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

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    54 repositories

    • SWAN

      Public
      Python
      •0•2•11•0•Updated Mar 30, 2026Mar 30, 2026

    • vetpathreview

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

    • Exact

      Public
      An open source online platform for collaborative image labeling of almost everything
      version-controlannotationscollaboration
      version-controlannotationscollaborationwhole-slide-imagingalgorithm-aided
      JavaScript
      •
      MIT License
      •19•62•18•1•Updated Mar 23, 2026Mar 23, 2026

    • MIDOG2025

      Public
      Analysis of the results of the MIDOG 2025 challenge
      HTML
      •0•0•0•0•Updated Mar 22, 2026Mar 22, 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

    • MIDOGpp

      Public
      A large, multi-domain mitotic Figure Dataset
      Python
      •
      MIT License
      •17•21•4•0•Updated Nov 8, 2025Nov 8, 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
      •11•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
      •11•80•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•21•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

    • EXACT-Sync

      Public
      Rest API sync with the EXACT Server https://github.com/ChristianMarzahl/Exact
      Python
      •
      MIT License
      •3•1•0•0•Updated May 30, 2025May 30, 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

    • MIDOG_2025_Guide

      Public
      This repository will guide you through the initial steps to get started with the MIDOG 2025 competition. Here, you’ll find information on accessing the datasets…
      Python
      •3•3•0•0•Updated Apr 17, 2025Apr 17, 2025

    • AMi-Br

      Public
      AMI-Br: A Dataset of Typical and Atypical Mitotic Figures on Human Breast Cancer
      Jupyter Notebook
      •0•11•0•0•Updated Apr 16, 2025Apr 16, 2025

    • HDV

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Apr 16, 2025Apr 16, 2025

    • WsiRegistration

      Public
      Robust quad-tree based registration on whole slide images (Marzahl et al.)
      Python
      •
      MIT License
      •5•0•0•0•Updated Apr 3, 2025Apr 3, 2025

    • CanineCutaneousTumors

      Public
      Jupyter Notebook
      •0•10•0•0•Updated Jan 9, 2025Jan 9, 2025

    • TCGA-BRCA-TumorArea-Coarse

      Public
      Coarse annotations of tumor areas from the TCGA-BRCA dataset
      Python
      •0•1•0•0•Updated Nov 7, 2024Nov 7, 2024
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