QuPath open ome tiff's first _Z0000.tif tif file shows abnormal stack instead of slice


I have several tif files(exported as ome tiff by other software, with “strip” option and XY dimension on single tif) to be processed in QuPath 0.2.0-m3 one by one.



The problem is that, when I drag & open PyramidalCell_Z000.tif, QuPath shows a stack(Z=65) with only first slice has image content, while all other slices are black.

However,when I drag & open other single file(PyramidalCell_Z001.tif,…), QuPath indeed shows a single slice.

So ther should be someting special for PyramidalCell_Z000.tif only.
Even when I change the file name “PyramidalCell_Z000” to random name, it still shows a not fully filled stack.

Later, I found that in other software if I export as Asjustable tiff instead of ome tiff, the problem disappears. All tif when dragged into QuPath, it shows a single slice.

QuPath is likely to be using Bio-Formats to open the files, which contain some logic for grouping files (e.g. see here and here). I don’t know what exactly the rules are, but I guess that is related.