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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. DeepProfiler DeepProfiler Public

    Morphological profiling using deep learning

    Python 109 40

  2. pycytominer pycytominer Public

    Python package for processing image-based profiling data

    Python 83 36

  3. cytominer cytominer Public

    Methods for Image-Based Cell Profiling

    R 49 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 27

  6. CytoTable CytoTable Public

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

    Python 7 5

Repositories

Showing 10 of 26 repositories
  • 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 7 BSD-3-Clause 5 64 2 Updated Dec 16, 2024
  • copairs Public

    Find pairs and compute metrics between them.

    cytomining/copairs’s past year of commit activity
    Python 9 BSD-3-Clause 5 10 2 Updated Dec 16, 2024
  • pycytominer Public

    Python package for processing image-based profiling data

    cytomining/pycytominer’s past year of commit activity
    Python 83 BSD-3-Clause 36 97 (1 issue needs help) 8 Updated Dec 12, 2024
  • DeepProfiler Public

    Morphological profiling using deep learning

    cytomining/DeepProfiler’s past year of commit activity
    Python 109 40 25 (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 12 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
  • evalzoo Public archive

    [Deprecated] Evaluate metrics using cytominer-eval and matric

    cytomining/evalzoo’s past year of commit activity
    HTML 1 BSD-3-Clause 2 1 0 Updated Sep 13, 2024
  • matric Public archive

    [Deprecated] Calculate quality metrics for readouts from high-throughput profiling experiments

    cytomining/matric’s past year of commit activity
    R 4 1 4 0 Updated Sep 13, 2024
  • matric-vm Public archive

    [Deprecated] Packer scripts for creating a matric VM

    cytomining/matric-vm’s past year of commit activity
    0 BSD-3-Clause 1 0 0 Updated Sep 13, 2024