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

[James Wainwright]

I've uploaded a sample dataset using the following link:

https://www.openmicroscopy.org/qa2/qa/upload/

James



On 25 November 2015 at 09:58, James Wainwright <jimboesq at gmail.com> wrote:

> 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
>>
>
>
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