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cytomining · GitHub
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!
Pinned
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Morphological profiling using deep learning
Python
124
46
Python package for processing image-based profiling data
Python
130
40
Methods for Image-Based Cell Profiling
R
51
28
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
Python
17
6
Find profile pairs and compute retrieval metrics between them.
Python
21
10
Single cell Morphology Quality Control (coSMicQC)
Python
10
3
Repositories
Showing 10 of 28 repositories
coSMicQC
Public
Single cell Morphology Quality Control (coSMicQC)
cytomining/coSMicQC’s past year of commit activity
Python
10
BSD-3-Clause
3
20
1
Updated Dec 29, 2025
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
8
BSD-3-Clause
2
23
1
Updated Dec 29, 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
17
BSD-3-Clause
6
75
2
Updated Dec 22, 2025
pycytominer
Public
Python package for processing image-based profiling data
cytomining/pycytominer’s past year of commit activity
copairs
Public
Find profile pairs and compute retrieval metrics between them.
cytomining/copairs’s past year of commit activity
Python
21
BSD-3-Clause
10
14
5
Updated Dec 8, 2025
cytomining/CytoTable-benchmarks’s past year of commit activity
Jupyter Notebook
0
BSD-3-Clause
1
0
0
Updated Oct 16, 2025
cytomining/profiling-template’s past year of commit activity
cytomining/profiling-handbook’s past year of commit activity
11
CC0-1.0
7
5
0
Updated Apr 15, 2025
cytomining/profiling-recipe’s past year of commit activity
DeepProfiler
Public
Morphological profiling using deep learning
cytomining/DeepProfiler’s past year of commit activity
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