Installation Guide

SubsetMask is a lightweight toolkit for coordinate-based subsetting of spatial transcriptomics datasets, with support for interactive region selection.

Install from local folder (downloaded or cloned)

✅ Step-by-step

  1. Clone or download the repository:

git clone https://github.com/RobinCarvajal/SubsetMask.git

Or download the ZIP and unzip it.

  1. Navigate into the project directory:

cd SubsetMask

  1. Install the package:

Regular install:

pip install .

Or editable/development install:

pip install -e .

📋 Requirements

SubsetMask requires:

  • Python 3.11+

  • pandas, numpy, geopandas, shapely, opencv-python, matplotlib, imageio, napari

If not using pyproject.toml, you can install dependencies manually:

pip install -r requirements.txt

🔍 Verifying the installation

After installation, you should be able to run:

import subsetmask as sm