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

    Apr 17, 2026J. Staforelli-Vivanco, R. Jofré, P. Coelho +12Salient Object DetectionExplainable Image Classification

    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

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

    Apr 16, 2026Yili Ren, Shiqi Wen, Li Hou +8Image SegmentationPromptable Image Segmentation

    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

  3. Multitasking Embedding for Embryo Blastocyst Grading Prediction (MEmEBG)

    Apr 14, 2026Nahid Khoshk Angabini, Mohsen Tajgardan, Mahesh Madhavan +3Automated GradingMicroscopy Image Analysis

    ⋆Department of Computer Science and Media Technology, Malmö University, Malmö, Sweden · ◦Faculty of Electrical and Computer Engineering, Qom University of Technology, Iran · †Kepler Universitätsklinikum, Linz, Austria

  4. Predicting Blastocyst Formation in IVF: Integrating DINOv2 and Attention-Based LSTM on Time-Lapse Embryo Images

    Apr 14, 2026Zahra Asghari Varzaneh, Niclas Wölner-Hanssen, Reza Khoshkangini +2Microscopy Image AnalysisRecurrent Neural Networks

    Sustainable Digitalisation Research Center, Department of Computer Science and Media Technology, Malmö University, Malmö, Sweden · School of Information Technology, Halmstad University, Halmstad, Sweden · Kepler Universitätsklinikum, Linz, Austria +1

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

    Apr 13, 2026Ben Isselmann, Dilara Göksu, Heinz Neumann +1Supervised Fine-TuningSelf-Supervised Pre-Training

    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

  6. Self-supervised Pretraining of Cell Segmentation Models

    Apr 12, 2026Kaden Stillwagon, Alexandra Dunnum VandeLoo, Benjamin Magondu +1Instance SegmentationMicroscopy Image Analysis

    School of Computer Science, Georgia Institute of Technology · School of Materials Science and Engineering, Georgia Institute of Technology · Department of Biomedical Engineering, Georgia Institute of Technology +1

  7. SIMPLER: H&E-Informed Representation Learning for Structured Illumination Microscopy

    Apr 11, 2026Abu Zahid Bin Aziz, Syed Fahim Ahmed, Gnanesh Rasineni +8Medical Image Representation LearningMicroscopy Image Analysis

    Kahlert School of Computing, University of Utah, Salt Lake City, UT 84112, USA · Scientific Computing & Imaging Institute, University of Utah, Salt Lake City, UT 84112, USA · Instapath Inc., Houston, TX 77021 +1

  8. Cluster-First Labelling: An Automated Pipeline for Segmentation and Morphological Clustering in Histology Whole Slide Images

    Apr 10, 2026Muhammad Haseeb Ahmad, Sharmila Rajendran, Damion Young +1Whole-Slide Image AnalysisMicroscopy Image Analysis

    Department of Engineering Science, University of Oxford, United Kingdom · Department of Physiology, Anatomy and Genetics, University of Oxford, United Kingdom · Medical Sciences Division, University of Oxford, United Kingdom

  9. Sampling-Aware 3D Spatial Analysis in Multiplexed Imaging

    Apr 9, 2026Ido Harlev, Tamar Oukhanov, Raz Ben-Uri +2Microscopy Image Analysis3D Reconstruction

    Weizmann Institute of Science, Israel

  10. A Mixture of Experts Foundation Model for Scanning Electron Microscopy Image Analysis

    Apr 7, 2026Sk Miraj Ahmed, Yuewei Lin, Chuntian Cao +9Microscopy Image AnalysisElectron Microscopy

    Computing and Data Sciences, Brookhaven National Laboratory, Upton, 11973, New York, USA. · Center for Functional Nanomaterials, Brookhaven National Laboratory, Upton, 11973, New York, USA. · Department of Material Sciences and Engineering, The University of Texas at Dallas, Richardson, 75080, Texas, USA.

  11. 3D Gaussian Splatting for Annular Dark Field Scanning Transmission Electron Microscopy Tomography Reconstruction

    Apr 6, 2026Beiyuan Zhang, Hesong Li, Ruiwen Shao +1Scanning Transmission Electron MicroscopyComputed Tomography

    Beijing Institute of Technology

  12. SAGE-GAN: Towards Realistic and Robust Segmentation of Spatially Ordered Nanoparticles via Attention-Guided GANs

    Apr 4, 2026Anindya Pal, Varun Ajith, Saumik Bhattacharya +1Electron MicroscopyImage Segmentation

    National Institute of Technology Durgapur, Department of Physics · Indian Institute of Technology Kharagpur

  13. AI-assisted Human-in-the-Loop Web Platform for Structural Characterization in Hard drive design

    Apr 1, 2026Utkarsh Pratiush, Huaixun Huyan, Maryam Zahiri Azar +4Microscopy Image AnalysisScientific Workflow Automation

    Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA · Western Digital corporation, 5601 Great Oaks Parkway, San Jose, CA 95119, USA

  14. Toward Generalizable Whole Brain Representations with High-Resolution Light-Sheet Data

    Mar 31, 2026Minyoung E. Kim, Dae Hee Yun, Aditi V. Patel +4Microscopy Image AnalysisObject Detection

    LifeCanvas Technologies

  15. Elucidating the Design Space of Flow Matching for Cellular Microscopy

    Mar 25, 2026Charles Jones, Emmanuel Noutahi, Jason Hartford +1Flow MatchingImage Generation

    Imperial College London · Valence Labs · University of Manchester

  16. λSplit: Self-Supervised Content-Aware Spectral Unmixing for Fluorescence Microscopy

    Mar 24, 2026Federico Carrara, Talley Lambert, Mehdi Seifi +1Spectral UnmixingMicroscopy Image Analysis

    Fondazione Human Technopole, Milan, Italy · Università Campus Bio-Medico, Rome, Italy · Harvard Medical School, Boston, MA, USA

  17. Boundary-Aware Instance Segmentation in Microscopy Imaging

    Mar 22, 2026Thomas Mendelson, Joshua Francois, Galit Lahav +1Instance SegmentationBoundary-Aware Segmentation

    The School of Electrical and Computer Engineering, Ben-Gurion University of the Negev · Department of Systems Biology, Harvard Medical School

  18. Evaluating Vision Foundation Models for Pixel and Object Classification in Microscopy

    Mar 20, 2026Carolin Teuber, Anwai Archit, Tobias Boothe +3Vision Foundation ModelsSemantic Segmentation

    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

  19. Ca2+ transient detection and segmentation with the Astronomically motivated algorithm for Background Estimation And Transient Segmentation (Astro-BEATS)

    Mar 19, 2026Bolin Fan, Anthony Bilodeau, Frederic Beaupre +4Microscopy Image AnalysisImage Segmentation

    Dunlap Institute for Astronomy and Astrophysics, University of Toronto, Toronto, Canada · David A. Dunlap Department for Astronomy and Astrophysics, University of Toronto, Toronto, Canada · CERVO Brain Research Center, Québec, Canada +4

  20. Statistical Characteristic-Guided Denoising for Rapid High-Resolution Transmission Electron Microscopy Imaging

    Mar 19, 2026Hesong Li, Ziqi Wu, Ruiwen Shao +1Scanning Transmission Electron MicroscopyImage Denoising

    Beijing Institute of Technology

  21. Revisiting foundation models for cell instance segmentation

    Mar 18, 2026Anwai Archit, Constantin PapeInstance SegmentationMicroscopy Image Analysis

    Georg-August-University Göttingen, Institute of Computer Science · CAIMed - Lower Saxony Center for AI & Causal Methods in Medicine, Göttingen · Cluster of Excellence Multiscale Bioimaging (MBExC), Georg-August-University Göttingen

  22. Novelty-Driven Target-Space Discovery in Automated Electron and Scanning Probe Microscopy

    Mar 17, 2026Utkarsh Pratiush, Kamyar Barakati, Boris N. Slautin +4Deep Kernel LearningScanning Transmission Electron Microscopy

    Department of Materials Science and Engineering, University of Tennessee, Knoxville, TN 37996, USA · Department of Chemistry, University of Washington, Seattle, WA 98195, USA · Pacific Northwest National Laboratory, Richland, WA 99354, USA

  23. Understanding Cell Fate Decisions with Temporal Attention

    Mar 17, 2026Florian Bürger, Martim Dias Gomes, Adrián E. Granada +2Microscopy Image AnalysisInterpretable ML

    Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany · Faculty of Mathematics and Natural Sciences, University of Cologne, Cologne, Germany · Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany +2

  24. Bridging the Simulation-to-Reality Gap in Electron Microscope Calibration via VAE-EM Estimation

    Mar 17, 2026Jilles S. van Hulst, W. P. M. H. Heemels, Duarte J. AntunesElectron MicroscopyScanning Transmission Electron Microscopy

    The authors are with the Control Systems Technology Section, Department of Mechanical Engineering, Eindhoven University of Technology, 5600 MB Eindhoven, The Netherlands.

  25. Self-Supervised ImageNet Representations for In Vivo Confocal Microscopy: Tortuosity Grading without Segmentation Maps

    Mar 16, 2026Kim Ouan, Noémie Moreau, Katarzyna BozekMedical Image ClassificationMicroscopy Image Analysis

    Faculty of Mathematics and Natural Sciences, University of Cologne, Germany · Institute for Biomedical Informatics, Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany · Center for Molecular Medicine Cologne (CMMC), Faculty of Medicine and University Hospital Cologne, University of Cologne, Germany +1

  26. A protocol for evaluating robustness to H&E staining variation in computational pathology models

    Mar 13, 2026Lydia A. Schönpflug, Nikki van den Berg, Sonali Andani +5Computational PathologyMicroscopy Image Analysis

  27. Nyxus: A Next Generation Image Feature Extraction Library for the Big Data and AI Era

    Mar 12, 2026Nicholas Schaub, Andriy Kharchenko, Hamdah Abbasi +3Medical Image AnalysisMicroscopy Image Analysis

    DSBU, Axle Research, 6116 Executive Blvd Suite 400, Rockville, 20852, MD, USA. · NGRF, NovaGen Research Fund, 6116 Executive Blvd Suite 400, Rockville, 20852, MD, USA. · NCATS, 9800 Medical Center Dr, Rockville, 20850, MD, USA.

  28. Leveraging Phytolith Research using Artificial Intelligence

    Mar 12, 2026Andrés G. Mejía Ramón, Kate Dudgeon, Nina Witteveen +6Microscopy Image Analysis

    Institut de Ciència i Tecnologia Ambientals, Universitat Autònoma de Barcelona Carrer de les Columnes s/n, Cerdanyola del Vallès, Barcelona, 08193, Espanya · Department of Anthropology, Smithsonian National Museum of Natural History, 1000 Madison Drive NW, Washington, D.C., 20560, United States · Smithsonian Tropical Research Institute, Luis Clement Avenue, Bldg. 401 Tupper, Ancón, Ciudad de Panamá, República de Panamá +5

  29. Single molecule localization microscopy challenge: a biologically inspired benchmark for long-sequence modeling

    Mar 11, 2026Fatemeh Valeh, Monika Farsang, Radu Grosu +1Sequence ModelingState Space Models

    Department of Biophysics, Technische Universität Wien, Vienna, Austria · Department of Informatics, Technische Universität Wien, Vienna, Austria

  30. Combining Microscopy Data and Metadata for Reconstruction of Cellular Traction Forces Using a Hybrid Vision Transformer-U-Net

    Mar 11, 2026Yunfei Huang, Elena Van der Vorst, Alexander Richard +1Microscopy Image AnalysisU-Net

    Fakultät Physik, Technische Universität Dortmund, Dortmund, 44227, Germany. · Faculty of Physics and Center for NanoScience, Ludwig-Maximilians-Universität München, Munich, 80752, Germany. · Department of Veterinary Sciences, Ludwig-Maximilians-Universität München, Munich, 80752, Germany.