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 UV

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

Install uv

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

Confirm that uv is installed

uv --version

Install ClearEx

Then, in the root directory of the cloned ClearEx repository, run:

# Create a virtual environment in the project root.
uv venv

# Activate virtual environment
source .venv/bin/activate

# If you want to operate the package in a non-editable mode, run:
uv sync

# Install the ClearEx package in editable mode with all core dependencies.
uv pip install -e .

# Optional - Install development dependencies
uv pip install -e ".[dev]"

# Optional - Install the documentation's dependencies.
uv pip install -e ".[docs]"

# Optional - Install the deconvolution dependencies. Requires slower installation.
uv pip install -e ".[decon]"

# Or install everything at once:
uv pip install -e ".[dev,docs,decon]"

Installation in a High Performance Computing environment.

There are several considerations for installation in a high performance computing (HPC) environment. While these are not unique to ClearEx, we provide some guidelines here to help you get started. Please see the INSTALLATION_NOTES.md file for more details.