Importing cellcharter


I am trying to import cellcharter to perform clustering on MERSCOPE data and I run into errors during the import:

I am using spatialdata==0.0.12 and the below commands for other dependencies
conda create -n cellcharter-env -c conda-forge python=3.10 mamba
conda activate cellcharter-env
mamba install pytorch==1.13.1 torchvision==0.14.1 torchaudio==0.13.1 pytorch-cuda=11.7 -c pytorch -c nvidia
pip install cellcharter
pip install scvi-tools==1.0.3

Any help would be greatly appreciated. Thank you!

Hi, welcome to our forum!

Can you please try again your code using the latest spatialdata version (0.0.15)? It should fix the issue, but if not please let me know.