Hi! I am not really sure if BioFormats is intended to handle this situation so, first a description!
I have a Prairie View set of tif files along with their xml and env files, with all of the appropriate metadata included to rebuild a 3D volume (PVScan version=“188.8.131.520” , BioFormats 5.8.2 first, and then 6.0.0). The Z stacks are not all equal in size since this was scanned on a live sample, and it is most efficient to only scan the area of interest (I wish this could be done on our 880!). That means the final volume would not be a cuboid.
Should it be possible to put together and view this kind of image with BioFormats? Currently when I open the xml file with Fiji/BioFormats plugin, it reads each tile as a separate Z stack and opens each correctly (with “Stitch tiles” checked). It does not put them all together though, in terms of their relative X Y and Z coordinates. When using other software and attempting to open these images, I generally see one of these stacks (QuPath (via BioFormats), Imaris).
Imaris reads each stack as a time series (not sure if that is relevant as I think they have their own reader).
I have hosted a sample data set here: https://drive.google.com/drive/folders/1tqyhZij6q7hMp9w7S0JsEpWquTzWfzQK?usp=sharing
Please let me know if there is any other information I can provide.
Cheers, and thank you for your time.