Please refer to our FAQ and look at our known issues before opening a bug report.
Describe the bug
With the current set up, we've noticed that when the source row is stitched with the rosetta compensated images, that row appears to be blacked out.
A couple causes for this:
img_sub_folder needs to be set to "rescaled", it is currently stitching the raw source images instead (considerably different values)
percent_norm can be increased to 99 instead of 98, currently producing nan values in the image because of very low signal values at 98th percentile (when scaling images down by 0.25)
Expected behavior
Be able to view the stitched with noodle images without issue.
Please refer to our FAQ and look at our known issues before opening a bug report.
Describe the bug With the current set up, we've noticed that when the source row is stitched with the rosetta compensated images, that row appears to be blacked out. A couple causes for this:
Expected behavior Be able to view the stitched with noodle images without issue.
To Reproduce Run the rosetta notebook.