Repositories list

• mcmicro

  Public
  Multiple-choice microscopy pipeline

  Nextflow

  •

  MIT License

  •61•134•65•2•Updated Jul 26, 2025Jul 26, 2025

• minerva-core-ui

  Public
  A microscopy viewer for non-experts

  TypeScript

  •

  MIT License

  •3•0•10•2•Updated Jul 24, 2025Jul 24, 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.

  microscopyomeminerva+ 1immunofluorescence

  JavaScript

  •

  MIT License

  •2•2•1•3•Updated Jul 17, 2025Jul 17, 2025

• gater

  Public
  JavaScript

  •

  MIT License

  •3•1•4•1•Updated Jul 11, 2025Jul 11, 2025

• minerva_analysis

  Public
  JavaScript

  •

  MIT License

  •7•26•22•4•Updated Jul 11, 2025Jul 11, 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.

  microscopyomeminerva+ 1immunofluorescence

  JavaScript

  •

  MIT License

  •5•4•2•4•Updated Jul 10, 2025Jul 10, 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•27•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

• ome-tiff-pyramid-tools

  Public
  Python tools for creating and manipulating OME-TIFF multi-resolution pyramid images.

  Python

  •

  MIT License

  •9•16•0•1•Updated Jul 2, 2025Jul 2, 2025

• cdk7-analysis

  Public
  R

  •0•0•0•0•Updated Jul 1, 2025Jul 1, 2025

• scimap

  Public
  Spatial Single-Cell Analysis Toolkit

  pythonspatial-analysisimage-analysis+ 2single-cell-analysispypi

  Python

  •

  MIT License

  •30•93•44•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

• harvardtissueatlas

  Public
  Harvard Tissue Atlas website

  SCSS

  •5•3•3•0•Updated Jun 20, 2025Jun 20, 2025

• peripheral-neuropathy

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

• okl-analysis

  Public
  Python

  •0•0•0•0•Updated May 27, 2025May 27, 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

  •439•0•2•0•Updated May 1, 2025May 1, 2025

• CRC_atlas_2022

  Public
  MATLAB

  •

  MIT License

  •4•16•4•0•Updated Apr 8, 2025Apr 8, 2025

• r-indra-gsea

  Public
  R

  •

  Other

  •0•0•0•0•Updated Apr 2, 2025Apr 2, 2025

• quantification

  Public
  Quantification module for mcmicro

  Python

  •14•9•7•1•Updated Apr 1, 2025Apr 1, 2025