Daily Papers

The rapid advancement of deep learning has facilitated the automated processing of electron microscopy (EM) big data stacks. However, designing a framework that eliminates manual labeling and adapts to domain gaps remains challenging. Current research remains entangled in the dilemma of pursuing complete automation while still requiring simulations or slight manual annotations. Here we demonstrate tandem generative adversarial network (tGAN), a fully label-free and simulation-free pipeline capable of generating EM images for computer vision training. The tGAN can assimilate key features from new data stacks, thus producing a tailored virtual dataset for the training of automated EM analysis tools. Using segmenting nanoparticles for analyzing size distribution of supported catalysts as the demonstration, our findings showcased that the recognition accuracy of tGAN even exceeds the manually-labeling method by 5%. It can also be adaptively deployed to various data domains without further manual manipulation, which is verified by transfer learning from HAADF-STEM to BF-TEM. This generalizability may enable it to extend its application to a broader range of imaging characterizations, liberating microscopists and materials scientists from tedious dataset annotations.

Current state-of-the-art methods for object detection rely on annotated bounding boxes of large data sets for training. However, obtaining such annotations is expensive and can require up to hundreds of hours of manual labor. This poses a challenge, especially since such annotations can only be provided by experts, as they require knowledge about the scientific domain. To tackle this challenge, we propose a domain-specific weakly supervised object detection algorithm that only relies on image-level annotations, which are significantly easier to acquire. Our method distills the knowledge of a pre-trained model, on the task of predicting the presence or absence of a virus in an image, to obtain a set of pseudo-labels that can be used to later train a state-of-the-art object detection model. To do so, we use an optimization approach with a shrinking receptive field to extract virus particles directly without specific network architectures. Through a set of extensive studies, we show how the proposed pseudo-labels are easier to obtain, and, more importantly, are able to outperform other existing weak labeling methods, and even ground truth labels, in cases where the time to obtain the annotation is limited.

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

The performance of advanced materials for extreme environments is underpinned by their microstructure, including the size and distribution of reinforcing phases. Chromium-based superalloys are a recently proposed alternative to conventional face-centred-cubic superalloys for high-temperature applications, such as Concentrated Solar Power, and their development requires efficient measurement of precipitate volume fraction and size distribution from electron microscopy images. Traditional fixed-threshold image processing is sensitive to background noise, generalises poorly across materials, and requires substantial manual measurement effort. To address these bottlenecks, this study proposes DT-SegNet, an end-to-end two-stage deep learning scheme based on YOLOv5 and SegFormer for object detection and segmentation in electron microscopy images. The approach combines the training efficiency of convolutional neural networks at the detection stage with the segmentation accuracy of a Vision Transformer. Numerical experiments show that DT-SegNet substantially outperforms state-of-the-art segmentation tools offered by Weka and ilastik across metrics including accuracy, precision, recall, and F1-score. The model provides a useful tool for alloy-development microstructure examinations and helps address the large datasets associated with high-throughput alloy development.

Austenitic 347H stainless steel offers superior mechanical properties and corrosion resistance required for extreme operating conditions such as high temperature. The change in microstructure due to composition and process variations is expected to impact material properties. Identifying microstructural features such as grain boundaries thus becomes an important task in the process-microstructure-properties loop. Applying convolutional neural network (CNN) based deep-learning models is a powerful technique to detect features from material micrographs in an automated manner. Manual labeling of the images for the segmentation task poses a major bottleneck for generating training data and labels in a reliable and reproducible way within a reasonable timeframe. In this study, we attempt to overcome such limitations by utilizing multi-modal microscopy to generate labels directly instead of manual labeling. We combine scanning electron microscopy (SEM) images of 347H stainless steel as training data and electron backscatter diffraction (EBSD) micrographs as pixel-wise labels for grain boundary detection as a semantic segmentation task. We demonstrate that despite producing instrumentation drift during data collection between two modes of microscopy, this method performs comparably to similar segmentation tasks that used manual labeling. Additionally, we find that naïve pixel-wise segmentation results in small gaps and missing boundaries in the predicted grain boundary map. By incorporating topological information during model training, the connectivity of the grain boundary network and segmentation performance is improved. Finally, our approach is validated by accurate computation on downstream tasks of predicting the underlying grain morphology distributions which are the ultimate quantities of interest for microstructural characterization.

Machine learning-based interatomic potentials and force fields depend critically on accurate atomic structures, yet such data are scarce due to the limited availability of experimentally resolved crystals. Although atomic-resolution electron microscopy offers a potential source of structural data, converting these images into simulation-ready formats remains labor-intensive and error-prone, creating a bottleneck for model training and validation. We introduce AutoMat, an end-to-end, agent-assisted pipeline that automatically transforms scanning transmission electron microscopy (STEM) images into atomic crystal structures and predicts their physical properties. AutoMat combines pattern-adaptive denoising, physics-guided template retrieval, symmetry-aware atomic reconstruction, fast relaxation and property prediction via MatterSim, and coordinated orchestration across all stages. We propose the first dedicated STEM2Mat-Bench for this task and evaluate performance using lattice RMSD, formation energy MAE, and structure-matching success rate. By orchestrating external tool calls, AutoMat enables a text-only LLM to outperform vision-language models in this domain, achieving closed-loop reasoning throughout the pipeline. In large-scale experiments over 450 structure samples, AutoMat substantially outperforms existing multimodal large language models and tools. These results validate both AutoMat and STEM2Mat-Bench, marking a key step toward bridging microscopy and atomistic simulation in materials science.The code and dataset are publicly available at https://github.com/yyt-2378/AutoMat and https://huggingface.co/datasets/yaotianvector/STEM2Mat.

The electron microscope (EM) remains the predominant technique for elucidating intricate details of the animal nervous system at the nanometer scale. However, accurately reconstructing the complex morphology of axons and myelin sheaths poses a significant challenge. Furthermore, the absence of publicly available, large-scale EM datasets encompassing complete cross sections of the corpus callosum, with dense ground truth segmentation for axons and myelin sheaths, hinders the advancement and evaluation of holistic corpus callosum reconstructions. To surmount these obstacles, we introduce the AxonCallosumEM dataset, comprising a 1.83 times 5.76mm EM image captured from the corpus callosum of the Rett Syndrome (RTT) mouse model, which entail extensive axon bundles. We meticulously proofread over 600,000 patches at a resolution of 1024 times 1024, thus providing a comprehensive ground truth for myelinated axons and myelin sheaths. Additionally, we extensively annotated three distinct regions within the dataset for the purposes of training, testing, and validation. Utilizing this dataset, we develop a fine-tuning methodology that adapts Segment Anything Model (SAM) to EM images segmentation tasks, called EM-SAM, enabling outperforms other state-of-the-art methods. Furthermore, we present the evaluation results of EM-SAM as a baseline.

Zero-shot and prompt-based technologies capitalized on using frequently occurring images to transform visual reasoning tasks, which explains why such technologies struggle with valuable yet scarce scientific image sets. In this work, we propose Zenesis, a comprehensive no-code interactive platform designed to minimize barriers posed by data readiness for scientific images. We develop lightweight multi-modal adaptation techniques that enable zero-shot operation on raw scientific data, along with human-in-the-loop refinement and heuristic-based temporal enhancement options. We demonstrate the performance of our approach through comprehensive comparison and validation on challenging Focused Ion Beam Scanning Electron Microscopy (FIB-SEM) data of catalyst-loaded membranes. Zenesis significantly outperforms baseline methods, achieving an average accuracy of 0.947, an Intersection over Union (IOU) of 0.858, and a Dice score of 0.923 for amorphous catalyst samples and accuracy of 0.987, an IOU of 0.857, and a Dice score of 0.923 for crystalline samples. These results mark a substantial improvement over traditional methods like Otsu thresholding and even advanced models like Segment Anything Model (SAM) when used in isolation. Our results demonstrate that Zenesis is a powerful tool for scientific applications, particularly in fields where high-quality annotated datasets are unavailable, accelerating accurate analysis of experimental imaging.

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.

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

TrueEBSD is an open-source MATLAB program for image alignment and spatial distortion correction of images and electron backscatter diffraction (EBSD) maps. We have re-implemented TrueEBSD as an add-on to MTEX, an established toolbox for EBSD data analysis. Spatial alignment enables correlative analysis methods, such as augmenting EBSD orientation maps with data from other imaging modes. The augmented EBSD maps can then be analysed further using MTEX. We demonstrate TrueEBSD on two example case studies: one for measuring Co phase fraction and WC contiguity in a WC-Co composite, and another for determining the relative susceptibility of grain boundaries to void formation in a copper polycrystal. In both examples, the EBSD map was augmented with scanning electron microscopy (SEM) image data. This enabled quantitative crystallographic measurements which would not be possible from analysing the EBSD maps and images separately.

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

In the field of integrated circuit manufacturing, the detection and classification of nanoscale wafer defects are critical for subsequent root cause analysis and yield enhancement. The complex background patterns observed in scanning electron microscope (SEM) images and the diverse textures of the defects pose significant challenges. Traditional methods usually suffer from insufficient data, labels, and poor transferability. In this paper, we propose a novel few-shot learning approach, SEM-CLIP, for accurate defect classification and segmentation. SEM-CLIP customizes the Contrastive Language-Image Pretraining (CLIP) model to better focus on defect areas and minimize background distractions, thereby enhancing segmentation accuracy. We employ text prompts enriched with domain knowledge as prior information to assist in precise analysis. Additionally, our approach incorporates feature engineering with textual guidance to categorize defects more effectively. SEM-CLIP requires little annotated data, substantially reducing labor demands in the semiconductor industry. Extensive experimental validation demonstrates that our model achieves impressive classification and segmentation results under few-shot learning scenarios.

Autoregressive next-token prediction is a standard pretraining method for large-scale language models, but its application to vision tasks is hindered by the non-sequential nature of image data, leading to cumulative errors. Most vision models employ masked autoencoder (MAE) based pretraining, which faces scalability issues. To address these challenges, we introduce TokenUnify, a novel pretraining method that integrates random token prediction, next-token prediction, and next-all token prediction. We provide theoretical evidence demonstrating that TokenUnify mitigates cumulative errors in visual autoregression. Cooperated with TokenUnify, we have assembled a large-scale electron microscopy (EM) image dataset with ultra-high resolution, ideal for creating spatially correlated long sequences. This dataset includes over 120 million annotated voxels, making it the largest neuron segmentation dataset to date and providing a unified benchmark for experimental validation. Leveraging the Mamba network inherently suited for long-sequence modeling on this dataset, TokenUnify not only reduces the computational complexity but also leads to a significant 45\% improvement in segmentation performance on downstream EM neuron segmentation tasks compared to existing methods. Furthermore, TokenUnify demonstrates superior scalability over MAE and traditional autoregressive methods, effectively bridging the gap between pretraining strategies for language and vision models. Code is available at https://github.com/ydchen0806/TokenUnify.

Large, carefully partitioned datasets are essential to train neural networks and standardize performance benchmarks. As a result, we have set up new repositories to make our electron microscopy datasets available to the wider community. There are three main datasets containing 19769 scanning transmission electron micrographs, 17266 transmission electron micrographs, and 98340 simulated exit wavefunctions, and multiple variants of each dataset for different applications. To visualize image datasets, we trained variational autoencoders to encode data as 64-dimensional multivariate normal distributions, which we cluster in two dimensions by t-distributed stochastic neighbor embedding. In addition, we have improved dataset visualization with variational autoencoders by introducing encoding normalization and regularization, adding an image gradient loss, and extending t-distributed stochastic neighbor embedding to account for encoded standard deviations. Our datasets, source code, pretrained models, and interactive visualizations are openly available at https://github.com/Jeffrey-Ede/datasets.

The state-of-the-art models for medical image segmentation are variants of U-Net and fully convolutional networks (FCN). Despite their success, these models have two limitations: (1) their optimal depth is apriori unknown, requiring extensive architecture search or inefficient ensemble of models of varying depths; and (2) their skip connections impose an unnecessarily restrictive fusion scheme, forcing aggregation only at the same-scale feature maps of the encoder and decoder sub-networks. To overcome these two limitations, we propose UNet++, a new neural architecture for semantic and instance segmentation, by (1) alleviating the unknown network depth with an efficient ensemble of U-Nets of varying depths, which partially share an encoder and co-learn simultaneously using deep supervision; (2) redesigning skip connections to aggregate features of varying semantic scales at the decoder sub-networks, leading to a highly flexible feature fusion scheme; and (3) devising a pruning scheme to accelerate the inference speed of UNet++. We have evaluated UNet++ using six different medical image segmentation datasets, covering multiple imaging modalities such as computed tomography (CT), magnetic resonance imaging (MRI), and electron microscopy (EM), and demonstrating that (1) UNet++ consistently outperforms the baseline models for the task of semantic segmentation across different datasets and backbone architectures; (2) UNet++ enhances segmentation quality of varying-size objects -- an improvement over the fixed-depth U-Net; (3) Mask RCNN++ (Mask R-CNN with UNet++ design) outperforms the original Mask R-CNN for the task of instance segmentation; and (4) pruned UNet++ models achieve significant speedup while showing only modest performance degradation. Our implementation and pre-trained models are available at https://github.com/MrGiovanni/UNetPlusPlus.

Medical images often contain artificial markers added by doctors, which can negatively affect the accuracy of AI-based diagnosis. To address this issue and recover the missing visual contents, inpainting techniques are highly needed. However, existing inpainting methods require manual mask input, limiting their application scenarios. In this paper, we introduce a novel blind inpainting method that automatically completes visual contents without specifying masks for target areas in an image. Our proposed model includes a mask-free reconstruction network and an object-aware discriminator. The reconstruction network consists of two branches that predict the corrupted regions with artificial markers and simultaneously recover the missing visual contents. The object-aware discriminator relies on the powerful recognition capabilities of the dense object detector to ensure that the markers of reconstructed images cannot be detected in any local regions. As a result, the reconstructed image can be close to the clean one as much as possible. Our proposed method is evaluated on different medical image datasets, covering multiple imaging modalities such as ultrasound (US), magnetic resonance imaging (MRI), and electron microscopy (EM), demonstrating that our method is effective and robust against various unknown missing region patterns.

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

Electron microscopy (EM) enables the reconstruction of neural circuits at the level of individual synapses, which has been transformative for scientific discoveries. However, due to the complex morphology, an accurate reconstruction of cortical axons has become a major challenge. Worse still, there is no publicly available large-scale EM dataset from the cortex that provides dense ground truth segmentation for axons, making it difficult to develop and evaluate large-scale axon reconstruction methods. To address this, we introduce the AxonEM dataset, which consists of two 30x30x30 um^3 EM image volumes from the human and mouse cortex, respectively. We thoroughly proofread over 18,000 axon instances to provide dense 3D axon instance segmentation, enabling large-scale evaluation of axon reconstruction methods. In addition, we densely annotate nine ground truth subvolumes for training, per each data volume. With this, we reproduce two published state-of-the-art methods and provide their evaluation results as a baseline. We publicly release our code and data at https://connectomics-bazaar.github.io/proj/AxonEM/index.html to foster the development of advanced methods.

Ultrafast electron microscopy (UEM) has found widespread applications in physics, chemistry, and materials science, enabling real-space imaging of dynamics on ultrafast timescales. Recent advances have pushed the temporal resolution of UEM into the attosecond regime, enabling the attomicroscopy technique to directly visualize electron motion. In this work, we extend the capabilities of this powerful imaging tool to investigate ultrafast electron dynamics in a biological system by imaging and controlling light induced electronic and chemical changes in the conductive network of multicellular cable bacteria. Using electron energy loss spectroscopy (EELS), we first observed a laser induced increase in {\pi}-electron density, accompanied by spectral peak broadening and a blueshift features indicative of enhanced conductivity and structural modification. We also traced the effect of ultrafast laser pumping on bulk plasmon electron oscillations by monitoring changes in the plasmon like resonance peak. Additionally, we visualized laser induced chemical structural changes in cable bacteria in real space. The imaging results revealed carbon enrichment alongside a depletion of nitrogen and oxygen, highlighting the controllability of chemical dynamics. Moreover, time resolved EELS measurements further revealed a picosecond scale decay and recovery of both {\pi}-electron and plasmonic features, attributed to electron phonon coupling. In addition to shedding light on the mechanism of electron motion in cable bacteria, these findings demonstrate ultrafast modulation and switching of conductivity, underscoring their potential as bio-optoelectronic components operating on ultrafast timescales.

Cryo-electron tomography (Cryo-ET) is a powerful tool in structural biology for 3D visualization of cells and biological systems at resolutions sufficient to identify individual proteins in situ. The measurements are collected by tilting the frozen specimen and exposing it to an electron beam of known dosage. As the biological samples are prone to electron damage, the samples can be exposed to only a limited dosage of electrons, leading to noisy and incomplete measurements. Thus, the reconstructions are noisy and incomplete, leading to the missing wedge problem. Currently, self-supervised learning is used to compensate for this issue. This typically involves, for each volume to recover, training a large 3D UNet on the initial noisy reconstruction, leading to large training time and memory requirements. In this work, we exploit the local nature of the forward model to train a lightweight network using only localized data from the measurements. This design provides flexibility in balancing computational and time requirements while reconstructing the volumes with high accuracy. We observe experimentally that this network can work well on unseen datasets, despite using a network trained on a few measurements.

Characterizing materials with electron micrographs poses significant challenges for automated labeling due to the complex nature of nanomaterial structures. To address this, we introduce a fully automated, end-to-end pipeline that leverages recent advances in Generative AI. It is designed for analyzing and understanding the microstructures of semiconductor materials with effectiveness comparable to that of human experts, contributing to the pursuit of Artificial General Intelligence (AGI) in nanomaterial identification. Our approach utilizes Large MultiModal Models (LMMs) such as GPT-4V, alongside text-to-image models like DALLE-3. We integrate a GPT-4 guided Visual Question Answering (VQA) method to analyze nanomaterial images, generate synthetic nanomaterial images via DALLE-3, and employ in-context learning with few-shot prompting in GPT-4V for accurate nanomaterial identification. Our method surpasses traditional techniques by enhancing the precision of nanomaterial identification and optimizing the process for high-throughput screening.

As the globalization of semiconductor design and manufacturing processes continues, the demand for defect detection during integrated circuit fabrication stages is becoming increasingly critical, playing a significant role in enhancing the yield of semiconductor products. Traditional wafer map defect pattern detection methods involve manual inspection using electron microscopes to collect sample images, which are then assessed by experts for defects. This approach is labor-intensive and inefficient. Consequently, there is a pressing need to develop a model capable of automatically detecting defects as an alternative to manual operations. In this paper, we propose a method that initially employs a pre-trained VAE model to obtain the fault distribution information of the wafer map. This information serves as guidance, combined with the original image set for semi-supervised model training. During the semi-supervised training, we utilize a teacher-student network for iterative learning. The model presented in this paper is validated on the benchmark dataset WM-811K wafer dataset. The experimental results demonstrate superior classification accuracy and detection performance compared to state-of-the-art models, fulfilling the requirements for industrial applications. Compared to the original architecture, we have achieved significant performance improvement.

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

Cryo-electron microscopy (cryo-EM) is a powerful technique in structural biology and drug discovery, enabling the study of biomolecules at high resolution. Significant advancements by structural biologists using cryo-EM have led to the production of over 38,626 protein density maps at various resolutions1. However, cryo-EM data processing algorithms have yet to fully benefit from our knowledge of biomolecular density maps, with only a few recent models being data-driven but limited to specific tasks. In this study, we present CryoFM, a foundation model designed as a generative model, learning the distribution of high-quality density maps and generalizing effectively to downstream tasks. Built on flow matching, CryoFM is trained to accurately capture the prior distribution of biomolecular density maps. Furthermore, we introduce a flow posterior sampling method that leverages CRYOFM as a flexible prior for several downstream tasks in cryo-EM and cryo-electron tomography (cryo-ET) without the need for fine-tuning, achieving state-of-the-art performance on most tasks and demonstrating its potential as a foundational model for broader applications in these fields.

The dynamics of biomolecules are crucial for our understanding of their functioning in living systems. However, current 3D imaging techniques, such as cryogenic electron microscopy (cryo-EM), require freezing the sample, which limits the observation of their conformational changes in real time. The innovative liquid-phase electron microscopy (liquid-phase EM) technique allows molecules to be placed in the native liquid environment, providing a unique opportunity to observe their dynamics. In this paper, we propose TEMPOR, a Temporal Electron MicroscoPy Object Reconstruction algorithm for liquid-phase EM that leverages an implicit neural representation (INR) and a dynamical variational auto-encoder (DVAE) to recover time series of molecular structures. We demonstrate its advantages in recovering different motion dynamics from two simulated datasets, 7bcq and Cas9. To our knowledge, our work is the first attempt to directly recover 3D structures of a temporally-varying particle from liquid-phase EM movies. It provides a promising new approach for studying molecules' 3D dynamics in structural biology.

Cryo-electron microscopy (cryo-EM) is a technique for reconstructing the 3-dimensional (3D) structure of biomolecules (especially large protein complexes and molecular assemblies). As the resolution increases to the near-atomic scale, building protein structures de novo from cryo-EM maps becomes possible. Recently, recognition-based de novo building methods have shown the potential to streamline this process. However, it cannot build a complete structure due to the low signal-to-noise ratio (SNR) problem. At the same time, AlphaFold has led to a great breakthrough in predicting protein structures. This has inspired us to combine fragment recognition and structure prediction methods to build a complete structure. In this paper, we propose a new method named FFF that bridges protein structure prediction and protein structure recognition with flexible fitting. First, a multi-level recognition network is used to capture various structural features from the input 3D cryo-EM map. Next, protein structural fragments are generated using pseudo peptide vectors and a protein sequence alignment method based on these extracted features. Finally, a complete structural model is constructed using the predicted protein fragments via flexible fitting. Based on our benchmark tests, FFF outperforms the baseline methods for building complete protein structures.

Quantitative microstructural characterization is fundamental to materials science, where electron micrograph (EM) provides indispensable high-resolution insights. However, progress in deep learning-based EM characterization has been hampered by the scarcity of large-scale, diverse, and expert-annotated datasets, due to acquisition costs, privacy concerns, and annotation complexity. To address this issue, we introduce UniEM-3M, the first large-scale and multimodal EM dataset for instance-level understanding. It comprises 5,091 high-resolution EMs, about 3 million instance segmentation labels, and image-level attribute-disentangled textual descriptions, a subset of which will be made publicly available. Furthermore, we are also releasing a text-to-image diffusion model trained on the entire collection to serve as both a powerful data augmentation tool and a proxy for the complete data distribution. To establish a rigorous benchmark, we evaluate various representative instance segmentation methods on the complete UniEM-3M and present UniEM-Net as a strong baseline model. Quantitative experiments demonstrate that this flow-based model outperforms other advanced methods on this challenging benchmark. Our multifaceted release of a partial dataset, a generative model, and a comprehensive benchmark -- available at huggingface -- will significantly accelerate progress in automated materials analysis.

Cryogenic Electron Tomography (CryoET) is a useful imaging technology in structural biology that is hindered by its need for manual annotations, especially in particle picking. Recent works have endeavored to remedy this issue with few-shot learning or contrastive learning techniques. However, supervised training is still inevitable for them. We instead choose to leverage the power of existing 2D foundation models and present a novel, training-free framework, CryoSAM. In addition to prompt-based single-particle instance segmentation, our approach can automatically search for similar features, facilitating full tomogram semantic segmentation with only one prompt. CryoSAM is composed of two major parts: 1) a prompt-based 3D segmentation system that uses prompts to complete single-particle instance segmentation recursively with Cross-Plane Self-Prompting, and 2) a Hierarchical Feature Matching mechanism that efficiently matches relevant features with extracted tomogram features. They collaborate to enable the segmentation of all particles of one category with just one particle-specific prompt. Our experiments show that CryoSAM outperforms existing works by a significant margin and requires even fewer annotations in particle picking. Further visualizations demonstrate its ability when dealing with full tomogram segmentation for various subcellular structures. Our code is available at: https://github.com/xulabs/aitom

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

Precision in identifying nanometer-scale device-killer defects is crucial in both semiconductor research and development as well as in production processes. The effectiveness of existing ML-based approaches in this context is largely limited by the scarcity of data, as the production of real semiconductor wafer data for training these models involves high financial and time costs. Moreover, the existing simulation methods fall short of replicating images with identical noise characteristics, surface roughness and stochastic variations at advanced nodes. We propose a method for generating synthetic semiconductor SEM images using a diffusion model within a limited data regime. In contrast to images generated through conventional simulation methods, SEM images generated through our proposed DL method closely resemble real SEM images, replicating their noise characteristics and surface roughness adaptively. Our main contributions, which are validated on three different real semiconductor datasets, are: i) proposing a patch-based generative framework utilizing DDPM to create SEM images with intended defect classes, addressing challenges related to class-imbalance and data insufficiency, ii) demonstrating generated synthetic images closely resemble real SEM images acquired from the tool, preserving all imaging conditions and metrology characteristics without any metadata supervision, iii) demonstrating a defect detector trained on generated defect dataset, either independently or combined with a limited real dataset, can achieve similar or improved performance on real wafer SEM images during validation/testing compared to exclusive training on a real defect dataset, iv) demonstrating the ability of the proposed approach to transfer defect types, critical dimensions, and imaging conditions from one specified CD/Pitch and metrology specifications to another, thereby highlighting its versatility.

We present two large datasets of labelled plant-images that are suited towards the training of machine learning and computer vision models. The first dataset encompasses as the day of writing over 1.2 million images of indoor-grown crops and weeds common to the Canadian Prairies and many US states. The second dataset consists of over 540,000 images of plants imaged in farmland. All indoor plant images are labelled by species and we provide rich etadata on the level of individual images. This comprehensive database allows to filter the datasets under user-defined specifications such as for example the crop-type or the age of the plant. Furthermore, the indoor dataset contains images of plants taken from a wide variety of angles, including profile shots, top-down shots, and angled perspectives. The images taken from plants in fields are all from a top-down perspective and contain usually multiple plants per image. For these images metadata is also available. In this paper we describe both datasets' characteristics with respect to plant variety, plant age, and number of images. We further introduce an open-access sample of the indoor-dataset that contains 1,000 images of each species covered in our dataset. These, in total 14,000 images, had been selected, such that they form a representative sample with respect to plant age and ndividual plants per species. This sample serves as a quick entry point for new users to the dataset, allowing them to explore the data on a small scale and find the parameters of data most useful for their application without having to deal with hundreds of thousands of individual images.

Electron-beam (e-beam) manipulation of single dopant atoms in an aberration-corrected scanning transmission electron microscope is emerging as a method for directed atomic motion and atom-by-atom assembly. Until now, the dopant species have been limited to atoms closely matched to carbon in terms of ionic radius and capable of strong covalent bonding with carbon atoms in the graphene lattice. In situ dopant insertion into a graphene lattice has thus far been demonstrated only for Si, which is ubiquitously present as a contaminant in this material. Here, we achieve in situ manipulation of Pt atoms and their insertion into the graphene host matrix using the e-beam deposited Pt on graphene as a host system. We further demonstrate a mechanism for stabilization of the Pt atom, enabled through the formation of Si-stabilized Pt heteroatomic clusters attached to the graphene surface. This study provides evidence toward the universality of the e-beam assembly approach, opening a pathway for exploring cluster chemistry through direct assembly.

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/ .

Finding scientifically interesting phenomena through slow, manual labeling campaigns severely limits our ability to explore the billions of galaxy images produced by telescopes. In this work, we develop a pipeline to create a semantic search engine from completely unlabeled image data. Our method leverages Vision-Language Models (VLMs) to generate descriptions for galaxy images, then contrastively aligns a pre-trained multimodal astronomy foundation model with these embedded descriptions to produce searchable embeddings at scale. We find that current VLMs provide descriptions that are sufficiently informative to train a semantic search model that outperforms direct image similarity search. Our model, AION-Search, achieves state-of-the-art zero-shot performance on finding rare phenomena despite training on randomly selected images with no deliberate curation for rare cases. Furthermore, we introduce a VLM-based re-ranking method that nearly doubles the recall for our most challenging targets in the top-100 results. For the first time, AION-Search enables flexible semantic search scalable to 140 million galaxy images, enabling discovery from previously infeasible searches. More broadly, our work provides an approach for making large, unlabeled scientific image archives semantically searchable, expanding data exploration capabilities in fields from Earth observation to microscopy. The code, data, and app are publicly available at https://github.com/NolanKoblischke/AION-Search

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

Large-scale cell microscopy screens are used in drug discovery and molecular biology research to study the effects of millions of chemical and genetic perturbations on cells. To use these images in downstream analysis, we need models that can map each image into a feature space that represents diverse biological phenotypes consistently, in the sense that perturbations with similar biological effects have similar representations. In this work, we present the largest foundation model for cell microscopy data to date, a new 1.9 billion-parameter ViT-G/8 MAE trained on over 8 billion microscopy image crops. Compared to a previous published ViT-L/8 MAE, our new model achieves a 60% improvement in linear separability of genetic perturbations and obtains the best overall performance on whole-genome biological relationship recall and replicate consistency benchmarks. Beyond scaling, we developed two key methods that improve performance: (1) training on a curated and diverse dataset; and, (2) using biologically motivated linear probing tasks to search across each transformer block for the best candidate representation of whole-genome screens. We find that many self-supervised vision transformers, pretrained on either natural or microscopy images, yield significantly more biologically meaningful representations of microscopy images in their intermediate blocks than in their typically used final blocks. More broadly, our approach and results provide insights toward a general strategy for successfully building foundation models for large-scale biological data.

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

Statistics of grain sizes and orientations in metals correlate to the material's mechanical properties. Reproducing representative volume elements for further analysis of deformation and failure in metals, like 316L stainless steel, is particularly important due to their wide use in manufacturing goods today. Two approaches, initially created for video games, were considered for the procedural generation of representative grain microstructures. The first is the Wave Function Collapse (WFC) algorithm, and the second is constraint propagation and probabilistic inference through Markov Junior, a free and open-source software. This study aimed to investigate these two algorithms' effectiveness in using reference electron backscatter diffraction (EBSD) maps and recreating a statistically similar one that could be used in further research. It utilized two stainless steel EBSD maps as references to test both algorithms. First, the WFC algorithm was too constricting and, thus, incapable of producing images that resembled EBSDs. The second, MarkovJunior, was much more effective in creating a Voronoi tessellation that could be used to create an EBSD map in Python. When comparing the results between the reference and the generated EBSD, we discovered that the orientation and volume fractions were extremely similar. With the study, it was concluded that MarkovJunior is an effective machine learning tool that can reproduce representative grain microstructures.

Quantifying cell morphology using images and machine learning has proven to be a powerful tool to study the response of cells to treatments. However, models used to quantify cellular morphology are typically trained with a single microscopy imaging type. This results in specialized models that cannot be reused across biological studies because the technical specifications do not match (e.g., different number of channels), or because the target experimental conditions are out of distribution. Here, we present CHAMMI-75, an open access dataset of heterogeneous, multi-channel microscopy images from 75 diverse biological studies. We curated this resource from publicly available sources to investigate cellular morphology models that are channel-adaptive and can process any microscopy image type. Our experiments show that training with CHAMMI-75 can improve performance in multi-channel bioimaging tasks primarily because of its high diversity in microscopy modalities. This work paves the way to create the next generation of cellular morphology models for biological studies.

In the image classification task, the most common approach is to resize all images in a dataset to a unique shape, while reducing their precision to a size which facilitates experimentation at scale. This practice has benefits from a computational perspective, but it entails negative side-effects on performance due to loss of information and image deformation. In this work we introduce the MAMe dataset, an image classification dataset with remarkable high resolution and variable shape properties. The goal of MAMe is to provide a tool for studying the impact of such properties in image classification, while motivating research in the field. The MAMe dataset contains thousands of artworks from three different museums, and proposes a classification task consisting on differentiating between 29 mediums (i.e. materials and techniques) supervised by art experts. After reviewing the singularity of MAMe in the context of current image classification tasks, a thorough description of the task is provided, together with dataset statistics. Experiments are conducted to evaluate the impact of using high resolution images, variable shape inputs and both properties at the same time. Results illustrate the positive impact in performance when using high resolution images, while highlighting the lack of solutions to exploit variable shapes. An additional experiment exposes the distinctiveness between the MAMe dataset and the prototypical ImageNet dataset. Finally, the baselines are inspected using explainability methods and expert knowledge, to gain insights on the challenges that remain ahead.

Understanding electron irradiation effects is vital not only for reliable transmission electron microscopy characterization, but increasingly also for the controlled manipulation of two-dimensional materials. The displacement cross sections of monolayer hBN are measured using aberration-corrected scanning transmission electron microscopy in near ultra-high vacuum at primary beam energies between 50 and 90 keV. Damage rates below 80 keV are up to three orders of magnitude lower than previously measured at edges under poorer residual vacuum conditions where chemical etching appears to have been dominant. Notably, is possible to create single vacancies in hBN using electron irradiation, with boron almost twice as likely as nitrogen to be ejected below 80 keV. Moreover, any damage at such low energies cannot be explained by elastic knock-on, even when accounting for vibrations of the atoms. A theoretical description is developed to account for lowering of the displacement threshold due to valence ionization resulting from inelastic scattering of probe electrons, modelled using charge-constrained density functional theory molecular dynamics. Although significant reductions are found depending on the constrained charge, quantitative predictions for realistic ionization states are currently not possible. Nonetheless, there is potential for defect-engineering of hBN at the level of single vacancies using electron irradiation.

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

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.

Continuous solid electrolyte interface (SEI) formation remains the limiting factor of the lifetime of silicon nanoparticles (SiNPs) based negative electrodes. Methods that could provide clear diagnosis of the electrode degradation are of utmost necessity to streamline further developments. We demonstrate that electron energy-loss spectroscopy (EELS) in a scanning transmission electron microscope (STEM) can be used to quickly map SEI components and quantify LixSi alloys from single experiments, with resolutions down to 5 nm. Exploiting the low-loss part of the EEL spectrum allowed us to circumvent the degradation phenomena that have so far crippled the application of this technique on such beam-sensitive compounds. Our results provide unprecedented insight into silicon aging mechanisms in full cell configuration. We observe the morphology of the SEI to be extremely heterogeneous at the particle scale but with clear chemical evolutions with extended cycling coming from both SEI accumulation and a transition from lithium-rich carbonate-like compounds to lithium-poor ones. Thanks to the retrieval of several results from a single dataset, we were able to correlate local discrepancies in lithiation to the initial crystallinity of silicon as well as to the local SEI chemistry and morphology. This study emphasizes how initial heterogeneities in the percolating electronic network and the porosity affect SiNPs aggregates along cycling. These findings pinpoint the crucial role of an optimized formulation in silicon-based thick electrodes.

Nanomaterials exhibit distinctive properties governed by parameters such as size, shape, and surface characteristics, which critically influence their applications and interactions across technological, biological, and environmental contexts. Accurate quantification and understanding of these materials are essential for advancing research and innovation. In this regard, deep learning segmentation networks have emerged as powerful tools that enable automated insights and replace subjective methods with precise quantitative analysis. However, their efficacy depends on representative annotated datasets, which are challenging to obtain due to the costly imaging of nanoparticles and the labor-intensive nature of manual annotations. To overcome these limitations, we introduce DiffRenderGAN, a novel generative model designed to produce annotated synthetic data. By integrating a differentiable renderer into a Generative Adversarial Network (GAN) framework, DiffRenderGAN optimizes textural rendering parameters to generate realistic, annotated nanoparticle images from non-annotated real microscopy images. This approach reduces the need for manual intervention and enhances segmentation performance compared to existing synthetic data methods by generating diverse and realistic data. Tested on multiple ion and electron microscopy cases, including titanium dioxide (TiO_2), silicon dioxide (SiO_2)), and silver nanowires (AgNW), DiffRenderGAN bridges the gap between synthetic and real data, advancing the quantification and understanding of complex nanomaterial systems.

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

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.

Cryo-EM is a powerful tool for understanding macromolecular structures, yet current methods for structure reconstruction are slow and computationally demanding. To accelerate research on pose estimation, we present CESPED, a new dataset specifically designed for Supervised Pose Estimation in Cryo-EM. Alongside CESPED, we provide a PyTorch package to simplify Cryo-EM data handling and model evaluation. We evaluated the performance of a baseline model, Image2Sphere, on CESPED, which showed promising results but also highlighted the need for further improvements. Additionally, we illustrate the potential of deep learning-based pose estimators to generalise across different samples, suggesting a promising path toward more efficient processing strategies. CESPED is available at https://github.com/oxpig/cesped.

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.

Scientific researchers frequently use the in situ synchrotron high-energy powder X-ray diffraction (XRD) technique to examine the crystallographic structures of materials in functional devices such as rechargeable battery materials. We propose a method for identifying artifacts in experimental XRD images. The proposed method uses deep learning convolutional neural network architectures, such as tunable U-Nets to identify the artifacts. In particular, the predicted artifacts are evaluated against the corresponding ground truth (manually implemented) using the overall true positive rate or recall. The result demonstrates that the U-Nets can consistently produce great recall performance at 92.4% on the test dataset, which is not included in the training, with a 34% reduction in average false positives in comparison to the conventional method. The U-Nets also reduce the time required to identify and separate artifacts by more than 50%. Furthermore, the exclusion of the artifacts shows major changes in the integrated 1D XRD pattern, enhancing further analysis of the post-processing XRD data.

In a previous study, structure of silica gels prepared in a high magnetic field was investigated. While a direct application of such anisotropic silica gels is for an optical anisotropic medium possessing chemical resistance, we show here their possibility of medium in materials processing. In this direction, for example, silica hydrogels have so far been used as media of crystal growth. In this paper, as opposed to the soft-wet state, dried silica gels have been investigated. We have found that lead (II) nanocrystallites were formed induced by electron irradiation to lead (II)-doped dried silica gels prepared in a high magnetic field such as B = 10 T. Hydrogels made from a sodium metasilicate solution doped with lead (II) acetate were prepared. The dried specimens were irradiated by electrons in a transmission electron microscope environment. Electron diffraction patterns indicated the crystallinity of lead (II) nanocrystallites depending on B. An advantage of this processing technique is that the crystallinity can be controlled through the strength of magnetic field B applied during gel preparation. Specific skills are not required to control the strength of magnetic field.

Vision-language datasets are vital for both text-to-image (T2I) and image-to-text (I2T) research. However, current datasets lack descriptions with fine-grained detail that would allow for richer associations to be learned by models. To fill the gap, we introduce Descriptions of Connected and Contrasting Images (DOCCI), a dataset with long, human-annotated English descriptions for 15k images that were taken, curated and donated by a single researcher intent on capturing key challenges such as spatial relations, counting, text rendering, world knowledge, and more. We instruct human annotators to create comprehensive descriptions for each image; these average 136 words in length and are crafted to clearly distinguish each image from those that are related or similar. Each description is highly compositional and typically encompasses multiple challenges. Through both quantitative and qualitative analyses, we demonstrate that DOCCI serves as an effective training resource for image-to-text generation -- a PaLI 5B model finetuned on DOCCI shows equal or superior results compared to highly-performant larger models like LLaVA-1.5 7B and InstructBLIP 7B. Furthermore, we show that DOCCI is a useful testbed for text-to-image generation, highlighting the limitations of current text-to-image models in capturing long descriptions and fine details.

We introduce a Three-Dimensional Convolutional Variational Autoencoder (3D-CVAE) for automated anomaly detection in Electron Energy Loss Spectroscopy Spectrum Imaging (EELS-SI) data. Our approach leverages the full three-dimensional structure of EELS-SI data to detect subtle spectral anomalies while preserving both spatial and spectral correlations across the datacube. By employing negative log-likelihood loss and training on bulk spectra, the model learns to reconstruct bulk features characteristic of the defect-free material. In exploring methods for anomaly detection, we evaluated both our 3D-CVAE approach and Principal Component Analysis (PCA), testing their performance using Fe L-edge peak shifts designed to simulate material defects. Our results show that 3D-CVAE achieves superior anomaly detection and maintains consistent performance across various shift magnitudes. The method demonstrates clear bimodal separation between normal and anomalous spectra, enabling reliable classification. Further analysis verifies that lower dimensional representations are robust to anomalies in the data. While performance advantages over PCA diminish with decreasing anomaly concentration, our method maintains high reconstruction quality even in challenging, noise-dominated spectral regions. This approach provides a robust framework for unsupervised automated detection of spectral anomalies in EELS-SI data, particularly valuable for analyzing complex material systems.

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

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.

Vision-language models hold considerable promise for ophthalmology, but their development depends on large-scale, high-quality image-text datasets that remain scarce. We present PubMed-Ophtha, a hierarchical dataset of 102,023 ophthalmological image-caption pairs extracted from 15,842 open-access articles in PubMed Central. Unlike existing datasets, figures are extracted directly from article PDFs at full resolution and decomposed into their constituent panels, panel identifiers, and individual images. Each image is annotated with its imaging modality -- color fundus photography, optical coherence tomography, retinal imaging, or other -- and a mark status indicating the presence of annotation marks such as arrows. Figure captions are split into panel-level subcaptions using a two-step LLM approach, achieving a mean average sentence BLEU score of 0.913 on human-annotated data. Panel and image detection models reach a mAP@0.50 of 0.909 and 0.892, respectively, and figure extraction achieves a median IoU of 0.997. To support reproducibility, we additionally release the human-annotated ground-truth data, all trained models, and the full dataset generation pipeline.

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

We present a method that uses a text-to-image model to generate consistent content across multiple image scales, enabling extreme semantic zooms into a scene, e.g., ranging from a wide-angle landscape view of a forest to a macro shot of an insect sitting on one of the tree branches. We achieve this through a joint multi-scale diffusion sampling approach that encourages consistency across different scales while preserving the integrity of each individual sampling process. Since each generated scale is guided by a different text prompt, our method enables deeper levels of zoom than traditional super-resolution methods that may struggle to create new contextual structure at vastly different scales. We compare our method qualitatively with alternative techniques in image super-resolution and outpainting, and show that our method is most effective at generating consistent multi-scale content.

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.

Neuronal morphology encodes critical information about circuit function, development, and disease, yet current methods analyze topology or graph structure in isolation. We introduce GraPHFormer, a multimodal architecture that unifies these complementary views through CLIP-style contrastive learning. Our vision branch processes a novel three-channel persistence image encoding unweighted, persistence-weighted, and radius-weighted topological densities via DINOv2-ViT-S. In parallel, a TreeLSTM encoder captures geometric and radial attributes from skeleton graphs. Both project to a shared embedding space trained with symmetric InfoNCE loss, augmented by persistence-space transformations that preserve topological semantics. Evaluated on six benchmarks (BIL-6, ACT-4, JML-4, N7, M1-Cell, M1-REG) spanning self-supervised and supervised settings, GraPHFormer achieves state-of-the-art performance on five benchmarks, significantly outperforming topology-only, graph-only, and morphometrics baselines. We demonstrate practical utility by discriminating glial morphologies across cortical regions and species, and detecting signatures of developmental and degenerative processes. Code: https://github.com/Uzshah/GraPHFormer

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

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

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

Diffusion models have revolutionized image generation, yet several challenges restrict their application to large-image domains, such as digital pathology and satellite imagery. Given that it is infeasible to directly train a model on 'whole' images from domains with potential gigapixel sizes, diffusion-based generative methods have focused on synthesizing small, fixed-size patches extracted from these images. However, generating small patches has limited applicability since patch-based models fail to capture the global structures and wider context of large images, which can be crucial for synthesizing (semantically) accurate samples. To overcome this limitation, we present ZoomLDM, a diffusion model tailored for generating images across multiple scales. Central to our approach is a novel magnification-aware conditioning mechanism that utilizes self-supervised learning (SSL) embeddings and allows the diffusion model to synthesize images at different 'zoom' levels, i.e., fixed-size patches extracted from large images at varying scales. ZoomLDM synthesizes coherent histopathology images that remain contextually accurate and detailed at different zoom levels, achieving state-of-the-art image generation quality across all scales and excelling in the data-scarce setting of generating thumbnails of entire large images. The multi-scale nature of ZoomLDM unlocks additional capabilities in large image generation, enabling computationally tractable and globally coherent image synthesis up to 4096 times 4096 pixels and 4times super-resolution. Additionally, multi-scale features extracted from ZoomLDM are highly effective in multiple instance learning experiments.

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.

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

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.

This paper introduces an innovative approach to Medical Vision-Language Pre-training (Med-VLP) area in the specialized context of radiograph representation learning. While conventional methods frequently merge textual annotations into unified reports, we acknowledge the intrinsic hierarchical relationship between the findings and impression section in radiograph datasets. To establish a targeted correspondence between images and texts, we propose a novel HybridMED framework to align global-level visual representations with impression and token-level visual representations with findings. Moreover, our framework incorporates a generation decoder that employs two proxy tasks, responsible for generating the impression from (1) images, via a captioning branch, and (2) findings, through a summarization branch. Additionally, knowledge distillation is leveraged to facilitate the training process. Experiments on the MIMIC-CXR dataset reveal that our summarization branch effectively distills knowledge to the captioning branch, enhancing model performance without significantly increasing parameter requirements due to the shared self-attention and feed-forward architecture.

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

Contrastive pretraining on parallel image-text data has attained great success in vision-language processing (VLP), as exemplified by CLIP and related methods. However, prior explorations tend to focus on general domains in the web. Biomedical images and text are rather different, but publicly available datasets are small and skew toward chest X-ray, thus severely limiting progress. In this paper, we conducted by far the largest study on biomedical VLP, using 15 million figure-caption pairs extracted from biomedical research articles in PubMed Central. Our dataset (PMC-15M) is two orders of magnitude larger than existing biomedical image-text datasets such as MIMIC-CXR, and spans a diverse range of biomedical images. The standard CLIP method is suboptimal for the biomedical domain. We propose BiomedCLIP with domain-specific adaptations tailored to biomedical VLP. We conducted extensive experiments and ablation studies on standard biomedical imaging tasks from retrieval to classification to visual question-answering (VQA). BiomedCLIP established new state of the art in a wide range of standard datasets, substantially outperformed prior VLP approaches. Surprisingly, BiomedCLIP even outperformed radiology-specific state-of-the-art models such as BioViL on radiology-specific tasks such as RSNA pneumonia detection, thus highlighting the utility in large-scale pretraining across all biomedical image types. We will release our models at https://aka.ms/biomedclip to facilitate future research in biomedical VLP.

We introduce MedMNIST v2, a large-scale MNIST-like dataset collection of standardized biomedical images, including 12 datasets for 2D and 6 datasets for 3D. All images are pre-processed into a small size of 28x28 (2D) or 28x28x28 (3D) with the corresponding classification labels so that no background knowledge is required for users. Covering primary data modalities in biomedical images, MedMNIST v2 is designed to perform classification on lightweight 2D and 3D images with various dataset scales (from 100 to 100,000) and diverse tasks (binary/multi-class, ordinal regression, and multi-label). The resulting dataset, consisting of 708,069 2D images and 10,214 3D images in total, could support numerous research / educational purposes in biomedical image analysis, computer vision, and machine learning. We benchmark several baseline methods on MedMNIST v2, including 2D / 3D neural networks and open-source / commercial AutoML tools. The data and code are publicly available at https://medmnist.com/.

Scientific archives now contain hundreds of petabytes of data across genomics, ecology, climate, and molecular biology that could reveal undiscovered patterns if systematically analyzed at scale. Large-scale, weakly-supervised datasets in language and vision have driven the development of foundation models whose internal representations encode structure (patterns, co-occurrences and statistical regularities) beyond their training objectives. Most existing methods extract structure only for pre-specified targets; they excel at confirmation but do not support open-ended discovery of unknown patterns. We ask whether sparse autoencoders (SAEs) can enable open-ended feature discovery from foundation model representations. We evaluate this question in controlled rediscovery studies, where the learned SAE features are tested for alignment with semantic concepts on a standard segmentation benchmark and compared against strong label-free alternatives on concept-alignment metrics. Applied to ecological imagery, the same procedure surfaces fine-grained anatomical structure without access to segmentation or part labels, providing a scientific case study with ground-truth validation. While our experiments focus on vision with an ecology case study, the method is domain-agnostic and applicable to models in other sciences (e.g., proteins, genomics, weather). Our results indicate that sparse decomposition provides a practical instrument for exploring what scientific foundation models have learned, an important prerequisite for moving from confirmation to genuine discovery.

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

Vision-Language Models (VLMs), such as recent Qwen and Gemini models, are positioned as general-purpose AI systems capable of reasoning across domains. Yet their capabilities in scientific imaging, especially on unfamiliar and potentially previously unseen data distributions, remain poorly understood. In this work, we assess whether generic VLMs, presumed to lack exposure to astronomical corpora, can perform morphology-based classification of radio galaxies using the MiraBest FR-I/FR-II dataset. We explore prompting strategies using natural language and schematic diagrams, and, to the best of our knowledge, we are the first to introduce visual in-context examples within prompts in astronomy. Additionally, we evaluate lightweight supervised adaptation via LoRA fine-tuning. Our findings reveal three trends: (i) even prompt-based approaches can achieve good performance, suggesting that VLMs encode useful priors for unfamiliar scientific domains; (ii) however, outputs are highly unstable, i.e. varying sharply with superficial prompt changes such as layout, ordering, or decoding temperature, even when semantic content is held constant; and (iii) with just 15M trainable parameters and no astronomy-specific pretraining, fine-tuned Qwen-VL achieves near state-of-the-art performance (3% Error rate), rivaling domain-specific models. These results suggest that the apparent "reasoning" of VLMs often reflects prompt sensitivity rather than genuine inference, raising caution for their use in scientific domains. At the same time, with minimal adaptation, generic VLMs can rival specialized models, offering a promising but fragile tool for scientific discovery.

Vision-language pre-training for chest X-rays has made significant strides, primarily by utilizing paired radiographs and radiology reports. However, existing approaches often face challenges in encoding medical knowledge effectively. While radiology reports provide insights into the current disease manifestation, medical definitions (as used by contemporary methods) tend to be overly abstract, creating a gap in knowledge. To address this, we propose DeViDe, a novel transformer-based method that leverages radiographic descriptions from the open web. These descriptions outline general visual characteristics of diseases in radiographs, and when combined with abstract definitions and radiology reports, provide a holistic snapshot of knowledge. DeViDe incorporates three key features for knowledge-augmented vision language alignment: First, a large-language model-based augmentation is employed to homogenise medical knowledge from diverse sources. Second, this knowledge is aligned with image information at various levels of granularity. Third, a novel projection layer is proposed to handle the complexity of aligning each image with multiple descriptions arising in a multi-label setting. In zero-shot settings, DeViDe performs comparably to fully supervised models on external datasets and achieves state-of-the-art results on three large-scale datasets. Additionally, fine-tuning DeViDe on four downstream tasks and six segmentation tasks showcases its superior performance across data from diverse distributions.

There is renewed interest in modeling and understanding the nervous system of the nematode Caenorhabditis elegans (C. elegans), as this small model system provides a path to bridge the gap between nervous system structure (connectivity) and function (physiology). However, existing physiology datasets, whether involving passive recording or stimulation, are in distinct formats, and connectome datasets require preprocessing before analysis can commence. Here we compile and homogenize datasets of neural activity and connectivity. Our neural activity dataset is derived from 11 C. elegans neuroimaging experiments, while our connectivity dataset is compiled from 9 connectome annotations based on 3 primary electron microscopy studies and 1 signal propagation study. Physiology datasets, collected under varying protocols, measure calcium fluorescence in labeled subsets of the worm's 300 neurons. Our preprocessing pipeline standardizes these datasets by consistently ordering labeled neurons and resampling traces to a common sampling rate, yielding recordings from approximately 900 worms and 250 uniquely labeled neurons. The connectome datasets, collected from electron microscopy reconstructions, represent the entire nervous system as a graph of connections. Our collection is accessible on HuggingFace, facilitating analysis of the structure-function relationship in biology using modern neural network architectures and enabling cross-lab and cross-animal comparisons.

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

Unsupervised denoising is a crucial challenge in real-world imaging applications. Unsupervised deep-learning methods have demonstrated impressive performance on benchmarks based on synthetic noise. However, no metrics are available to evaluate these methods in an unsupervised fashion. This is highly problematic for the many practical applications where ground-truth clean images are not available. In this work, we propose two novel metrics: the unsupervised mean squared error (MSE) and the unsupervised peak signal-to-noise ratio (PSNR), which are computed using only noisy data. We provide a theoretical analysis of these metrics, showing that they are asymptotically consistent estimators of the supervised MSE and PSNR. Controlled numerical experiments with synthetic noise confirm that they provide accurate approximations in practice. We validate our approach on real-world data from two imaging modalities: videos in raw format and transmission electron microscopy. Our results demonstrate that the proposed metrics enable unsupervised evaluation of denoising methods based exclusively on noisy data.

The rapid advancement of Large Language Models (LLMs) and Large Multimodal Models (LMMs) has heightened the demand for AI-based scientific assistants capable of understanding scientific articles and figures. Despite progress, there remains a significant gap in evaluating models' comprehension of professional, graduate-level, and even PhD-level scientific content. Current datasets and benchmarks primarily focus on relatively simple scientific tasks and figures, lacking comprehensive assessments across diverse advanced scientific disciplines. To bridge this gap, we collected a multimodal, multidisciplinary dataset from open-access scientific articles published in Nature Communications journals. This dataset spans 72 scientific disciplines, ensuring both diversity and quality. We created benchmarks with various tasks and settings to comprehensively evaluate LMMs' capabilities in understanding scientific figures and content. Our evaluation revealed that these tasks are highly challenging: many open-source models struggled significantly, and even GPT-4V and GPT-4o faced difficulties. We also explored using our dataset as training resources by constructing visual instruction-following data, enabling the 7B LLaVA model to achieve performance comparable to GPT-4V/o on our benchmark. Additionally, we investigated the use of our interleaved article texts and figure images for pre-training LMMs, resulting in improvements on the material generation task. The source dataset, including articles, figures, constructed benchmarks, and visual instruction-following data, is open-sourced.

Over the last five years, deep generative models have gradually been adopted for various tasks in biological research. Notably, image-to-image translation methods showed to be effective in revealing subtle phenotypic cell variations otherwise invisible to the human eye. Current methods to achieve this goal mainly rely on Generative Adversarial Networks (GANs). However, these models are known to suffer from some shortcomings such as training instability and mode collapse. Furthermore, the lack of robustness to invert a real image into the latent of a trained GAN prevents flexible editing of real images. In this work, we propose PhenDiff, an image-to-image translation method based on conditional diffusion models to identify subtle phenotypes in microscopy images. We evaluate this approach on biological datasets against previous work such as CycleGAN. We show that PhenDiff outperforms this baseline in terms of quality and diversity of the generated images. We then apply this method to display invisible phenotypic changes triggered by a rare neurodevelopmental disorder on microscopy images of organoids. Altogether, we demonstrate that PhenDiff is able to perform high quality biological image-to-image translation allowing to spot subtle phenotype variations on a real image.

Accurate disease interpretation from radiology remains challenging due to imaging heterogeneity. Achieving expert-level diagnostic decisions requires integration of subtle image features with clinical knowledge. Yet major vision-language models (VLMs) treat images as holistic entities and overlook fine-grained image details that are vital for disease diagnosis. Clinicians analyze images by utilizing their prior medical knowledge and identify anatomical structures as important region of interests (ROIs). Inspired from this human-centric workflow, we introduce Anatomy-VLM, a fine-grained, vision-language model that incorporates multi-scale information. First, we design a model encoder to localize key anatomical features from entire medical images. Second, these regions are enriched with structured knowledge for contextually-aware interpretation. Finally, the model encoder aligns multi-scale medical information to generate clinically-interpretable disease prediction. Anatomy-VLM achieves outstanding performance on both in- and out-of-distribution datasets. We also validate the performance of Anatomy-VLM on downstream image segmentation tasks, suggesting that its fine-grained alignment captures anatomical and pathology-related knowledge. Furthermore, the Anatomy-VLM's encoder facilitates zero-shot anatomy-wise interpretation, providing its strong expert-level clinical interpretation capabilities.

We present Cephalo, a series of multimodal vision large language models (V-LLMs) designed for materials science applications, integrating visual and linguistic data for enhanced understanding and interaction within human-AI and multi-agent AI frameworks. A key innovation of Cephalo is its advanced dataset generation method, which employs a sophisticated algorithm to accurately detect and separate images and their corresponding textual descriptions from PDF documents, such as scientific papers. The method includes a careful refinement of image-text pairs through integrated vision and language processing, ensuring high-quality, contextually relevant, and well reasoned training data. Cephalo is trained on integrated image and text data extracted from thousands of scientific papers and science-focused Wikipedia pages demonstrates can interpret complex visual scenes, generate precise language descriptions, and answer queries about images effectively. The combination of a vision encoder with an autoregressive transformer supports complex natural language understanding in an integrated model, which can be coupled with other generative methods to create an image-to-text-to-image or image-to-text-to-3D pipeline. To explore the development of larger models from smaller ones, we merge sets of layers that originate from different pre-trained source models. This hybrid approach allows us to leverage the domain-specific expertise and general conversational capabilities to harness the strengths of multiple models. We examine the models in diverse use cases that incorporate biological materials, fracture and engineering analysis, protein biophysics, and bio-inspired design based on insect behavior. Generative applications include bio-inspired designs, including pollen-inspired architected materials, as well as the synthesis of bio-inspired material microstructures from a photograph of a solar eclipse.

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.

Electronic band structure (BS) and crystal structure are the two complementary identifiers of solid state materials. While convenient instruments and reconstruction algorithms have made large, empirical, crystal structure databases possible, extracting quasiparticle dispersion (closely related to BS) from photoemission band mapping data is currently limited by the available computational methods. To cope with the growing size and scale of photoemission data, we develop a pipeline including probabilistic machine learning and the associated data processing, optimization and evaluation methods for band structure reconstruction, leveraging theoretical calculations. The pipeline reconstructs all 14 valence bands of a semiconductor and shows excellent performance on benchmarks and other materials datasets. The reconstruction uncovers previously inaccessible momentum-space structural information on both global and local scales, while realizing a path towards integration with materials science databases. Our approach illustrates the potential of combining machine learning and domain knowledge for scalable feature extraction in multidimensional data.

Microscopic interpretation of histopathology images underlies many important diagnostic and treatment decisions. While advances in vision-language modeling raise new opportunities for analysis of such images, the gigapixel-scale size of whole slide images (WSIs) introduces unique challenges. Additionally, pathology reports simultaneously highlight key findings from small regions while also aggregating interpretation across multiple slides, often making it difficult to create robust image-text pairs. As such, pathology reports remain a largely untapped source of supervision in computational pathology, with most efforts relying on region-of-interest annotations or self-supervision at the patch-level. In this work, we develop a vision-language model based on the BLIP-2 framework using WSIs paired with curated text from pathology reports. This enables applications utilizing a shared image-text embedding space, such as text or image retrieval for finding cases of interest, as well as integration of the WSI encoder with a frozen large language model (LLM) for WSI-based generative text capabilities such as report generation or AI-in-the-loop interactions. We utilize a de-identified dataset of over 350,000 WSIs and diagnostic text pairs, spanning a wide range of diagnoses, procedure types, and tissue types. We present pathologist evaluation of text generation and text retrieval using WSI embeddings, as well as results for WSI classification and workflow prioritization (slide-level triaging). Model-generated text for WSIs was rated by pathologists as accurate, without clinically significant error or omission, for 78% of WSIs on average. This work demonstrates exciting potential capabilities for language-aligned WSI embeddings.

Power batteries are essential components in electric vehicles, where internal structural defects can pose serious safety risks. We conduct a comprehensive study on a new task, power battery detection (PBD), which aims to localize the dense endpoints of cathode and anode plates from industrial X-ray images for quality inspection. Manual inspection is inefficient and error-prone, while traditional vision algorithms struggle with densely packed plates, low contrast, scale variation, and imaging artifacts. To address this issue and drive more attention into this meaningful task, we present PBD5K, the first large-scale benchmark for this task, consisting of 5,000 X-ray images from nine battery types with fine-grained annotations and eight types of real-world visual interference. To support scalable and consistent labeling, we develop an intelligent annotation pipeline that combines image filtering, model-assisted pre-labeling, cross-verification, and layered quality evaluation. We formulate PBD as a point-level segmentation problem and propose MDCNeXt, a model designed to extract and integrate multi-dimensional structure clues including point, line, and count information from the plate itself. To improve discrimination between plates and suppress visual interference, MDCNeXt incorporates two state space modules. The first is a prompt-filtered module that learns contrastive relationships guided by task-specific prompts. The second is a density-aware reordering module that refines segmentation in regions with high plate density. In addition, we propose a distance-adaptive mask generation strategy to provide robust supervision under varying spatial distributions of anode and cathode positions. The source code and datasets will be publicly available at https://github.com/Xiaoqi-Zhao-DLUT/X-ray-PBD{PBD5K}.

This paper considers open-set recognition (OSR) of plankton images. Plankton include a diverse range of microscopic aquatic organisms that have an important role in marine ecosystems as primary producers and as a base of food webs. Given their sensitivity to environmental changes, fluctuations in plankton populations offer valuable information about oceans' health and climate change motivating their monitoring. Modern automatic plankton imaging devices enable the collection of large-scale plankton image datasets, facilitating species-level analysis. Plankton species recognition can be seen as an image classification task and is typically solved using deep learning-based image recognition models. However, data collection in real aquatic environments results in imaging devices capturing a variety of non-plankton particles and plankton species not present in the training set. This creates a challenging fine-grained OSR problem, characterized by subtle differences between taxonomically close plankton species. We address this challenge by conducting extensive experiments on three OSR approaches using both phyto- and zooplankton images analyzing also on the effect of the rejection thresholds for OSR. The results demonstrate that high OSR accuracy can be obtained promoting the use of these methods in operational plankton research. We have made the data publicly available to the research community.

Recent advances in the development of vision-language models (VLMs) are yielding remarkable success in recognizing visual semantic content, including impressive instances of compositional image understanding. Here, we introduce the novel task of Visual Data-Type Identification, a basic perceptual skill with implications for data curation (e.g., noisy data-removal from large datasets, domain-specific retrieval) and autonomous vision (e.g., distinguishing changing weather conditions from camera lens staining). We develop two datasets consisting of animal images altered across a diverse set of 27 visual data-types, spanning four broad categories. An extensive zero-shot evaluation of 39 VLMs, ranging from 100M to 80B parameters, shows a nuanced performance landscape. While VLMs are reasonably good at identifying certain stylistic data-types, such as cartoons and sketches, they struggle with simpler data-types arising from basic manipulations like image rotations or additive noise. Our findings reveal that (i) model scaling alone yields marginal gains for contrastively-trained models like CLIP, and (ii) there is a pronounced drop in performance for the largest auto-regressively trained VLMs like OpenFlamingo. This finding points to a blind spot in current frontier VLMs: they excel in recognizing semantic content but fail to acquire an understanding of visual data-types through scaling. By analyzing the pre-training distributions of these models and incorporating data-type information into the captions during fine-tuning, we achieve a significant enhancement in performance. By exploring this previously uncharted task, we aim to set the stage for further advancing VLMs to equip them with visual data-type understanding. Code and datasets are released at https://github.com/bethgelab/DataTypeIdentification.

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.

Identifying subtle phenotypic variations in cellular images is critical for advancing biological research and accelerating drug discovery. These variations are often masked by the inherent cellular heterogeneity, making it challenging to distinguish differences between experimental conditions. Recent advancements in deep generative models have demonstrated significant potential for revealing these nuanced phenotypes through image translation, opening new frontiers in cellular and molecular biology as well as the identification of novel biomarkers. Among these generative models, diffusion models stand out for their ability to produce high-quality, realistic images. However, training diffusion models typically requires large datasets and substantial computational resources, both of which can be limited in biological research. In this work, we propose a novel approach that leverages pre-trained latent diffusion models to uncover subtle phenotypic changes. We validate our approach qualitatively and quantitatively on several small datasets of microscopy images. Our findings reveal that our approach enables effective detection of phenotypic variations, capturing both visually apparent and imperceptible differences. Ultimately, our results highlight the promising potential of this approach for phenotype detection, especially in contexts constrained by limited data and computational capacity.

Medical image classification in radiology faces significant challenges, particularly in generalizing to unseen pathologies. In contrast, CLIP offers a promising solution by leveraging multimodal learning to improve zero-shot classification performance. However, in the medical domain, lesions can be small and might not be well represented in the embedding space. Therefore, in this paper, we explore the potential of visual prompt engineering to enhance the capabilities of Vision Language Models (VLMs) in radiology. Leveraging BiomedCLIP, trained on extensive biomedical image-text pairs, we investigate the impact of embedding visual markers directly within radiological images to guide the model's attention to critical regions. Our evaluation on the JSRT dataset, focusing on lung nodule malignancy classification, demonstrates that incorporating visual prompts x2013 such as arrows, circles, and contours x2013 significantly improves classification metrics including AUROC, AUPRC, F1 score, and accuracy. Moreover, the study provides attention maps, showcasing enhanced model interpretability and focus on clinically relevant areas. These findings underscore the efficacy of visual prompt engineering as a straightforward yet powerful approach to advance VLM performance in medical image analysis.

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

In quality control, microstructures are investigated rigorously to ensure structural integrity, exclude the presence of critical volume defects, and validate the formation of the target microstructure. For quenched, hierarchically-structured steels, the morphology of the bainitic and martensitic microstructures are of major concern to guarantee the reliability of the material under service conditions. Therefore, industries conduct small sample-size inspections of materials cross-sections through metallographers to validate the needle morphology of such microstructures. We demonstrate round-robin test results revealing that this visual grading is afflicted by pronounced subjectivity despite the thorough training of personnel. Instead, we propose a deep learning image classification approach that distinguishes steels based on their microstructure type and classifies their needle length alluding to the ISO 643 grain size assessment standard. This classification approach facilitates the reliable, objective, and automated classification of hierarchically structured steels. Specifically, an accuracy of 96% and roughly 91% is attained for the distinction of martensite/bainite subtypes and needle length, respectively. This is achieved on an image dataset that contains significant variance and labeling noise as it is acquired over more than ten years from multiple plants, alloys, etchant applications, and light optical microscopes by many metallographers (raters). Interpretability analysis gives insights into the decision-making of these models and allows for estimating their generalization capability.

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

The detection and classification of exfoliated two-dimensional (2D) material flakes from optical microscope images can be automated using computer vision algorithms. This has the potential to increase the accuracy and objectivity of classification and the efficiency of sample fabrication, and it allows for large-scale data collection. Existing algorithms often exhibit challenges in identifying low-contrast materials and typically require large amounts of training data. Here, we present a deep learning model, called MaskTerial, that uses an instance segmentation network to reliably identify 2D material flakes. The model is extensively pre-trained using a synthetic data generator, that generates realistic microscopy images from unlabeled data. This results in a model that can to quickly adapt to new materials with as little as 5 to 10 images. Furthermore, an uncertainty estimation model is used to finally classify the predictions based on optical contrast. We evaluate our method on eight different datasets comprising five different 2D materials and demonstrate significant improvements over existing techniques in the detection of low-contrast materials such as hexagonal boron nitride.

Text-conditioned generative models for volumetric medical imaging provide semantic control but lack explicit anatomical guidance, often resulting in outputs that are spatially ambiguous or anatomically inconsistent. In contrast, structure-driven methods ensure strong anatomical consistency but typically assume access to ground-truth annotations, which are unavailable when the target image is to be synthesized. We propose a retrieval-augmented approach for Text-to-CT generation that integrates semantic and anatomical information under a realistic inference setting. Given a radiology report, our method retrieves a semantically related clinical case using a 3D vision-language encoder and leverages its associated anatomical annotation as a structural proxy. This proxy is injected into a text-conditioned latent diffusion model via a ControlNet branch, providing coarse anatomical guidance while maintaining semantic flexibility. Experiments on the CT-RATE dataset show that retrieval-augmented generation improves image fidelity and clinical consistency compared to text-only baselines, while additionally enabling explicit spatial controllability, a capability inherently absent in such approaches. Further analysis highlights the importance of retrieval quality, with semantically aligned proxies yielding consistent gains across all evaluation axes. This work introduces a principled and scalable mechanism to bridge semantic conditioning and anatomical plausibility in volumetric medical image synthesis. Code will be released.

Pixel-level segmentation of structural cracks across various scenarios remains a considerable challenge. Current methods encounter challenges in effectively modeling crack morphology and texture, facing challenges in balancing segmentation quality with low computational resource usage. To overcome these limitations, we propose a lightweight Structure-Aware Vision Mamba Network (SCSegamba), capable of generating high-quality pixel-level segmentation maps by leveraging both the morphological information and texture cues of crack pixels with minimal computational cost. Specifically, we developed a Structure-Aware Visual State Space module (SAVSS), which incorporates a lightweight Gated Bottleneck Convolution (GBC) and a Structure-Aware Scanning Strategy (SASS). The key insight of GBC lies in its effectiveness in modeling the morphological information of cracks, while the SASS enhances the perception of crack topology and texture by strengthening the continuity of semantic information between crack pixels. Experiments on crack benchmark datasets demonstrate that our method outperforms other state-of-the-art (SOTA) methods, achieving the highest performance with only 2.8M parameters. On the multi-scenario dataset, our method reached 0.8390 in F1 score and 0.8479 in mIoU. The code is available at https://github.com/Karl1109/SCSegamba.

The polarization of an X-ray beam that produces electrons with velocity components perpendicular to the beam generates an azimuthal distribution of the ejected electrons. We present methods for simulating and for analyzing the angular dependence of electron detections which enable us to derive simple analytical expressions for useful statistical properties of observable data. The derivations are verified by simulations. While we confirm the results of previous work on this topic, we provide an extension needed for analytical treatment of the full range of possible polarization amplitudes.

Medical vision-language models (VLMs) have shown increasing potential for clinical image interpretation, including lesion detection and report generation. However, their practical utility remains limited by insufficient sensitivity to subtle lesions, whose visual evidence is often sparse, low-contrast, and embedded within complex anatomical context. As local visual tokens are aggregated, these weak lesion cues can become underrepresented in global image representations, making them difficult for medical VLMs to recognize. Existing efforts to improve lesion sensitivity mainly rely on medical-domain vision-encoder pre-training, clinical-term-guided alignment, or trainable pathological representation enhancement. Although effective, these approaches usually require additional training or model-specific adaptation and may overfit to particular disease morphologies, limiting their applicability to frozen medical VLMs. To address these limitations, we propose EasyLens, a training-free plug-and-play subtle-lesion representation amplifier for medical VLMs. EasyLens first constructs EasyBank, a pathology-anatomy prototype space that provides lesion-related prototypes and anatomy-aware normal references for comparing suspicious patches against both pathological and normal anatomical patterns. To avoid blindly amplifying normal tissues, EasyTag selects lesion-relevant patches through counterfactual prototype reasoning. To counteract the dilution of subtle lesion cues in global image representations, EasyAmplifier strengthens the selected lesion-relevant patch representations through morphology-guided residual enhancement, thereby increasing their contribution to the global image embedding. Experiments on multiple medical image datasets and frozen medical VLM backbones show that EasyLens improves subtle-lesion detection and outperforms existing encoder-enhancement baselines.

We introduce a new -- currently 42 gigabyte -- ``living'' dataset of phone images of dog feces, annotated with manually drawn or AI-assisted polygon labels. There are 6k full resolution images and 4k detailed polygon annotations. The collection and annotation of images started in late 2020 and the dataset grows by roughly 1GB a month. We train VIT and MaskRCNN baseline models to explore the difficulty of the dataset. The best model achieves a pixelwise average precision of 0.858 on a 691-image validation set and 0.847 on a small independently captured 30-image contributor test set. The most recent snapshot of dataset is made publicly available through three different distribution methods: one centralized (Girder) and two decentralized (IPFS and BitTorrent). We study of the trade-offs between distribution methods and discuss the feasibility of each with respect to reliably sharing open scientific data. The code to reproduce the experiments is hosted on GitHub, and the data is published under the Creative Commons Attribution 4.0 International license. Model weights are made publicly available with the dataset. Experimental hardware, time, energy, and emissions are quantified.

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

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

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

To synthesize high-fidelity samples, diffusion models typically require auxiliary data to guide the generation process. However, it is impractical to procure the painstaking patch-level annotation effort required in specialized domains like histopathology and satellite imagery; it is often performed by domain experts and involves hundreds of millions of patches. Modern-day self-supervised learning (SSL) representations encode rich semantic and visual information. In this paper, we posit that such representations are expressive enough to act as proxies to fine-grained human labels. We introduce a novel approach that trains diffusion models conditioned on embeddings from SSL. Our diffusion models successfully project these features back to high-quality histopathology and remote sensing images. In addition, we construct larger images by assembling spatially consistent patches inferred from SSL embeddings, preserving long-range dependencies. Augmenting real data by generating variations of real images improves downstream classifier accuracy for patch-level and larger, image-scale classification tasks. Our models are effective even on datasets not encountered during training, demonstrating their robustness and generalizability. Generating images from learned embeddings is agnostic to the source of the embeddings. The SSL embeddings used to generate a large image can either be extracted from a reference image, or sampled from an auxiliary model conditioned on any related modality (e.g. class labels, text, genomic data). As proof of concept, we introduce the text-to-large image synthesis paradigm where we successfully synthesize large pathology and satellite images out of text descriptions.

Large language models (LLMs) are increasingly used to assist scientists across diverse workflows. A key challenge is generating high-quality figures from textual descriptions, often represented as TikZ programs that can be rendered as scientific images. Prior research has proposed a variety of datasets and modeling approaches for this task. However, existing datasets for Text-to-TikZ are too small and noisy to capture the complexity of TikZ, causing mismatches between text and rendered figures. Moreover, prior approaches rely solely on supervised fine-tuning (SFT), which does not expose the model to the rendered semantics of the figure, often resulting in errors such as looping, irrelevant content, and incorrect spatial relations. To address these issues, we construct DaTikZ-V4, a dataset more than four times larger and substantially higher in quality than DaTikZ-V3, enriched with LLM-generated figure descriptions. Using this dataset, we train TikZilla, a family of small open-source Qwen models (3B and 8B) with a two-stage pipeline of SFT followed by reinforcement learning (RL). For RL, we leverage an image encoder trained via inverse graphics to provide semantically faithful reward signals. Extensive human evaluations with over 1,000 judgments show that TikZilla improves by 1.5-2 points over its base models on a 5-point scale, surpasses GPT-4o by 0.5 points, and matches GPT-5 in the image-based evaluation, while operating at much smaller model sizes. Code, data, and models will be made available.

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

Text-rich images, where text serves as the central visual element guiding the overall understanding, are prevalent in real-world applications, such as presentation slides, scanned documents, and webpage snapshots. Tasks involving multiple text-rich images are especially challenging, as they require not only understanding the content of individual images but reasoning about inter-relationships and logical flows across multiple visual inputs. Despite the importance of these scenarios, current multimodal large language models (MLLMs) struggle to handle such tasks due to two key challenges: (1) the scarcity of high-quality instruction tuning datasets for text-rich multi-image scenarios, and (2) the difficulty in balancing image resolution with visual feature sequence length. To address these challenges, we propose \OurMethod, a MLLM designed specifically for handling vision-language tasks involving multiple text-rich images. First, we curated about one million high-quality multimodal instruction-tuning data, tailored to text-rich, multi-image scenarios. Second, we developed an adaptive high-resolution multi-image encoding module to dynamically optimize the allocation of visual sequence length based on the original aspect ratios and resolutions of the input images. Experiments across a wide range of benchmarks demonstrate our model's superior capabilities in text-rich, multi-image evaluations and competitive performance in general domain evaluations.

Recent innovations in light sheet microscopy, paired with developments in tissue clearing techniques, enable the 3D imaging of large mammalian tissues with cellular resolution. Combined with the progress in large-scale data analysis, driven by deep learning, these innovations empower researchers to rapidly investigate the morphological and functional properties of diverse biological samples. Segmentation, a crucial preliminary step in the analysis process, can be automated using domain-specific deep learning models with expert-level performance. However, these models exhibit high sensitivity to domain shifts, leading to a significant drop in accuracy when applied to data outside their training distribution. To address this limitation, and inspired by the recent success of self-supervised learning in training generalizable models, we organized the SELMA3D Challenge during the MICCAI 2024 conference. SELMA3D provides a vast collection of light-sheet images from cleared mice and human brains, comprising 35 large 3D images-each with over 1000^3 voxels-and 315 annotated small patches for finetuning, preliminary testing and final testing. The dataset encompasses diverse biological structures, including vessel-like and spot-like structures. Five teams participated in all phases of the challenge, and their proposed methods are reviewed in this paper. Quantitative and qualitative results from most participating teams demonstrate that self-supervised learning on large datasets improves segmentation model performance and generalization. We will continue to support and extend SELMA3D as an inaugural MICCAI challenge focused on self-supervised learning for 3D microscopy image segmentation.

Multimodal learning has revolutionized general domain tasks, yet its application in scientific discovery is hindered by the profound semantic gap between complex scientific imagery and sparse textual descriptions. We present S1-MMAlign, a large-scale, multi-disciplinary multimodal dataset comprising over 15.5 million high-quality image-text pairs derived from 2.5 million open-access scientific papers. Spanning disciplines from physics and biology to engineering, the dataset captures diverse visual modalities including experimental setups, heatmaps, and microscopic imagery. To address the pervasive issue of weak alignment in raw scientific captions, we introduce an AI-ready semantic enhancement pipeline that utilizes the Qwen-VL multimodal large model series to recaption images by synthesizing context from paper abstracts and citation contexts. Technical validation demonstrates that this enhancement significantly improves data quality: SciBERT-based pseudo-perplexity metrics show reduced semantic ambiguity, while CLIP scores indicate an 18.21% improvement in image-text alignment. S1-MMAlign provides a foundational resource for advancing scientific reasoning and cross-modal understanding in the era of AI for Science. The dataset is publicly available at https://huggingface.co/datasets/ScienceOne-AI/S1-MMAlign.

Reliable anomaly detection in photovoltaic (PV) modules is critical for maintaining solar energy efficiency. However, developing robust computer vision models for PV inspection is constrained by the scarcity of large-scale, diverse, and balanced datasets. This study introduces PV-DDPM, a spatially conditioned denoising diffusion probabilistic model that generates anomalous electroluminescence (EL) images across four PV cell types: multi-crystalline silicon (multi-c-Si), mono-crystalline silicon (mono-c-Si), half-cut multi-c-Si, and interdigitated back contact (IBC) with dogbone interconnect. PV-DDPM enables controlled synthesis of single-defect and multi-defect scenarios by conditioning on binary masks representing structural features and defect positions. To the best of our knowledge, this is the first framework that jointly models multiple PV cell types while supporting simultaneous generation of diverse anomaly types. We also introduce E-SCDD, an enhanced version of the SCDD dataset, comprising 1,000 pixel-wise annotated EL images spanning 30 semantic classes, and 1,768 unlabeled synthetic samples. Quantitative evaluation shows our generated images achieve a Fréchet Inception Distance (FID) of 4.10 and Kernel Inception Distance (KID) of 0.0023 pm 0.0007 across all categories. Training the vision--language anomaly detection model AA-CLIP on E-SCDD, compared to the SCDD dataset, improves pixel-level AUC and average precision by 1.70 and 8.34 points, respectively.

Whole Slide Images (WSIs) exhibit hierarchical structure, where diagnostic information emerges from cellular morphology, regional tissue organization, and global context. Existing Computational Pathology (CPath) Multimodal Large Language Models (MLLMs) typically compress an entire WSI into a single embedding, which hinders fine-grained grounding and ignores how pathologists synthesize evidence across different scales. We introduce MLLM-HWSI, a Hierarchical WSI-level MLLM that aligns visual features with pathology language at four distinct scales, cell as word, patch as phrase, region as sentence, and WSI as paragraph to support interpretable evidence-grounded reasoning. MLLM-HWSI decomposes each WSI into multi-scale embeddings with scale-specific projectors and jointly enforces (i) a hierarchical contrastive objective and (ii) a cross-scale consistency loss, preserving semantic coherence from cells to the WSI. We compute diagnostically relevant patches and aggregate segmented cell embeddings into a compact cellular token per-patch using a lightweight Cell-Cell Attention Fusion (CCAF) transformer. The projected multi-scale tokens are fused with text tokens and fed to an instruction-tuned LLM for open-ended reasoning, VQA, report, and caption generation tasks. Trained in three stages, MLLM-HWSI achieves new SOTA results on 13 WSI-level benchmarks across six CPath tasks. By aligning language with multi-scale visual evidence, MLLM-HWSI provides accurate, interpretable outputs that mirror diagnostic workflows and advance holistic WSI understanding. Code is available at: https://github.com/BasitAlawode/HWSI-MLLM{GitHub}.

The materials science literature encodes decades of experimental knowledge in figures, yet this visual record remains locked away and inaccessible to AI at scale. The core difficulty is structural: most scientific figures are compound, with a single caption describing multiple sub-panels simultaneously, making direct image-text pairing unreliable. We present MatMMExtract, an end-to-end open-source pipeline that resolves this by decomposing compound figures into individual sub-panels and generating structured, grounded annotations using a large language model guided by a curated materials science taxonomy. Applied to 14,810 open-access articles, MatMMExtract produces MatSciFig; 391,606 panel-level image-text pairs from 180,571 figures, each annotated with a sub-caption, a two-level visualisation category spanning 19 classes and over 100 subtypes, and a scientific summary. To enable accurate panel localisation, we introduce MaterialScope, a domain-specific detection dataset of 2,811 manually annotated materials science figures, on which a fine-tuned YOLO12-m detector achieves mAP_50 of 0.9227. Among six benchmarked language models, Gemini 3.1 Flash Lite delivers the best cost-quality trade-off for annotation generation, with 82% of outputs rated good and a hallucination rate of 4.8%. A dual-encoder retrieval baseline on MatSciFig achieves a 4.4 times improvement in R@1 over zero-shot CLIP, demonstrating the dataset's immediate utility for vision-language learning. All resources are released openly to the community.

Large annotated datasets are essential for training robust Computer-Aided Diagnosis (CAD) models for breast cancer detection or risk prediction. However, acquiring such datasets with fine-detailed annotation is both costly and time-consuming. Vision-Language Models (VLMs), such as CLIP, which are pre-trained on large image-text pairs, offer a promising solution by enhancing robustness and data efficiency in medical imaging tasks. This paper introduces a novel Multi-View Mammography and Language Model for breast cancer classification and risk prediction, trained on a dataset of paired mammogram images and synthetic radiology reports. Our MV-MLM leverages multi-view supervision to learn rich representations from extensive radiology data by employing cross-modal self-supervision across image-text pairs. This includes multiple views and the corresponding pseudo-radiology reports. We propose a novel joint visual-textual learning strategy to enhance generalization and accuracy performance over different data types and tasks to distinguish breast tissues or cancer characteristics(calcification, mass) and utilize these patterns to understand mammography images and predict cancer risk. We evaluated our method on both private and publicly available datasets, demonstrating that the proposed model achieves state-of-the-art performance in three classification tasks: (1) malignancy classification, (2) subtype classification, and (3) image-based cancer risk prediction. Furthermore, the model exhibits strong data efficiency, outperforming existing fully supervised or VLM baselines while trained on synthetic text reports and without the need for actual radiology reports.