Dependencies

• cellmaps_utils

• cellmaps_imagedownloader

• cellmaps_ppidownloader

• cellmaps_image_embedding

• cellmaps_ppi_embedding

• cellmaps_coembedding

• cellmaps_generate_hierarchy

• cellmaps_hierarchyeval

• networkx

• scipy

• tqdm

Compatibility

• Python 3.8 - 3.11

OS Requirements

This package is supported for macOS and Linux. The package has been tested on the following systems:

• macOS: Ventura (13.5)

• Linux: Rocky Linux 8

Installation

Install from PyPi

pip install cellmaps_pipeline

Install from Github

git clone https://github.com/idekerlab/cellmaps_pipeline
cd cellmaps_pipeline
pip install -r requirements_dev.txt
make dist
pip install dist/cellmaps_pipeline*whl

Run make command with no arguments to see other build/deploy options including creation of Docker image

make

Output:

clean                remove all build, test, coverage and Python artifacts
clean-build          remove build artifacts
clean-pyc            remove Python file artifacts
clean-test           remove test and coverage artifacts
lint                 check style with flake8
test                 run tests quickly with the default Python
test-all             run tests on every Python version with tox
coverage             check code coverage quickly with the default Python
docs                 generate Sphinx HTML documentation, including API docs
servedocs            compile the docs watching for changes
testrelease          package and upload a TEST release
release              package and upload a release
dist                 builds source and wheel package
install              install the package to the active Python's site-packages
dockerbuild          build docker image and store in local repository
dockerpush           push image to dockerhub

Expected install time: ~30-40s

Before running tests, please install pip install -r requirements_dev.txt and pip install -r requirements.txt.

For developers

# From base directory of this repo cellmaps_pipeline
pip uninstall cellmaps_pipeline -y ; make clean dist; pip install dist/cellmaps_pipeline*whl

Needed files

• samples file: CSV file with list of IF images to download (see sample samples file in examples folder)

• unique file: CSV file of unique samples (see sample unique file in examples folder)

• bait list file: TSV file of baits used for AP-MS experiments

• edge list file: TSV file of edges for protein interaction network

• provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)

Usage

For information invoke cellmaps_pipelinecmd.py -h

Instruction for running cellmaps_pipeline on your data can be found here.

Example usage (Demo)

cellmaps_pipelinecmd.py ./cellmaps_pipeline_outdir --samples examples/samples.csv --unique examples/unique.csv --edgelist examples/edgelist.tsv --baitlist examples/baitlist.tsv --provenance examples/provenance.json

Expected run time for demo: ~55min (macOS: Ventura 13.5, M2 Processor)

Coming soon...

Cite

If you find this tool useful, please cite:

Lenkiewicz, J., Churas, C., Hu, M., Qian, G., Jain, M., Levinson, M. A., … & Schaffer, L. V. (2025). Cell Mapping Toolkit: An end-to-end pipeline for mapping subcellular organization. Bioinformatics, 41(6), btaf205, https://doi.org/10.1093/bioinformatics/btaf205.

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.

1.4.0 (2026-07-27)

• implementation of networkfromebedding cytoscape web service app that takes the embedding file and outputs a CX2Network wrapped in the result json structure for cytoscape web apps.

• implementation of communitydetection cytoscape web service app that takes a CX2Network as input from the service app, runs hidef community detection with multiple ppi cutoffs

• Updated dependency cellmaps_coembedding to 1.6.0 from 1.2.2

• Updated dependency cellmaps_generate_hierarchy to 0.3.0.post1 from 0.2.4

1.3.0 (2025-07-22)

• Updated dependency cellmaps_utils to 0.9.0 from 0.8.0

• Updated dependency cellmaps_image_embedding to 0.3.3 from 0.3.2

• Updated dependency cellmaps_ppi_embedding to 0.4.3 from 0.4.2

• Updated dependency cellmaps_coembedding to 1.3.1 from 1.2.2

1.2.0 (2025-05-19)

• Updated dependency cellmaps_utils to 0.8.0 from 0.7.0

• Updated dependency cellmaps_imagedownloader to 0.3.0 from 0.2.1

• Updated dependency cellmaps_ppidownloader to 0.2.2 from 0.2.1

• Updated dependency cellmaps_image_embedding to 0.3.2 from 0.3.1

• Updated dependency cellmaps_ppi_embedding to 0.4.2 from 0.4.1

• Updated dependency cellmaps_coembedding to 1.2.2 from 1.2.0

• Updated dependency cellmaps_generate_hierarchy to 0.2.4 from 0.2.3

• Updated dependency cellmaps_hierarchyeval to 0.2.2 from 0.2.1

• Updated to PEP 517 compliant build system

1.1.0 (2025-03-20)

• Unique flag is no longer required to run the pipeline

• Updated versions of packages

1.0.0 (2024-12-09)

• First release on PyPI.