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    28 repositories

    • CytoDataFrame

      Public
      An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
      image-analysissingle-celldataframesimage-based-profiling
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •2•7•23•1•Updated Dec 8, 2025Dec 8, 2025

    • copairs

      Public
      Find profile pairs and compute retrieval metrics between them.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•21•13•5•Updated Dec 8, 2025Dec 8, 2025

    • coSMicQC

      Public
      Single cell Morphology Quality Control (coSMicQC)
      quality-controlimage-based-profilingmicroscopy-image-analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•10•20•1•Updated Dec 7, 2025Dec 7, 2025

    • CytoTable

      Public
      Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
      pythoncellprofilersingle-cell-analysisway-lab
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •6•17•75•1•Updated Dec 7, 2025Dec 7, 2025

    • pycytominer

      Public
      Python package for processing image-based profiling data
      pythonimage-processingcellprofilermicroscopycarpenter-labmorphological-profilingcytominerway-lab
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •40•129•95•10•Updated Dec 6, 2025Dec 6, 2025

    • CytoTable-benchmarks

      Public
      Benchmarks for CytoTable and related.
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Oct 16, 2025Oct 16, 2025

    • profiling-template

      Public template
      Image-based Profiling Template
      BSD 3-Clause "New" or "Revised" License
      •1•0•10•0•Updated Jun 27, 2025Jun 27, 2025

    • profiling-handbook

      Public
      Image-based Profiling Handbook
      guidehandbookcellprofilermorphological-profilingcytomining
      Creative Commons Zero v1.0 Universal
      •7•12•5•0•Updated Apr 15, 2025Apr 15, 2025

    • profiling-recipe

      Public
      Image-based Profiling Recipe
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •33•10•12•3•Updated Feb 7, 2025Feb 7, 2025

    • DeepProfiler

      Public
      Morphological profiling using deep learning
      Python
      •
      Other
      •45•124•26•4•Updated Oct 19, 2024Oct 19, 2024

    • pipeline-examples

      Public
      Example pipelines for training purposes
      Jupyter Notebook
      •3•1•1•0•Updated Oct 19, 2024Oct 19, 2024

    • cytominer-database

      Public
      [DEPRECATED] A package for storing morphological profiling data.
      databaseprofilingmicroscopy
      Python
      •
      Other
      •11•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
      •12•7•23•1•Updated Sep 13, 2024Sep 13, 2024

    • evalzoo

      Public archive
      [Deprecated] Evaluate metrics using cytominer-eval and matric
      HTML
      •
      BSD 3-Clause "New" or "Revised" License
      •2•1•1•0•Updated Sep 13, 2024Sep 13, 2024

    • matric

      Public archive
      [Deprecated] Calculate quality metrics for readouts from high-throughput profiling experiments
      R
      •
      Other
      •1•4•4•0•Updated Sep 13, 2024Sep 13, 2024

    • matric-vm

      Public archive
      [Deprecated] Packer scripts for creating a matric VM
      BSD 3-Clause "New" or "Revised" License
      •1•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • cytominer-transport

      Public archive
      [Deprecated]
      Python
      •
      Other
      •2•1•4•0•Updated Sep 13, 2024Sep 13, 2024

    • cytotools

      Public archive
      [Deprecated] Command-line Tools to Get Things Done Using Cytominer
      R
      •
      Other
      •0•0•7•3•Updated Sep 13, 2024Sep 13, 2024

    • cytoplot

      Public archive
      [Deprecated] Package for visualizing high-dimensional single-cell data
      profilingmicroscopy
      R
      •
      Other
      •2•4•5•0•Updated Sep 13, 2024Sep 13, 2024

    • cytostats

      Public archive
      [Deprecated] Statistical Functions for Single-Cell Analysis
      C++
      •
      Other
      •0•1•1•0•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•51•6•1•Updated May 8, 2024May 8, 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
      documentationdeep-learning
      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

    • cytominergallery

      Public archive
      [Deprecated] A Gallery of Cytominer Vignettes
      vignetteprofilingmicroscopy
      R
      •
      Other
      •6•1•1•4•Updated Jul 20, 2022Jul 20, 2022

    • cytominer-python

      Public archive
      DEPRECATED A Python package for mining patterns in perturbations
      biologyprofilingmicroscopy
      Jupyter Notebook
      •
      Other
      •1•1•0•0•Updated May 4, 2017May 4, 2017