Repositories list

• NuclearIDTracker

  Public
  Predicts cell types based on nucleus features (morphology, neighborhood). Allows for observing cell types in mouse small intestinal organoid time lapses.

  Jupyter Notebook

  •00 forks in RodriguezColmanLab/NuclearIDTracker•00 stars in RodriguezColmanLab/NuclearIDTracker•00 issues in RodriguezColmanLab/NuclearIDTracker•00 pull requests in RodriguezColmanLab/NuclearIDTracker•Updated Oct 28, 2026Oct 28, 2026

• CellPhenTracker

  Public
  Set of OrganoidTracker plugins to measure and analyse fluorescent intensities.

  Python

  •00 forks in RodriguezColmanLab/CellPhenTracker•00 stars in RodriguezColmanLab/CellPhenTracker•00 issues in RodriguezColmanLab/CellPhenTracker•00 pull requests in RodriguezColmanLab/CellPhenTracker•Updated Sep 16, 2026Sep 16, 2026

• dpct

  Public
  Dynamic Programming Cell Tracking Solver

  C++

  •

  MIT License

  •11 fork in RodriguezColmanLab/dpct•00 stars in RodriguezColmanLab/dpct•00 issues in RodriguezColmanLab/dpct•00 pull requests in RodriguezColmanLab/dpct•Updated Sep 9, 2026Sep 9, 2026

• napari-organoidtracker

  Public
  Allows you to read OrganoidTracker files into Napari

  Python

  •

  GNU General Public License v3.0

  •00 forks in RodriguezColmanLab/napari-organoidtracker•00 stars in RodriguezColmanLab/napari-organoidtracker•00 issues in RodriguezColmanLab/napari-organoidtracker•00 pull requests in RodriguezColmanLab/napari-organoidtracker•Updated Sep 8, 2026Sep 8, 2026

• Metaboglobe

  Public
  Plot KEGG pathways with highlighted fluxes/metabolites

  Python

  •00 forks in RodriguezColmanLab/Metaboglobe•00 stars in RodriguezColmanLab/Metaboglobe•00 issues in RodriguezColmanLab/Metaboglobe•00 pull requests in RodriguezColmanLab/Metaboglobe•Updated Aug 24, 2026Aug 24, 2026

• KaryoMetab

  Public
  Reproducible computational workflow for the joint inference of chromosomal instability (CIN) patterns and metabolic states from single-cell RNA-seq data

  R

  •

  Other

  •00 forks in RodriguezColmanLab/KaryoMetab•22 stars in RodriguezColmanLab/KaryoMetab•00 issues in RodriguezColmanLab/KaryoMetab•00 pull requests in RodriguezColmanLab/KaryoMetab•Updated Jul 2, 2026Jul 2, 2026

• CMMCells

  Public
  Game for the open day of the CMM Utrecht

  Game Maker Language

  •

  MIT License

  •00 forks in RodriguezColmanLab/CMMCells•00 stars in RodriguezColmanLab/CMMCells•00 issues in RodriguezColmanLab/CMMCells•00 pull requests in RodriguezColmanLab/CMMCells•Updated May 6, 2025May 6, 2025

• in_vitro_droplet_assay

  Public
  Python

  •

  MIT License

  •11 fork in RodriguezColmanLab/in_vitro_droplet_assay•00 stars in RodriguezColmanLab/in_vitro_droplet_assay•00 issues in RodriguezColmanLab/in_vitro_droplet_assay•00 pull requests in RodriguezColmanLab/in_vitro_droplet_assay•Updated Dec 13, 2023Dec 13, 2023

• .github

  Public
  00 forks in RodriguezColmanLab/.github•00 stars in RodriguezColmanLab/.github•00 issues in RodriguezColmanLab/.github•00 pull requests in RodriguezColmanLab/.github•Updated Jan 25, 2023Jan 25, 2023