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Spatial Single Cell Analysis in Python
Hi squidpy team, Thank you for a great tool! I think the sq.pl.spatial_scatter function might not be working as expected. Setting return_ax = True, should return Axes object, but it's...
Initial data is coming up in which perturbation screens have been analysed using spatial technologies. This workstream should deal with tools to analyse and compare these data. @Zethson
Currently, squidpy focusses mostly on local [spatial neighborhoods ](https://squidpy.readthedocs.io/en/stable/notebooks/tutorials/tutorial_vizgen_mouse_liver.html#neighborhood-enrichment) for niche analysis purposes. However, there are other definitions which one could use. Including other options could increase tool usage and...
A future extension of the commonly 2D spatial data would be to include "layered" 2.5D data which can then be analysed in 3D. `spatialdata` already allows for storing it, however,...
Hello All, I was wondering if there is any effort to port some of the squidpy tools (e.g. segmentation) to R. For example as Velociraptor R package does for scvelo....
Dear squidpy developers, Thank you for creating this useful tool. Squidpy has been extremely helpful in the analysis of spatial transcriptome data, aiding our research. Currently, we are performing analyses...
Dear Squidpy developers: I'm not quite sure some of the parameters in ```squidpy.gr.spatial_neighbors()``` function. I noticed that there are parameters of ```n_neighs``` and ```radius``` for the generic coordinates data, what's...
## Description WARNING: Failed to open the url with default certificates, trying with certifi. Visium_FFPE_Mouse_Brain. Error: HTTP Error 403: Forbidden WARNING: Failed to open the url with default certificates, trying...
Hi Squidpy developers: I am looking for using squidpy to measure the spatial autocorrelation (like Moran's I ) for genes in spatial dataset. I was wondering if the result would...
Hi, thanks for developing this tool! Have you considered to add Geographically Weighted Regression (GWR) for evaluating gene-gene correlation? Fig4 in this perspective: https://www.sciencedirect.com/science/article/pii/S0092867423012199 Thanks again!
