Giovanni Palla
Giovanni Palla
hi @josiejenyne it looks like the `fov_key` which is hardcoded as "fov" is not correct for your file. Again this is possibly because the company changed the spec or because...
hi, thank youf ro your interest in squidpy, what do you mean "export the cropped spot as numpy arrays"? with the function generate_spot_crops you should be able to do just...
closing due to inactivity
hi @Rafael-Silva-Oliveira , could increase the memory available on your system and try to run it again>?
I think we might be hitting performance issues on various tools on squidpy with this huge number of cells. I think make the algorithms more memory efficient is not trivial...
after trying different combinations, this seems to work: `scanpy==1.6.0 anndata==0.7.5 umap==0.4.6 numpy==1.18.2 scipy==1.4.1 pandas==1.1.3 scikit-learn==0.23.2 statsmodels==0.11.1 python-igraph==0.8.3 leidenalg==0.8.3`
just pinging this as I was trying today but had to create new env with python3.9
hi @ankitbioinfo I believe the suggested code has an error ```python ncem.data = customLoader(...) ``` should be ```python from ncem.data import customLoader loader = customLoader(...) ```
we discussed this extensively in the past and I still think it's a pretty bad and unique ux design, wrong arguments should always errors, I understand that we had other...