In the ABC Atlas webinar ( https://www.youtube.com/watch?v=fuqpSZp7uk0) you mentioned that each MERFISH z plane was segmented separately and then combined. How did you match cells when combining? Based on the distance of the cell centroid?
Sorry for the late reply. I also must have misspoken. The z-planes were segmented each segmented separately, they were segmented with all z-planes at once in 3D.