Morphomics 2.0.0

morphOMICs: a python package for the topological and statistical analysis of microglia morphology (appliable to any cell structure)

morphOMICs

morphOMICs is a Python package containing tools for analyzing microglia morphology using a topological data analysis approach. Note that this algorithm is designed not only for microglia applications but also for any dynamic branching structures across natural sciences.

• Overview
• Required Dependencies
• Installation Guide
• Usage

Overview

morphOMICs is a topological data analysis approach which combines the Topological Morphology Descriptor (TMD) with bootstrapping approach, dimensionality reduction strategies to visualize microglial morphological signatures and their relationships across different biological conditions.

Required Dependencies

Python : 3.9

numpy : 1.8.1+, scipy : 0.13.3+, pickle : 4.0+, enum34 : 1.0.4+, scikit-learn : 0.19.1+, tomli: 2.0.1+, matplotlib : 3.2.0+, ipyvolume: 0.6.1+

Additional dependencies: umap-learn : 0.3.10+, morphon: 0.0.8+, pylmeasure: 0.2.0+, fa2 (https://github.com/AminAlam/forceatlas2)

Installation Guide

Using PyPi

conda create -n morphology python=3.9
conda activate morphology
pip install morphomics

Using Source Code

conda create -n morphology python=3.9
conda activate morphology

git clone https://github.com/siegert-lab/morphOMICs.git
cd morphOMICs
pip install -e .

Usage

To run a typical morphOMICs pipeline, create a parameter file with filename Morphomics.Parameters.[Parameters ID].toml (see examples). The parameter file is build such that it modularizes the steps required to generate the phenotypic spectrum. Once you have completed filling up the necessary information in the parameter file, run python3 run_morphomics.py [path-to-parameter-file]

To get started, download a demo folder containing sample traces, a parameter file and tutorial Jupyter notebooks HERE. Once downloaded, place the extracted folder morphOMICs_v2_Tutorials inside morphomics_v2. On the terminal, cd to morphOMICs_v2_Tutorials and run python3 ../run_morphomics.py Morphomics.Parameters.1.toml You can also follow each steps in the protocol in Jupyter notebook in morphOMICs_v2_Tutorials/morphOMICs_v2_Tutorial.ipynb.