Black lines in pixel-decoded images

[stsai7]

Hi,

I am running into an issue where the pixel decoded images seem to have a black line (sometimes 2) running through the image for some reason (see example image below). I am using the run_together pipeline on MERSCOPE data. Do you know what might be the cause of this and how to fix it?

Thanks!

[hyunminkang]

This could happen when the data is not properly sorted (or an incorrect sort axis was specified), but in that case, we usually see much more black space. As this is is a really small gap, so I wonder if the gap actually exist in the original data? If not, please check if the input data was properly sorted.

[stsai7]

Hi! I am so sorry for the delayed reply. The input data seems to be sorted correctly and I don't think that this is in the original data (see screenshot below of the same data but in the MERSCOPE visualizer). Do you have any other potential ideas? I can also send the sorted file if that would be helpful. Thank you so much for your help!