[ome-users] Problem with OME-TIFF writer

[Melissa Linkert]

Hi Sebi,

> 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.

It sounds like you are encountering an open issue in python-bioformats:

https://github.com/CellProfiler/python-bioformats/issues/23

the summary of which is that OME-TIFF files are detected as plain
TIFF files by default.

There are a few ways of changing that, as mentioned in the issue.
I would expect that one or all would resolve the problem, but if not,
I would recommend contacting the python-bioformats team directly.

Regards,
-Melissa

On Fri, May 08, 2015 at 09:52:59AM +0200, Sebastian Rhode wrote:
> 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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