ClearEx

Scalable Analytics for Cleared and Expanded Tissue Imaging.

ClearEx is an open source Python package for scalable analytics of cleared and expanded tissue imaging data. It relies heavily on next-generation file formats and cloud-based chunk computing to accelerate image analysis workflows, enabling tissue-scale computer vision and machine learning.

Installation with pip

We recommend installing ClearEx in a dedicated Anaconda environment:

conda create -n clearex python=3.12
conda activate clearex
cd to/your/cloned/clearex/directory
pip install -e .

Install with uv

You can also manage dependencies using uv, which provides faster installs and lockfile support. First, install uv via the official script:

curl -Ls https://astral.sh/uv/install | sh

Then install ClearEx and optional development extras:

uv pip install -e .          # core install
uv pip install -e '.[dev]'   # development extras

uv is compatible with existing pip or conda workflows, so you can continue to use those tools if preferred.

Launching the CLI

Once installed and the environment is active, start the ClearEx command line interface by running:

clearex

Follow the prompts to perform image registration.