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.
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 .Once installed and the environment is active, start the ClearEx command line interface by running:
clearexFollow the prompts to perform image registration.