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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. DeepProfiler DeepProfiler Public

    Morphological profiling using deep learning

    Python 123 47

  2. pycytominer pycytominer Public

    Python package for processing image-based profiling data

    Python 135 40

  3. cytominer cytominer Public

    Methods for Image-Based Cell Profiling

    R 51 28

  4. CytoTable CytoTable Public

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

    Python 17 6

  5. copairs copairs Public

    Find profile pairs and compute retrieval metrics between them.

    Python 22 11

  6. coSMicQC coSMicQC Public

    Single cell Morphology Quality Control (coSMicQC)

    Python 10 3

Repositories

Showing 10 of 28 repositories
  • coSMicQC Public

    Single cell Morphology Quality Control (coSMicQC)

    cytomining/coSMicQC’s past year of commit activity
    Python 10 BSD-3-Clause 3 21 1 Updated Feb 10, 2026
  • 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 17 BSD-3-Clause 6 76 3 Updated Feb 9, 2026
  • pycytominer Public

    Python package for processing image-based profiling data

    cytomining/pycytominer’s past year of commit activity
    Python 135 BSD-3-Clause 40 95 (1 issue needs help) 11 Updated Feb 9, 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 27 2 Updated Feb 9, 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 7 Updated Jan 27, 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 0 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 123 47 26 (1 issue needs help) 4 Updated Oct 19, 2024
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