Repositories list

• CytoTable

  Public
  Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.

  pythoncellprofilersingle-cell-analysis+ 1way-lab

  Python

  •

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

  •6•9•66•2•Updated Mar 26, 2025Mar 26, 2025

• pycytominer

  Public
  Python package for processing image-based profiling data

  pythonimage-processingcellprofiler+ 5microscopycarpenter-labmorphological-profilingcytominerway-lab

  Python

  •

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

  •39•104•100•12•Updated Mar 12, 2025Mar 12, 2025

• copairs

  Public
  Find profile pairs and compute metrics between them.

  Python

  •

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

  •6•10•10•1•Updated Mar 10, 2025Mar 10, 2025

• profiling-recipe

  Public
  Image-based Profiling Recipe

  Python

  •

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

  •28•8•12•3•Updated Feb 7, 2025Feb 7, 2025

• profiling-template

  Public template
  Image-based Profiling Template

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

  •1•0•10•0•Updated Jan 27, 2025Jan 27, 2025

• DeepProfiler

  Public
  Morphological profiling using deep learning

  Python

  •

  Other

  •41•116•26•4•Updated Oct 19, 2024Oct 19, 2024

• pipeline-examples

  Public
  Example pipelines for training purposes

  Jupyter Notebook

  •2•1•1•0•Updated Oct 19, 2024Oct 19, 2024

• cytominer-database

  Public
  [DEPRECATED] A package for storing morphological profiling data.

  databaseprofilingmicroscopy

  Python

  •

  Other

  •12•10•13•1•Updated Oct 10, 2024Oct 10, 2024

• cytominer-eval

  Public
  [Deprecated] Common Evaluation Metrics for DataFrames

  Python

  •

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

  •11•7•23•1•Updated Sep 13, 2024Sep 13, 2024

• cytominer-vm

  Public
  [DEPRECATED] Packer scripts to create VMs for running image-based profiling workflows on a cluster

  virtual-machineimage-processingprovisioning

  Shell

  •

  MIT License

  •2•2•4•0•Updated Sep 13, 2024Sep 13, 2024

• cytominer

  Public
  Methods for Image-Based Cell Profiling

  rprofilingmicroscopy

  R

  •

  Other

  •28•50•6•1•Updated May 8, 2024May 8, 2024

• profiling-handbook

  Public
  Image-based Profiling Handbook

  guidecellprofilermorphological-profiling+ 2cytomininghandbook

  Creative Commons Zero v1.0 Universal

  •7•9•5•0•Updated Mar 21, 2024Mar 21, 2024

• CytoTable-benchmarks

  Public
  Benchmarks for CytoTable and related.

  Jupyter Notebook

  •

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

  •1•0•2•0•Updated Feb 22, 2024Feb 22, 2024

• .github

  Public
  A special GitHub repository for setting the Cytomining organization profile and default community health files.

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

  •2•1•1•0•Updated Feb 2, 2024Feb 2, 2024

• DeepProfiler-handbook

  Public
  Documentation for installing and using of DeepProfiler

  deep-learningdocumentation

  HTML

  •3•8•6•1•Updated Jan 2, 2024Jan 2, 2024

• cytomining.github.io

  Public
  Cytomining organization GitHub Pages configuration.

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

  •1•0•0•0•Updated Nov 14, 2023Nov 14, 2023

• pycytominer-Docker

  Public
  Dockerfile

  •

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

  •2•1•1•0•Updated Nov 13, 2023Nov 13, 2023