[ome-users] Problem with OME-TIFF writer

[Sebastian Rhode]

Hi guys,

i encounter a strange behavior and I am not sure, if this is a bug or I do
something wrong.

This is the z-Stack:
https://dl.dropboxusercontent.com/u/623476/Beads_63X_NA1.35_xy%3D0.042_z%3D0.1.czi

When I open this via Fiji (up-to-date 20150508) I get a z-Stack with 100
focal planes - OK --> see screenshot

[image: Inline-Bild 1]

When I load this CZI vai Python Bioformats (bioformats_package 5.1.1 +
python_bioformats 1.0.4) , it also works fine --> see screenshot

[image: Inline-Bild 2]

Now I go back to Fiji and use the BioFormats exporter to write an OME-TIFF
from the open CZI and save it to disk.

File can be found here:
https://dl.dropboxusercontent.com/u/623476/63X_NA1.35_xy%3D0.042_z%3D0.1.ome.tiff

When I open the OME-TIFF in Fiji I get a z-stack with 100 planes and the
correct z.spacing (as expected). But when I open the OME-TIFF via
python-bioformats The dimensions get mixed up --> see screenshot below.

So I am wondering why the python stuff seems to work for the CZI, but not
for the exported OME-TIFF while it always seems to be OK for Fiji itself no
matter if I open the CZI or the exported OME-TIFF.

And why is the z-spacing wrong? I think because the python assumes it is a
NOT a z-stack.

Sebi

[image: Inline-Bild 3]
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