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cytomining

17 indexed repositories · View on GitHub

pycytominer
Python package for image-based profiling

Python · 145 stars
DeepProfiler
Morphological profiling using deep learning

Python · 129 stars
cytominer
Methods for Image-Based Cell Profiling

R · 52 stars
copairs
Find profile pairs and compute retrieval metrics between them.

Python · 24 stars
CytoTable
Harmonize high-content image analysis tool outputs for processing with Pycytominer and other Cytomining tools.

Python · 21 stars
CytoDataFrame
An in-memory data analysis format for single-cell profiles alongside their corresponding images and segmentation masks.

Python · 13 stars
profiling-recipe
Image-based Profiling Recipe

Python · 11 stars
profiling-handbook
Image-based Profiling Handbook

11 stars
coSMicQC
Single cell Morphology Quality Control (coSMicQC)

Python · 11 stars
cytominer-database
[DEPRECATED] A package for storing morphological profiling data.

Python · 10 stars
DeepProfiler-handbook
Documentation for installing and using of DeepProfiler

HTML · 8 stars
cytominer-eval
[Deprecated] Common Evaluation Metrics for DataFrames

Python · 7 stars
cytominer-vm
[DEPRECATED] Packer scripts to create VMs for running image-based profiling workflows on a cluster

Shell · 2 stars
pycytominer-Docker

Dockerfile · 1 star
pipeline-examples
Example pipelines for training purposes

Jupyter Notebook · 1 star
.github
A special GitHub repository for setting the Cytomining organization profile and default community health files.

1 star
profiling-template
Image-based Profiling Template

0 stars

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303 open issues indexed

Enhancements via automated Docker image builds, `cell-locations` extra, and commit hash specification Open

enhancement

cytomining/pycytominer-Docker#2 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Issue on page /docs/03-images.html Open

cytomining/DeepProfiler-handbook#12 · 8 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
A few Issues on page /docs/04-metadata.html Open

cytomining/DeepProfiler-handbook#13 · 5 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
Improvements to profiling chapter - Issue on page /docs/07-profiling.html Open

cytomining/DeepProfiler-handbook#17 · 5 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Pycytominer section in downstream analysis Open

cytomining/DeepProfiler-handbook#18 · 3 comments · 0 reactions · 2 assignees · Indexed Sep 15, 2026
Add training instructions for Cell Painting CNN-1 / Issue on page /docs/07-train.html Open

cytomining/DeepProfiler-handbook#20 · 1 comment · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Some additional supporting code. Open

cytomining/DeepProfiler-handbook#21 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
Implement stepwise feature selection algorithm to remove linear dependencies Open

feature request

cytomining/cytominer#19 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Create a subpopulation report Open

feature request

cytomining/cytominer#111 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Consider adding cytominer on conda Open

cytomining/cytominer#132 · 14 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update cytominer-pipeline vignette to reflect current practices Open

cytomining/cytominer#144 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Rename whiten -> spherize Open

cytomining/cytominer#150 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Increasing the column limits Open

cytomining/cytominer#157 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Update VM Open

cytomining/cytominer-vm#4 · 12 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
EFS not giving write access initially Open

cytomining/cytominer-vm#7 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add Git Credential Manager to VM Open

cytomining/cytominer-vm#8 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
SSH timeout Open

cytomining/cytominer-vm#9 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add an `Audit` test applying to more than one group Open

cytomining/cytominer-eval#3 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Evaluation metrics with full vs. subset profiles Open

cytomining/cytominer-eval#4 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
percent_strong outputs nan when no replicates are present Open

enhancement good first issue

cytomining/cytominer-eval#15 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Option to not have to recalculate melted similarity matrix Open

enhancement good first issue

cytomining/cytominer-eval#16 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Calculate MOA enrichment as an evaluation metric Open

enhancement

cytomining/cytominer-eval#17 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Define percent strong Open

documentation

cytomining/cytominer-eval#21 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Define precision and recall @ k Open

documentation

cytomining/cytominer-eval#22 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Implement Mahalanobis distance to negative controls Open

cytomining/cytominer-eval#23 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add reporting option to percent_strong Open

enhancement good first issue

cytomining/cytominer-eval#24 · 0 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
Support multiple columns as replicate indicators Open

enhancement

cytomining/cytominer-eval#28 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add option to summarize replicate z-scores from controls as medians Open

enhancement

cytomining/cytominer-eval#38 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Running metric_melt several times Open

cytomining/cytominer-eval#51 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Further optimizations Open

cytomining/cytominer-eval#53 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
assert melt in enrichment Open

enhancement good first issue

cytomining/cytominer-eval#54 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Upgrade to minimum pandas 1.2 and deprecate python 3.5 Open

question

cytomining/cytominer-eval#56 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Figure out why percent replicating is apparently insensitive to number of replicates Open

question

cytomining/cytominer-eval#60 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
`precision_recall()` counts within group connections twice but not between group connections Open

cytomining/cytominer-eval#62 · 14 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Remaining tests for the new precision recall Open

cytomining/cytominer-eval#64 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add Precision at R to precision at k Open

cytomining/cytominer-eval#65 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add https link for cytominer-eval installation Open

cytomining/cytominer-eval#66 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Issues with groupby columns Open

cytomining/cytominer-eval#67 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Add Demo of Hit@k Open

cytomining/cytominer-eval#68 · 0 comments · 0 reactions · 1 assignee · Indexed Sep 15, 2026
calculate_precision_recall() fails when replicate_groups has just one member Open

cytomining/cytominer-eval#69 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Specify external dependencies Open

Enhancement

cytomining/cytominer-database#21 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Allow searching for CSVs at arbitrary depths Open

Enhancement

cytomining/cytominer-database#88 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Don't ingest objects when cell count = 0 Open

Enhancement

cytomining/cytominer-database#91 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Handle very large datasets (>100M single cells) Open

Feature

cytomining/cytominer-database#96 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Ingest fails when columns don't align across sets Open

Bug

cytomining/cytominer-database#100 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
License file in MANIFEST.in Open

cytomining/cytominer-database#112 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Explicitly test for nan being handled correctly Open

cytomining/cytominer-database#123 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Other ways of creating db backends or obviating the need for a db Open

Notes

cytomining/cytominer-database#124 · 7 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Cytominer learning Open

cytomining/cytominer-database#125 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Integrate the use of a reference schema for the '--sqlite' option (done for `--parquet`) Open

cytomining/cytominer-database#127 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026

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