Installation

CellRefiner requires Python >= 3.9 and NVIDIA GPU with CUDA support.

Step 1: Create and activate a virtual environment

We recommend using conda or mamba for environment management.

conda create -n cellrefiner_env python=3.9
conda activate cellrefiner_env

Step 2: Install cellrefiner from GitHub

pip install git+https://github.com/XiangyuKuang/cellrefiner.git

Step 3: Install CuPy (Optional)

CuPy installation will accelerate preprocessing.spatial_mapping()

We recommend installing CuPy and CUDA toolkit via conda to avoid compatibility issues:

conda install cupy cudatoolkit -c conda-forge