Cell Maps ImmunoFluorescent Image Downloader

The Cell Maps Image Downloader is part of the Cell Mapping Toolkit

Downloads ImmunoFluorescent image data from Human Protein Atlas or from a CM4AI RO-Crate

• Free software: MIT license
• Documentation: https://cellmaps-imagedownloader.readthedocs.io.

Dependencies

• cellmaps_utils
• requests
• mygene
• tqdm

Compatibility

• Python 3.8 - 3.11

Installation

pip install cellmaps_imagedownloader

Or directly from source:

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

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

Needed files

• samples file: CSV file with list of IF images to download (see sample samples file in examples folder)
• unique file (optional/deprecated): CSV file of unique samples (see sample unique file in examples folder)
• provenance: file containing provenance information about input files in JSON format (see sample provenance file in examples folder)

Usage

For information invoke cellmaps_imagedownloadercmd.py -h

Example usage

cellmaps_imagedownloadercmd.py ./cellmaps_imagedownloader_outdir  --samples examples/samples.csv --provenance examples/provenance.json

Outputs

Every run writes the following artifacts to the output directory:

• blue, red, green, yellow – directories containing downloaded images in different color spectrum.
• proteinatlas.xml.gz – a gzipped XML file containing information fetched from the `Human Protein Atlas`_. This file is only present when the automatic HPA workflow was executed.
• ro-crate-metadata.json – metadata in RO-Crate_ format, a community effort to establish a lightweight approach to packaging research data with their metadata.
• samples.csv or samplescopy.csv – copy of the provided samples file or one generated from the Human Protein Atlas fallback or from the CM4AI table.
• README.txt – human-readable summary of the tool version and output structure.
• task_<timestamp>_start.json / task_<timestamp>_finish.json – provenance records emitted by :mod:`cellmaps_utils.logutils`.
• Optional files such as unique.csv/uniquecopy.csv only appear when --unique or --cm4ai_table arguments were provided.

Via Docker

Example usage

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.

Credits

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