Ted Zhang and Bob Murphy, Carnegie Mellon University V1.4.1 May 8, 2024
SPRM is a statistical modeling program used to calculate a range of descriptors/features from multichannel cell images. It uses these descriptors for clustering of cells and saves them for use for comparison and content-based search of the images. It can be used with any type of multichannel 2D or 3D image (e.g., CODEX, IMS).
Two OMETIFF files from the output of CytoKit - 4D Multiplexed intensity Image (3D for multiple channels) 4D Indexed Image (3D for multiple segmentations) containing one channel for each type of segmentation (currently “cells”, “nucleus”, “cell membrane” and “nuclear membrane”).
[python_path] SPRM.py --img-dir [img_dir_path] --mask-dir [mask_dir_path] --optional-img-dir [optional_img_dir_path]SPRM takes in three command line arguments that specify the path in the following order:
Image directory path
Mask directory path
Options image file path
- Python 3.8 or newer
- AICSImageIO
- Matplotlib
- Numba
- NumPy
- Pandas
- Pillow
- Pint
- scikit-learn
- SciPy
- Shapely
For more information on specific analytical tools and outputs of SPRM:
Code in this repository is formatted with black and isort.
A pre-commit hook configuration is provided, which runs black and isort before committing.
Run pre-commit install in each clone of this repository which you will use for development (after pip install pre-commit
into an appropriate Python environment, if necessary).
Robert F. Murphy - murphy@cmu.edu
Ted (Ce) Zhang - tedz@andrew.cmu.edu