We routinely take whole well tiled images on our Zeiss, run the resulting multiscene CZI file through “Split Scenes” in Zen, and then use a macro to run large numbers of of individual scene CZIs through FIJI to use either Grid/Collection or MIST-based stitching. This has never worked in the Java 8 versions of Fiji, as it appears BioFormats in Java 8 will only open the Pyramidal Hierarchy files as whole well image with overlaps determined by stage position, and cannot open the individual tiles. I have been waiting for an update to correct this, but none has come. Our workaround has been to use the last Java6 build of FIJI. However, this is no longer an option and we need to upgrade some version of the Java8 builds.
Can anyone advise how to correct this issue so we can open tiled czi files as image stacks?