Microscopy Image Analysis

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Overview

Microscopy image analysis turns images from biological and materials microscopes into measurements, such as cell counts, tissue structure, particle properties, and cell motion. Common approaches include classical image processing and deep learning for segmentation, detection, classification, tracking, and 2D or 3D reconstruction; newer work also uses self-supervised and foundation models, physics-informed methods, synthetic data, and expert interaction. These tools can make analysis more scalable and reproducible, but performance often depends on microscope settings, sample type, image quality, and the amount of expert annotation available. A central challenge is establishing reliable generalization and evaluation: strong benchmark scores may not ensure robust measurements on new acquisitions, and visual quality metrics may miss errors that affect downstream scientific conclusions.

Latest papers

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199 papers15 papers in the last four weeks, down 42% on the four weeks before. 0.1% of all new papers.

  1. Neural Blind Deconvolution for Image Scanning Microscopy

    Oct 29, 2026Eliot Guez, Nathan Buskulic, Lisa Cuneo +2Microscopy Image AnalysisImage Super-Resolution

    MaLGa Center, DIBRIS, University of Genoa, Italy · CSLM, Italian Institute of Technology, Italy · MMS, Italian Institute of Technology, Italy

  2. Progressively Refining SAM for Accurate Phytoplankton Segmentation

    Oct 27, 2026Jialin Li, Jinkun Jiang, Yuezun Li +1Instance SegmentationSegment Anything Models

    School of Computer Science and Technology, Ocean University of China, Qingdao, China

  3. CellTrack-Bench: Microscopic Cell Tracking Benchmark for Vision-Language Models

    Oct 22, 2026Ilan Theodoro, Jordão Bragantini, Loïc A. RoyerVLM EvaluationMicroscopy Image Analysis

    Biohub San Francisco, CA

  4. Cross-polarization pairing for label-free few-shot thin-section classification

    Oct 17, 2026Bingchen YanFew-Shot Image ClassificationMicroscopy Image Analysis

    School of Computer Science and Information Security, Guilin University of Electronic Technology, Guilin, 541004, China

  5. MicroCLIP: Connecting Text and Microscopy Images via Contrastive Language--Image Pretraining

    Oct 13, 2026Yanran Ruan, Zhixiang Wei, Shiyao Hong +5Fluorescence MicroscopyMicroscopy Image Analysis

    University of Science and Technology of China

  6. Background2Background: a self-supervised background removal framework for high dimensional microscopy

    Oct 13, 2026Guangrui Ding, Haonan Lin, Rong Tang +8Microscopy Image AnalysisSelf-Supervised Learning

    Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA, 02215 · Photonics Center, Boston University, Boston, MA, USA, 02215 · The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, 30332 +2

  7. Protein Crystallization Segmentation and Classification Using Subordinate Color Channel in Fluorescence Microscopy Images

    Oct 11, 2026Truong X. Tran, Marc L. Pusey, Ramazan S. AygunFluorescence MicroscopyMicroscopy Image Analysis

    Data Media Lab, Computer Science Department, The University of Alabama in Huntsville, USA. · XpressGenes, Inc, Huntsville, Alabama, USA. · Chemistry Departement, The University of Alabama in Huntsville, USA.

  8. Detection of extremely rare dead cells in fluorescence microscopy images

    Oct 9, 2026Prateek Verma, Benjamin Butter, Jian Zhang +1Microscopy Image AnalysisFluorescence Microscopy

    Department of Electrical Engineering and Computer Science University of Arkansas, Fayetteville, Arkansas, USA · Department of Biomedical Engineering University of Arkansas, Fayetteville, Arkansas, USA

  9. Label-free cell counting and viability prediction with brightfield imaging and deep learning

    Oct 7, 2026Amir Reza Vazifeh, Christian Zeigler, Sornanathan Meyyappan +2Microscopy Image Analysis

    Department of Electrical and Computer Engineering, Princeton University, Princeton, NJ 08544, USA · Waters Corporation, Immerse Cambridge, 301 Binney Street, Suite 102, Cambridge, MA 02142, USA · Waters Corporation, 34 Maple St, Milford, MA 01757, USA +1

  10. Representation Bias, Correction Transfer, and Resolution Sensitivity in Three-Dimensional Mitochondrial Morphometry

    Oct 6, 2026Farouk Ganiyu Adewumi, Timothy OladunniMicroscopy Image AnalysisUncertainty Calibration

    Department of Computer Science, Morgan State University, Baltimore, MD 21251 USA

  11. Patch-based Querying Identifies Structures of Interest in Electron Microscopy

    Oct 5, 2026Niels Vyncke, Nicolas Nadisic, Yvan Saeys +1Image RetrievalMicroscopy Image Analysis

    Department of Telecommunications and Information Processing, Sint-Pietersnieuwstraat 41, Ghent, 9000, Belgium · Royal Institute for Cultural Heritage (KIK-IRPA), Jubelpark 1, Brussels, 1000, Belgium · Department of Mathematics, Computer Science and Statistics, Krijgslaan 281, Ghent, 9000, Belgium

  12. Feature identification for parameter extraction and defect detection using machine learning

    Oct 5, 2026Yan Guo, Helda Pahlavani, Artem Khachaturiants +5Semiconductor ManufacturingIndustrial Inspection

    Nearfield Instruments, B.V. (The Netherlands)

  13. COMPASS: Comet Object Measurement Pipeline with Automated Selection and Scoring

    Oct 3, 2026Jack Roberts, Canya Lu, Alexis Michelle Lawson +4Microscopy Image Analysis

    Department of Computer Science, Brown University, Providence, RI, USA · Department of Computer Science, Bryn Mawr College, Bryn Mawr, PA, USA · Department of Biology, University of Maryland, College Park, MD, USA +2

  14. CellSplat4D: PSF-Aware 4D Gaussian Splatting for Sparse Robotic Live-Cell Imaging

    Oct 3, 2026Yingda Tao, Guoyu Lu4D ReconstructionMicroscopy Image Analysis

    Indiana University Bloomington

  15. An Automated and Reproducible Workflow for Crack Identification and Damage Assessment of Fusion Materials

    Oct 2, 2026Rinkle Juneja, Viktor Reshniak, Richard K. Archibald +4Microscopy Image AnalysisMaterials Science

    Oak Ridge National Laboratory, Oak Ridge, TN 37831

  16. A Fully Automatic Pipeline for 3D Dendrite Instance Segmentation in SBF-SEM

    Oct 2, 2026Zewen Zhuo, Ilya Belevich, Eija Jokitalo +23D Instance SegmentationInstance Segmentation

    A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland

  17. MorphoBranch: A Fine-Structure-Preserving Workbench for Morphometric Analysis of Branched Cellular Structures

    Oct 1, 2026Song Zhiying, Ling Hanyi, Wu Junyi +1Image SegmentationMicroscopy Image Analysis

    School of Data Science, Zhejiang University of Finance and Economics, Hangzhou, 310018, China · College of Biomedical Engineering & Instrument Science, Zhejiang University, Hangzhou, 310027, China · School of Information Technology and Artificial Intelligence, Zhejiang University of Finance and Economics, Hangzhou, 310018, China

  18. AxonSynth: Domain-Randomized Synthetic Data for Zero-Shot 3D Axon Segmentation in Light-Sheet Microscopy

    Sep 25, 2026Edward Gaibor, Kyriaki-Margarita Bintsi, Chiara Mauri +9Domain RandomizationSynthetic-to-Real Domain Adaptation

    Department of Computer Science, University of Massachusetts Boston, Boston, MA, USA · Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital and Harvard Medical School, Charlestown, MA, USA · Universidad San Sebastián, Chile +4

  19. Universal Drift Correction for Multidimensional Scanning Microscopy

    Sep 25, 2026Sangjoon Lee, William Millsaps, Dasol Yoon +7Microscopy Image AnalysisDeformable Image Registration

    Department of Materials Science and Engineering, Stanford University, Stanford, CA 94305, USA · Stanford Nano Shared Facilities, Stanford University, Stanford, CA 94305, USA

  20. Leakage-Safe Machine Learning for Hydrogen Embrittlement Detection in 316L Stainless Steel: A Region-Held-Out Evaluation of Texture and Deep Features in SEM Micrographs

    Sep 23, 2026Muhammad Awais, Muhammad Yaseen, Abdul Shakoor +3Materials ScienceMicroscopy Image Analysis

    Dipartimento di Fisica e Astronomia “G. Galilei”, Università di Padova, Italy · Institute of Physics, Bahauddin Zakariya University, Multan, Pakistan

  21. RootQuantV2: Adapting a Vision Foundation Model for Root-Trait Regression from Minirhizotron Imagery

    Sep 22, 2026Kinjalk Parth, Sebastian Varela, Andrew D. B. LeakeyPlant PhenotypingVision Foundation Model Adaptation

    Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA · Center for Advanced Bioenergy and Bioproducts Innovation, Urbana, IL 61801, USA

  22. MiTHras: Task-specific Hierarchical Semi-supervised Contrastive Masked Autoencoder for Mitotic Figure Analysis

    Sep 21, 2026Trinh T. L. Vuong, Simon Graham, Quoc Dang Vu +5Contrastive LearningMasked Autoencoders

    Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, USA · Histofy Ltd, Coventry, United Kingdom · Department of Pathology, University Medical Center Ho Chi Minh City, Ho Chi Minh City, Vietnam +1

  23. Spatial Action Review: A Visual Analytics Dashboard for Auditing Language-to-Action Hand-offs in Electron Microscopy

    Sep 21, 2026Samia Mohinta, Albert CardonaHuman-in-the-Loop EvaluationMultimodal QA

    University of Cambridge, UK · MRC Laboratory of Molecular Biology, UK

  24. SomaNet: Weakly Supervised Learning for Instance Soma Segmentation in 3D Electron Microscopy with Partial Annotations

    Sep 19, 2026Mohammad Khateri, Morteza Ghahremani, Jussi Tohka +1Electron MicroscopyInstance Segmentation

    A. I. Virtanen Institute for Molecular Sciences, Faculty of Health Sciences, University of Eastern Finland, Finland

  25. Reconstructed holograms and explanation-aware evaluation for low-cost computational pollen analysis in veterinary cytology

    Sep 19, 2026Swarn Warshaneyan, Joial Danyal, Blaž Cugmas +4Microscopy Image AnalysisExplainable Image Classification

    Institute of Electronics and Computer Science (EDI), Riga, Latvia · Faculty of Science and Technology, University of Latvia, Riga, Latvia

  26. Learning 3D biophysical cell properties from 2D images and cell-population statistics

    Sep 18, 2026Santiago Hernández-Orozco, Hector ZenilMicroscopy Image Analysis

    Algocyte | Oxford Immune Algorithmics, Oxford University Innovation & London Institute for Healthcare Engineering, UK · Algorithmic Dynamics Lab, Department of Biomedical Computing, School of Biomedical Engineering and Imaging Sciences, King’s Institute for AI, King’s College London, UK

  27. Catena: A Comprehensive Software Suite for Large-Scale Connectomics

    Sep 18, 2026Samia Mohinta, Pedro Gómez-Gálvez, Shi Yan Lee +5Electron MicroscopyMicroscopy Image Analysis

    Dept. of Physiology, Development and Neuroscience, University of Cambridge, UK · MRC Laboratory of Molecular Biology, UK · HHMI Janelia, USA +1

  28. A benchmark dataset and baseline methods for four-dimensional STEM diffraction patterns

    Sep 18, 2026Yuyan Guan, Haoran Zhang, Zian Mao +7Scanning Transmission Electron MicroscopyMicroscopy Image Analysis

    Global Institute of Future Technology, Shanghai Jiao Tong University, Shanghai 200240, China · Global College, Shanghai Jiao Tong University, Shanghai 200240, China · Contemporary Amperex Technology Co., Ltd., Ningde, P.R. China +1

  29. Training Neural Networks to Approach the Optimum Bayes Estimator in Dense Multi-Emitter Localization

    Sep 17, 2026Yi Sun, Mona Sharifi, Muzna YummanMicroscopy Image Analysis

    Electrical Engineering Department Applied and Embodied AI Lab The City College of City University of New York New York, NY 10031, USA

  30. Toward AI-Assisted Poultry Coccidiosis Diagnosis: Evaluating Gemini and BiomedParse on Eimeria Microscopy Images

    Sep 16, 2026Ali Alsalama, Ahmed Kubba, Manar Abu TalibMicroscopy Image AnalysisMultimodal Model Evaluation

    Department of Computer Science, College of Computing and Informatics, University of Sharjah, Sharjah, United Arab Emirates