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    181 repositories

    • scimap

      Public
      Spatial Single-Cell Analysis Toolkit
      pythonpypispatial-analysis
      pythonpypispatial-analysisimage-analysissingle-cell-analysis
      Python
      •
      MIT License
      •36•110•48•6•Updated Mar 11, 2026Mar 11, 2026

    • minerva-core-ui

      Public
      A microscopy viewer for non-experts
      TypeScript
      •
      MIT License
      •3•1•10•1•Updated Mar 5, 2026Mar 5, 2026

    • minerva-annotation-demo

      Public
      JavaScript
      •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • mcmicro-lsp

      Public
      mcmicro helpers for local use within the LSP (especially O2)
      Shell
      •
      MIT License
      •0•0•0•0•Updated Mar 5, 2026Mar 5, 2026

    • mcmicro

      Public
      Multiple-choice microscopy pipeline
      Nextflow
      •
      MIT License
      •64•149•64•2•Updated Feb 27, 2026Feb 27, 2026

    • vae-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •2•4•0•0•Updated Feb 21, 2026Feb 21, 2026

    • okl-analysis

      Public
      Python
      •0•0•0•0•Updated Feb 20, 2026Feb 20, 2026

    • ashlar

      Public
      ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
      Python
      •
      MIT License
      •53•166•59•12•Updated Feb 19, 2026Feb 19, 2026

    • palom

      Public
      Piecewise alignment for layers of mosaics
      Python
      •
      MIT License
      •10•40•7•1•Updated Feb 18, 2026Feb 18, 2026

    • Christensen-Wala-PI3K-PD1

      Public
      Data repository and links for Christensen, Wala et al. 2026. Nat Comms.
      0•0•0•0•Updated Feb 17, 2026Feb 17, 2026

    • minerva-cloud-ui

      Public
      Minerva Cloud is a novel cloud-based (AWS) software for high-dimensional image management, storage and visualization.
      microscopyomeminerva
      microscopyomeminervaimmunofluorescence
      JavaScript
      •
      MIT License
      •2•2•1•12•Updated Feb 13, 2026Feb 13, 2026

    • cylinter

      Public
      An Interactive Image Segmentation Filter for Multiplex Microscopy
      Python
      •
      MIT License
      •12•31•1•0•Updated Feb 12, 2026Feb 12, 2026

    • cdk7-analysis

      Public
      R
      •0•0•0•0•Updated Feb 12, 2026Feb 12, 2026

    • TB-3D-TLS-2026

      Public
      Multidimensional Spatial Characterization of Tertiary Lymphoid Structures in Human Pulmonary TB Lung Granulomas
      0•0•0•0•Updated Feb 9, 2026Feb 9, 2026

    • cycif.org

      Public
      cycif.org GitHub Pages Website
      JavaScript
      •
      MIT License
      •9•3•6•4•Updated Feb 5, 2026Feb 5, 2026

    • Chen-Santagata-Kidney-2026

      Public
      MATLAB
      •
      MIT License
      •1•0•0•0•Updated Jan 27, 2026Jan 27, 2026

    • orion-fish-ms-2026

      Public
      Kader_Santagata_ORION-FISH 2026
      R
      •1•0•0•0•Updated Jan 25, 2026Jan 25, 2026

    • lsp-idc-minerva

      Public
      IDC DicomWeb Minerva Demo page
      JavaScript
      •0•0•0•0•Updated Jan 22, 2026Jan 22, 2026

    • lsp-idc-minerva-crc02

      Public
      IDC DicomWeb Minerva Demo page - CRC02
      JavaScript
      •0•0•0•0•Updated Jan 20, 2026Jan 20, 2026

    • 2025-Vallius-Shi-Novikov-melanoma-PCAII

      Public
      Custom codes for Vallius, Shi, Novikov et al. manuscript 2025
      Jupyter Notebook
      •1•0•0•0•Updated Jan 18, 2026Jan 18, 2026

    • vae

      Public
      Python
      •
      MIT License
      •2•4•0•0•Updated Jan 11, 2026Jan 11, 2026

    • 2025_Williams_Pant_Melanoma-TRM

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

    • mccellpose

      Public
      Alternative interface to the Cellpose cell segmentation algorithm that uses constant memory
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•2•1•Updated Jan 5, 2026Jan 5, 2026

    • ad-personalized

      Public
      TYK2 mediates neuroinflammation in dementia with Alzheimer’s disease
      R
      •
      MIT License
      •0•0•0•0•Updated Dec 30, 2025Dec 30, 2025

    • PCa

      Public
      Spatial analysis of the prostate TME
      R
      •0•0•0•0•Updated Dec 19, 2025Dec 19, 2025

    • harvardtissueatlas

      Public
      Harvard Tissue Atlas website
      SCSS
      •5•3•3•0•Updated Dec 16, 2025Dec 16, 2025

    • basicpy-docker-mcmicro

      Public
      Python
      •4•0•0•0•Updated Dec 3, 2025Dec 3, 2025

    • peripheral-neuropathy

      Public
      0•0•0•0•Updated Dec 2, 2025Dec 2, 2025

    • 2025_Shi_Exceptional_Responder_Manuscript

      Public
      Dissecting the Mechanisms of Persistent Residual Disease Following Immunotherapy in Metastatic Melanoma
      Jupyter Notebook
      •0•0•0•0•Updated Dec 2, 2025Dec 2, 2025

    • minerva-author

      Public
      Tool to create images and configuration files for Minerva-Story
      Python
      •
      MIT License
      •15•16•27•1•Updated Dec 1, 2025Dec 1, 2025