Giovanni Palla comments

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                                            Giovanni Palla

Co-occurrence gives 'nan' if n_splits>1 in large dataset

hi @Mena-SA-Kamel , since 1.5 it should have been fixed, could you try and install the latest version of squidpy?

sq.gr.ripley() cost too much memory

hi @wangjiawen2013 , I can see the problem, unfort I don't have capacity to write a memory efficient implementation. Any help would be highly appreciated.

When attempting to install, dependency "pygeos" gives: module 'configparser' has no attribute 'SafeConfigParser'

hi @azguan yes this is a known issue ith python 3.12 we will fix it soon but don't have an estimate now, easier it is to not use python3.12 with...

After removing rows with only NaN interactions, none remain.

hi @asmlgkj are you using log normalized data?

Import from QuPath or CODEX Dataset

Hi @andreevg04 , unforutnatley I don't have a lot of experience with qupath. Can I suggest to take a look at this tutorials from spatialdata https://spatialdata.scverse.org/en/latest/tutorials/notebooks/notebooks/examples/models2.html to understand how to...

Working on 3D segmentation matrix

> Could anyone provide guidance on how I might resolve this issue and successfully visualize my images? could you try to `squeeze()` the numpy array? I'm not sure how the...

MultiScaleImage datatree.DataTree attrs in sdata object lost when writing to disk

hi @simone-codeluppi , thanks for reporting this, so the transformation is stored in attrs of each scale, e.g. in the example above ```python img_scaled2= Image2DModel.parse( img, dims=("c","y","x"), chunks=(1, 1000, 1000),...

MultiScaleImage datatree.DataTree attrs in sdata object lost when writing to disk

hi @simone-codeluppi will close this but feel free to reopen if necessary

multiprocessing for dataloader

hi @xiao233333 , thank you for the interest in spatialdata. Can you share how did you created the train_dataset that you pass to the dataloader?

sdata does not save when chunks are not equal

I think this could be an issue with the parser