Cytomining

Open-source tools for every stage of the single-cell image-based profiling workflow.

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README.md

Welcome to Cytomining!

See our homepage here: cytomining.github.io

Cytomining is a software ecosystem that maintains essential tools, workflows, and best practices for single-cell image-based profiling and microscopy data analysis research. We are proud members of the CytoData scientific community.

Our Tools

Tool		Description
	pycytominer	Python package for image-based profiling bioinformatics
	CytoTable	Harmonize high-content image analysis tool outputs
	coSMicQC	Single-cell morphology quality control
	CytoDataFrame	In-memory data format for single-cell profiles alongside images
	copairs	Find profile pairs and compute retrieval metrics
	DeepProfiler	Morphological profiling using deep learning

Experimental tools (Cytomining Roadmap)

The following tools are under active development in the WayScience organization and represent the next generation of the Cytomining ecosystem.

Tool		Description
	buscar	Perturbation hit calling for high-content screening
	zedprofiler	CPU-first 3D image feature extraction for high-content profiling
	OME-arrow	OME specifications via Apache Arrow for fast, queryable bioimage data
	iceberg-bioimage	Format-agnostic framework for cataloging and querying bioimaging data

Get involved

See the links below to get started!

💬 Join the community on Discord
📺 Watch image-based profiling videos at our YouTube channel
😃 Check out our amazing community of contributors
🏫 Learn more about the CytoData community we are part of
📫 Subscribe to our mailing list
🌈 Please abide our community Code of Conduct

Pinned Loading

pycytominer pycytominer Public

Python package for image-based profiling

Python 144 42
CytoTable CytoTable Public

Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.

Python 21 6
coSMicQC coSMicQC Public

Single cell Morphology Quality Control (coSMicQC)

Python 11 3
CytoDataFrame CytoDataFrame Public

An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

Python 13 2
DeepProfiler DeepProfiler Public

Morphological profiling using deep learning

Python 129 52
copairs copairs Public

Find profile pairs and compute retrieval metrics between them.

Python 24 11

Repositories

Type Language Sort

copairs Public
Find profile pairs and compute retrieval metrics between them.

cytomining/copairs's past year of commit activity

Python 24 BSD-3-Clause 11 14 14 Updated Aug 28, 2026
pycytominer Public
Python package for image-based profiling

cytomining/pycytominer's past year of commit activity

Python 144 BSD-3-Clause 42 43 (1 issue needs help) 1 Updated Aug 27, 2026
CytoTable Public
Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.

cytomining/CytoTable's past year of commit activity

Python 21 BSD-3-Clause 6 81 1 Updated Aug 19, 2026
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 13 BSD-3-Clause 2 33 2 Updated Aug 5, 2026
cytomining.github.io Public
Cytomining organization GitHub Pages configuration.

cytomining/cytomining.github.io's past year of commit activity

HTML 0 BSD-3-Clause 2 0 0 Updated Aug 5, 2026
DeepProfiler Public
Morphological profiling using deep learning

cytomining/DeepProfiler's past year of commit activity

Python 129 BSD-3-Clause 52 25 (1 issue needs help) 0 Updated Aug 5, 2026
coSMicQC Public
Single cell Morphology Quality Control (coSMicQC)

cytomining/coSMicQC's past year of commit activity

Python 11 BSD-3-Clause 3 23 0 Updated Aug 3, 2026
.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 May 22, 2026
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 9, 2026
CytoTable-benchmarks Public
Benchmarks for CytoTable and related.

cytomining/CytoTable-benchmarks's past year of commit activity

Jupyter Notebook 0 BSD-3-Clause 1 0 0 Updated Oct 16, 2025