Installation

Installation#

We recommend installing CellPick in an isolated environment using pipx:

pipx install cellpick

Note

You can install pipx using pip install pipx. Running pipx ensurepath will add pipx (and cellpick) to your PATH.

This will install the cellpick command globally, isolated from your other Python packages.

Alternative Installation Methods#

Using pip#

You can also install CellPick using pip directly:

pip install cellpick

Using conda#

For conda users, you can create a dedicated environment:

conda create -n cellpick python=3.11
conda activate cellpick
pip install cellpick

SpatialData Support#

To use CellPick with SpatialData (.zarr) files, you need to install the optional SpatialData dependencies:

pip install cellpick[spatialdata]

Or install SpatialData separately:

pip install spatialdata spatialdata-io

Note

SpatialData support requires Python 3.9 or higher.

Contents