[ome-users] Z-dimension bug with Andor TIFF

[James Wainwright]

Hi there,

I don't think this has been fixed?

I've tested in version 5.1.6 and the OME metadata still shows:

PositionZ="0.0"

It does however show:

TheZ="2" for the third Z slice, which is sort of correct, but this must
then be translated back to a Z position by the user who would need to look
further up in the OME metadata at the following entry:

PhysicalSizeZ

To make matters worse, it doesn't seem possible to copy or paste this OME
metadata any more! I can select a line, and use CTRL-A to select all, but
cannot paste it (presumably because I cannot copy it).

Finally, I'm convinced that once upon a time, I was able to simply drag a
TIFF onto FIJI and it would auto-load Bioformats because it recognised it
as a compatible file. Could this feature be enabled again?

Thanks!

James



On 29 September 2015 at 14:58, James Wainwright <jimboesq at gmail.com> wrote:

> Hi again,
>
> A user has pointed out, and I have confirmed, that the Z dimension is
> incorrectly sized when opening an Andor TIFF with Bioformats. I guess this
> is similar to Bug 12964, which I previously reported.
>
> Basically, Bioformats seems to ignore the actual Z-step used and uses the
> frame number instead - i.e. 1um Z-step for everything.
>
> I've uploaded a dataset created by the latest version of Andor iQ (3.3.2)
> here:
>
> http://www.andor.com/ftp/8670/Protocol1.zip
>
> The text file should show the correct metadata, namely:
>
> XY (pixels) = 0.696
> Z (Z-step) = 0.86
>
> Let me know if it helps or if you need more!
>
> Thanks a lot!
>
> James
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20151125/afd0e385/attachment.html>