Simon Frerich comments

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                                            Simon Frerich

Best practise for sample integration

Hi @giovp, thanks for your reply, I will have a look!

adata$uns error: Conversion from numpy array type 20 is not supported

The bug is due to `adata.uns['rank_genes_groups']`, after deleting `rank_genes_groups` it works perfectly

Convert log_eFC to log_2FC in differential gene expression chapter

Just FYI, [here](https://github.com/RGLab/MAST/issues/100#issuecomment-429132244) the MAST developer says "the base of the logarithm is whatever you set it to be when you log transform your counts", which means that you would...

Missing filtered table in polygon_query() of MERFISH data

Hi, thanks for the quick reply. Here's a gif showing how I create the manual annotations. I save the layer using shift+E. Does that help? ![output2](https://github.com/scverse/spatialdata/assets/70199914/9a5ca8e3-b9cb-4b42-8231-b7e76f61f023) package versions: anndata 0.10.8...

Missing filtered table in polygon_query() of MERFISH data

Thank you, and sorry for the delay. Even when loading a saved SpatialData file with associated Zarr store I found that the output of ``sd.polygon_query()`` with ``filter_tables=True`` does not contain...

Question about x_min, x_max in MerscopeSample().load_transcripts()

@EliHei2 Thanks for the great tool! Do you suggest using the workaround for now, or is full MERSCOPE/MERFISH support coming soon?