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cytomining

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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. Morphological profiling using deep learning

    Python 123 48

  2. Python package for processing image-based profiling data

    Python 134 40

  3. Methods for Image-Based Cell Profiling

    R 51 28

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

    Python 17 6

  5. Find profile pairs and compute retrieval metrics between them.

    Python 22 11

  6. Single cell Morphology Quality Control (coSMicQC)

    Python 10 3

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Showing 10 of 28 repositories

  • pycytominer Public

    Python package for processing image-based profiling data

    cytomining/pycytominer’s past year of commit activity

  • 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 30 0

    Updated Mar 3, 2026

  • coSMicQC Public

    Single cell Morphology Quality Control (coSMicQC)

    cytomining/coSMicQC’s past year of commit activity

    Python

    10

    BSD-3-Clause

    3 21 0

    Updated Mar 3, 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 1

    Updated Mar 1, 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 Mar 1, 2026

  • cytomining/profiling-template’s past year of commit activity

  • cytomining/CytoTable-benchmarks’s past year of commit activity

    Jupyter Notebook 0 BSD-3-Clause

    1 0 0

    Updated Oct 16, 2025

  • cytomining/profiling-handbook’s past year of commit activity

    11

    CC0-1.0

    7 5 0

    Updated Apr 15, 2025

  • cytomining/profiling-recipe’s past year of commit activity

  • DeepProfiler Public

    Morphological profiling using deep learning

    cytomining/DeepProfiler’s past year of commit activity