they often overlook the model's ability to capture the complex, distance-dependent visibility loss present in highly turbid environments. In this work, we propose an improved synthetic data generation pipeline that includes the commonly omitted forward scattering term, while also considering a nonuniform medium. Additionally, we collected the BUCKET dataset under controlled turbidity conditions to acquire real turbid footage with the corresponding reference images. Our results demonstrate qualitative improvements over the reference model, particularly under increasing turbidity, with a selection rate of 82. 5\% by survey participants. Data and code can be accessed on the project page: vap.aau.dk/sea-ing-through-scattered-rays.

Unsustainable fishing practices worldwide pose a major threat to marine resources and ecosystems. Identifying vessels that do not show up in conventional monitoring systems -- known as ``dark vessels'' -- is key to managing and securing the health of marine environments. With the rise of satellite-based synthetic aperture radar (SAR) imaging and modern machine learning (ML), it is now possible to automate detection of dark vessels day or night, under all-weather conditions. SAR images, however, require a domain-specific treatment and are not widely accessible to the ML community. Maritime objects (vessels and offshore infrastructure) are relatively small and sparse, challenging traditional computer vision approaches. We present the largest labeled dataset for training ML models to detect and characterize vessels and ocean structures in SAR imagery. xView3-SAR consists of nearly 1,000 analysis-ready SAR images from the Sentinel-1 mission that are, on average, 29,400-by-24,400 pixels each. The images are annotated using a combination of automated and manual analysis. Co-located bathymetry and wind state rasters accompany every SAR image. We also provide an overview of the xView3 Computer Vision Challenge, an international competition using xView3-SAR for ship detection and characterization at large scale. We release the data (https://iuu.xview.us/{https://iuu.xview.us/}) and code (https://github.com/DIUx-xView{https://github.com/DIUx-xView}) to support ongoing development and evaluation of ML approaches for this important application.

Images are increasingly becoming the currency for documenting biodiversity on the planet, providing novel opportunities for accelerating scientific discoveries in the field of organismal biology, especially with the advent of large vision-language models (VLMs). We ask if pre-trained VLMs can aid scientists in answering a range of biologically relevant questions without any additional fine-tuning. In this paper, we evaluate the effectiveness of 12 state-of-the-art (SOTA) VLMs in the field of organismal biology using a novel dataset, VLM4Bio, consisting of 469K question-answer pairs involving 30K images from three groups of organisms: fishes, birds, and butterflies, covering five biologically relevant tasks. We also explore the effects of applying prompting techniques and tests for reasoning hallucination on the performance of VLMs, shedding new light on the capabilities of current SOTA VLMs in answering biologically relevant questions using images. The code and datasets for running all the analyses reported in this paper can be found at https://github.com/sammarfy/VLM4Bio.

Artificial Intelligence (AI) Foundation models (FMs), pre-trained on massive unlabelled datasets, have the potential to drastically change AI applications in ocean science, where labelled data are often sparse and expensive to collect. In this work, we describe a new foundation model using the Prithvi-EO Vision Transformer architecture which has been pre-trained to reconstruct data from the Sentinel-3 Ocean and Land Colour Instrument (OLCI). We evaluate the model by fine-tuning on two downstream marine earth observation tasks. We first assess model performance compared to current baseline models used to quantify chlorophyll concentration. We then evaluate the FMs ability to refine remote sensing-based estimates of ocean primary production. Our results demonstrate the utility of self-trained FMs for marine monitoring, in particular for making use of small amounts of high quality labelled data and in capturing detailed spatial patterns of ocean colour whilst matching point observations. We conclude that this new generation of geospatial AI models has the potential to provide more robust, data-driven insights into ocean ecosystems and their role in global climate processes.

This work investigates descriptive captions as an additional source of supervision for biological multimodal foundation models. Images and captions can be viewed as complementary samples from the latent morphospace of a species, each capturing certain biological traits. Incorporating captions during training encourages alignment with this shared latent structure, emphasizing potentially diagnostic characters while suppressing spurious correlations. The main challenge, however, lies in obtaining faithful, instance-specific captions at scale. This requirement has limited the utilization of natural language supervision in organismal biology compared with many other scientific domains. We complement this gap by generating synthetic captions with multimodal large language models (MLLMs), guided by Wikipedia-derived visual information and taxon-tailored format examples. These domain-specific contexts help reduce hallucination and yield accurate, instance-based descriptive captions. Using these captions, we train BIOCAP (i.e., BIOCLIP with Captions), a biological foundation model that captures rich semantics and achieves strong performance in species classification and text-image retrieval. These results demonstrate the value of descriptive captions beyond labels in bridging biological images with multimodal foundation models.

Coral reefs are vital yet vulnerable ecosystems that require continuous monitoring to support conservation. While coral reef images provide essential information in coral monitoring, interpreting such images remains challenging due to the need for domain expertise. Visual Question Answering (VQA), powered by Large Vision-Language Models (LVLMs), has great potential in user-friendly interaction with coral reef images. However, applying VQA to coral imagery demands a dedicated dataset that addresses two key challenges: domain-specific annotations and multidimensional questions. In this work, we introduce CoralVQA, the first large-scale VQA dataset for coral reef analysis. It contains 12,805 real-world coral images from 67 coral genera collected from 3 oceans, along with 277,653 question-answer pairs that comprehensively assess ecological and health-related conditions. To construct this dataset, we develop a semi-automatic data construction pipeline in collaboration with marine biologists to ensure both scalability and professional-grade data quality. CoralVQA presents novel challenges and provides a comprehensive benchmark for studying vision-language reasoning in the context of coral reef images. By evaluating several state-of-the-art LVLMs, we reveal key limitations and opportunities. These insights form a foundation for future LVLM development, with a particular emphasis on supporting coral conservation efforts.

In this paper, we present the first large-scale dataset for semantic Segmentation of Underwater IMagery (SUIM). It contains over 1500 images with pixel annotations for eight object categories: fish (vertebrates), reefs (invertebrates), aquatic plants, wrecks/ruins, human divers, robots, and sea-floor. The images have been rigorously collected during oceanic explorations and human-robot collaborative experiments, and annotated by human participants. We also present a benchmark evaluation of state-of-the-art semantic segmentation approaches based on standard performance metrics. In addition, we present SUIM-Net, a fully-convolutional encoder-decoder model that balances the trade-off between performance and computational efficiency. It offers competitive performance while ensuring fast end-to-end inference, which is essential for its use in the autonomy pipeline of visually-guided underwater robots. In particular, we demonstrate its usability benefits for visual servoing, saliency prediction, and detailed scene understanding. With a variety of use cases, the proposed model and benchmark dataset open up promising opportunities for future research in underwater robot vision.

A database of images of approximately 960 unique plants belonging to 12 species at several growth stages is made publicly available. It comprises annotated RGB images with a physical resolution of roughly 10 pixels per mm. To standardise the evaluation of classification results obtained with the database, a benchmark based on f_{1} scores is proposed. The dataset is available at https://vision.eng.au.dk/plant-seedlings-dataset

With the exacerbation of the biodiversity and climate crises, macroecological pursuits such as global biodiversity mapping become more urgent. Remote sensing offers a wealth of Earth observation data for ecological studies, but the scarcity of labeled datasets remains a major challenge. Recently, self-supervised learning has enabled learning representations from unlabeled data, triggering the development of pretrained geospatial models with generalizable features. However, these models are often trained on datasets biased toward areas of high human activity, leaving entire ecological regions underrepresented. Additionally, while some datasets attempt to address seasonality through multi-date imagery, they typically follow calendar seasons rather than local phenological cycles. To better capture vegetation seasonality at a global scale, we propose a simple phenology-informed sampling strategy and introduce corresponding SSL4Eco, a multi-date Sentinel-2 dataset, on which we train an existing model with a season-contrastive objective. We compare representations learned from SSL4Eco against other datasets on diverse ecological downstream tasks and demonstrate that our straightforward sampling method consistently improves representation quality, highlighting the importance of dataset construction. The model pretrained on SSL4Eco reaches state of the art performance on 7 out of 8 downstream tasks spanning (multi-label) classification and regression. We release our code, data, and model weights to support macroecological and computer vision research at https://github.com/PlekhanovaElena/ssl4eco.

Foundation models trained at scale exhibit remarkable emergent behaviors, learning new capabilities beyond their initial training objectives. We find such emergent behaviors in biological vision models via large-scale contrastive vision-language training. To achieve this, we first curate TreeOfLife-200M, comprising 214 million images of living organisms, the largest and most diverse biological organism image dataset to date. We then train BioCLIP 2 on TreeOfLife-200M to distinguish different species. Despite the narrow training objective, BioCLIP 2 yields extraordinary accuracy when applied to various biological visual tasks such as habitat classification and trait prediction. We identify emergent properties in the learned embedding space of BioCLIP 2. At the inter-species level, the embedding distribution of different species aligns closely with functional and ecological meanings (e.g., beak sizes and habitats). At the intra-species level, instead of being diminished, the intra-species variations (e.g., life stages and sexes) are preserved and better separated in subspaces orthogonal to inter-species distinctions. We provide formal proof and analyses to explain why hierarchical supervision and contrastive objectives encourage these emergent properties. Crucially, our results reveal that these properties become increasingly significant with larger-scale training data, leading to a biologically meaningful embedding space.

Global plant maps of plant traits, such as leaf nitrogen or plant height, are essential for understanding ecosystem processes, including the carbon and energy cycles of the Earth system. However, existing trait maps remain limited by the high cost and sparse geographic coverage of field-based measurements. Citizen science initiatives offer a largely untapped resource to overcome these limitations, with over 50 million geotagged plant photographs worldwide capturing valuable visual information on plant morphology and physiology. In this study, we introduce PlantTraitNet, a multi-modal, multi-task uncertainty-aware deep learning framework that predictsfour key plant traits (plant height, leaf area, specific leaf area, and nitrogen content) from citizen science photos using weak supervision. By aggregating individual trait predictions across space, we generate global maps of trait distributions. We validate these maps against independent vegetation survey data (sPlotOpen) and benchmark them against leading global trait products. Our results show that PlantTraitNet consistently outperforms existing trait maps across all evaluated traits, demonstrating that citizen science imagery, when integrated with computer vision and geospatial AI, enables not only scalable but also more accurate global trait mapping. This approach offers a powerful new pathway for ecological research and Earth system modeling.

Deep generative vision models are now able to synthesize realistic-looking satellite imagery. But, the possibility of hallucinations prevents their adoption for risk-sensitive applications, such as generating materials for communicating climate change. To demonstrate this issue, we train a generative adversarial network (pix2pixHD) to create synthetic satellite imagery of future flooding and reforestation events. We find that a pure deep learning-based model can generate photorealistic flood visualizations but hallucinates floods at locations that were not susceptible to flooding. To address this issue, we propose to condition and evaluate generative vision models on segmentation maps of physics-based flood models. We show that our physics-conditioned model outperforms the pure deep learning-based model and a handcrafted baseline. We evaluate the generalization capability of our method to different remote sensing data and different climate-related events (reforestation). We publish our code and dataset which includes the data for a third case study of melting Arctic sea ice and >30,000 labeled HD image triplets -- or the equivalent of 5.5 million images at 128x128 pixels -- for segmentation guided image-to-image translation in Earth observation. Code and data is available at https://github.com/blutjens/eie-earth-public.

Existing image classification datasets used in computer vision tend to have a uniform distribution of images across object categories. In contrast, the natural world is heavily imbalanced, as some species are more abundant and easier to photograph than others. To encourage further progress in challenging real world conditions we present the iNaturalist species classification and detection dataset, consisting of 859,000 images from over 5,000 different species of plants and animals. It features visually similar species, captured in a wide variety of situations, from all over the world. Images were collected with different camera types, have varying image quality, feature a large class imbalance, and have been verified by multiple citizen scientists. We discuss the collection of the dataset and present extensive baseline experiments using state-of-the-art computer vision classification and detection models. Results show that current non-ensemble based methods achieve only 67% top one classification accuracy, illustrating the difficulty of the dataset. Specifically, we observe poor results for classes with small numbers of training examples suggesting more attention is needed in low-shot learning.

In many computer vision applications, images are acquired with arbitrary or random rotations and translations, and in such setups, it is desirable to obtain semantic representations disentangled from the image orientation. Examples of such applications include semiconductor wafer defect inspection, plankton microscope images, and inference on single-particle cryo-electron microscopy (cryo-EM) micro-graphs. In this work, we propose Invariant Representation Learning with Implicit Neural Representation (IRL-INR), which uses an implicit neural representation (INR) with a hypernetwork to obtain semantic representations disentangled from the orientation of the image. We show that IRL-INR can effectively learn disentangled semantic representations on more complex images compared to those considered in prior works and show that these semantic representations synergize well with SCAN to produce state-of-the-art unsupervised clustering results.

Fishes are integral to both ecological systems and economic sectors, and studying fish traits is crucial for understanding biodiversity patterns and macro-evolution trends. To enable the analysis of visual traits from fish images, we introduce the Fish-Visual Trait Analysis (Fish-Vista) dataset - a large, annotated collection of about 60K fish images spanning 1900 different species, supporting several challenging and biologically relevant tasks including species classification, trait identification, and trait segmentation. These images have been curated through a sophisticated data processing pipeline applied to a cumulative set of images obtained from various museum collections. Fish-Vista provides fine-grained labels of various visual traits present in each image. It also offers pixel-level annotations of 9 different traits for 2427 fish images, facilitating additional trait segmentation and localization tasks. The ultimate goal of Fish-Vista is to provide a clean, carefully curated, high-resolution dataset that can serve as a foundation for accelerating biological discoveries using advances in AI. Finally, we provide a comprehensive analysis of state-of-the-art deep learning techniques on Fish-Vista.

Recent technological advances in synthetic data have enabled the generation of images with such high quality that human beings cannot tell the difference between real-life photographs and Artificial Intelligence (AI) generated images. Given the critical necessity of data reliability and authentication, this article proposes to enhance our ability to recognise AI-generated images through computer vision. Initially, a synthetic dataset is generated that mirrors the ten classes of the already available CIFAR-10 dataset with latent diffusion which provides a contrasting set of images for comparison to real photographs. The model is capable of generating complex visual attributes, such as photorealistic reflections in water. The two sets of data present as a binary classification problem with regard to whether the photograph is real or generated by AI. This study then proposes the use of a Convolutional Neural Network (CNN) to classify the images into two categories; Real or Fake. Following hyperparameter tuning and the training of 36 individual network topologies, the optimal approach could correctly classify the images with 92.98% accuracy. Finally, this study implements explainable AI via Gradient Class Activation Mapping to explore which features within the images are useful for classification. Interpretation reveals interesting concepts within the image, in particular, noting that the actual entity itself does not hold useful information for classification; instead, the model focuses on small visual imperfections in the background of the images. The complete dataset engineered for this study, referred to as the CIFAKE dataset, is made publicly available to the research community for future work.

Robust visual recognition in underwater environments remains a significant challenge due to complex distortions such as turbidity, low illumination, and occlusion, which severely degrade the performance of standard vision systems. This paper introduces AQUA20, a comprehensive benchmark dataset comprising 8,171 underwater images across 20 marine species reflecting real-world environmental challenges such as illumination, turbidity, occlusions, etc., providing a valuable resource for underwater visual understanding. Thirteen state-of-the-art deep learning models, including lightweight CNNs (SqueezeNet, MobileNetV2) and transformer-based architectures (ViT, ConvNeXt), were evaluated to benchmark their performance in classifying marine species under challenging conditions. Our experimental results show ConvNeXt achieving the best performance, with a Top-3 accuracy of 98.82% and a Top-1 accuracy of 90.69%, as well as the highest overall F1-score of 88.92% with moderately large parameter size. The results obtained from our other benchmark models also demonstrate trade-offs between complexity and performance. We also provide an extensive explainability analysis using GRAD-CAM and LIME for interpreting the strengths and pitfalls of the models. Our results reveal substantial room for improvement in underwater species recognition and demonstrate the value of AQUA20 as a foundation for future research in this domain. The dataset is publicly available at: https://huggingface.co/datasets/taufiktrf/AQUA20.

Recent advances in large language models (LLMs) have enabled multimodal foundation models to tackle both image understanding and generation within a unified framework. Despite these gains, unified models often underperform compared to specialized models in either task. A key challenge in developing unified models lies in the inherent differences between the visual features needed for image understanding versus generation, as well as the distinct training processes required for each modality. In this work, we introduce Pisces, an auto-regressive multimodal foundation model that addresses this challenge through a novel decoupled visual encoding architecture and tailored training techniques optimized for multimodal generation. Combined with meticulous data curation, pretraining, and finetuning, Pisces achieves competitive performance in both image understanding and image generation. We evaluate Pisces on over 20 public benchmarks for image understanding, where it demonstrates strong performance across a wide range of tasks. Additionally, on GenEval, a widely adopted benchmark for image generation, Pisces exhibits robust generative capabilities. Our extensive analysis reveals the synergistic relationship between image understanding and generation, and the benefits of using separate visual encoders, advancing the field of unified multimodal models.

Remote sensing has significantly advanced water detection by applying semantic segmentation techniques to satellite imagery. However, semantic segmentation remains challenging due to the substantial amount of annotated data required. This is particularly problematic in wetland detection, where water extent varies over time and space, necessitating multiple annotations for the same area. In this paper, we present DeepAqua, a self-supervised deep learning model that leverages knowledge distillation to eliminate the need for manual annotations during the training phase. DeepAqua utilizes the Normalized Difference Water Index (NDWI) as a teacher model to train a Convolutional Neural Network (CNN) for segmenting water from Synthetic Aperture Radar (SAR) images. To train the student model, we exploit cases where optical- and radar-based water masks coincide, enabling the detection of both open and vegetated water surfaces. Our model represents a significant advancement in computer vision techniques by effectively training semantic segmentation models without any manually annotated data. This approach offers a practical solution for monitoring wetland water extent changes without needing ground truth data, making it highly adaptable and scalable for wetland conservation efforts.

Crop biomass, a critical indicator of plant growth, health, and productivity, is invaluable for crop breeding programs and agronomic research. However, the accurate and scalable quantification of crop biomass remains inaccessible due to limitations in existing measurement methods. One of the obstacles impeding the advancement of current crop biomass prediction methodologies is the scarcity of publicly available datasets. Addressing this gap, we introduce a new dataset in this domain, i.e. Multi-modality dataset for crop biomass estimation (MMCBE). Comprising 216 sets of multi-view drone images, coupled with LiDAR point clouds, and hand-labelled ground truth, MMCBE represents the first multi-modality one in the field. This dataset aims to establish benchmark methods for crop biomass quantification and foster the development of vision-based approaches. We have rigorously evaluated state-of-the-art crop biomass estimation methods using MMCBE and ventured into additional potential applications, such as 3D crop reconstruction from drone imagery and novel-view rendering. With this publication, we are making our comprehensive dataset available to the broader community.

Developing computer vision-based rice phenotyping techniques is crucial for precision field management and accelerating breeding, thereby continuously advancing rice production. Among phenotyping tasks, distinguishing image components is a key prerequisite for characterizing plant growth and development at the organ scale, enabling deeper insights into eco-physiological processes. However, due to the fine structure of rice organs and complex illumination within the canopy, this task remains highly challenging, underscoring the need for a high-quality training dataset. Such datasets are scarce, both due to a lack of large, representative collections of rice field images and the time-intensive nature of annotation. To address this gap, we established the first comprehensive multi-class rice semantic segmentation dataset, RiceSEG. We gathered nearly 50,000 high-resolution, ground-based images from five major rice-growing countries (China, Japan, India, the Philippines, and Tanzania), encompassing over 6,000 genotypes across all growth stages. From these original images, 3,078 representative samples were selected and annotated with six classes (background, green vegetation, senescent vegetation, panicle, weeds, and duckweed) to form the RiceSEG dataset. Notably, the sub-dataset from China spans all major genotypes and rice-growing environments from the northeast to the south. Both state-of-the-art convolutional neural networks and transformer-based semantic segmentation models were used as baselines. While these models perform reasonably well in segmenting background and green vegetation, they face difficulties during the reproductive stage, when canopy structures are more complex and multiple classes are involved. These findings highlight the importance of our dataset for developing specialized segmentation models for rice and other crops.

Coral reefs are declining worldwide due to climate change and local stressors. To inform effective conservation or restoration, monitoring at the highest possible spatial and temporal resolution is necessary. Conventional coral reef surveying methods are limited in scalability due to their reliance on expert labor time, motivating the use of computer vision tools to automate the identification and abundance estimation of live corals from images. However, the design and evaluation of such tools has been impeded by the lack of large high quality datasets. We release the Coralscapes dataset, the first general-purpose dense semantic segmentation dataset for coral reefs, covering 2075 images, 39 benthic classes, and 174k segmentation masks annotated by experts. Coralscapes has a similar scope and the same structure as the widely used Cityscapes dataset for urban scene segmentation, allowing benchmarking of semantic segmentation models in a new challenging domain which requires expert knowledge to annotate. We benchmark a wide range of semantic segmentation models, and find that transfer learning from Coralscapes to existing smaller datasets consistently leads to state-of-the-art performance. Coralscapes will catalyze research on efficient, scalable, and standardized coral reef surveying methods based on computer vision, and holds the potential to streamline the development of underwater ecological robotics.

Automated fish documentation processes are in the near future expected to play an essential role in sustainable fisheries management and for addressing challenges of overfishing. In this paper, we present a novel and publicly available dataset named AutoFish designed for fine-grained fish analysis. The dataset comprises 1,500 images of 454 specimens of visually similar fish placed in various constellations on a white conveyor belt and annotated with instance segmentation masks, IDs, and length measurements. The data was collected in a controlled environment using an RGB camera. The annotation procedure involved manual point annotations, initial segmentation masks proposed by the Segment Anything Model (SAM), and subsequent manual correction of the masks. We establish baseline instance segmentation results using two variations of the Mask2Former architecture, with the best performing model reaching an mAP of 89.15%. Additionally, we present two baseline length estimation methods, the best performing being a custom MobileNetV2-based regression model reaching an MAE of 0.62cm in images with no occlusion and 1.38cm in images with occlusion. Link to project page: https://vap.aau.dk/autofish/.

Climate change is negatively impacting the world's biodiversity. To build automated systems to monitor these negative biodiversity impacts, large-scale, volunteer-collected datasets like iNaturalist are built from community-identified, natural imagery. However, such volunteer-based data are opportunistic and lack a structured sampling strategy, resulting in geographic, temporal, observation quality, and socioeconomic, biases that stymie uptake of these models for downstream biodiversity monitoring tasks. Here we introduce DivShift North American West Coast (DivShift-NAWC), a curated dataset of almost 8 million iNaturalist plant images across the western coast of North America, for exploring the effects of these biases on deep learning model performance. We compare model performance across four known biases and observe that they indeed confound model performance. We suggest practical strategies for curating datasets to train deep learning models for monitoring climate change's impacts on the world's biodiversity.

Underwater image restoration algorithms seek to restore the color, contrast, and appearance of a scene that is imaged underwater. They are a critical tool in applications ranging from marine ecology and aquaculture to underwater construction and archaeology. While existing pixel-domain diffusion-based image restoration approaches are effective at restoring simple scenes with limited depth variation, they are computationally intensive and often generate unrealistic artifacts when applied to scenes with complex geometry and significant depth variation. In this work we overcome these limitations by combining a novel network architecture (SLURPP) with an accurate synthetic data generation pipeline. SLURPP combines pretrained latent diffusion models -- which encode strong priors on the geometry and depth of scenes -- with an explicit scene decomposition -- which allows one to model and account for the effects of light attenuation and backscattering. To train SLURPP we design a physics-based underwater image synthesis pipeline that applies varied and realistic underwater degradation effects to existing terrestrial image datasets. This approach enables the generation of diverse training data with dense medium/degradation annotations. We evaluate our method extensively on both synthetic and real-world benchmarks and demonstrate state-of-the-art performance. Notably, SLURPP is over 200X faster than existing diffusion-based methods while offering ~ 3 dB improvement in PSNR on synthetic benchmarks. It also offers compelling qualitative improvements on real-world data. Project website https://tianfwang.github.io/slurpp/.

ImageNet-1K linear-probe transfer accuracy remains the default proxy for visual representation quality, yet it no longer predicts performance on scientific imagery. Across 46 modern vision model checkpoints, ImageNet top-1 accuracy explains only 34% of variance on ecology tasks and mis-ranks 30% of models above 75% accuracy. We present BioBench, an open ecology vision benchmark that captures what ImageNet misses. BioBench unifies 9 publicly released, application-driven tasks, 4 taxonomic kingdoms, and 6 acquisition modalities (drone RGB, web video, micrographs, in-situ and specimen photos, camera-trap frames), totaling 3.1M images. A single Python API downloads data, fits lightweight classifiers to frozen backbones, and reports class-balanced macro-F1 (plus domain metrics for FishNet and FungiCLEF); ViT-L models evaluate in 6 hours on an A6000 GPU. BioBench provides new signal for computer vision in ecology and a template recipe for building reliable AI-for-science benchmarks in any domain. Code and predictions are available at https://github.com/samuelstevens/biobench and results at https://samuelstevens.me/biobench.

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.

Unprecedented access to multi-temporal satellite imagery has opened new perspectives for a variety of Earth observation tasks. Among them, pixel-precise panoptic segmentation of agricultural parcels has major economic and environmental implications. While researchers have explored this problem for single images, we argue that the complex temporal patterns of crop phenology are better addressed with temporal sequences of images. In this paper, we present the first end-to-end, single-stage method for panoptic segmentation of Satellite Image Time Series (SITS). This module can be combined with our novel image sequence encoding network which relies on temporal self-attention to extract rich and adaptive multi-scale spatio-temporal features. We also introduce PASTIS, the first open-access SITS dataset with panoptic annotations. We demonstrate the superiority of our encoder for semantic segmentation against multiple competing architectures, and set up the first state-of-the-art of panoptic segmentation of SITS. Our implementation and PASTIS are publicly available.

Correlative computational microscopy is accelerating the mapping of dynamic biological systems by integrating morphological and molecular measurements across spatial scales, from organelles to entire organisms. Visualization, measurement, and prediction of interactions among the components of biological systems can be accelerated by generalist computational imaging frameworks that relax the trade-offs imposed by multiplex dynamic imaging. This work reports a generalist framework for wave optical imaging of the architectural order (waveOrder) among biomolecules for encoding and decoding multiple specimen properties from a minimal set of acquired channels, with or without fluorescent labels. waveOrder expresses material properties in terms of elegant physically motivated basis vectors directly interpretable as phase, absorption, birefringence, diattenuation, and fluorophore density; and it expresses image data in terms of directly measurable Stokes parameters. We report a corresponding multi-channel reconstruction algorithm to recover specimen properties in multiple contrast modes. With this framework, we implement multiple 3D computational microscopy methods, including quantitative phase imaging, quantitative label-free imaging with phase and polarization, and fluorescence deconvolution imaging, across scales ranging from organelles to whole zebrafish. These advances are available via an extensible open-source computational imaging library, waveOrder, and a napari plugin, recOrder.

In recent years, remarkable advancements have been achieved in the field of image generation, primarily driven by the escalating demand for high-quality outcomes across various image generation subtasks, such as inpainting, denoising, and super resolution. A major effort is devoted to exploring the application of super-resolution techniques to enhance the quality of low-resolution images. In this context, our method explores in depth the problem of ship image super resolution, which is crucial for coastal and port surveillance. We investigate the opportunity given by the growing interest in text-to-image diffusion models, taking advantage of the prior knowledge that such foundation models have already learned. In particular, we present a diffusion-model-based architecture that leverages text conditioning during training while being class-aware, to best preserve the crucial details of the ships during the generation of the super-resoluted image. Since the specificity of this task and the scarcity availability of off-the-shelf data, we also introduce a large labeled ship dataset scraped from online ship images, mostly from ShipSpotting\url{www.shipspotting.com} website. Our method achieves more robust results than other deep learning models previously employed for super resolution, as proven by the multiple experiments performed. Moreover, we investigate how this model can benefit downstream tasks, such as classification and object detection, thus emphasizing practical implementation in a real-world scenario. Experimental results show flexibility, reliability, and impressive performance of the proposed framework over state-of-the-art methods for different tasks. The code is available at: https://github.com/LuigiSigillo/ShipinSight .

Accurate identification of crop and weed species is critical for precision agriculture and sustainable farming. However, it remains a challenging task due to a variety of factors -- a high degree of visual similarity among species, environmental variability, and a continued lack of large, agriculture-specific image data. We introduce iNatAg, a large-scale image dataset which contains over 4.7 million images of 2,959 distinct crop and weed species, with precise annotations along the taxonomic hierarchy from binary crop/weed labels to specific species labels. Curated from the broader iNaturalist database, iNatAg contains data from every continent and accurately reflects the variability of natural image captures and environments. Enabled by this data, we train benchmark models built upon the Swin Transformer architecture and evaluate the impact of various modifications such as the incorporation of geospatial data and LoRA finetuning. Our best models achieve state-of-the-art performance across all taxonomic classification tasks, achieving 92.38\% on crop and weed classification. Furthermore, the scale of our dataset enables us to explore incorrect misclassifications and unlock new analytic possiblities for plant species. By combining large-scale species coverage, multi-task labels, and geographic diversity, iNatAg provides a new foundation for building robust, geolocation-aware agricultural classification systems. We release the iNatAg dataset publicly through AgML (https://github.com/Project-AgML/AgML), enabling direct access and integration into agricultural machine learning workflows.

Plant diseases pose significant threats to agriculture. It necessitates proper diagnosis and effective treatment to safeguard crop yields. To automate the diagnosis process, image segmentation is usually adopted for precisely identifying diseased regions, thereby advancing precision agriculture. Developing robust image segmentation models for plant diseases demands high-quality annotations across numerous images. However, existing plant disease datasets typically lack segmentation labels and are often confined to controlled laboratory settings, which do not adequately reflect the complexity of natural environments. Motivated by this fact, we established PlantSeg, a large-scale segmentation dataset for plant diseases. PlantSeg distinguishes itself from existing datasets in three key aspects. (1) Annotation type: Unlike the majority of existing datasets that only contain class labels or bounding boxes, each image in PlantSeg includes detailed and high-quality segmentation masks, associated with plant types and disease names. (2) Image source: Unlike typical datasets that contain images from laboratory settings, PlantSeg primarily comprises in-the-wild plant disease images. This choice enhances the practical applicability, as the trained models can be applied for integrated disease management. (3) Scale: PlantSeg is extensive, featuring 11,400 images with disease segmentation masks and an additional 8,000 healthy plant images categorized by plant type. Extensive technical experiments validate the high quality of PlantSeg's annotations. This dataset not only allows researchers to evaluate their image classification methods but also provides a critical foundation for developing and benchmarking advanced plant disease segmentation algorithms.

Benchmarking multi-object tracking and object detection model performance is an essential step in machine learning model development, as it allows researchers to evaluate model detection and tracker performance on human-generated 'test' data, facilitating consistent comparisons between models and trackers and aiding performance optimization. In this study, a novel benchmark video dataset was developed and used to assess the performance of several Monterey Bay Aquarium Research Institute object detection models and a FathomNet single-class object detection model together with several trackers. The dataset consists of four video sequences representing midwater and benthic deep-sea habitats. Performance was evaluated using Higher Order Tracking Accuracy, a metric that balances detection, localization, and association accuracy. To the best of our knowledge, this is the first publicly available benchmark for multi-object tracking in deep-sea video footage. We provide the benchmark data, a clearly documented workflow for generating additional benchmark videos, as well as example Python notebooks for computing metrics.

India loses 35% of the annual crop yield due to plant diseases. Early detection of plant diseases remains difficult due to the lack of lab infrastructure and expertise. In this paper, we explore the possibility of computer vision approaches for scalable and early plant disease detection. The lack of availability of sufficiently large-scale non-lab data set remains a major challenge for enabling vision based plant disease detection. Against this background, we present PlantDoc: a dataset for visual plant disease detection. Our dataset contains 2,598 data points in total across 13 plant species and up to 17 classes of diseases, involving approximately 300 human hours of effort in annotating internet scraped images. To show the efficacy of our dataset, we learn 3 models for the task of plant disease classification. Our results show that modelling using our dataset can increase the classification accuracy by up to 31%. We believe that our dataset can help reduce the entry barrier of computer vision techniques in plant disease detection.

Remote individual animal identification is important for food safety, sport, and animal conservation. Numerous existing remote individual animal identification studies have focused on RGB images. In this paper, we tackle individual penguin identification using hyperspectral (HS) images. To the best of our knowledge, it is the first work to analyze spectral differences between penguin individuals using an HS camera. We have constructed a novel penguin HS image dataset, including 990 hyperspectral images of 27 penguins. We experimentally demonstrate that the spectral information of HS image pixels can be used for individual penguin identification. The experimental results show the effectiveness of using HS images for individual penguin identification. The dataset and source code are available here: https://033labcodes.github.io/igrass24_penguin/

Clouds play a significant role in global temperature regulation through their effect on planetary albedo. Anthropogenic emissions of aerosols can alter the albedo of clouds, but the extent of this effect, and its consequent impact on temperature change, remains uncertain. Human-induced clouds caused by ship aerosol emissions, commonly referred to as ship tracks, provide visible manifestations of this effect distinct from adjacent cloud regions and therefore serve as a useful sandbox to study human-induced clouds. However, the lack of large-scale ship track data makes it difficult to deduce their general effects on cloud formation. Towards developing automated approaches to localize ship tracks at scale, we present CloudTracks, a dataset containing 3,560 satellite images labeled with more than 12,000 ship track instance annotations. We train semantic segmentation and instance segmentation model baselines on our dataset and find that our best model substantially outperforms previous state-of-the-art for ship track localization (61.29 vs. 48.65 IoU). We also find that the best instance segmentation model is able to identify the number of ship tracks in each image more accurately than the previous state-of-the-art (1.64 vs. 4.99 MAE). However, we identify cases where the best model struggles to accurately localize and count ship tracks, so we believe CloudTracks will stimulate novel machine learning approaches to better detect elongated and overlapping features in satellite images. We release our dataset openly at {zenodo.org/records/10042922}.

We introduce an effective strategy to generate an annotated synthetic dataset of microbiological images of Petri dishes that can be used to train deep learning models in a fully supervised fashion. The developed generator employs traditional computer vision algorithms together with a neural style transfer method for data augmentation. We show that the method is able to synthesize a dataset of realistic looking images that can be used to train a neural network model capable of localising, segmenting, and classifying five different microbial species. Our method requires significantly fewer resources to obtain a useful dataset than collecting and labeling a whole large set of real images with annotations. We show that starting with only 100 real images, we can generate data to train a detector that achieves comparable results (detection mAP = 0.416, and counting MAE = 4.49) to the same detector but trained on a real, several dozen times bigger dataset (mAP = 0.520, MAE = 4.31), containing over 7k images. We prove the usefulness of the method in microbe detection and segmentation, but we expect that it is general and flexible and can also be applicable in other domains of science and industry to detect various objects.

Reconstructing subsurface ocean dynamics, such as vertical velocity fields, from incomplete surface observations poses a critical challenge in Earth science, a field long hampered by the lack of standardized, analysis-ready benchmarks. To systematically address this issue and catalyze research, we first build and release KD48, a high-resolution ocean dynamics benchmark derived from petascale simulations and curated with expert-driven denoising. Building on this benchmark, we introduce VISION, a novel reconstruction paradigm based on Dynamic Prompting designed to tackle the core problem of missing data in real-world observations. The essence of VISION lies in its ability to generate a visual prompt on-the-fly from any available subset of observations, which encodes both data availability and the ocean's physical state. More importantly, we design a State-conditioned Prompting module that efficiently injects this prompt into a universal backbone, endowed with geometry- and scale-aware operators, to guide its adaptive adjustment of computational strategies. This mechanism enables VISION to precisely handle the challenges posed by varying input combinations. Extensive experiments on the KD48 benchmark demonstrate that VISION not only substantially outperforms state-of-the-art models but also exhibits strong generalization under extreme data missing scenarios. By providing a high-quality benchmark and a robust model, our work establishes a solid infrastructure for ocean science research under data uncertainty. Our codes are available at: https://github.com/YuanGao-YG/VISION.

We present the Caltech Fish Counting Dataset (CFC), a large-scale dataset for detecting, tracking, and counting fish in sonar videos. We identify sonar videos as a rich source of data for advancing low signal-to-noise computer vision applications and tackling domain generalization in multiple-object tracking (MOT) and counting. In comparison to existing MOT and counting datasets, which are largely restricted to videos of people and vehicles in cities, CFC is sourced from a natural-world domain where targets are not easily resolvable and appearance features cannot be easily leveraged for target re-identification. With over half a million annotations in over 1,500 videos sourced from seven different sonar cameras, CFC allows researchers to train MOT and counting algorithms and evaluate generalization performance at unseen test locations. We perform extensive baseline experiments and identify key challenges and opportunities for advancing the state of the art in generalization in MOT and counting.

Vision-driven field monitoring is central to digital agriculture, yet models built on general-domain pretrained backbones often fail to generalize across tasks, owing to the interaction of fine, variable canopy structures with fluctuating field conditions. We present FoMo4Wheat, one of the first crop-domain vision foundation model pretrained with self-supervision on ImAg4Wheat, the largest and most diverse wheat image dataset to date (2.5 million high-resolution images collected over a decade at 30 global sites, spanning >2,000 genotypes and >500 environmental conditions). This wheat-specific pretraining yields representations that are robust for wheat and transferable to other crops and weeds. Across ten in-field vision tasks at canopy and organ levels, FoMo4Wheat models consistently outperform state-of-the-art models pretrained on general-domain dataset. These results demonstrate the value of crop-specific foundation models for reliable in-field perception and chart a path toward a universal crop foundation model with cross-species and cross-task capabilities. FoMo4Wheat models and the ImAg4Wheat dataset are publicly available online: https://github.com/PheniX-Lab/FoMo4Wheat and https://huggingface.co/PheniX-Lab/FoMo4Wheat. The demonstration website is: https://fomo4wheat.phenix-lab.com/.

Accurate image-based bathymetric mapping in shallow waters remains challenging due to the complex optical distortions such as wave induced patterns, scattering and sunglint, introduced by the dynamic water surface, the water column properties, and solar illumination. In this work, we introduce Sea-Undistort, a comprehensive synthetic dataset of 1200 paired 512x512 through-water scenes rendered in Blender. Each pair comprises a distortion-free and a distorted view, featuring realistic water effects such as sun glint, waves, and scattering over diverse seabeds. Accompanied by per-image metadata such as camera parameters, sun position, and average depth, Sea-Undistort enables supervised training that is otherwise infeasible in real environments. We use Sea-Undistort to benchmark two state-of-the-art image restoration methods alongside an enhanced lightweight diffusion-based framework with an early-fusion sun-glint mask. When applied to real aerial data, the enhanced diffusion model delivers more complete Digital Surface Models (DSMs) of the seabed, especially in deeper areas, reduces bathymetric errors, suppresses glint and scattering, and crisply restores fine seabed details. Dataset, weights, and code are publicly available at https://www.magicbathy.eu/Sea-Undistort.html.

Addressing the current lack of a standardized habitat classification system for cultivated land ecosystems, incomplete coverage of habitat types, and the inability of existing models to effectively integrate semantic and texture features-resulting in insufficient segmentation accuracy and blurred boundaries for multi-scale habitats (e.g., large-scale field plots and micro-habitats)-this study developed a comprehensively annotated ultra-high-resolution remote sensing image dataset encompassing 15 categories of cultivated land system habitats. Furthermore, we propose a Dynamic-Weighted Feature Fusion Network (DWFF-Net). The encoder of this model utilizes a frozen-parameter DINOv3 to extract foundational features. By analyzing the relationships between different category images and feature maps, we introduce a data-level adaptive dynamic weighting strategy for feature fusion. The decoder incorporates a dynamic weight computation network to achieve thorough integration of multi-layer features, and a hybrid loss function is adopted to optimize model training. Experimental results on the constructed dataset demonstrate that the proposed model achieves a mean Intersection over Union (mIoU) of 0.6979 and an F1-score of 0.8049, outperforming the baseline network by 0.021 and 0.0161, respectively. Ablation studies further confirm the complementary nature of multi-layer feature fusion, which effectively improves the IoU for micro-habitat categories such as field ridges. This study establishes a habitat identification framework for cultivated land systems based on adaptive multi-layer feature fusion, enabling sub-meter precision habitat mapping at a low cost and providing robust technical support for fine-grained habitat monitoring in cultivated landscapes.

Rip currents are strong, localized and narrow currents of water that flow outwards into the sea, causing numerous beach-related injuries and fatalities worldwide. Accurate identification of rip currents remains challenging due to their amorphous nature and the lack of annotated data, which often requires expert knowledge. To address these issues, we present RipVIS, a large-scale video instance segmentation benchmark explicitly designed for rip current segmentation. RipVIS is an order of magnitude larger than previous datasets, featuring 184 videos (212,328 frames), of which 150 videos (163,528 frames) are with rip currents, collected from various sources, including drones, mobile phones, and fixed beach cameras. Our dataset encompasses diverse visual contexts, such as wave-breaking patterns, sediment flows, and water color variations, across multiple global locations, including USA, Mexico, Costa Rica, Portugal, Italy, Greece, Romania, Sri Lanka, Australia and New Zealand. Most videos are annotated at 5 FPS to ensure accuracy in dynamic scenarios, supplemented by an additional 34 videos (48,800 frames) without rip currents. We conduct comprehensive experiments with Mask R-CNN, Cascade Mask R-CNN, SparseInst and YOLO11, fine-tuning these models for the task of rip current segmentation. Results are reported in terms of multiple metrics, with a particular focus on the F_2 score to prioritize recall and reduce false negatives. To enhance segmentation performance, we introduce a novel post-processing step based on Temporal Confidence Aggregation (TCA). RipVIS aims to set a new standard for rip current segmentation, contributing towards safer beach environments. We offer a benchmark website to share data, models, and results with the research community, encouraging ongoing collaboration and future contributions, at https://ripvis.ai.

This paper deals with 3D reconstruction of seabirds which recently came into focus of environmental scientists as valuable bio-indicators for environmental change. Such 3D information is beneficial for analyzing the bird's behavior and physiological shape, for example by tracking motion, shape, and appearance changes. From a computer vision perspective birds are especially challenging due to their rapid and oftentimes non-rigid motions. We propose an approach to reconstruct the 3D pose and shape from monocular videos of a specific breed of seabird - the common murre. Our approach comprises a full pipeline of detection, tracking, segmentation, and temporally consistent 3D reconstruction. Additionally, we propose a temporal loss that extends current single-image 3D bird pose estimators to the temporal domain. Moreover, we provide a real-world dataset of 10000 frames of video observations on average capture nine birds simultaneously, comprising a large variety of motions and interactions, including a smaller test set with bird-specific keypoint labels. Using our temporal optimization, we achieve state-of-the-art performance for the challenging sequences in our dataset.

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/ .

Image datasets are essential not only in validating existing methods in computer vision but also in developing new methods. Most existing image datasets focus on trichromatic intensity images to mimic human vision. However, polarization and spectrum, the wave properties of light that animals in harsh environments and with limited brain capacity often rely on, remain underrepresented in existing datasets. Although spectro-polarimetric datasets exist, these datasets have insufficient object diversity, limited illumination conditions, linear-only polarization data, and inadequate image count. Here, we introduce two spectro-polarimetric datasets: trichromatic Stokes images and hyperspectral Stokes images. These novel datasets encompass both linear and circular polarization; they introduce multiple spectral channels; and they feature a broad selection of real-world scenes. With our dataset in hand, we analyze the spectro-polarimetric image statistics, develop efficient representations of such high-dimensional data, and evaluate spectral dependency of shape-from-polarization methods. As such, the proposed dataset promises a foundation for data-driven spectro-polarimetric imaging and vision research. Dataset and code will be publicly available.

As the global food security landscape continues to evolve, the need for accurate and reliable crop disease diagnosis has never been more pressing. To address global food security concerns, we extend the widely used PlantVillage dataset with additional apple leaf disease classes, enhancing diversity and complexity. Experimental evaluations on both original and extended datasets reveal that existing models struggle with the new additions, highlighting the need for more robust and generalizable computer vision models. Test F1 scores of 99.63% and 97.87% were obtained on the original and extended datasets, respectively. Our study provides a more challenging and diverse benchmark, paving the way for the development of accurate and reliable models for identifying apple leaf diseases under varying imaging conditions. The expanded dataset is available at https://www.kaggle.com/datasets/akinyemijoseph/apple-leaf-disease-dataset-6-classes-v2 enabling future research to build upon our findings.

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.

This paper explores the feasibility of using text-to-image models in a zero-shot setup to generate images for taxonomy concepts. While text-based methods for taxonomy enrichment are well-established, the potential of the visual dimension remains unexplored. To address this, we propose a comprehensive benchmark for Taxonomy Image Generation that assesses models' abilities to understand taxonomy concepts and generate relevant, high-quality images. The benchmark includes common-sense and randomly sampled WordNet concepts, alongside the LLM generated predictions. The 12 models are evaluated using 9 novel taxonomy-related text-to-image metrics and human feedback. Moreover, we pioneer the use of pairwise evaluation with GPT-4 feedback for image generation. Experimental results show that the ranking of models differs significantly from standard T2I tasks. Playground-v2 and FLUX consistently outperform across metrics and subsets and the retrieval-based approach performs poorly. These findings highlight the potential for automating the curation of structured data resources.

We introduce COU: Common Objects Underwater, an instance-segmented image dataset of commonly found man-made objects in multiple aquatic and marine environments. COU contains approximately 10K segmented images, annotated from images collected during a number of underwater robot field trials in diverse locations. COU has been created to address the lack of datasets with robust class coverage curated for underwater instance segmentation, which is particularly useful for training light-weight, real-time capable detectors for Autonomous Underwater Vehicles (AUVs). In addition, COU addresses the lack of diversity in object classes since the commonly available underwater image datasets focus only on marine life. Currently, COU contains images from both closed-water (pool) and open-water (lakes and oceans) environments, of 24 different classes of objects including marine debris, dive tools, and AUVs. To assess the efficacy of COU in training underwater object detectors, we use three state-of-the-art models to evaluate its performance and accuracy, using a combination of standard accuracy and efficiency metrics. The improved performance of COU-trained detectors over those solely trained on terrestrial data demonstrates the clear advantage of training with annotated underwater images. We make COU available for broad use under open-source licenses.

This work tackles 3D scene reconstruction for a video fly-over perspective problem in the maritime domain, with a specific emphasis on geometrically and visually sound reconstructions. This will allow for downstream tasks such as segmentation, navigation, and localization. To our knowledge, there is no dataset available in this domain. As such, we propose a novel maritime 3D scene reconstruction benchmarking dataset, named as MTReD (Maritime Three-Dimensional Reconstruction Dataset). The MTReD comprises 19 fly-over videos curated from the Internet containing ships, islands, and coastlines. As the task is aimed towards geometrical consistency and visual completeness, the dataset uses two metrics: (1) Reprojection error; and (2) Perception based metrics. We find that existing perception-based metrics, such as Learned Perceptual Image Patch Similarity (LPIPS), do not appropriately measure the completeness of a reconstructed image. Thus, we propose a novel semantic similarity metric utilizing DINOv2 features coined DiFPS (DinoV2 Features Perception Similarity). We perform initial evaluation on two baselines: (1) Structured from Motion (SfM) through Colmap; and (2) the recent state-of-the-art MASt3R model. We find that the reconstructed scenes by MASt3R have higher reprojection errors, but superior perception based metric scores. To this end, some pre-processing methods are explored, and we find a pre-processing method which improves both the reprojection error and perception-based score. We envisage our proposed MTReD to stimulate further research in these directions. The dataset and all the code will be made available in https://github.com/RuiYiYong/MTReD.

The continuous operation of Earth-orbiting satellites generates vast and ever-growing archives of Remote Sensing (RS) images. Natural language presents an intuitive interface for accessing, querying, and interpreting the data from such archives. However, existing Vision-Language Models (VLMs) are predominantly trained on web-scraped, noisy image-text data, exhibiting limited exposure to the specialized domain of RS. This deficiency results in poor performance on RS-specific tasks, as commonly used datasets often lack detailed, scientifically accurate textual descriptions and instead emphasize solely on attributes like date and location. To bridge this critical gap, we introduce GAIA, a novel dataset designed for multi-scale, multi-sensor, and multi-modal RS image analysis. GAIA comprises of 205,150 meticulously curated RS image-text pairs, representing a diverse range of RS modalities associated to different spatial resolutions. Unlike existing vision-language datasets in RS, GAIA specifically focuses on capturing a diverse range of RS applications, providing unique information about environmental changes, natural disasters, and various other dynamic phenomena. The dataset provides a spatially and temporally balanced distribution, spanning across the globe, covering the last 25 years with a balanced temporal distribution of observations. GAIA's construction involved a two-stage process: (1) targeted web-scraping of images and accompanying text from reputable RS-related sources, and (2) generation of five high-quality, scientifically grounded synthetic captions for each image using carefully crafted prompts that leverage the advanced vision-language capabilities of GPT-4o. Our extensive experiments, including fine-tuning of CLIP and BLIP2 models, demonstrate that GAIA significantly improves performance on RS image classification, cross-modal retrieval and image captioning tasks.

Berry picking has long-standing traditions in Finland, yet it is challenging and can potentially be dangerous. The integration of drones equipped with advanced imaging techniques represents a transformative leap forward, optimising harvests and promising sustainable practices. We propose WildBe, the first image dataset of wild berries captured in peatlands and under the canopy of Finnish forests using drones. Unlike previous and related datasets, WildBe includes new varieties of berries, such as bilberries, cloudberries, lingonberries, and crowberries, captured under severe light variations and in cluttered environments. WildBe features 3,516 images, including a total of 18,468 annotated bounding boxes. We carry out a comprehensive analysis of WildBe using six popular object detectors, assessing their effectiveness in berry detection across different forest regions and camera types. We will release WildBe publicly.

Accurately quantifying tree cover is an important metric for ecosystem monitoring and for assessing progress in restored sites. Recent works have shown that deep learning-based segmentation algorithms are capable of accurately mapping trees at country and continental scales using high-resolution aerial and satellite imagery. Mapping at high (ideally sub-meter) resolution is necessary to identify individual trees, however there are few open-access datasets containing instance level annotations and those that exist are small or not geographically diverse. We present a novel open-access dataset for individual tree crown delineation (TCD) in high-resolution aerial imagery sourced from OpenAerialMap (OAM). Our dataset, OAM-TCD, comprises 5072 2048x2048 px images at 10 cm/px resolution with associated human-labeled instance masks for over 280k individual and 56k groups of trees. By sampling imagery from around the world, we are able to better capture the diversity and morphology of trees in different terrestrial biomes and in both urban and natural environments. Using our dataset, we train reference instance and semantic segmentation models that compare favorably to existing state-of-the-art models. We assess performance through k-fold cross-validation and comparison with existing datasets; additionally we demonstrate compelling results on independent aerial imagery captured over Switzerland and compare to municipal tree inventories and LIDAR-derived canopy maps in the city of Zurich. Our dataset, models and training/benchmark code are publicly released under permissive open-source licenses: Creative Commons (majority CC BY 4.0), and Apache 2.0 respectively.

In situ imageomics leverages machine learning techniques to infer biological traits from images collected in the field, or in situ, to study individuals organisms, groups of wildlife, and whole ecosystems. Such datasets provide real-time social and environmental context to inferred biological traits, which can enable new, data-driven conservation and ecosystem management. The development of machine learning techniques to extract biological traits from images are impeded by the volume and quality data required to train these models. Autonomous, unmanned aerial vehicles (UAVs), are well suited to collect in situ imageomics data as they can traverse remote terrain quickly to collect large volumes of data with greater consistency and reliability compared to manually piloted UAV missions. However, little guidance exists on optimizing autonomous UAV missions for the purposes of remote sensing for conservation and biodiversity monitoring. The UAV video dataset curated by KABR: In-Situ Dataset for Kenyan Animal Behavior Recognition from Drone Videos required three weeks to collect, a time-consuming and expensive endeavor. Our analysis of KABR revealed that a third of the videos gathered were unusable for the purposes of inferring wildlife behavior. We analyzed the flight telemetry data from portions of UAV videos that were usable for inferring wildlife behavior, and demonstrate how these insights can be integrated into an autonomous remote sensing system to track wildlife in real time. Our autonomous remote sensing system optimizes the UAV's actions to increase the yield of usable data, and matches the flight path of an expert pilot with an 87% accuracy rate, representing an 18.2% improvement in accuracy over previously proposed methods.

Automated pollen recognition is vital to paleoclimatology, biodiversity monitoring, and public health, yet conventional methods are hampered by inefficiency and subjectivity. Existing deep learning models often struggle to achieve the requisite localization accuracy for microscopic targets like pollen, which are characterized by their minute size, indistinct edges, and complex backgrounds. To overcome this limitation, we introduce HieraEdgeNet, a multi-scale edge-enhancement framework. The framework's core innovation is the introduction of three synergistic modules: the Hierarchical Edge Module (HEM), which explicitly extracts a multi-scale pyramid of edge features that corresponds to the semantic hierarchy at early network stages; the Synergistic Edge Fusion (SEF) module, for deeply fusing these edge priors with semantic information at each respective scale; and the Cross Stage Partial Omni-Kernel Module (CSPOKM), which maximally refines the most detail-rich feature layers using an Omni-Kernel operator - comprising anisotropic large-kernel convolutions and mixed-domain attention - all within a computationally efficient Cross-Stage Partial (CSP) framework. On a large-scale dataset comprising 120 pollen classes, HieraEdgeNet achieves a mean Average Precision ([email protected]) of 0.9501, significantly outperforming state-of-the-art baseline models such as YOLOv12n and RT-DETR. Furthermore, qualitative analysis confirms that our approach generates feature representations that are more precisely focused on object boundaries. By systematically integrating edge information, HieraEdgeNet provides a robust and powerful solution for high-precision, high-efficiency automated detection of microscopic objects.

Remote sensing imagery, despite its broad applications in helping achieve Sustainable Development Goals and tackle climate change, has not yet benefited from the recent advancements of versatile, task-agnostic vision language models (VLMs). A key reason is that the large-scale, semantically diverse image-text dataset required for developing VLMs is still absent for remote sensing images. Unlike natural images, remote sensing images and their associated text descriptions cannot be efficiently collected from the public Internet at scale. In this work, we bridge this gap by using geo-coordinates to automatically connect open, unlabeled remote sensing images with rich semantics covered in OpenStreetMap, and thus construct SkyScript, a comprehensive vision-language dataset for remote sensing images, comprising 2.6 million image-text pairs covering 29K distinct semantic tags. With continual pre-training on this dataset, we obtain a VLM that surpasses baseline models with a 6.2% average accuracy gain in zero-shot scene classification across seven benchmark datasets. It also demonstrates the ability of zero-shot transfer for fine-grained object attribute classification and cross-modal retrieval. We hope this dataset can support the advancement of VLMs for various multi-modal tasks in remote sensing, such as open-vocabulary classification, retrieval, captioning, and text-to-image synthesis.

An early, non-invasive, and on-site detection of nutrient deficiencies is critical to enable timely actions to prevent major losses of crops caused by lack of nutrients. While acquiring labeled data is very expensive, collecting images from multiple views of a crop is straightforward. Despite its relevance for practical applications, unsupervised domain adaptation where multiple views are available for the labeled source domain as well as the unlabeled target domain is an unexplored research area. In this work, we thus propose an approach that leverages multiple camera views in the source and target domain for unsupervised domain adaptation. We evaluate the proposed approach on two nutrient deficiency datasets. The proposed method achieves state-of-the-art results on both datasets compared to other unsupervised domain adaptation methods. The dataset and source code are available at https://github.com/jh-yi/MV-Match.

Automatic monitoring of tree plantations plays a crucial role in agriculture. Flawless monitoring of tree health helps farmers make informed decisions regarding their management by taking appropriate action. Use of drone images for automatic plantation monitoring can enhance the accuracy of the monitoring process, while still being affordable to small farmers in developing countries such as India. Small, low cost drones equipped with an RGB camera can capture high-resolution images of agricultural fields, allowing for detailed analysis of the well-being of the plantations. Existing methods of automated plantation monitoring are mostly based on satellite images, which are difficult to get for the farmers. We propose an automated system for plantation health monitoring using drone images, which are becoming easier to get for the farmers. We propose a dataset of images of trees with three categories: ``Good health", ``Stunted", and ``Dead". We annotate the dataset using CVAT annotation tool, for use in research purposes. We experiment with different well-known CNN models to observe their performance on the proposed dataset. The initial low accuracy levels show the complexity of the proposed dataset. Further, our study revealed that, depth-wise convolution operation embedded in a deep CNN model, can enhance the performance of the model on drone dataset. Further, we apply state-of-the-art object detection models to identify individual trees to better monitor them automatically.

This study introduces a novel dataset for segmenting flooded areas in satellite images. After reviewing 77 existing benchmarks utilizing satellite imagery, we identified a shortage of suitable datasets for this specific task. To fill this gap, we collected satellite imagery of the 2019 Midwestern USA floods from Planet Explorer by Planet Labs (Image opyright 2024 Planet Labs PBC). The dataset consists of 10 satellite images per location, each containing both flooded and non-flooded areas. We selected ten locations from each of the five states: Iowa, Kansas, Montana, Nebraska, and South Dakota. The dataset ensures uniform resolution and resizing during data processing. For evaluating semantic segmentation performance, we tested state-of-the-art models in computer vision and remote sensing on our dataset. Additionally, we conducted an ablation study varying window sizes to capture temporal characteristics. Overall, the models demonstrated modest results, suggesting a requirement for future multimodal and temporal learning strategies. The dataset will be publicly available on <https://github.com/youngsunjang/SDSU_MidWest_Flood_2019>.

There exist no publicly available annotated underwater multi-object tracking (MOT) datasets captured in turbid environments. To remedy this we propose the BrackishMOT dataset with focus on tracking schools of small fish, which is a notoriously difficult MOT task. BrackishMOT consists of 98 sequences captured in the wild. Alongside the novel dataset, we present baseline results by training a state-of-the-art tracker. Additionally, we propose a framework for creating synthetic sequences in order to expand the dataset. The framework consists of animated fish models and realistic underwater environments. We analyse the effects of including synthetic data during training and show that a combination of real and synthetic underwater training data can enhance tracking performance. Links to code and data can be found at https://www.vap.aau.dk/brackishmot

The application of artificial intelligence (AI) in three-dimensional (3D) agricultural research, particularly for maize, has been limited by the scarcity of large-scale, diverse datasets. While 2D image datasets are abundant, they fail to capture essential structural details such as leaf architecture, plant volume, and spatial arrangements that 3D data provide. To address this limitation, we present AgriField3D (https://baskargroup.github.io/AgriField3D/), a curated dataset of 3D point clouds of field-grown maize plants from a diverse genetic panel, designed to be AI-ready for advancing agricultural research. Our dataset comprises over 1,000 high-quality point clouds collected using a Terrestrial Laser Scanner, complemented by procedural models that provide structured, parametric representations of maize plants. These procedural models, generated using Non-Uniform Rational B-Splines (NURBS) and optimized via a two-step process combining Particle Swarm Optimization (PSO) and differentiable programming, enable precise, scalable reconstructions of leaf surfaces and plant architectures. To enhance usability, we performed graph-based segmentation to isolate individual leaves and stalks, ensuring consistent labeling across all samples. We also conducted rigorous manual quality control on all datasets, correcting errors in segmentation, ensuring accurate leaf ordering, and validating metadata annotations. The dataset further includes metadata detailing plant morphology and quality, alongside multi-resolution subsampled versions (100k, 50k, 10k points) optimized for various computational needs. By integrating point cloud data of field grown plants with high-fidelity procedural models and ensuring meticulous manual validation, AgriField3D provides a comprehensive foundation for AI-driven phenotyping, plant structural analysis, and 3D applications in agricultural research.

Coral reefs are fast-changing and complex ecosystems that are crucial to monitor and study. Biological hotspot detection can help coral reef managers prioritize limited resources for monitoring and intervention tasks. Here, we explore the use of autonomous underwater vehicles (AUVs) with cameras, coupled with visual detectors and photogrammetry, to map and identify these hotspots. This approach can provide high spatial resolution information in fast feedback cycles. To the best of our knowledge, we present one of the first attempts at using an AUV to gather visually-observed, fine-grain biological hotspot maps in concert with topography of a coral reefs. Our hotspot maps correlate with rugosity, an established proxy metric for coral reef biodiversity and abundance, as well as with our visual inspections of the 3D reconstruction. We also investigate issues of scaling this approach when applied to new reefs by using these visual detectors pre-trained on large public datasets.

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.

In this paper, we present a complete refractive Structure-from-Motion (RSfM) framework for underwater 3D reconstruction using refractive camera setups (for both, flat- and dome-port underwater housings). Despite notable achievements in refractive multi-view geometry over the past decade, a robust, complete and publicly available solution for such tasks is not available at present, and often practical applications have to resort to approximating refraction effects by the intrinsic (distortion) parameters of a pinhole camera model. To fill this gap, we have integrated refraction considerations throughout the entire SfM process within the state-of-the-art, open-source SfM framework COLMAP. Numerical simulations and reconstruction results on synthetically generated but photo-realistic images with ground truth validate that enabling refraction does not compromise accuracy or robustness as compared to in-air reconstructions. Finally, we demonstrate the capability of our approach for large-scale refractive scenarios using a dataset consisting of nearly 6000 images. The implementation is released as open-source at: https://cau-git.rz.uni-kiel.de/inf-ag-koeser/colmap_underwater.