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@cytomining

cytomining

Cytomining organization logo

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 98 39

  2. pycytominer pycytominer Public

    Python package for processing image-based profiling data

    Python 70 32

  3. cytominer cytominer Public

    Methods for Image-Based Cell Profiling

    R 46 28

  4. cytominer-eval cytominer-eval Public

    Common Evaluation Metrics for DataFrames

    Python 7 11

  5. profiling-recipe profiling-recipe Public

    Image-based Profiling Recipe

    Python 8 26

  6. CytoTable CytoTable Public

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

    Python 4 5

Repositories

Showing 10 of 26 repositories
  • pycytominer Public

    Python package for processing image-based profiling data

    cytomining/pycytominer’s past year of commit activity
    Python 70 BSD-3-Clause 32 91 (1 issue needs help) 8 Updated Jul 6, 2024
  • 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 4 BSD-3-Clause 5 62 2 Updated Jul 6, 2024
  • copairs Public

    Find pairs and compute metrics between them.

    cytomining/copairs’s past year of commit activity
    Python 6 BSD-3-Clause 5 9 1 Updated Jun 6, 2024
  • DeepProfiler Public

    Morphological profiling using deep learning

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

    Image-based Profiling Recipe

    cytomining/profiling-recipe’s past year of commit activity
    Python 8 BSD-3-Clause 26 11 (1 issue needs help) 2 Updated May 20, 2024
  • cytominer Public

    Methods for Image-Based Cell Profiling

    cytomining/cytominer’s past year of commit activity
    R 46 28 6 1 Updated May 8, 2024
  • profiling-handbook Public

    Image-based Profiling Handbook

    cytomining/profiling-handbook’s past year of commit activity
    8 CC0-1.0 7 5 0 Updated Mar 21, 2024
  • CytoTable-benchmarks Public

    Benchmarks for CytoTable and related.

    cytomining/CytoTable-benchmarks’s past year of commit activity
    Jupyter Notebook 0 BSD-3-Clause 1 2 0 Updated Feb 22, 2024
  • .github Public

    A special GitHub repository for setting the Cytomining organization profile and default community health files.

    cytomining/.github’s past year of commit activity
    1 BSD-3-Clause 2 1 0 Updated Feb 2, 2024
  • 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 12, 2024

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