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    169 repositories

    • gater

      Public
      JavaScript
      •
      MIT License
      •3•1•4•1•Updated Aug 20, 2025Aug 20, 2025

    • minerva_analysis

      Public
      JavaScript
      •
      MIT License
      •7•26•22•4•Updated Aug 20, 2025Aug 20, 2025

    • minerva-core-ui

      Public
      A microscopy viewer for non-experts
      HTML
      •
      MIT License
      •3•0•10•2•Updated Aug 20, 2025Aug 20, 2025

    • okl-analysis

      Public
      Python
      •0•0•0•0•Updated Aug 14, 2025Aug 14, 2025

    • mcmicro

      Public
      Multiple-choice microscopy pipeline
      Nextflow
      •
      MIT License
      •61•136•66•2•Updated Aug 14, 2025Aug 14, 2025

    • minerva-author-ui

      Public
      Minerva Author is an authoring tool used to create Minerva narrated stories via selection of specific channel groupings and image views.
      microscopyomeminervaimmunofluorescence
      JavaScript
      •
      MIT License
      •5•4•2•4•Updated Aug 12, 2025Aug 12, 2025

    • Image-Analysis-Guides

      Public
      mostly single cell image analysis and instructions for relevant tasks related to our imaging platform
      Jupyter Notebook
      •0•0•0•0•Updated Aug 12, 2025Aug 12, 2025

    • ashlar

      Public
      ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration
      Python
      •
      MIT License
      •46•149•56•9•Updated Aug 11, 2025Aug 11, 2025

    • cylinter

      Public
      An Interactive Image Segmentation Filter for Multiplex Microscopy
      Python
      •
      MIT License
      •13•31•3•1•Updated Aug 11, 2025Aug 11, 2025

    • ome-tiff-pyramid-tools

      Public
      Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.
      Python
      •
      MIT License
      •9•17•0•1•Updated Aug 8, 2025Aug 8, 2025

    • harvardtissueatlas

      Public
      Harvard Tissue Atlas website
      SCSS
      •5•3•3•0•Updated Aug 8, 2025Aug 8, 2025

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

      Public
      Custom codes for Vallius, Shi, Novikov et al. manuscript 2025
      Jupyter Notebook
      •1•0•0•0•Updated Jul 22, 2025Jul 22, 2025

    • 2025_Williams_Pant_Melanoma-TRM

      Public
      Python
      •0•0•0•0•Updated Jul 18, 2025Jul 18, 2025

    • minerva-cloud-ui

      Public
      Minerva Cloud is a novel cloud-based (AWS) software for high-dimensional image management, storage and visualization.
      microscopyomeminervaimmunofluorescence
      JavaScript
      •
      MIT License
      •2•2•1•3•Updated Jul 17, 2025Jul 17, 2025

    • vae-paper

      Public
      Jupyter Notebook
      •
      MIT License
      •2•3•0•0•Updated Jul 7, 2025Jul 7, 2025

    • palom

      Public
      Piecewise alignment for layers of mosaics
      Python
      •
      MIT License
      •7•28•6•1•Updated Jul 7, 2025Jul 7, 2025

    • vae

      Public
      Python
      •
      MIT License
      •1•2•0•0•Updated Jul 7, 2025Jul 7, 2025

    • mel-3d-mis

      Public
      MATLAB
      •1•0•0•0•Updated Jul 4, 2025Jul 4, 2025

    • cdk7-analysis

      Public
      R
      •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

    • scimap

      Public
      Spatial Single-Cell Analysis Toolkit
      pythonspatial-analysisimage-analysissingle-cell-analysispypi
      Python
      •
      MIT License
      •31•94•45•2•Updated Jun 30, 2025Jun 30, 2025

    • ad-rna-editing

      Public
      R
      •1•0•0•0•Updated Jun 24, 2025Jun 24, 2025

    • orion-crc

      Public
      MATLAB
      •
      MIT License
      •3•18•1•0•Updated Jun 24, 2025Jun 24, 2025

    • cycif.org

      Public
      cycif.org GitHub Pages Website
      JavaScript
      •
      MIT License
      •9•2•6•4•Updated Jun 20, 2025Jun 20, 2025

    • minerva-browser

      Public
      JavaScript
      •
      MIT License
      •5•5•10•3•Updated Jun 20, 2025Jun 20, 2025

    • peripheral-neuropathy

      Public
      0•0•0•0•Updated May 28, 2025May 28, 2025

    • minerva-author

      Public
      Tool to create images and configuration files for Minerva-Story
      Python
      •
      MIT License
      •15•16•25•1•Updated May 15, 2025May 15, 2025

    • bftools-docker

      Public
      BioFormats Tools Docker Image
      dockertoolsbio-formats
      Dockerfile
      •
      MIT License
      •0•0•0•0•Updated May 12, 2025May 12, 2025

    • Eddy

      Public
      The marker localization mapper and mask merger of the quantification folder (MCMICRO)
      Python
      •0•0•0•0•Updated May 9, 2025May 9, 2025

    • ad-personalized

      Public
      R
      •
      MIT License
      •0•0•0•0•Updated May 7, 2025May 7, 2025

    • python-intermediate-may-institute-2025

      Public
      Intermediate Python, data visualization and statistics
      HTML
      •
      Other
      •438•0•2•0•Updated May 1, 2025May 1, 2025