Repositories list

• harvardtissueatlas

  Public
  Harvard Tissue Atlas website

  SCSS

  •6•3•2•0•Updated Dec 9, 2024Dec 9, 2024

• stic-ms-2024

  Public
  Custom codes related to Kader, Lin, Hug manuscript 2024

  R

  •1•0•0•0•Updated Dec 6, 2024Dec 6, 2024

• cycif.org

  Public
  cycif.org GitHub Pages Website

  JavaScript

  •

  MIT License

  •9•2•4•4•Updated Dec 6, 2024Dec 6, 2024

• CRC_atlas_2022

  Public
  MATLAB

  •

  MIT License

  •4•12•1•0•Updated Dec 5, 2024Dec 5, 2024

• minerva-core-ui

  Public
  A microscopy viewer for non-experts

  TypeScript

  •

  MIT License

  •2•0•10•2•Updated Dec 4, 2024Dec 4, 2024

• scimap

  Public
  Spatial Single-Cell Analysis Toolkit

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

  Python

  •

  MIT License

  •27•78•37•2•Updated Dec 4, 2024Dec 4, 2024

• mcmicro

  Public
  Multiple-choice microscopy pipeline

  Nextflow

  •

  MIT License

  •58•115•57•2•Updated Dec 4, 2024Dec 4, 2024

• minerva-browser

  Public
  JavaScript

  •

  MIT License

  •5•4•10•3•Updated Nov 27, 2024Nov 27, 2024

• ashlar

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

  Python

  •

  MIT License

  •43•131•54•12•Updated Nov 25, 2024Nov 25, 2024

• prostate

  Public
  Analysis of prostate cancer CyCIF data

  R

  •0•0•0•0•Updated Nov 23, 2024Nov 23, 2024

• 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 Nov 21, 2024Nov 21, 2024

• omero-oauth

  Public
  OMERO.web application to allow OAuth2 login to OMERO

  Python

  •

  GNU Affero General Public License v3.0

  •3•1•0•0•Updated Nov 19, 2024Nov 19, 2024

• ad-rna-editing

  Public
  R

  •0•0•0•0•Updated Nov 7, 2024Nov 7, 2024

• okl-analysis

  Public
  Python

  •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

• palom

  Public
  Piecewise alignment for layers of mosaics

  Python

  •

  MIT License

  •4•20•4•2•Updated Nov 3, 2024Nov 3, 2024

• minerva-author

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

  Python

  •

  MIT License

  •14•15•19•1•Updated Nov 1, 2024Nov 1, 2024

• cylinter

  Public
  An Interactive Image Segmentation Filter for Multiplex Microscopy

  Python

  •

  MIT License

  •12•26•0•1•Updated Oct 31, 2024Oct 31, 2024

• mcmicro-lsp

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

  Shell

  •

  MIT License

  •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• sarek-variant-calling-pipeline

  Public
  Shell

  •0•0•0•0•Updated Oct 24, 2024Oct 24, 2024

• mcqc

  Public
  Quality control module for mcmicro

  Python

  •

  MIT License

  •0•0•0•0•Updated Oct 22, 2024Oct 22, 2024

• ad-personalized

  Public
  R

  •

  MIT License

  •0•0•0•0•Updated Oct 9, 2024Oct 9, 2024

• vae-paper

  Public
  Jupyter Notebook

  •

  MIT License

  •2•2•0•0•Updated Oct 4, 2024Oct 4, 2024

• beta-segmentinator

  Public
  Python

  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• gater

  Public
  JavaScript

  •

  MIT License

  •3•1•1•1•Updated Sep 16, 2024Sep 16, 2024

• minerva_analysis

  Public
  JavaScript

  •

  MIT License

  •6•26•21•4•Updated Sep 16, 2024Sep 16, 2024

• mel-3d-mis

  Public
  MATLAB

  •1•0•0•0•Updated Sep 11, 2024Sep 11, 2024

• plateviewer

  Public
  Renders HTS microscopy image data into a Minerva Story for visual review

  Nextflow

  •

  MIT License

  •0•0•2•0•Updated Sep 3, 2024Sep 3, 2024

• ludwigtumoratlas.org

  Public
  Ludwig Tumor Atlas website

  SCSS

  •1•1•0•1•Updated Aug 27, 2024Aug 27, 2024

• quantification

  Public
  Quantification module for mcmicro

  Python

  •14•9•6•1•Updated Aug 9, 2024Aug 9, 2024

• biospecimen-disease-research-terminology

  Public
  Clinical disease terminology for annotation of biospecimen records

  Python

  •

  MIT License

  •1•0•0•0•Updated Aug 2, 2024Aug 2, 2024