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@DeepMicroscopy DeepMicroscopy - Generating Deep Insights from Deep Learning in Microscopy

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    60 repositories

    • Exact

      Public
      An open source online platform for collaborative image labeling of almost everything
      version-controlannotationscollaboration
      version-controlannotationscollaborationwhole-slide-imagingalgorithm-aided
      JavaScript
      •
      MIT License
      •20•65•17•0•Updated Oct 27, 2026Oct 27, 2026

    • SWAN

      Public
      Python
      •0•2•12•1•Updated Oct 26, 2026Oct 26, 2026

    • EXACT-Sync

      Public
      Rest API sync with the EXACT Server https://github.com/ChristianMarzahl/Exact
      Python
      •
      MIT License
      •3•1•0•0•Updated Oct 19, 2026Oct 19, 2026

    • FreeLeaf

      Public
      An free and open latex collaborative suite
      TypeScript
      •
      GNU Affero General Public License v3.0
      •0•7•0•0•Updated Oct 19, 2026Oct 19, 2026

    • resource-efficient-MFdet

      Public
      Python
      •1•0•0•0•Updated Sep 14, 2026Sep 14, 2026

    • FM4MFdet

      Public
      Foundation Models for Mitotic Figure Detection
      Python
      •0•0•0•0•Updated Aug 17, 2026Aug 17, 2026

    • MitoSim

      Public
      3D Simulation of Mitotic Figures and their appearance in H&E
      HTML
      •0•0•0•0•Updated Jul 24, 2026Jul 24, 2026

    • DICOM_Anonymizer

      Public
      Python
      •1•1•0•0•Updated Jul 20, 2026Jul 20, 2026

    • RetroScope

      Public
      An Open Framework for Motorizing and Digitizing Vintage Microscopes
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 7, 2026Jul 7, 2026

    • MIDOG2025

      Public
      Analysis of the results of the MIDOG 2025 challenge
      HTML
      •0•0•0•0•Updated Jun 19, 2026Jun 19, 2026

    • MIDOGpp

      Public
      A large, multi-domain mitotic Figure Dataset
      Python
      •
      MIT License
      •17•29•2•0•Updated Apr 24, 2026Apr 24, 2026

    • vetpathreview

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Mar 30, 2026Mar 30, 2026

    • AgenticPathologyReports

      Public
      Repository for the paper "Errare algorithmicum est - Exploring General-Purpose Autonomous Multimodal Agents for Pathology Report Generation"
      HTML
      •1•1•0•0•Updated Mar 5, 2026Mar 5, 2026

    • MIDOG25_T1_evaluation_docker

      Public
      Repository for the evaluation script of submissions on MIDOG'25 on grand-challenge.
      Python
      •0•0•0•0•Updated Dec 30, 2025Dec 30, 2025

    • AMi-Br_Benchmark

      Public
      Code for the paper 'Benchmarking Deep Learning and Vision Foundation Models for Atypical vs. Normal Mitosis Classification with Cross-Dataset Evaluation'
      Jupyter Notebook
      •
      MIT License
      •2•2•1•0•Updated Dec 12, 2025Dec 12, 2025

    • FoundationModelComparison

      Public
      Code for our arxiv preprint: https://arxiv.org/abs/2508.04441
      Python
      •1•0•0•0•Updated Dec 12, 2025Dec 12, 2025

    • DECOMP

      Public
      Python
      •0•0•0•0•Updated Dec 9, 2025Dec 9, 2025

    • MIDOG25_T1_reference_docker

      Public
      Reference algorithm for the MIDOG 2025 challenge, track 1 (Mitosis Detection)
      Python
      •1•0•0•0•Updated Aug 30, 2025Aug 30, 2025

    • Annotation-free-VLM-specialization

      Public
      Python
      •0•2•1•0•Updated Aug 11, 2025Aug 11, 2025

    • MIDOG_reference_docker

      Public
      Reference implementation of domain-adversarial training on a RetinaNet (to use as template in the MIDOG challenge)
      Python
      •9•8•2•0•Updated Jul 30, 2025Jul 30, 2025

    • MIDOG25_T2_reference_docker

      Public
      Reference algorithm for the MIDOG 2025 challenge, track 2 (Atypical Mitosis Classification)
      Python
      •1•0•0•0•Updated Jul 30, 2025Jul 30, 2025

    • SlideRunner

      Public
      SlideRunner is a tool for massive cell annotations in whole slide images
      Python
      •
      GNU General Public License v3.0
      •12•82•4•2•Updated Jul 29, 2025Jul 29, 2025

    • MIDOG_evaluation_docker

      Public
      Evaluation container for the MIDOG 2021 challenge on grand-challenge.org
      Python
      •1•0•0•0•Updated Jul 29, 2025Jul 29, 2025

    • MIDOG25_T2_evaluation_docker

      Public
      Evaluation docker container for MIDOG2025 on grand-challenge.org
      Python
      •0•0•0•0•Updated Jul 28, 2025Jul 28, 2025

    • ChroMa-GI

      Public
      Code for the paper 'Chromosome Mask-Conditioned Generative Inpainting for Improved Atypical vs. Normal Mitosis Classification'
      Jupyter Notebook
      •1•1•0•0•Updated Jun 30, 2025Jun 30, 2025

    • MITOS_WSI_CCMCT

      Public
      Large-Scale Canine Cutaneous Mast Cell Tumor Dataset for Mitotic Figure Assessment on Whole Slide Images
      Jupyter Notebook
      •10•31•1•0•Updated Jun 9, 2025Jun 9, 2025

    • MITOS_WSI_CMC

      Public
      Large-Scale Canine Mammary Carcinoma Dataset for Mitotic Figure Assessment on Whole Slide Images
      Jupyter Notebook
      •10•22•2•0•Updated Jun 9, 2025Jun 9, 2025

    • timm_parameters

      Public
      Comprehensive collection of configuration parameters for all deep learning models available in the timm (PyTorch Image Models) library.
      Jupyter Notebook
      •0•0•0•0•Updated Jun 4, 2025Jun 4, 2025

    • FELIX

      Public
      Felinae Evaluation with Layperson and ML Interaction EXperience Dataset (FELIX)
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•1•0•0•Updated May 19, 2025May 19, 2025

    • EXACT-QueueRunner

      Public
      Repository for EXACT QueueRunner, a service that executes processing for jobs available on EXACT.
      Python
      •
      MIT License
      •2•2•0•0•Updated May 16, 2025May 16, 2025
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