Microscopy Image Analysis

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13 papers in the last four weeks, up 117% on the four weeks before. 0.1% of all new papers.

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Latest papers 125

May 21, 2026cs.CV

Detection of Virus and Small Cell Patches in Foci Images Using Switchable Convolution and Feature Pyramid Networks

Accurate detection and counting of virus patches in focus-forming unit (FFU) images, also known as foci images, are important for quantifying viral infection and analyzing cellular structures. This task is challenging because biomedical targets often vary substantially in size, density, contrast, and shape. In this paper, we propose an enhanced YOLOv2-based detector that integrates a Feature Pyramid Network (FPN) to improve multi-scale feature representation. We also incorporate a switchable atrous convolution mechanism to adapt the receptive field for fine-grained targets in dense microscopy images. The proposed method is evaluated on biomedical foci image datasets for virus patch and small cell patch detection. For small cell patch detection, the model achieves a mean average precision (mAP) of 40.5% at a 25% Intersection over Union (IoU) threshold. For FFU virus patch detection, the model achieves an mAP of 68%. These results indicate that combining FPN-based feature fusion with switchable convolution improves the suitability of YOLOv2 for specialized biomedical object detection tasks

Amrita Singh, Snehasis Mukherjee

Small Object Detection Object Detection Convolutional Neural Networks Microscopy Image Analysis

May 21, 2026cs.CV

Virtual 3D H&E Staining from Phase-contrast Back-illumination Interference Tomography

Three-dimensional (3D) histopathology of unprocessed tissues has the potential to transform disease management by enabling volumetric characterization of tissue microarchitecture and in-vivo assessment. Back-illumination Interference Tomography (BIT) is a new phase microscopy technology that provides rapid, non-destructive volumetric imaging of unprocessed tissues. However, translating BIT volumes into clinically interpretable H&E images remains challenging, particularly due to shift-variant contrast and the absence of quantitative validation benchmarks. We introduce HistoBIT3D, the first voxel-wise paired BIT and fluorescence-labeled nuclei dataset, enabling quantitative evaluation of structural preservation in unsupervised virtual staining against ground-truth nuclear distributions. Using this dataset, we present a novel virtual staining framework that translates BIT volumes with shift-variant contrast into realistic H&E volumes by leveraging bidirectional multiscale content consistency and cross-domain style reuse to enhance structural fidelity and perceptual realism. Our method achieves state-of-the-art realism metrics while significantly improving 3D nuclei segmentation accuracy and boundary preservation under zero-shot Cellpose evaluation. Together, these contributions establish a quantitatively validated, structurally faithful, and scalable pipeline for 3D virtual H&E staining, advancing the paradigm of slide-free, volumetric computational histopathology. Our data and code are available at: https://github.com/aasong113/HistoBIT3D_VirtualStaining.

Anthony Song, Boyan Zhou, Mayank Golhar +3

Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA · Department of Pathology, Johns Hopkins Hospital,2026 Baltimore, MD, USA

Computational Pathology Image-to-Image Translation Virtual Staining Microscopy Image Analysis

May 19, 2026cs.CV

A Human-in-the-Loop Framework for Efficient Prompt Selection in Microscopy Vision-Language Models

Deep-learning pipelines for microscopy image classification often require expensive, labor- and time-intensive expert annotation to produce high-quality ground truth for training. Recent work has shown that prompt tuning of vision-language models (VLMs) can reduce manual annotation by constructing a small prompt set of expert-verified image-caption exemplars that is reused as few-shot context to classify all remaining images at inference time. To further reduce effort, the VLM can draft captions for candidate exemplars, which experts then verify and lightly edit instead of writing text de novo. However, two practical questions remain unaddressed: (1) which unlabeled images should be prioritized for verification, and (2) how many verified exemplars are needed to reach a performance target. In this work, we address these questions by formulating prompt-set construction as a target-driven active learning problem that prioritizes which images to annotate. We study three complementary selection criteria under strict low-resource constraints with small unlabeled pools. Experiments show that our methods reach the target performance with substantially fewer expert-verified images than random selection, achieving 100% test accuracy with as few as 20 annotated images on average. More broadly, our human-in-the-loop framework demonstrates a human-centered use of generative AI in biomedical image analysis, where experts remain actively involved in verifying and refining model output while significantly reducing annotation cost. Code and data will be publicly available.

Abhiram Kandiyana, Ankur Mali, Lawrence O. Hall +2

University of South Florida, USA · SRC Biosciences, USA

Vision-Language Models Human-in-the-Loop Annotation Few-Shot Image Classification Microscopy Image Analysis

May 15, 2026cs.CV

End-to-end plaque counting and virus titration from laboratory plate images with deep learning

Plaque assays remain the gold standard readout of virus infectivity; however, plaque counting from plate images is labor-intensive and prone to inter-operator variability. We present an end-to-end, computer-aided workflow for cytopathic effect-based virus titration directly from laboratory plaque assay images. The proposed approach combines two models derived from the Segment Anything Model (SAM): a SAM2-based well-segmentation module that localizes assay wells across heterogeneous imaging conditions, and a SAM-based plaque-segmentation model that detects and enumerates plaques within each well. The method was evaluated on a mixed dataset comprising private plaque assay images of Mayaro virus and Coxsackievirus B3, together with public Vaccinia virus images from the VACVPlaque dataset. The pipeline outputs per-well plaque counts, automatically computes plaque-forming units per milliliter (PFU/mL), and is integrated into a web-based platform that allows users to review results and organize experiments. On held-out plates (17 from MAYV/CVB3 and 22 from VACV), the workflow generalized across two plate formats (6-well and 12-well) and showed strong agreement with manual annotations (Pearson correlation coefficients of 0.92 for MAYV/CVB3 and 0.88 for VACV). Automated plaque counts were further compared with annotations from four independent experts, demonstrating high concordance. The proposed system will be open sourced and publicly released upon acceptance of this manuscript to enable reproducible, scalable, and audit-ready plaque assay analysis while substantially reducing manual annotation effort.

Eugenia Moris, Alicia Costábile, Sebastián Rey +11

Arionkoder LLC, Boston, MA 02114, United States · Laboratory of Experimental Virus Evolution, Pasteur Institute of Montevideo, Montevideo, 11400, Uruguay · Laboratory of Molecular Virology, Faculty of Sciences, University of the Republic, Montevideo, 11400, Uruguay +3

Image Segmentation Microscopy Image Analysis

May 14, 2026cs.CV

MorphoHELM: A Comprehensive Benchmark for Evaluating Representations for Microscopy-Based Morphology Assays

Microscopy images contain rich information about how cells respond to perturbations, making them essential to applications like drug screening. To quantify images, researchers often use representation extraction methods, and recent years have seen a proliferation of deep learning methods. While measuring the quality of these representations is essential, evaluation remains fragmented, with each proposed model evaluated on different tasks and datasets, using custom pipelines and metrics, making it difficult to fairly compare models. Here, we introduce MorphoHELM, a comprehensive open benchmark for evaluating feature extraction methods for Cell Painting, the most widely-used morphological profiling assay. MorphoHELM consolidates evaluation standards in the field, extends and corrects them to be more robust, and evaluates on the widest range of methods to date. A defining feature of the benchmark is that each task is evaluated at different degrees of batch effects (or technical noise), directly quantifying how the ability of methods to detect biological signal degrades as noise increases. Together, these properties enable MorphoHELM to detect trade-offs between methods, and we demonstrate that models that excel at certain kinds of biological signal are weaker at others. We show that no existing model outperforms classic computer vision analytic strategies across all settings, which remain the strongest general use-case representations. All datasets, code, and evaluation tools are publicly available at https://github.com/microsoft/MorphoHELM.

Emre Hayir, Lorin Crawford, Alex X. Lu

Microsoft Research New England

Microscopy Image Analysis

May 14, 2026cs.CV

MicroscopyMatching: Towards a Ready-to-use Framework for Microscopy Image Analysis in Diverse Conditions

Analyzing microscopy images to extract biological object properties (e.g., their morphological organization, temporal dynamics, and population density) is fundamental to various biomedical research. Yet conducting this manually is costly and time-consuming. Though deep learning-based approaches have been explored to automate this process, the substantial diversity of microscopy analysis settings in practice (including variations of biological object types, sample processing protocols, imaging equipment, and analysis tasks, etc.) often renders them ineffective. As a result, these approaches typically require extensive adaptation for different settings, which, however, can impose burdens that are often practically unsustainable for laboratories, forcing biomedical researchers to still commonly rely on manual analysis, thereby severely bottlenecking the pace of biomedical research progress. This situation has created a pressing and long-standing need for a reliable and broadly applicable microscopy image analysis tool, yet such a tool is still missing. To address this gap, we present the first ready-to-use microscopy image analysis framework, MicroscopyMatching, that can reliably perform key analysis tasks (including segmentation, tracking, and counting) across diverse microscopy analysis settings. From a fundamentally different perspective, MicroscopyMatching reformulates diverse microscopy image analysis tasks as a unified matching problem, effectively handling this problem by exploiting the robust matching capability from pre-trained latent diffusion models.

Xiaofei Hui, Haoxuan Qu, Hossein Rahmani +3

School of Computing and Communications, Lancaster University, Lancaster, LA1 4WA, UK. · Department of Cell Biology, Harvard Medical School, Boston, MA 02115, USA. · Department of Molecular and Cellular Biology, Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.

Image Segmentation Image Matching Object Counting Microscopy Image Analysis Multi-Object Tracking

May 14, 2026cs.CV

Towards Label-Free Single-Cell Phenotyping Using Multi-Task Learning

Label-free single-cell imaging offers a scalable, non-invasive alternative to fluorescence-based cytometry, yet inferring molecular phenotypes directly from bright-field morphology remains challenging. We present a unified Deep Learning (DL) framework that jointly performs White Blood Cell (WBC) classification and continuous protein-expression regression from label-free Differential Phase Contrast (DPC) images. Our model employs a Hybrid architecture that fuses convolutional fine-grained texture features with transformer-based global representations through a learnable cross-branch gating module, enabling robust morpho-molecular inference from DPC images. To support downstream interpretability, we further incorporate a Large Language Model (LLM) that generates concise, biologically grounded summaries of the predicted cell states. Experiments on the Berkeley Single Cell Computational Microscopy (BSCCM) and Blood Cells Image benchmarks demonstrate strong performance, achieving a 91.3% WBC classification accuracy and a 0.72 Pearson correlation for CD16 expression regression on BSCCM. These results underscore the promise of label-free single-cell imaging for cost-effective hematological profiling, enabling simultaneous phenotype identification and quantitative biomarker estimation without fluorescent staining. The source code is available at https://github.com/saqibnaziir/Single-Cell-Phenotyping.

Saqib Nazir, Ardhendu Behera

Department of Computer Science, Edge Hill University, UK

Multi-Task Learning Microscopy Image Analysis

May 13, 2026physics.optics

DeepFilters: Scattering-Aware Pupil Engineering with Learned Digital Filter Reconstruction for Extended Depth of Field Microscopy

Extended depth of field microscopy encodes axial information into a single acquisition through engineered point spread functions, but conventional and deep optics approaches are subject to degradation in scattering tissue. We introduce DeepFilters, a scattering-aware deep optics framework that jointly optimizes a parameterized pupil filter and a digital-filter-based reconstruction network through a calibrated differentiable forward model to achieve broad generalization without retraining. Incorporating empirical scattering kernels, physics-guided regularization, and a hybrid genetic-gradient initialization strategy, DeepFilters extends the PSF from 16 micron to >400 micron in clear media and enables signal recovery beyond 120 micron deep in biological tissues, validated across fixed brain slices and sea urchin embryos.

Joseph L. Greene, Suet YIng Chan, Qilin Deng +8

Boston University, Department of Electrical and Computer Engineering, Boston, MA, 02215 · Current Address: Georgia Tech Research Institute, Electro-Optical Systems Lab, Atlanta, GA, 30332 · Boston University, Department of Biology, Boston, MA, 02215 +3

Image Reconstruction Microscopy Image Analysis Image Inverse Problems

May 13, 2026cs.CV

Bayesian In Vivo Tracking of Synapses using Joint Poisson Deconvolution and Diffeomorphic Registration

Synapses are densely packed submicron structures that dynamically reorganize during learning and memory formation. Longitudinal \textit{in vivo} imaging of fluorescently tagged synaptic receptors offers a promising opportunity to study large-scale synaptic dynamics and how these processes are disrupted in neurological disease. However, in vivo imaging with 2-photon microscopy uses low laser power and therefore suffers from low signal-to-noise ratio (SNR) and high shot noise, nonlinear tissue motion between days, nonstationary fluctuations in synaptic fluorescence, and significant blur induced by the microscope point spread function (PSF). Together, these factors make it challenging to detect and track synapses, especially in regions with high synaptic density. This paper presents a novel template-based framework for modeling synapses as varying luminance point sources that move under a nonlinear tissue deformation. Taking a unified Bayesian approach, we apply this model to microscopy data by deriving a posterior that incorporates a diffeomorphic mapping for domain warping, a Gaussian point spread function for the imaging process, and a Poisson observation model for raw photon counts. The Bayesian solution simultaneously: (1) Constructs a probabilistic template of synapse locations, (2) denoises and deconvolves the image data, (3) infers fluorescence intensities, (4) performs diffeomorphic image registration to correct for tissue motion, and (5) provides confidence regions for these parameter estimates. We demonstrate the framework on both a 2D+t simulated dataset and a 3D+t longitudinal \textit{in vivo} microscopy dataset of fluorescent synapses imaged in a mouse over two weeks.

Shashwat Kumar, Dominic M. Padova, Binish Narang +6

Department of Biomedical Engineering, Johns Hopkins University · Department of Neuroscience, Johns Hopkins University · Kavli Neuroscience Discovery Institute, Johns Hopkins University +2

Bayesian Inverse Problems Longitudinal Medical Image Analysis Neuroimaging Microscopy Image Analysis Image Inverse Problems

May 11, 2026cs.CV

Automated Detection of Abnormalities in Zebrafish Development

Zebrafish embryos are a valuable model for drug discovery due to their optical transparency and genetic similarity to humans. However, current evaluations rely on manual inspection, which is costly and labor-intensive. While machine learning offers automation potential, progress is limited by the lack of comprehensive datasets. To address this, we introduce a large-scale dataset of high-resolution microscopic image sequences capturing zebrafish embryonic development under both control conditions and exposure to compounds (3,4-dichloroaniline). This dataset, with expert annotations at fine-grained temporal levels, supports two benchmarking tasks: (1) fertility classification, assessing zebrafish egg viability (130,368 images), and (2) toxicity assessment, detecting malformations induced by toxic exposure over time (55,296 images). Alongside the dataset, we present the first transformer-based baseline model that integrates spatiotemporal features to predict developmental abnormalities at early stages. Experimental results present the model's effectiveness, achieving 98% accuracy in fertility classification and 92% in toxicity assessment. These findings underscore the potential of automated approaches to enhance zebrafish-based toxicity analysis.

Sarath Sivaprasad, Hui-Po Wang, Anna-Lisa Jäckel +4

CISPA Helmholtz Center for Information Security, Saarbrücken, Germany · Helmholtz Institute for Pharmaceutical Research Saarland, Saarbrücken, Germany

Toxicity Detection Microscopy Image Analysis

May 8, 2026cs.CV

MicroDiffuse3D: A Foundation Model for 3D Microscopy Imaging Restoration

Chemical imaging enables label-free visualization of cells, tissues and living systems while providing direct biochemical information that is difficult to obtain with conventional fluorescence microscopy. Despite its promise in applications ranging from intraoperative diagnosis to drug-response analysis, its broader use remains limited by slow data acquisition, particularly for three-dimensional imaging. Here we present MicroDiffuse3D, a pretrained foundation model for 3D microscopy image restoration that recovers high-quality volumetric structure from degraded low-resolution measurements acquired at substantially higher throughput. We evaluated MicroDiffuse3D across three challenging restoration settings, including 3D super-resolution under 16-fold volumetric sparsity, joint degradation in resolution and noise, and 3D denoising in the low signal-to-noise ratio (SNR) regime, where the model delivered clear gains over strong baselines. Under the sparse 3D super-resolution setting, MicroDiffuse3D produced clearer continuity across depth with fewer artifacts and improved segmentation quality by 10.58% and line-profile concordance by 15.59%. Together, our results establish pretrained 3D restoration as a broadly applicable strategy for overcoming the throughput and SNR limitations in volumetric chemical imaging, enabling high-resolution analysis at scales and speeds that were previously difficult to achieve.

Yongkang Li, Brian Wong, King Wai Chiu +5

Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA. · Department of Chemistry, University of Washington, Seattle, WA, USA

Image Restoration Microscopy Image Analysis Image Super-Resolution Image Denoising

May 6, 2026q-bio.BM

Enhancing Cryo-EM Density Map Segmentation in Phenix for Improved Atomic Model Building

We introduce PhenixCraft, a fully automated pipeline for building atomic models from cryo-EM density maps. By integrating AlphaFold predictions, we enhance the map-segmentation step in Phenix during model building, addressing challenges posed by noise and artifacts that traditionally hinder this step. Our results demonstrate PhenixCraft's superior performance in TM-scores and sequence accuracy, significantly improving upon the limitations and inefficiencies of traditional model building using Phenix.

Chenwei Zhang

Department of Computer Science The University of British Columbia Vancouver, Canada

AI-Assisted Scientific Research Cryo-Electron Microscopy Microscopy Image Analysis

May 3, 2026physics.app-ph

Continuous quantification of viral plaque dynamics using ultra-large-area label-free imaging enables rapid antiviral susceptibility testing

The plaque reduction assay (PRA) remains the gold standard for antiviral susceptibility testing, evaluating drug potency by measuring reductions in plaque-forming units (PFUs). However, the traditional PRA is time-consuming, labor-intensive, prone to manual counting errors, and offers limited scalability. Moreover, its reliance on destructive fixation and chemical staining reduces the assay to a static, endpoint observation, obscuring the dynamic, time-resolved kinetics of dose-dependent viral inhibition. Here, we introduce a label-free, time-resolved PRA platform that transforms the conventional assay into a continuous, high-dimensional measurement of viral infection dynamics. Our system integrates a compact lens-free imaging setup with a custom-designed ultra-large-area (100 cm^2) thin-film transistor (TFT) image sensor and deep learning-based algorithms to autonomously quantify PFU dynamics within an incubator. Validated using herpes simplex virus type-1 (HSV-1) treated with acyclovir, the platform matched chemically-stained ground truth measurements with zero false positives while accelerating readout by ~26 hours. Crucially, our system revealed that increasing drug concentrations induce temporally distinct delays and suppress new PFU formation, enabling conclusive drug efficacy evaluations within ~60 hours post-infection. This scalable, label-free framework redefines antiviral susceptibility testing as a rapid, time-resolved and information-rich measurement framework, providing a generalizable platform for virology research, high-throughput drug screening, and clinical diagnostics.

Merve Eryilmaz, Yuzhu Li, Xiao Wang +8

Department of Electrical and Computer Engineering, University of California, Los Angeles, CA, USA, 90095 · Department of Bioengineering, University of California, Los Angeles, CA, USA, 90095 · 3California NanoSystems Institute (CNSI), University of California, Los Angeles, CA, USA, 90095 +5

Microscopy Image Analysis

May 1, 2026eess.IV

Multi-frame Restoration for High-rate Lissajous Confocal Laser Endomicroscopy

Lissajous confocal laser endomicroscopy (CLE) is a promising solution for high speed in vivo optical biopsy for handheld scenarios. However, Lissajous scanning traces a resonant trajectory and samples only the visited pixels per frame; at high frame rates, many pixels remain unvisited, creating structured holes. In this work, we introduce the first benchmark for high-rate Lissajous CLE, consisting of low-quality video clips paired with high-quality reference images. The reference images are wide-FOV mosaics obtained by stitching stabilized, slow-scan frames of the same tissue, enabling temporally aligned supervision. Using this dataset, we propose MIRA, a lightweight recurrent framework for Lissajous CLE restoration that iteratively aggregates temporal context through feature reuse and displacement alignment. Our experiments demonstrate that MIRA outperforms both lightweight and high-complexity baselines in restoration quality while maintaining a favorable computational efficiency suitable for clinical deployment.

Minhee Lee, Sangyoon Lee, Jiwook Lee +4

POSTECH, Pohang, Republic of Korea · VPIX Medical, Seoul, Republic of Korea

Endoscopy Medical Imaging Recurrent Neural Networks Image Restoration Video Restoration Medical Image Benchmarks+1

Apr 29, 2026cs.CV

MTCurv: Deep learning for direct microtubule curvature mapping in noisy fluorescence microscopy images

Accurate quantification of the geometry of curvilinear biological structures is essential for understanding cellular mechanics and disease-related morphological alterations. Microtubule curvature is a key descriptor of filament rigidity and mechanical perturbations. However, reliable curvature extraction from fluorescence microscopy images remains challenging due to noise, low contrast, and partial filament visibility. Existing approaches rely on segmentation pipelines with pre or post-processing, which are highly sensitive to segmentation errors and often fail under adverse imaging conditions. In this work, we propose MTCurv, a deep learning framework for direct, segmenta-tion-free regression of microtubule curvature maps from noisy microscopy images. Leveraging a synthetic dataset with pixel-wise curvature annotations, we reformulated curvature estimation as a regression problem and adapted an attention-based residual U-Net. To reduce hallucinations and enforce spatial coherence, we introduced a gradient-aware loss combining Mean Squared Error with a gradient consistency term. Beyond model and loss design, we evaluated commonly used regression and image quality metrics, revealing that many perceptual and blind metrics are poorly suited for curvature estimation. Correlation-based metrics, particularly Spearman correlation, emerged as more reliable indicators of curvature prediction quality. Experiments on two datasets of increasing difficulty demonstrated that MTCurv accurately recovers local microtubule curvatures, even in the presence of background fluorescence. Ablation studies highlighted the contribution of both residual encoding and attention-based decoding. Overall, this work provides a practical tool for filament curvature analysis and methodological insights for geometry-aware regression in biomedical imaging. Datasets and code are made available.

Achraf Ait Laydi, Sidi Mohamed Sid'El Moctar, Yousef El Mourabit +1

TIAD Laboratory, Sciences and Technology Faculty, Sultan Moulay Slimane Univ., Beni Mellal, Morocco. · CNRS, Univ. Rennes, IGDR (Institut de Génétique et Développement de Rennes), UMR6290, 35000 Rennes, France

Convolutional Neural Networks Microscopy Image Analysis

Apr 28, 2026cs.CV

A Data-Centric Framework for Intraoperative Fluorescence Lifetime Imaging for Glioma Surgical Guidance

Accurate intraoperative assessment of glioma infiltration is essential for maximizing tumor resection while preserving functional brain tissue. Fluorescence lifetime imaging (FLIm) offers real-time, label-free biochemical contrast, but its clinical utility is challenged by biological heterogeneity, class imbalance, and variability in histopathological labeling. We present a data-centric AI (DC-AI) framework that integrates confident learning (CL), class refinement, and targeted label evaluation to develop a robust multi-class FLIm classifier for glioblastoma (GBM) resection margins. FLIm data were collected from 192 tissue margins across 31 newly diagnosed IDH-wildtype GBM patients and initially labeled into seven tumor cellularity classes by an expert neuropathologist. CL was applied to quantify FLIm point-level confidence, identify label inconsistencies, and guide iterative class merging into a three-class scheme ("low", "moderate", "high"). The resulting high-fidelity dataset enabled training a model that achieved 96% accuracy in the three-class task. SHAP analysis revealed class-specific FLIm feature importance, highlighting distinct optical signatures across the infiltration spectrum. Targeted FLIm analysis further identified biological (e.g., gray matter composition) and acquisition-related (e.g., blood contamination) contributors to low-confidence predictions. Blinded re-evaluation of margins flagged by CL demonstrated intra-pathologist variability, underscoring the value of selective relabeling rather than exhaustive review. Together, these findings demonstrate that a DC-AI framework can systematically improve data reliability, enhance model robustness, and refine biological interpretation of FLIm signals, supporting the development of clinically actionable optical tools for real-time glioma margin assessment.

Silvia Noble Anbunesan, Mohamed Abul Hassan, Jinyi Qi +4

University of California, Davis · Department of Biomedical Engineering · Department of Pathology and Laboratory Medicine +1

Medical Image Analysis Medical Image Classification Brain Tumor Classification Microscopy Image Analysis

Apr 27, 2026cs.LG

Contrastive Image-Metadata Pre-Training for Materials Transmission Electron Microscopy

The transmission electron microscope facilitates the highest-resolution imaging of any instrument ever created, and its limiting factor is no longer spatial resolution but dose efficiency. Low electron doses avoid sample damage but produce noisy images for which, unlike in classical computer vision, there is no ground truth. Autonomous materials experimentation poses a related problem, since closed-loop instruments need representations grounded in the microscope state at acquisition. Both demand representations grounded in how an image was acquired. We release 7,330 paired high-angle annular dark-field scanning-TEM (HAADF-STEM) images and their seven-dimensional acquisition metadata, and propose Contrastive Image-Metadata Pre-training (CIMP), a CLIP-style encoder that aligns the two modalities and reaches 84.4% Top-1 cross-modal retrieval on a held-out split. All seven parameters are individually recoverable from the frozen visual embedding through a linear probe, and we use the embedding to condition a metadata-conditioned style-transfer model that re-renders experimental images under different acquisition parameters. Virtually scaling dwell time and beam current of low-dose images turns this model into a physics-informed denoiser; in a blind user study, experimental microscopists prefer it over the current state-of-the-art denoiser for STEM imagery on 70.2% of trials.

Georgia Channing, Debora Keller, Marta D. Rossell +3

Hugging Face · University of Oxford · Empa Dübendorf +1

Cross-Modal Alignment Multimodal Contrastive Learning Microscopy Image Analysis Image Denoising

Apr 27, 2026cs.CV

Aycromo: An Open-Source Platform for Automatic Chromosome Detection in Metaphase Images Based on Deep Learning

Chromosome analysis is a fundamental step in the diagnosis of genetic diseases, but the manual karyotyping workflow is time-consuming and heavily dependent on expert specialists, often requiring several days per patient. Although Deep Learning models have achieved high performance in chromosome detection, most proposed solutions remain restricted to research prototypes or lack graphical interfaces suitable for clinical use. In this work, we present Aycromo, an open-source desktop platform for AI-assisted cytogenetic analysis. Built on Electron and ONNX Runtime, the tool allows cytogeneticists to load pre-trained models, compare architectures through an integrated benchmarking module, and manually correct detections via an interactive annotation interface, all without command-line interaction. Preliminary experiments on metaphase images from the CRCN-NE dataset demonstrate that YOLOv11 achieves 99.40% mAP@50, while the platform reduces per-slide analysis to seconds

Jorge L. A. Lima, Filipe R. Cordeiro

Visual Computing Lab, Department of Computing, Universidade Federal Rural de Pernambuco (UFRPE), Brazil

Medical Diagnosis Microscopy Image Analysis

Apr 24, 2026eess.IV

Multimodal Diffusion to Mutually Enhance Polarized Light and Low Resolution EBSD Data

In spite of the utility of 3-D electron back-scattered diffraction (EBSD) microscopy, the data collection process can be time-consuming with serial-sectioning. Hence, it is natural to look at other modalities, such as polarized light (PL) data, to accelerate EBSD data collection, supplemented with shared information. Complementarily, features in chaotic PL data could even be enriched with a handful of EBSD measurements. To inherently learn the complex dynamics between EBSD and PL to solve these inverse problems, we use an unconditional multimodal diffusion model, motivated by progress in diffusion models for inverse problems. Although trained solely on synthetic data once, our model has strong generalizable capabilities on real data which can be low-resolution, noisy, corrupted, and misregistered. With inference-time scaling, we show gains in performance on a variety of objectives including grain boundary prediction, super-resolution, and denoising. With our model, we demonstrate that there is little difference from full resolution performance with only 25% (1/4 the resolution) of EBSD data and corrupted PL data.

Harry Dong, Timofey Efimov, Megna Shah +4

Department of Electrical and Computer Engineering, Carnegie Mellon University, USA · Materials and Manufacturing Directorate, Air Force Research Laboratory, USA · Department of Materials Science and Engineering, Carnegie Mellon University, USA +1

Diffusion Models for Image Restoration Materials Science Microscopy Image Analysis Inverse Problems Multimodal Diffusion Models

Apr 22, 2026cs.AI

InVitroVision: a Multi-Modal AI Model for Automated Description of Embryo Development using Natural Language

The application of artificial intelligence (AI) in IVF has shown promise in improving consistency and standardization of decisions, but often relies on annotated data and does not make use of the multimodal nature of IVF data. We investigated whether foundational vision-language models can be fine-tuned to predict natural language descriptions of embryo morphology and development. Using a publicly available embryo time-lapse dataset, we fine-tuned PaliGemma-2, a multi-modal vision-language model, with only 1,000 images and corresponding captions, describing embryo morphology, embryonic cell cycle and developmental stage. Our results show that the fine-tuned model, InVitroVision, outperformed a commercial model, ChatGPT 5.2, and base models in overall metrics, with performance improving with larger training datasets. This study demonstrates the potential of foundational vision-language models to generalize to IVF tasks with limited data, enabling the prediction of natural language descriptions of embryo morphology and development. This approach may facilitate the use of large language models to retrieve information and scientific evidence from relevant publications and guidelines, and has implications for few-shot adaptation to multiple downstream tasks in IVF.

Nicklas Neu, Thomas Ebner, Jasmin Primus +4

Software Competence Center Hagenberg GmbH,Softwarepark 32a,Hagenberg, 4232, Upper Austria, Austria · Kinderwunsch Zentrum Kepler Universitätsklinikum,Krankenhausstraße 26, Linz, 4021 Upper Austria, Austria · Wunschkind Klinik Dr. Brunbauer, Ebendorferstraße 6/4 Vienna, 1010, Vienna, Austria

VLM Adaptation Medical VLMs Microscopy Image Analysis

Apr 21, 2026cs.CV

Learning to count small and clustered objects with application to bacterial colonies

Automated bacterial colony counting from images is an important technique to obtain data required for the development of vaccines and antibiotics. However, bacterial colonies present unique machine vision challenges that affect counting, including (1) small physical size, (2) object clustering, (3) high data annotation cost, and (4) limited cross-species generalisation. While FamNet is an established object counting technique effective for clustered objects and costly data annotation, its effectiveness for small colony sizes and cross-species generalisation remains unknown. To address the first three challenges, we propose ACFamNet, an extension of FamNet that handles small and clustered objects using a novel region of interest pooling with alignment and optimised feature engineering. To address all four challenges above, we introduce ACFamNet Pro, which augments ACFamNet with multi-head attention and residual connections, enabling dynamic weighting of objects and improved gradient flow. Experiments show that ACFamNet Pro achieves a mean normalised absolute error (MNAE) of 9.64% under 5-fold cross-validation, outperforming ACFamNet and FamNet by 2.23% and 12.71%, respectively.

Minghua Zheng, Na Helian, Peter C. R. Lane +2

King’s College London, St Thomas Street, London, SE1 1UL, United Kingdom · University of Hertfordshire, College Lane, Hatfield, AL10 9AB, United Kingdom · Synoptics Ltd, Beacon House, Nuffield Road, Cambridge, CB4 1TF, United Kingdom

Object Counting Cross-Domain Generalization Microscopy Image Analysis

Apr 21, 2026cs.CV

Investigation of cardinality classification for bacterial colony counting using explainable artificial intelligence

Automatic bacterial colony counting is a highly sought-after technology in modern biological laboratories because it eliminates manual counting effort. Previous work has observed that MicrobiaNet, currently the best-performing cardinality classification model for colony counting, has difficulty distinguishing colonies of three or more individuals. However, it is unclear if this is due to properties of the data together with inherent characteristics of the MicrobiaNet model. By analysing MicrobiaNet with explainable artificial intelligence (XAI), we demonstrate that XAI can provide insights into how data properties constrain cardinality classification performance in colony counting. Our results show that high visual similarity across classes is the key issue hindering further performance improvement, revising prior assertions about MicrobiaNet. These findings suggest future work should focus on models that explicitly incorporate visual similarity or explore density estimation approaches, with broader implications for neural network classifiers trained on imbalanced datasets.

Minghua Zheng, Na Helian, Peter C. R. Lane +2

King’s College London, St Thomas Street, London, SE1 1UL, United Kingdom · University of Hertfordshire, College Lane, Hatfield, AL10 9AB, United Kingdom · Synoptics Ltd, Beacon House, Nuffield Road, Cambridge, CB4 1TF, United Kingdom

Object Counting Classification Microscopy Image Analysis

Apr 21, 2026cs.CV

Bridging Foundation Models and ASTM Metallurgical Standards for Automated Grain Size Estimation from Microscopy Images

Extracting standardized metallurgical metrics from microscopy images remains challenging due to complex grain morphology and the data demands of supervised segmentation. To bridge foundational computer vision with practical metallurgical evaluation, we propose an automated pipeline for dense instance segmentation and grain size estimation that adapts Cellpose-SAM to microstructures and integrates its topology-aware gradient tracking with an ASTM E112 Jeffries planimetric module. We systematically benchmark this pipeline against a classical convolutional network (U-Net), an adaptive-prompting vision foundation model (MatSAM) and a contemporary vision-language model (Qwen2.5-VL-7B). Our evaluations reveal that while the out-of-the-box vision-language model struggles with the localized spatial reasoning required for dense microscopic counting and MatSAM suffers from over-segmentation despite its domain-specific prompt generation, our adapted pipeline successfully maintains topological separation. Furthermore, experiments across progressively reduced training splits demonstrate exceptional few-shot scalability; utilizing only two training samples, the proposed system predicts the ASTM grain size number (G) with a mean absolute percentage error (MAPE) as low as 1.50%, while robustness testing across varying target grain counts empirically validates the ASTM 50-grain sampling minimum. These results highlight the efficacy of application-level foundation model integration for highly accurate, automated materials characterization. Our project repository is available at https://github.com/mueez-overflow/ASTM-Grain-Size-Estimator.

Abdul Mueez, Shruti Vyas

University of Central Florida

Vision Foundation Models Instance Segmentation Industrial Inspection Microscopy Image Analysis

Apr 20, 2026cs.CV

Rabies diagnosis in low-data settings: A comparative study on the impact of data augmentation and transfer learning

Rabies remains a major public health concern across many African and Asian countries, where accurate diagnosis is critical for effective epidemiological surveillance. The gold standard diagnostic methods rely heavily on fluorescence microscopy, necessitating skilled laboratory personnel for the accurate interpretation of results. Such expertise is often scarce, particularly in regions with low annual sample volumes. This paper presents an automated, AI-driven diagnostic system designed to address these challenges. We developed a robust pipeline utilizing fluorescent image analysis through transfer learning with four deep learning architectures: EfficientNetB0, EfficientNetB2, VGG16, and Vision Transformer (ViTB16). Three distinct data augmentation strategies were evaluated to enhance model generalization on a dataset of 155 microscopic images (123 positive and 32 negative). Our results demonstrate that TrivialAugmentWide was the most effective augmentation technique, as it preserved critical fluorescent patterns while improving model robustness. The EfficientNetB0 model, utilizing Geometric & Color augmentation and selected through stratified 3fold cross-validation, achieved optimal classification performance on cropped images. Despite constraints posed by class imbalance and a limited dataset size, this work confirms the viability of deep learning for automating rabies diagnosis. The proposed method enables fast and reliable detection with significant potential for further optimization. An online tool was deployed to facilitate practical access, establishing a framework for future medical imaging applications. This research underscores the potential of optimized deep learning models to transform rabies diagnostics and improve public health outcomes.

Khalil Akremi, Mariem Handous, Zied Bouslama +4

University of Carthage, Engineering School of Statistics and Information Analysis, Tunis, Tunisia. · University of Tunis-El-Manar, Rabies Laboratory, Institut Pasteur de Tunis, Tunis, Tunisia. · World Health Organization, Country Oﬀice Tunisia. +1

Data Augmentation Medical Diagnosis Medical Image Classification Transfer Learning Microscopy Image Analysis

Apr 20, 2026cs.CV

PlankFormer: Robust Plankton Instance Segmentation via MAE-Pretrained Vision Transformers and Pseudo Community Image Generation

Plankton monitoring is essential for assessing aquatic ecosystems but is limited by the labor-intensive nature of manual microscopic analysis. Automating the segmentation of plankton from crowded images is crucial, however, it faces two major challenges: (i) the scarcity of pixel-level annotated datasets and (ii) the difficulty of distinguishing plankton from debris and overlapping individuals using conventional CNN-based methods. To address these issues, we propose PlankFormer, a novel framework for plankton instance segmentation. First, to overcome the data shortage, we introduce a method to generate labeled Pseudo Community Images (PCI) by synthesizing individual plankton images onto diverse backgrounds, including those created by generative models. Second, we propose a segmentation model utilizing a Vision Transformer (ViT) backbone with a Mask2Former decoder. To robustly capture the global structural features of plankton against occlusion and debris, we employ a Masked Autoencoder (MAE) for self-supervised pre-training on unlabeled individual images. Experimental results on real-world datasets demonstrate that our method significantly outperforms conventional methods, such as Mask R-CNN, particularly in challenging environments with high debris density. We demonstrate that our synthetic training strategy and MAE-based architecture enable high-precision segmentation with requiring less manual annotations for individual plankton images.

Masaharu Miyazaki, Yurie Otake, Koichi Ito +3

Graduate School of Information Sciences, Tohoku University 6-6-05, Aramaki Aza Aoba, Sendai, 9808579, Japan. · The Center for Ecological Research, Kyoto University, 2–509–3, Hirano, Otsu-shi, Shiga-ken, 5202113, Japan. · Graduate School of Life Sciences, Tohoku University, 6–3, Aramaki Aza Aoba, Aoba-ku, Sendai-shi, 9808578, Japan.

Instance Segmentation Synthetic Data Generation Microscopy Image Analysis

Apr 18, 2026cs.LG

Applications of deep generative models to DNA reaction kinetics and to cryogenic electron microscopy

This dissertation explores how deep generative models can advance the analysis of challenging biological problems by integrating domain knowledge with deep learning. It focuses on two areas: DNA reaction kinetics and cryogenic electron microscopy (cryo-EM). In the first part, we present ViDa, a biophysics-informed framework leveraging variational autoencoders (VAEs) and geometric scattering transforms to generate biophysically-plausible embeddings of DNA reaction kinetics simulations. These embeddings are reduced to a two-dimensional space to visualize DNA hybridization and toehold-mediated strand displacement reactions. ViDa preserves structure and clusters trajectory ensembles into reaction pathways, making simulation results more interpretable and revealing new mechanistic insights. In the second part, we address key challenges in cryo-EM density map interpretation and protein structure modeling. We provide a comprehensive review and benchmarking of deep learning methods for atomic model building, with improved evaluation metrics and practical guidance. We then present Struc2mapGAN, a generative adversarial network that synthesizes high-fidelity experimental-like cryo-EM density maps from protein structures. Finally, we present CryoSAMU, a structure-aware multimodal U-Net that enhances intermediate-resolution cryo-EM maps by integrating density features with structural embeddings from protein language models via cross-attention. Overall, these contributions demonstrate the potential of deep generative models to interpret DNA reaction mechanisms and advance cryo-EM density map analysis and protein structure modeling.

Chenwei Zhang

THE UNIVERSITY OF BRITISH COLUMBIA (Vancouver)

Image Reconstruction Cryo-Electron Microscopy Generative Adversarial Networks Microscopy Image Analysis

Apr 17, 2026cs.CV

Automated Palynological Analysis System: Integrating Deep Metric Learning, Detection and Classification in Bright Field Microscopy

Traditional melissopalynology is a time-consuming and subjective process, often taking 4-6 hours per sample. We present an automated, high-throughput microscopy system that integrates H_\infty robust mechanical control with advanced deep learning pipelines for the precise counting, classification, and morphological analysis of pollen grains from Bio Bio region in south central territory in Chile. Our system employs U^2-Net for salient object detection and a DINOv2 Vision Transformer backbone trained via Deep Metric Learning for classification. By integrating Gradient-Weighted Attention, the model provides human-interpretable texture and diagnostic feature annotations. The system achieves a 95.8% classification recall and at least 6x processing speedup compared to manual expert analysis.

J. Staforelli-Vivanco, R. Jofré, P. Coelho +12

Facultad de Ingeniería, Universidad Andres Bello, Talcahuano, CCP-THNO 7100 Chile · Universidad Arturo Prat, Sede Victoria, Chile · Laboratory of Palynology and Plant Ecology, School of Sciences and Technologies, University of Concepción, Los Angeles Campus

Salient Object Detection Explainable Image Classification Microscopy Image Analysis Image Classification

Apr 16, 2026cs.CV

From Boundaries to Semantics: Prompt-Guided Multi-Task Learning for Petrographic Thin-section Segmentation

Grain-edge segmentation (GES) and lithology semantic segmentation (LSS) are two pivotal tasks for quantifying rock fabric and composition. However, these two tasks are often treated separately, and the segmentation quality is implausible albeit expensive, time-consuming, and expert-annotated datasets have been used. Recently, foundation models, especially the Segment Anything Model (SAM), have demonstrated impressive robustness for boundary alignment. However, directly adapting SAM to joint GES and LSS is nontrivial due to 1) severe domain gap induced by extinction-dependent color variations and ultra-fine grain boundaries, and 2) lacking novel modules for joint learning on multi-angle petrographic image stacks. In this paper, we propose Petro-SAM, a novel two-stage, multi-task framework that can achieve high-quality joint GES and LSS on petrographic images. Specifically, based on SAM, we introduce a Merge Block to integrate seven polarized views, effectively solving the extinction issue. Moreover, we introduce multi-scale feature fusion and color-entropy priors to refine the detection.

Yili Ren, Shiqi Wen, Li Hou +8

Research Institute of Petroleum Exploration and Development (RIPED) · The Hong Kong University of Science and Technology (Guangzhou) · The Hong Kong University of Science and Technology +1

Image Segmentation Promptable Image Segmentation Multi-Task Learning Semantic Segmentation Microscopy Image Analysis

Apr 13, 2026cs.CV

Using Deep Learning Models Pretrained by Self-Supervised Learning for Protein Localization

Background: Task-specific microscopy datasets are often small, making it difficult to train deep learning models that learn robust features. While self-supervised learning (SSL) has shown promise through pretraining on large, domain-specific datasets, generalizability across datasets with differing staining protocols and channel configurations remains underexplored. We investigated the generalizability of SSL models pretrained on ImageNet-1k and HPA FOV, evaluating their embeddings on OpenCell with and without fine-tuning, two channel-mismatch strategies, and varying fine-tuning data fractions. We additionally analyzed single-cell embeddings on a labeled OpenCell subset. Result: DINO-based ViT backbones pretrained on HPA FOV or ImageNet-1k transfer well to OpenCell even without fine-tuning. Fine-tuning further improved performance to 0.704

\pm

0.027 (17 classes, multi-class labels). At the single-cell level, the HPA single-cell-pretrained model achieved the highest k-nearest neighbor performance across all neighborhood sizes (macro

F_1

\geq

0.515). Conclusion: SSL methods like DINO, pretrained on large domain-relevant datasets, enable effective use of deep learning features for fine-tuning on small, task-specific microscopy datasets.

Ben Isselmann, Dilara Göksu, Heinz Neumann +1

Department of Mathematics and Natural Sciences, Hochschule Darmstadt, Schoeﬀerstraße 3, Darmstadt, 64295, Hessen, Germany. · Department of Chemical Engineering and Biotechnology, Hochschule Darmstadt, Stephanstrasse 7, Darmstadt, 64295, Hessen, Germany. · European University of Technology, European Union. +1

Supervised Fine-Tuning Self-Supervised Pre-Training Self-Supervised Visual Representation Learning Microscopy Image Analysis

Mar 20, 2026cs.CV

Evaluating Vision Foundation Models for Pixel and Object Classification in Microscopy

Deep learning underlies most modern approaches and tools in computer vision, including biomedical imaging. However, for interactive semantic segmentation (often called pixel classification in this context) and interactive object-level classification (object classification), feature-based shallow learning remains widely used. This is due to the diversity of data in this domain, the lack of large pretraining datasets, and the need for computational and label efficiency. In contrast, state-of-the-art tools for many other vision tasks in microscopy - most notably cellular instance segmentation - already rely on deep learning and have recently benefited substantially from vision foundation models (VFMs), particularly SAM. Here, we investigate whether VFMs can also improve pixel and object classification compared to current approaches. To this end, we evaluate several VFMs, including general-purpose models (SAM, SAM2, SAM3, DINOv3) and domain-specific ones (

μ

SAM, PathoSAM, KRONOS), in combination with shallow learning and attentive probing on five diverse and challenging datasets. Our results demonstrate consistent improvements over hand-crafted features and provide a clear pathway toward practical improvements. Furthermore, our study establishes a benchmark for VFMs in microscopy and informs future developments in this area.

Carolin Teuber, Anwai Archit, Tobias Boothe +3

Georg-August-University Göttingen, Institute of Computer Science · Department of Tissue Dynamics and Regeneration, Max Planck Institute for Multidisciplinary Sciences, Göttingen · Georg-August-University Göttingen, Faculty of Biology and Psychology +3

Vision Foundation Models Semantic Segmentation Microscopy Image Analysis