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@cytomining

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. DeepProfiler Public

    Morphological profiling using deep learning

    Python 114 41

  2. pycytominer Public

    Python package for processing image-based profiling data

    Python 97 39

  3. cytominer Public

    Methods for Image-Based Cell Profiling

    R 50 28

  4. cytominer-eval Public

    [Deprecated] Common Evaluation Metrics for DataFrames

    Python 7 11

  5. profiling-recipe Public

    Image-based Profiling Recipe

    Python 8 28

  6. CytoTable Public

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

    Python 9 6

Repositories

Showing 10 of 26 repositories
  • pycytominer Public

    Python package for processing image-based profiling data

    Python 97 BSD-3-Clause 39 100 (1 issue needs help) 13 Updated Mar 6, 2025
  • copairs Public

    Find pairs and compute metrics between them.

    Python 10 BSD-3-Clause 6 8 2 Updated Feb 21, 2025
  • CytoTable Public

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

    Python 9 BSD-3-Clause 6 65 2 Updated Feb 18, 2025
  • profiling-recipe Public

    Image-based Profiling Recipe

    Python 8 BSD-3-Clause 28 12 (1 issue needs help) 3 Updated Feb 7, 2025
  • profiling-template Public template

    Image-based Profiling Template

    0 BSD-3-Clause 1 10 (1 issue needs help) 0 Updated Jan 27, 2025
  • DeepProfiler Public

    Morphological profiling using deep learning

    Python 114 41 26 (1 issue needs help) 4 Updated Oct 19, 2024
  • pipeline-examples Public

    Example pipelines for training purposes

    Jupyter Notebook 1 2 1 0 Updated Oct 19, 2024
  • cytominer-database Public

    [DEPRECATED] A package for storing morphological profiling data.

    Python 10 12 13 1 Updated Oct 10, 2024
  • cytominer-eval Public

    [Deprecated] Common Evaluation Metrics for DataFrames

    Python 7 BSD-3-Clause 11 23 (4 issues need help) 1 Updated Sep 13, 2024
  • evalzoo Public archive

    [Deprecated] Evaluate metrics using cytominer-eval and matric

    HTML 1 BSD-3-Clause 2 1 0 Updated Sep 13, 2024

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