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

[Curtis Rueden]

Hi James,

> 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?

In the Edit > Options > ImageJ2... dialog, there is an option "Use SCIFIO
when opening files (BETA!)". When checked, that option will override
ImageJ1's default file handling to make the File > Open command use SCIFIO,
which will include calling Bio-Formats for TIFF files which have custom
TIFF readers.

Without this option checked, the default ImageJ1 TIFF handling will always
be used, with all its limitations: it may do a limited or incorrect job
importing the data if it is a special flavored TIFF of which ImageJ1 is
ignorant., or issue an error message in some cases.

For details, see: http://imagej.net/SCIFIO

Alternately, if you run Plugins > Bio-Formats > Bio-Formats Plugins
Shortcut Window, you can then drag-and-drop files onto the window which
appears to open them directly with Bio-Formats.

Regards,
Curtis


On Wed, Nov 25, 2015 at 3:58 AM, 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
>>
>
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20151125/a951db18/attachment.html>