Quick Start Guide

Installation

SpatialCells can currently only be installed from source. To install, download code from the repository and change to the code folder.

Run the following commands from the root directory of SpatialCells:

pip install -r requirements.txt
pip install .

It is recommended to install SpatialCells in a virtual environment, such as conda. A conda environment can be created with the following yaml file:

conda env create --name spatialcells --file=conda.yaml
pip install .

The conda.yaml is specified as follows:

name: spatial-cells-env

channels:
  - conda-forge
  - defaults

dependencies:
  - python>=3.7, <3.11
  - ipykernel
  - matplotlib>=3.7.0
  - pandas>=2.0.3
  - seaborn>=0.12.2
  - shapely>=2.0
  - tqdm
  - pip
  - pip:
      - anndata==0.9.2
      - scanpy==1.9.4