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YangLabHKUST / UCS

Code for "UCS: a unified approach to cell segmentation for subcellular spatial transcriptomics"
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Error in scvi version when running the downstream process (analyse.py) #4

Open devianggr opened 1 week ago

devianggr commented 1 week ago

Hi,

Thanks for providing the repo!

Currently, I am doing segmentation of my Vizgen and Xenium datasets. And I am curious about the downstream process you provided in this repo. However, when I wanted to run the analyse.py, I encountered a problem, especially with the scvi version.

DeprecationWarning: scvi is deprecated, please uninstall scvi via pip uninstall scvi and install the new scvi-tools package at github.com/YosefLab/scvi-tools warnings.warn(deprecation_msg, DeprecationWarning)

In this case, I have even tried to install a new scvi-tools, however, it led again to another error : ImportError: cannot import name 'AlignedViewMixin' from 'anndata._core.aligned_mapping'

Since I am not so familiar with bioinformatic analysis, it would be nice if you could help solve this issue.

Thanks again for considering my issue! I am looking forward to your response.

Best regards, Devi

chenyhvvvv commented 1 week ago

Hi, have you followed the instruction to install UCS? You can try to reinstall UCS and ignore the warning and then try to run the notebook. Since python package Warning is different from Error and may not influence the code.

devianggr commented 1 week ago

Hi,

thanks for the suggestion! I reinstalled everything, and still, the same problem occurred image

Best, Devi

chenyhvvvv commented 1 week ago

Try to reinstall scvi and anndata: pip install scvi_tools==1.1.2 pip install anndata==0.10.8