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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 115 42

  2. pycytominer pycytominer Public

    Python package for processing image-based profiling data

    Python 110 39

  3. cytominer cytominer Public

    Methods for Image-Based Cell Profiling

    R 50 28

  4. cytominer-eval cytominer-eval Public

    [Deprecated] Common Evaluation Metrics for DataFrames

    Python 7 11

  5. profiling-recipe profiling-recipe Public

    Image-based Profiling Recipe

    Python 8 28

  6. CytoTable CytoTable Public

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

    Python 10 6

Repositories

Showing 10 of 26 repositories
  • profiling-handbook Public

    Image-based Profiling Handbook

    cytomining/profiling-handbook’s past year of commit activity
    9 CC0-1.0 7 5 0 Updated Apr 15, 2025
  • 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 10 BSD-3-Clause 6 66 2 Updated Apr 14, 2025
  • pycytominer Public

    Python package for processing image-based profiling data

    cytomining/pycytominer’s past year of commit activity
    Python 110 BSD-3-Clause 39 101 (1 issue needs help) 11 Updated Apr 2, 2025
  • copairs Public

    Find profile pairs and compute metrics between them.

    cytomining/copairs’s past year of commit activity
    Python 10 BSD-3-Clause 6 10 1 Updated Mar 10, 2025
  • profiling-recipe Public

    Image-based Profiling Recipe

    cytomining/profiling-recipe’s past year of commit activity
    Python 8 BSD-3-Clause 28 12 (1 issue needs help) 3 Updated Feb 7, 2025
  • 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 27, 2025
  • DeepProfiler Public

    Morphological profiling using deep learning

    cytomining/DeepProfiler’s past year of commit activity
    Python 115 42 26 (1 issue needs help) 4 Updated Oct 19, 2024
  • pipeline-examples Public

    Example pipelines for training purposes

    cytomining/pipeline-examples’s past year of commit activity
    Jupyter Notebook 1 2 1 0 Updated Oct 19, 2024
  • cytominer-database Public

    [DEPRECATED] A package for storing morphological profiling data.

    cytomining/cytominer-database’s past year of commit activity
    Python 10 11 13 1 Updated Oct 10, 2024
  • cytominer-eval Public

    [Deprecated] Common Evaluation Metrics for DataFrames

    cytomining/cytominer-eval’s past year of commit activity
    Python 7 BSD-3-Clause 11 23 (4 issues need help) 1 Updated Sep 13, 2024
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