Installation

Installation#

Make sure you have Conda installed on your system before proceeding with these steps. If not, you can install Miniconda or Anaconda from https://docs.conda.io/en/latest/miniconda.html.

Create and activate a conda environment#

conda create --name insitupy python=3.13
conda activate insitupy

Install Jupyter kernel#

To ensure that the InSituPy package is available as a kernel in Jupyter notebooks within your conda environment, you can follow the instructions here.

Install InSituPy#

Method 1: Install from PyPi#

pip install insitupy-spatial

This base installation includes napari and related visualization dependencies.

InSituPy currently requires zarr>=3.0.0 and targets the zarr v3 format. Legacy zarr v2 workflows will be only partially supported in the future.

Optional: Install with SpatialData support (spatialdata>=0.7.2)#

pip install insitupy-spatial[spatialdata]

Method 2: Installation from Cloned Repository#

  1. Clone the repository to your local machine:

    git clone https://github.com/SpatialPathology/InSituPy.git

  2. Navigate to the cloned repository and select the right branch:

    cd InSituPy

# Optionally: switch to dev branch
git checkout dev

  3. Install the required packages using pip within the conda environment:

    # basic installation
pip install .

# for developmental purposes add the -e flag
pip install -e .

Method 3: Direct Installation from GitHub#

  1. Install directly from GitHub:

    pip install git+https://github.com/SpatialPathology/InSituPy.git