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# MorphOMICs

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`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.
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- [Overview](#overview)
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- [Required Dependencies](#required-dependencies)
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- [Installation Guide](#installation-guide)
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- [Usage](#usage)

# Overview
`MorphOMICs` is a novel 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 : 3.7+

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numpy : 1.8.1+, scipy : 0.13.3+, pickle : 4.0+, enum34 : 1.0.4+, scikit-learn : 0.19.1+, matplotlib : 3.2.0+
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Additioal dependencies:
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anndata : 0.7+, umap-learn : 0.3.10+, palantir : 1.0.0+, harmonypy : 0.1.4+
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# Installation Guide
```
git clone https://git.ist.ac.at/rcubero/morphomics
cd morphomics
python3 setup.py install
```

# Usage
The easiest way to navigate through `MorphOMICs` is to run the demo notebook:
  - `cd demo`
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  - `jupyter notebook`
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  - Copy the url it generates, it looks something like this: `http://127.0.0.1:8888/?token=a4d016c37e162499e17b2993e69073fac0018bd9a779b762`
  - Open it in your browser
  - Then open `Morphomics_demo.ipynb`
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