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

[James Wainwright]

Many thanks David and Curtis!

On 25 November 2015 at 10:03, James Wainwright <jimboesq at gmail.com> wrote:

> 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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