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    100 repositories

    • prop-fusion-gene-expression-overlay

      Public
      Proposal to prepare and visualize per-cell gene expression data from Xenium Ranger output overlaid on co-registered H&E whole slide images (WSI) in the FUSION 2…
      proposalfusionxenium
      proposalfusionxenium
      R
      •0•0•0•0•Updated Apr 30, 2026Apr 30, 2026

    • prop-spot-annotation

      Public
      Proposal of how to add grouped cell type annotations to a Seurat RDS file output by the FUSION label transfer step, as a precursor to spot annotation. This is a…
      R
      •0•0•0•0•Updated Apr 23, 2026Apr 23, 2026

    • fusion-packages

      Public
      Python package distributions built from fusion repositories and utility functions
      Jupyter Notebook
      •
      MIT License
      •0•0•2•0•Updated Apr 14, 2026Apr 14, 2026

    • Instance-to-Instance-DSA-Data-Transfer

      Public
      Python
      •0•0•1•1•Updated Apr 6, 2026Apr 6, 2026

    • Spatial-Omics-Plugins

      Public
      Python
      •0•0•0•0•Updated Apr 1, 2026Apr 1, 2026

    • CombinedFeatureExtraction

      Public
      Python
      •0•1•0•0•Updated Mar 31, 2026Mar 31, 2026

    • HistoLens

      Public
      MATLAB
      •
      MIT License
      •2•3•0•0•Updated Mar 25, 2026Mar 25, 2026

    • ComPRePS

      Public
      ComPRePS wiki page
      HTML
      •0•1•0•0•Updated Mar 23, 2026Mar 23, 2026

    • Multi-Compartment-Segmentation

      Public
      fusioncompreps
      fusioncompreps
      Python
      •2•5•0•13•Updated Mar 17, 2026Mar 17, 2026

    • procurement-biopsy-pathomics-ml

      Public
      Code used for training and testing machine learning models with donor clinical and pathomic biopsy features to predict kidney transplant recipient outcomes for …
      R
      •
      MIT License
      •1•0•0•0•Updated Mar 16, 2026Mar 16, 2026

    • kidney_hfm_eval

      Public
      This repository contains code to extract features from 11 different foundation models and do linear, kNN probing on the extracted features
      Python
      •
      MIT License
      •1•2•0•0•Updated Mar 10, 2026Mar 10, 2026

    • temp-visium-analysis

      Public
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Mar 9, 2026Mar 9, 2026

    • svs_scanned_dates_extraction

      Public
      Python
      •0•0•0•0•Updated Mar 6, 2026Mar 6, 2026

    • FUSION1_documentation_assets

      Public
      Holds documentation resources
      assetsishaqfusion1
      assetsishaqfusion1
      HTML
      •0•0•0•0•Updated Feb 26, 2026Feb 26, 2026

    • Athena-HiPerGator-Metadata-CSV

      Public
      Python
      •0•0•0•0•Updated Feb 19, 2026Feb 19, 2026

    • DA-Collagen-Segment

      Public
      Deep Learning for Collagen Segmentation with Domain Adaptation — PyTorch-based framework for training, evaluating, and benchmarking collagen segmentation models…
      Python
      •0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • Tubule_Lumen_Filter_Plugin

      Public
      This plugin filters the lumen based on area threshold by taking input as nuclei and sub compartment segmentation json files and outputs a refined sub compartmen…
      Python
      •0•0•0•0•Updated Jan 30, 2026Jan 30, 2026

    • wsi_annotations_kit

      Public
      utility functions for generation, conversion, and saving annotation files for various whole slide image viewers
      Python
      •
      MIT License
      •3•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • FL_flower_framework

      Public
      Flower: A Friendly Federated AI Framework
      Python
      •
      Apache License 2.0
      •1.2k•0•0•0•Updated Jan 8, 2026Jan 8, 2026

    • Histo-cloud

      Public
      Python
      •
      Apache License 2.0
      •4•21•2•4•Updated Dec 30, 2025Dec 30, 2025

    • IFTA_segmentation

      Public
      GNU General Public License v3.0
      •1•2•1•2•Updated Dec 17, 2025Dec 17, 2025

    • ome-tiff-converter

      Public
      Python
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • Cell-Segmentation

      Public
      Python
      •0•0•0•0•Updated Dec 1, 2025Dec 1, 2025

    • Nuclei_Segmentation

      Public
      Nuclei segmentation code for EEL5934
      Python
      •0•0•0•0•Updated Nov 12, 2025Nov 12, 2025

    • Artery-Feature-Extraction

      Public
      Feature extraction from various parts of arteries including intima, media
      Python
      •0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • FUSION2.0-Documentation

      Public
      0•0•0•0•Updated Oct 31, 2025Oct 31, 2025

    • nexus_annotator

      Public
      A platform for accelerating ground-truth data collection for various disease groups including DN, FSGS and Tx
      Python
      •
      Apache License 2.0
      •5•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • girder_worker

      Public
      Distributed task execution engine with Girder integration, developed by Kitware
      Python
      •
      Apache License 2.0
      •32•0•2•0•Updated Oct 20, 2025Oct 20, 2025

    • KPMP_DN_RO1-Model

      Public
      Patient-level multi-task model for diabetic nephropathy prediction using glomeruli and WSI: KPMP Batch 1 dataset. Implemented by Dhiraj
      Python
      •0•0•0•0•Updated Oct 10, 2025Oct 10, 2025

    • Intimal_Arterial_Fibrosis_Segmentation

      Public
      Python
      •0•0•0•0•Updated Sep 30, 2025Sep 30, 2025
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