# 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](https://docs.conda.io/en/latest/miniconda.html).

## Create and activate a conda environment

   ```bash
   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](https://ipython.readthedocs.io/en/stable/install/kernel_install.html).

## Install InSituPy

### Method 1: Install from PyPi

   ```bash
   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`)

   ```bash
   pip install insitupy-spatial[spatialdata]
   ```

### Method 2: Installation from Cloned Repository

1. **Clone the repository to your local machine:**

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

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

   ```bash
   cd InSituPy

   # Optionally: switch to dev branch
   git checkout dev
   ```

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

   ```bash
   # 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:**

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