Hello, I try to run spaceranger count after realizing a manual alignment of cytAssist image and microscope image. But while everything seems fine during the manual alignment done on Loupe Browser, and while I don’t get any error during spaceranger count run, the web summary show weird results:

First, the fiducials are not in the proper position while I indicated their positions in Loupe Browser Secondly and most importantly, my cytAssist image is now not detected (cf screenshot). As a consequence it does not detect any UMI.

Has anyone encountered such an issue?

I use spaceranger 3.0.1

I join here all screenshots showing the issue.

Thanks a bunch!