[ome-devel] ome-tiff issue?

[Melissa Linkert]

Hi Daniel,

> I got an ome-tiff file (originally a multi-series Leica .LIF) that
> was opened with the latest Fiji using the BioFormats library. It is
> a 3 channel stack with around 300 z-slices. One of the series was
> selected when opening the file, then cropped in X&Y and finally
> exported to a stack as ome-tiff using BioFormats.
> 
> What strikes me is that the Y dimension reported by the ome-tiff
> file header is 255 whereas the actual Y dimension is 175. Does
> anybody know whether this is intended?

No, that is not expected, and unfortunately I have not been able to
duplicate the problem so far.

When you open the exported OME-TIFF file, are the images the correct size?
Does "Help > Update Fiji" show that the installed version of Bio-Formats
is up to date?

If Bio-Formats was up to date when this OME-TIFF was created, then it
would be very helpful if you could send the original file and indicate
which series was exported.  If Bio-Formats was not up to date, then
please try updating and see if that solves the problem.

Regards,
-Melissa

On Mon, Jan 21, 2013 at 12:30:12PM +0100, Daniel Sevilla Sanchez wrote:
> Dear List,
> 
> I am wondering whether ome-tiff files may have a disagreement
> between the dimensions reported by the file header and the
> dimensions contained in the file itself.
> 
> I got an ome-tiff file (originally a multi-series Leica .LIF) that
> was opened with the latest Fiji using the BioFormats library. It is
> a 3 channel stack with around 300 z-slices. One of the series was
> selected when opening the file, then cropped in X&Y and finally
> exported to a stack as ome-tiff using BioFormats.
> 
> What strikes me is that the Y dimension reported by the ome-tiff
> file header is 255 whereas the actual Y dimension is 175. Does
> anybody know whether this is intended?
> 
> Thanks a lot in advance.
> 
> Best regards,
> Daniel Sevilla
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