csi_analysis: Analytical modules and pipelines for CSI-Cancer

This package contains classes and functions for running modular analysis pipelines on data types commonly used by CSI-Cancer. Currently, this only includes whole-slide images (immunoflourescent scans). In particular, this package is meant to provide abstract base classes that can be fit into an then run in a standard pipeline. This will enable more interchangeability and easier development of new modules, such as for image segmentation or feature extraction.

While much of the functionality is specific to the CSI-Cancer organization, some of the functionality and structure may be beneficial for the broader community. Other packages in the CSI-Cancer organization may depend on this package.

Structure

Currently, this package contains the main module: csi_scan_pipeline.py. This module contains the abstract base classes for the pipeline, as well as the ScanPipeline class, which is the main class for running the pipeline. This class contains the run() method, which handles parallelization, logging, and passing data between the module components. 4

Documentation

For more detailed documentation, open up docs/index.html in your browser.

To regenerate the documentation, ensure that you have installed the package and then run:

make_docs

Installation

If you haven't yet, make sure to set up an SSH key for GitHub.

1. Activate your conda (conda activate yourenv) or venv (source path/to/your/venv/bin/activate) environment first.
2. Clone csi_images and install:

cd ~/path/to/your/repositories
git clone git@github.com:CSI-Cancer/csi_analysis.git
pip install ./csi_analysis

Alternatively, you can "editable" install the package, which will allow you to make changes to the package and have them reflected in your environment without reinstalling:

pip install -e ./csi_analysis

This will add symbolic links to your site-packages directory instead of copying the package files over.