Open Beiusxzw opened 1 month ago
Hi, to help with debugging, can you let me know the dimensions of nuclei.tif
and all_genes_sum.tif
? And how many nuclei are in nuclei.tif
(the maximum pixel value in this image)?
Here is the information of nuclei.tif and all_genes_sum.tif, thanks!
Thanks for the info. Seems like the the transcript image is slightly larger (in height) than the DAPI image. They should be the same size. I suppose a workaround is to pad the DAPI image along the top or bottom border, and then run the pipeline using this image instead. It might take a little trial and error to find the right amount of padding to get the two images aligned
Thank a lot for your comments! I will try to pad the DAPI image or filter the input transcript file by maximum coordinates.
I have encountered an error during training bidcell model with a stereoseq dataset.