cellmaps-image-embedding 0.3.3

A tool to generate embeddings from HPA IF images

Cell Maps ImmunoFluorescent Image Embedder

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

Generate embeddings from ImmunoFluorescent image data from Human Protein Atlas

• Free software: MIT license

• Documentation: https://cellmaps-image-embedding.readthedocs.io.

Dependencies

• cellmaps_utils

• tqdm

• numpy

• pandas>=0.23.1

• torch

• torchvision

• opencv-python

• mlcrate

• scikit-image

• scikit-learn>=0.19.0

• Pillow

Compatibility

• Python 3.8 - 3.11

Installation

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

For developers

To deploy development versions of this package

Below are steps to make changes to this code base, deploy, and then run against those changes.

1. Make changes

   Modify code in this repo as desired

2. Build and deploy

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

Needed files

The output directory for the image downloads is required (see Cell Maps Image Downloader). Optionally, a path to the image embedding model can be provided.

Usage

For information invoke cellmaps_image_embeddingcmd.py -h

Example usage

cellmaps_image_embeddingcmd.py ./cellmaps_image_embedding_outdir --inputdir ./cellmaps_imagedownloader_outdir

Via Docker

Example usage

Coming soon...

Credits

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

History

0.3.3 (2025-07-03)

• Fix for UD-3116, missing header 0 row

0.3.2 (2025-05-13)

• Updated to PEP 517 compliant build system

0.3.1 (2025-03-18)

• Add version bounds for required packages.

• Bug fix for change in pytorch 2.6.

0.3.0 (2024-12-02)

• Added README generation.

• Refactor code.

0.2.1 (2024-09-06)

• Bug fix in --inputdir argument.

0.2.0 (2024-08-29)

• Added --provenance flag to pass a path to json file with provenance information. This removes the necessity of input directory to be an RO-Crate.

• Bug fixes

  • Resolved an issue in embedding generation process where images associated with multiple genes were not correctly handled (ambiguous antibodies).

0.1.0 (2024-02-01)

• First release on PyPI.