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cytomining

README.md
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Welcome to Cytomining!

Cytomining is a software ecosystem that maintains essential tools, workflows, and best practices for single-cell image-based profiling and microscopy data analysis research.

See the links below to get started!

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  1. pycytominer pycytominer Public

    Python package for processing image-based profiling data

    Python 136 40

  2. CytoTable CytoTable Public

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

    Python 18 6

  3. coSMicQC coSMicQC Public

    Single cell Morphology Quality Control (coSMicQC)

    Python 11 3

  4. CytoDataFrame CytoDataFrame Public

    An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

    Python 11 2

  5. DeepProfiler DeepProfiler Public

    Morphological profiling using deep learning

    Python 124 49

  6. copairs copairs Public

    Find profile pairs and compute retrieval metrics between them.

    Python 22 11

Repositories

Showing 10 of 28 repositories
  • CytoTable Public

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

    cytomining/CytoTable’s past year of commit activity
    Python 18 BSD-3-Clause 6 77 2 Updated Apr 2, 2026
  • pycytominer Public

    Python package for processing image-based profiling data

    cytomining/pycytominer’s past year of commit activity
    Python 136 BSD-3-Clause 40 60 (1 issue needs help) 7 Updated Apr 2, 2026
  • copairs Public

    Find profile pairs and compute retrieval metrics between them.

    cytomining/copairs’s past year of commit activity
    Python 22 BSD-3-Clause 11 14 5 Updated Apr 1, 2026
  • CytoDataFrame Public

    An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

    cytomining/CytoDataFrame’s past year of commit activity
    Python 11 BSD-3-Clause 2 33 1 Updated Apr 1, 2026
  • coSMicQC Public

    Single cell Morphology Quality Control (coSMicQC)

    cytomining/coSMicQC’s past year of commit activity
    Python 11 BSD-3-Clause 3 21 3 Updated Mar 30, 2026
  • profiling-template Public template

    Image-based Profiling Template

    cytomining/profiling-template’s past year of commit activity
    0 BSD-3-Clause 1 10 (1 issue needs help) 0 Updated Jan 9, 2026
  • CytoTable-benchmarks Public

    Benchmarks for CytoTable and related.

    cytomining/CytoTable-benchmarks’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 1 0 0 Updated Oct 16, 2025
  • profiling-handbook Public

    Image-based Profiling Handbook

    cytomining/profiling-handbook’s past year of commit activity
    11 CC0-1.0 7 5 1 Updated Apr 15, 2025
  • profiling-recipe Public

    Image-based Profiling Recipe

    cytomining/profiling-recipe’s past year of commit activity
    Python 11 BSD-3-Clause 34 12 (1 issue needs help) 3 Updated Feb 7, 2025
  • DeepProfiler Public

    Morphological profiling using deep learning

    cytomining/DeepProfiler’s past year of commit activity
    Python 124 49 26 (1 issue needs help) 4 Updated Oct 19, 2024
View all repositories

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