Hi Masoud,
After having investigating several hours about this problem, i can confirm you this is definitely a bug with Bio-Formats :-/ Icy is using version 5.9.2 of Bio-Formats but it looks like the bug is also present on the last version anyway.
The problem comes from when we force un-grouping files (which Icy does when you select Separate files and when using drag & drop operation for a single file, ImageJ is always using grouping), in this case Bio-Formats has a bug parsing metadata of this multi series OME TIFF files.
The bug happen at line 688 from loci.formats.in.OMETiffReader class in initFile(..) function :
Pixels pix = img.getPixels();
List<Plane> planes = pix.copyPlaneList();
for (int p=0; p<planes.size(); p++) {
Plane plane = planes.get(p);
if (plane.getTheZ().getValue() >= core.get(i).sizeZ ||
plane.getTheC().getValue() >= core.get(i).sizeC ||
plane.getTheT().getValue() >= core.get(i).sizeT)
{
pix.removePlane(planes.get(p));
}
}
I guess they should used pix.getSizeZ() instead of core.get(i).sizeZ as at this point as core isn’t yet fully filled.
Still hopefully there a way to display a single dataset, just try to open the associated metadata.txt file instead of the .tif file, in my case that is enough to get the proper dataset to open (unfortunately we cannot just disable un-grouping as other things would break).
Hope that helps.
– Stephane
