Repositories list

• Volumetric-CyCIF

  Public
  Python

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• cdk7-analysis

  Public
  R

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jun 3, 2026Jun 3, 2026

• minerva-author

  Public
  Tool to create images and configuration files for Minerva-Story

  Python

  •

  MIT License

  •1515 forks•1616 stars•2727 issues•11 pull request•Updated Jun 1, 2026Jun 1, 2026

• mccellpose

  Public
  Alternative interface to the Cellpose cell segmentation algorithm that uses constant memory

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •11 fork•00 stars•55 issues•00 pull requests•Updated Jun 1, 2026Jun 1, 2026

• ad-rna-editing

  Public
  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• ad-personalized

  Public
  TYK2 mediates neuroinflammation in dementia with Alzheimer’s disease

  R

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2026May 29, 2026

• palom

  Public
  Piecewise alignment for layers of mosaics

  Python

  •

  MIT License

  •1010 forks•5757 stars•77 issues•11 pull request•Updated May 28, 2026May 28, 2026

• Zhao-FMSAE-2026

  Public
  Jupyter Notebook

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 26, 2026May 26, 2026

• minerva-core-ui

  Public
  A microscopy viewer for non-experts

  TypeScript

  •

  MIT License

  •33 forks•11 star•1212 issues•33 pull requests•Updated May 22, 2026May 22, 2026

• mcmicro

  Public
  Multiple-choice microscopy pipeline

  Nextflow

  •

  MIT License

  •6464 forks•152152 stars•6464 issues•22 pull requests•Updated May 21, 2026May 21, 2026

• Santagata-Ependymoma-2026

  Public
  Jupyter Notebook

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 21, 2026May 21, 2026

• TB-3D-TLS-2026

  Public
  Multidimensional Spatial Characterization of Tertiary Lymphoid Structures in Human Pulmonary TB Lung Granulomas

  00 forks•00 stars•00 issues•00 pull requests•Updated May 15, 2026May 15, 2026

• harvardtissueatlas

  Public
  Harvard Tissue Atlas website

  SCSS

  •55 forks•33 stars•33 issues•00 pull requests•Updated May 14, 2026May 14, 2026

• ashlar

  Public
  ASHLAR: Alignment by Simultaneous Harmonization of Layer/Adjacency Registration

  Python

  •

  MIT License

  •5454 forks•175175 stars•6060 issues•1313 pull requests•Updated May 14, 2026May 14, 2026

• mcmicro-lsp

  Public
  mcmicro helpers for local use within the LSP (especially O2)

  Shell

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 14, 2026May 14, 2026

• omero-oauth

  Public
  OMERO.web application to allow OAuth2 login to OMERO

  Python

  •

  GNU Affero General Public License v3.0

  •44 forks•11 star•00 issues•00 pull requests•Updated May 5, 2026May 5, 2026

• okl-analysis

  Public
  Python

  •11 fork•00 stars•00 issues•00 pull requests•Updated Apr 28, 2026Apr 28, 2026

• tlsR

  Public
  Detection and Spatial Analysis of Tertiary Lymphoid Structures

  HTML

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 23, 2026Apr 23, 2026

• minerva-annotation-demo

  Public
  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Apr 13, 2026Apr 13, 2026

• cylinter

  Public
  An Interactive Image Segmentation Filter for Multiplex Microscopy

  Python

  •

  MIT License

  •1313 forks•3333 stars•11 issue•00 pull requests•Updated Apr 9, 2026Apr 9, 2026

• Chen-Santagata-Kidney-2026

  Public
  MATLAB

  •

  MIT License

  •22 forks•00 stars•00 issues•00 pull requests•Updated Apr 6, 2026Apr 6, 2026

• vae-paper

  Public
  Jupyter Notebook

  •

  MIT License

  •22 forks•44 stars•00 issues•00 pull requests•Updated Mar 31, 2026Mar 31, 2026

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

  Public
  Custom codes for Vallius, Shi, Novikov et al. manuscript 2025

  Jupyter Notebook

  •11 fork•00 stars•00 issues•00 pull requests•Updated Mar 26, 2026Mar 26, 2026

• orion-fish-ms-2026

  Public
  Kader_Santagata_ORION-FISH 2026

  Python

  •22 forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2026Mar 19, 2026

• scimap

  Public
  Spatial Single-Cell Analysis Toolkit

  pythonpypispatial-analysis+ 2

  pythonpypispatial-analysisimage-analysissingle-cell-analysis

  Python

  •

  MIT License

  •3636 forks•111111 stars•4747 issues•66 pull requests•Updated Mar 11, 2026Mar 11, 2026

• Christensen-Wala-PI3K-PD1

  Public
  Data repository and links for Christensen, Wala et al. 2026. Nat Comms.

  00 forks•00 stars•00 issues•00 pull requests•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+ 1

  microscopyomeminervaimmunofluorescence

  JavaScript

  •

  MIT License

  •22 forks•22 stars•11 issue•1212 pull requests•Updated Feb 13, 2026Feb 13, 2026

• cycif.org

  Public
  cycif.org GitHub Pages Website

  JavaScript

  •

  MIT License

  •99 forks•33 stars•66 issues•44 pull requests•Updated Feb 5, 2026Feb 5, 2026

• lsp-idc-minerva

  Public
  IDC DicomWeb Minerva Demo page

  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 22, 2026Jan 22, 2026

• lsp-idc-minerva-crc02

  Public
  IDC DicomWeb Minerva Demo page - CRC02

  JavaScript

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 20, 2026Jan 20, 2026