No project description provided
Project description
Morpheus: Generating Therapeutic Strategies from Multiplexed Tissue Images
Introduction
Morpheus is an integrated deep learning framework that takes large scale spatial omics profiles of patient tumors, and combines a formulation of T-cell infiltration prediction as a self-supervised machine learning problem with a counterfactual optimization strategy to generate minimal tumor perturbations predicted to boost T-cell infiltration.
Getting Started
Prerequisites
- Python >=3.9, <3.12
- PyTorch Lightning 2.2.0 or higher
- CUDA 11.7 or higher (for GPU acceleration)
- Other dependencies listed in
requirements.txt
Note numpy 2.0 or above not currently supported
Installation
Using pip (PyPI)
Run the following in the command line
pip install morpheus-spatial
From Source
To install Morpheus from source, clone the repository and install the dependencies:
git clone https://github.com/neonine2/morpheus-spatial.git
cd morpheus-spatial
pip install -r requirements.txt
pip install .
Tutorial
See tutorial_notebook.ipynb
for a complete, self-contained workflow on using Morpheus to generate therapeutic strategies.
Known Issues
OpenMP Conflicts on macOS
Some users may encounter warnings about conflicting OpenMP libraries. If you see a warning about Intel OpenMP and LLVM OpenMP being loaded at the same time, try the following solution:
Set this environment variable before running your Python script or notebook:
export KMP_DUPLICATE_LIB_OK=TRUE
Alternatively, you can set this in your Python code:
import os
os.environ['KMP_DUPLICATE_LIB_OK'] = 'TRUE'
If issues persist, please open an issue on our GitHub repository.
Repository Structure
assets/
: Contains images and other assets used in the documentation and the project.examples/
: Example scripts and notebooks demonstrating various use cases of the Morpheus framework.tutorial.ipynb
: A notebook demonstrating how to reproduce the primary analyses of the paper.
reproduction/
: Includes Jupyter notebooks and scripts for reproducing the main analyses presented in the associated research paper.reproduction_notebook.ipynb
: A notebook demonstrating how to reproduce the primary analyses of the paper.
src/
: The main package directory containing all core modules and functions.tests/
: Contains unit tests for the different modules of the package.requirements.txt
: A file listing all Python dependencies required to run the project.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Hashes for morpheus_spatial-0.10.0-py3-none-any.whl
Algorithm | Hash digest | |
---|---|---|
SHA256 | 0e44ccd540fad5de5a93741b7b83c30660b9cf727cbf6bb7beda21f8220eba7c |
|
MD5 | 7080ee0c808b47471c4c06fba60149e0 |
|
BLAKE2b-256 | 5b4a894a7d19ad981b9cd75598ce7fd69942182de7771d7b9d7206051ac74135 |