cytomining

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28 repositories

pycytominer
Public
Python package for processing image-based profiling data
python image-processing cellprofiler
python image-processing cellprofiler microscopy carpenter-lab morphological-profiling cytominer way-lab
Python
•
BSD 3-Clause "New" or "Revised" License
•40•134•99•8•Updated Mar 4, 2026Mar 4, 2026
CytoDataFrame
Public
An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.
image-analysis single-cell dataframes
image-analysis single-cell dataframes image-based-profiling
Python
•
BSD 3-Clause "New" or "Revised" License
•2•11•30•0•Updated Mar 3, 2026Mar 3, 2026
coSMicQC
Public
Single cell Morphology Quality Control (coSMicQC)
quality-control image-based-profiling microscopy-image-analysis
quality-control image-based-profiling microscopy-image-analysis
Python
•
BSD 3-Clause "New" or "Revised" License
•3•10•21•0•Updated Mar 3, 2026Mar 3, 2026
CytoTable
Public
Transform CellProfiler and DeepProfiler data for processing image-based profiling readouts with Pycytominer and other Cytomining tools.
python cellprofiler single-cell-analysis
python cellprofiler single-cell-analysis way-lab
Python
•
BSD 3-Clause "New" or "Revised" License
•6•17•76•1•Updated Mar 1, 2026Mar 1, 2026
copairs
Public
Find profile pairs and compute retrieval metrics between them.
Python
•
BSD 3-Clause "New" or "Revised" License
•11•22•14•7•Updated Mar 1, 2026Mar 1, 2026
profiling-template
Public template
Image-based Profiling Template
BSD 3-Clause "New" or "Revised" License
•1•0•10•0•Updated Jan 9, 2026Jan 9, 2026
CytoTable-benchmarks
Public
Benchmarks for CytoTable and related.
Jupyter Notebook
•
BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Oct 16, 2025Oct 16, 2025
profiling-handbook
Public
Image-based Profiling Handbook
guide handbook cellprofiler
guide handbook cellprofiler morphological-profiling cytomining
Creative Commons Zero v1.0 Universal
•7•11•5•0•Updated Apr 15, 2025Apr 15, 2025
profiling-recipe
Public
Image-based Profiling Recipe
Python
•
BSD 3-Clause "New" or "Revised" License
•34•11•12•3•Updated Feb 7, 2025Feb 7, 2025
DeepProfiler
Public
Morphological profiling using deep learning
Python
•
Other
•48•123•26•4•Updated Oct 19, 2024Oct 19, 2024
pipeline-examples
Public
Example pipelines for training purposes
Jupyter Notebook
•3•1•1•0•Updated Oct 19, 2024Oct 19, 2024
cytominer-database
Public
[DEPRECATED] A package for storing morphological profiling data.
database profiling microscopy
database profiling microscopy
Python
•
Other
•11•10•13•1•Updated Oct 10, 2024Oct 10, 2024
cytominer-eval
Public
[Deprecated] Common Evaluation Metrics for DataFrames
Python
•
BSD 3-Clause "New" or "Revised" License
•12•7•23•1•Updated Sep 13, 2024Sep 13, 2024
evalzoo
Public archive
[Deprecated] Evaluate metrics using cytominer-eval and matric
HTML
•
BSD 3-Clause "New" or "Revised" License
•2•1•1•0•Updated Sep 13, 2024Sep 13, 2024
matric
Public archive
[Deprecated] Calculate quality metrics for readouts from high-throughput profiling experiments
R
•
Other
•1•4•4•0•Updated Sep 13, 2024Sep 13, 2024
matric-vm
Public archive
[Deprecated] Packer scripts for creating a matric VM
BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Sep 13, 2024Sep 13, 2024
cytominer-transport
Public archive
[Deprecated]
Python
•
Other
•2•1•4•0•Updated Sep 13, 2024Sep 13, 2024
cytotools
Public archive
[Deprecated] Command-line Tools to Get Things Done Using Cytominer
R
•
Other
•0•0•7•3•Updated Sep 13, 2024Sep 13, 2024
cytoplot
Public archive
[Deprecated] Package for visualizing high-dimensional single-cell data
profiling microscopy
profiling microscopy
R
•
Other
•2•4•5•0•Updated Sep 13, 2024Sep 13, 2024
cytostats
Public archive
[Deprecated] Statistical Functions for Single-Cell Analysis
C++
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Other
•0•1•1•0•Updated Sep 13, 2024Sep 13, 2024
cytominer-vm
Public
[DEPRECATED] Packer scripts to create VMs for running image-based profiling workflows on a cluster
virtual-machine image-processing provisioning
virtual-machine image-processing provisioning
Shell
•
MIT License
•2•2•4•0•Updated Sep 13, 2024Sep 13, 2024
cytominer
Public
Methods for Image-Based Cell Profiling
r profiling microscopy
r profiling microscopy
R
•
Other
•28•51•6•1•Updated May 8, 2024May 8, 2024
.github
Public
A special GitHub repository for setting the Cytomining organization profile and default community health files.
BSD 3-Clause "New" or "Revised" License
•2•1•1•0•Updated Feb 2, 2024Feb 2, 2024
DeepProfiler-handbook
Public
Documentation for installing and using of DeepProfiler
documentation deep-learning
documentation deep-learning
HTML
•3•8•6•1•Updated Jan 2, 2024Jan 2, 2024
cytomining.github.io
Public
Cytomining organization GitHub Pages configuration.
BSD 3-Clause "New" or "Revised" License
•1•0•0•0•Updated Nov 14, 2023Nov 14, 2023
pycytominer-Docker
Public
Dockerfile
•
BSD 3-Clause "New" or "Revised" License
•2•1•1•0•Updated Nov 13, 2023Nov 13, 2023
cytominergallery
Public archive
[Deprecated] A Gallery of Cytominer Vignettes
vignette profiling microscopy
vignette profiling microscopy
R
•
Other
•6•1•1•4•Updated Jul 20, 2022Jul 20, 2022
cytominer-python
Public archive
DEPRECATED A Python package for mining patterns in perturbations
biology profiling microscopy
biology profiling microscopy
Jupyter Notebook
•
Other
•1•1•0•0•Updated May 4, 2017May 4, 2017