Michael Kunst

apply image rotation when plotting tissue / cellxgene

1

## Imege rotation Hi, when plotting cell position on top of images (sc.pl.spatial) would it be possible to apply a predefined rotation to it? This could either be an argument...

bug loading vizgen data

13

## Description Trouble using vizgen data with sq.read.vizgen(). Function is expected 8 columns in metadata file mine has 9 ## Minimal reproducible example ```python adata = sq.read.vizgen( path=data_path, counts_file=os.path.join(data_path,section,file_path,cbg_file), meta_file=os.path.join(data_path,section,file_path,meta_file),...

problem creating anndata file from MERSCOPE vpt output

3

Hi, I'm trying to create a spatialdata object of a MERSCOPE experiment from the vpt output file but there is an index mismatch error when generating the anndata file Here...

how to handle empty tiles

3

Hi, the images from my spatial transcriptomics data don't fill the entire image so we I split up the image into smaller tiles I get an error that there are...

issue loading MERSCOPE results

3

Hi, when trying to read in a MERSCOPE results I'm getting the following error Cell In[10], line 1 ----> 1 sdata = sdio.merscope("/allen/programs/celltypes/production/mfish/mfishmerscopemouseatlas/1288760920/region_0") File /allen/programs/celltypes/workgroups/rnaseqanalysis/mFISH/michaelkunst/github_projects/spatialdata-io/src/spatialdata_io/readers/merscope.py:192, in merscope(path, vpt_outputs, z_layers, region_name,...