Hi, I'm a bioinformatician at a research institute processing in-house generated 10X Visium-HD datasets. I've noticed that the microscopy images sometimes have tissue structures that are completely absent from the Cytassist image (including inside the borders). I asked the wet-lab researcher performing the experiments and they told me that it's because they use consecutive tissue sections, one for the microscopy H&E high resolution imaging and another for the actual run with the Cytassist. I don't see anywhere in the 10X guidelines that this is standard protocol and I think this can cause image misalignment issues. Does anyone have experience with this that can clarify if it's standard procedure to use consecutive tissue sections? And that 10X's Spaceranger is prepared to deal with this? Many thanks submitted by /u/Different_Basket2544 [link] [comments]