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    30 repositories

    • CellProfiler-plugins

      Public
      Community-contributed and experimental CellProfiler modules.
      Python
      •70•68•31•12•Updated Aug 1, 2025Aug 1, 2025

    • CellProfiler

      Public
      An open-source application for biological image analysis
      Python
      •
      Other
      •400•1k•312•26•Updated Aug 1, 2025Aug 1, 2025

    • CellProfiler-Analyst

      Public
      Open-source software for exploring and analyzing large, high-dimensional image-derived data.
      machine-learningcellprofilerimage-analysiscellprofiler-analyst
      Python
      •
      Other
      •75•158•68•1•Updated Jul 21, 2025Jul 21, 2025

    • prokaryote

      Public
      CellProfiler’s Java dependencies
      Java
      •
      GNU General Public License v3.0
      •11•2•3•2•Updated Jul 12, 2025Jul 12, 2025

    • python-bioformats

      Public
      Read and write life sciences file formats
      Python
      •
      Other
      •48•140•72•5•Updated Jun 12, 2025Jun 12, 2025

    • python-javabridge

      Public
      Python wrapper for the Java Native Interface
      Python
      •
      Other
      •64•23•13•2•Updated Jun 12, 2025Jun 12, 2025

    • tutorials

      Public
      CellProfiler tutorial pipelines and images
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •86•93•3•0•Updated May 7, 2025May 7, 2025

    • centrosome

      Public
      An open source image processing library
      Python
      •
      Other
      •37•19•31•2•Updated Mar 31, 2025Mar 31, 2025

    • core

      Public
      Core classes and components used by CellProfiler
      Python
      •
      Other
      •24•6•0•0•Updated Nov 12, 2024Nov 12, 2024

    • .github

      Public
      Default files are stored here, such as code of conduct
      0•0•0•0•Updated Oct 27, 2024Oct 27, 2024

    • distribution

      Public
      Everything needed to build CellProfiler for your favorite environment.
      Python
      •
      Other
      •6•4•13•0•Updated Sep 26, 2024Sep 26, 2024

    • CellProfiler-Explorer

      Public
      Web app for exploring CellProfiler data and combining with metadata
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Dec 20, 2023Dec 20, 2023

    • examples

      Public
      Example CellProfiler pipelines.
      Makefile
      •
      BSD 3-Clause "New" or "Revised" License
      •14•15•5•1•Updated Jul 19, 2022Jul 19, 2022

    • library

      Public archive
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•2•0•0•Updated Mar 2, 2022Mar 2, 2022

    • pyinstaller

      Public
      Freeze (package) Python programs into stand-alone executables
      Python
      •
      Other
      •2k•0•0•0•Updated Jun 24, 2020Jun 24, 2020

    • cellprofiler.github.com

      Public archive
      CellProfiler Website
      carpenter-lab
      JavaScript
      •4•2•6•0•Updated May 5, 2020May 5, 2020

    • stitching

      Public
      Image stitching
      Python
      •
      Other
      •6•12•3•1•Updated Dec 23, 2018Dec 23, 2018

    • meoir

      Public
      Profiling modules from CellProfiler-Analyst for exploring and analyzing large, high-dimensional image-derived data. http://cellprofiler.org
      Python
      •1•1•0•0•Updated Sep 23, 2018Sep 23, 2018

    • notebooks

      Public
      Jupyter notebooks for CellProfiler and friends
      Jupyter Notebook
      •6•13•2•0•Updated Mar 23, 2018Mar 23, 2018

    • CellProfiler-1.0

      Public archive
      ⚠️ ARCHIVED ⚠️ CellProfiler 1.0 (Matlab-based), current version at: CellProfiler/CellProfiler
      MATLAB
      •
      Other
      •8•9•0•0•Updated Jan 24, 2018Jan 24, 2018

    • RFC

      Public
      A place to propose new features for CellProfiler
      0•0•0•0•Updated Nov 30, 2017Nov 30, 2017

    • docker

      Public archive
      Makefile
      •10•2•0•0•Updated Nov 16, 2017Nov 16, 2017

    • cellprofiler.github.com-backup

      Public archive
      OLD cp website repo. Current repo is here: https://github.com/CellProfiler/cellprofiler.github.com. We are currently in the process of transferring any remaining and relevant issues to the current Github repo so that this repo can then be deleted.
      HTML
      •
      Other
      •2•3•3•0•Updated Feb 8, 2017Feb 8, 2017

    • BatchProfiler

      Public archive
      Python
      •1•1•13•1•Updated Apr 4, 2016Apr 4, 2016

    • tutorial

      Public archive
      Python
      •3•0•2•0•Updated Mar 2, 2016Mar 2, 2016

    • jenkins

      Public archive
      Shell
      •2•1•3•1•Updated Jan 12, 2016Jan 12, 2016

    • knime-bridge

      Public
      ZMQ connection between CellProfiler and Knime
      Java
      •
      BSD 3-Clause "New" or "Revised" License
      •1•1•4•0•Updated Aug 25, 2015Aug 25, 2015

    • CellProfiler-rpm

      Public archive
      1•0•0•0•Updated Apr 13, 2015Apr 13, 2015

    • CellProfiler-build

      Public archive
      Infrastructure for continuous integration and automatic builds of CellProfiler internally at the Broad institute
      Python
      •
      GNU General Public License v2.0
      •3•1•0•0•Updated Apr 13, 2015Apr 13, 2015

    • CPCharm

      Public archive
      Python
      •2•3•0•0•Updated Jan 23, 2015Jan 23, 2015