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

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    37 repositories

    • Exact

      Public
      An open source online platform for collaborative image labeling of almost everything
      version-controlannotationscollaborationwhole-slide-imagingalgorithm-aided
      JavaScript
      •
      MIT License
      •17•55•11•0•Updated Nov 20, 2024Nov 20, 2024

    • FELIX

      Public
      Felinae Evaluation with Layperson and ML Interaction EXperience Dataset (FELIX)
      Jupyter Notebook
      •
      Creative Commons Attribution Share Alike 4.0 International
      •0•0•0•0•Updated Nov 12, 2024Nov 12, 2024

    • TCGA-BRCA-TumorArea-Coarse

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

    • AMI-Br

      Public
      AMI-Br: A Dataset of Typical and Atypical Mitotic Figures on Human Breast Cancer
      0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

    • TUPAC16_AlternativeLabels

      Public
      Alternative training set for the TUPAC16 auxiliary mitotic figure data set
      Jupyter Notebook
      •4•11•0•0•Updated Oct 22, 2024Oct 22, 2024

    • EXACT-QueueRunner

      Public
      Repository for EXACT QueueRunner, a service that executes processing for jobs available on EXACT.
      Python
      •
      MIT License
      •2•0•0•0•Updated Sep 5, 2024Sep 5, 2024

    • deep-learning-optimizing-linear-regresision-github-starter-course

      Public
      deep-learning-optimizing-linear-regresision-github-starter-course created by GitHub Classroom
      0•0•0•0•Updated Aug 20, 2024Aug 20, 2024

    • Prototype-sampling

      Public
      Python
      •0•0•0•0•Updated Jul 10, 2024Jul 10, 2024

    • QuiltCleaner

      Public
      Automatic cleaning of the QUILT-1M pathology dataset
      Jupyter Notebook
      •
      MIT License
      •0•3•0•0•Updated Jul 5, 2024Jul 5, 2024

    • nnUNet

      Public
      Python
      •
      Apache License 2.0
      •1.8k•2•0•0•Updated Jun 24, 2024Jun 24, 2024

    • CD3-Detection

      Public
      Python
      •0•0•0•0•Updated Jun 5, 2024Jun 5, 2024

    • MIDOGpp

      Public
      A large, multi-domain mitotic Figure Dataset
      Python
      •
      MIT License
      •8•13•1•1•Updated May 22, 2024May 22, 2024

    • Histopathology-Datasets

      Public
      Ressources of histopathology datasets
      46•0•0•0•Updated Apr 29, 2024Apr 29, 2024

    • MITOS_WSI_CCMCT

      Public
      Large-Scale Canine Cutaneous Mast Cell Tumor Dataset for Mitotic Figure Assessment on Whole Slide Images
      Jupyter Notebook
      •10•28•0•0•Updated Apr 29, 2024Apr 29, 2024

    • nnUNet-for-pathology

      Public
      Adapted nnUNet framework with additional features to suit the requirements for pathology applications
      Python
      •
      Apache License 2.0
      •1.8k•0•0•0•Updated Apr 8, 2024Apr 8, 2024

    • AIRoV

      Public
      JavaScript
      •0•0•0•0•Updated Mar 18, 2024Mar 18, 2024

    • EXACT-Sync

      Public
      Rest API sync with the EXACT Server https://github.com/ChristianMarzahl/Exact
      Python
      •
      MIT License
      •3•0•0•0•Updated Feb 13, 2024Feb 13, 2024

    • SlideRunner

      Public
      SlideRunner is a tool for massive cell annotations in whole slide images
      Python
      •
      GNU General Public License v3.0
      •10•75•5•2•Updated Oct 4, 2023Oct 4, 2023

    • MIDOG_evaluation_docker

      Public
      Evaluation container for the MIDOG 2021 challenge on grand-challenge.org
      Python
      •1•0•0•0•Updated Sep 4, 2023Sep 4, 2023

    • MultiScanner_SCC

      Public
      Python
      •0•7•0•0•Updated Aug 22, 2023Aug 22, 2023

    • COSAS

      Public
      Python
      •5•0•0•0•Updated Jul 19, 2023Jul 19, 2023

    • VisualRepresentationSurvey

      Public
      Jupyter Notebook
      •1•0•0•0•Updated Jul 18, 2023Jul 18, 2023

    • AdaptiveRegionSelection

      Public
      Python
      •3•6•1•0•Updated Jul 17, 2023Jul 17, 2023

    • CrossScannerRegistration

      Public
      Python
      •1•2•0•0•Updated Jun 5, 2023Jun 5, 2023

    • Cox_AMIL

      Public
      Code for our BVM workshop submission "Attention-based Multiple Instance Learning for Survival Prediction on Lung Cancer Tissue Microarrays"
      deep-learninglung-cancercomputational-pathologytissue-microarray-analysismultiple-instance-learninghistopathology
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •3•7•1•0•Updated Dec 16, 2022Dec 16, 2022

    • HierarchicalFCOS

      Public
      Automatic Subtyping for Atypical and Typical Mitosis using a Hierarchical Anchor-Free Object Detector
      Jupyter Notebook
      •
      MIT License
      •2•0•0•0•Updated Dec 12, 2022Dec 12, 2022

    • WsiRegistration

      Public
      Robust quad-tree based registration on whole slide images (Marzahl et al.)
      Python
      •
      MIT License
      •5•0•0•0•Updated Sep 19, 2022Sep 19, 2022

    • SlideRunner_dataAccess

      Public
      Data access routines (database and images) for SlideRunner
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Aug 12, 2022Aug 12, 2022

    • MIDOG_LaTeX_template

      Public
      LaTeX Template for short papers for the MIDOG challenge, based upon the HenriquesLab bioRxiv template
      TeX
      •0•0•1•0•Updated Aug 5, 2022Aug 5, 2022

    • 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 25, 2022Jul 25, 2022