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Installation

Run these commands from a checkout of this repository.

Python 3.12 and uv are required.

uv sync

On Windows and Linux, this includes the default gpu dependency group, which selects the CUDA extra for deconvolution and registration. Plain uv sync and uv run keep CuPy and its NVIDIA runtime dependencies installed; you do not need to repeat --extra gpu. The explicit extra remains supported.

To deliberately omit the default GPU group (for a non-CUDA environment):

uv sync --no-group gpu

Native Windows also requires the pure-Python cucim.skimage package from a local cuCIM checkout because RAPIDS does not publish its standard wheel there.

cuCIM on Windows

Install cuCIM from the tagged source checkout using an editable installation:

  1. In the Start menu, right-click Miniforge Prompt and select Run as Administrator so Git can create symbolic links.
  2. Enable symbolic links globally for Git:
git config --global --add core.symlinks true
  1. Change to this project's directory and activate the environment created by uv sync:
cd /d C:\Users\qi2lab\Documents\github\opm-processing-v2
.venv\Scripts\activate.bat
  1. Install cuCIM:
pip install -e "git+https://github.com/rapidsai/cucim.git@v26.08.00#egg=cucim-cu12&subdirectory=python/cucim"

Continue with the first workflow.