[ome-users] Fiji: Wrong image calibration when reading DM3 Format

[Roger Leigh]

On 19/07/14 11:53, Thorsten Wagner wrote:
> Hi,
>
> I updated Fiji (and bioformats) today and recognized a wrong image
> calibration when reading the following image with Fiji:
> https://dl.dropboxusercontent.com/u/560426/60kx_HAADF_03.zip
>
> With bioformats 5.0.0 (revision cd2a5db, built 24 Feb.) the image
> calibration is correct: 1.69x1.69µm
>
> With bioformats 5.0.2 (revision 0c4215a, built 27 Mai.) the wrong image
> calibration is read: 1024x1.69 pixels
>
> Could this be a bug?

I think so.  I can reproduce this with 5.0.0, 5.0.1 and 5.0.3-rc
(current dev_5_0).  I don't see it working correctly with 5.0.0 (same
revision, but my own build).

The problem is that PhysicalSizeX is set to 1.0 which messes up the
pixel aspect ratio.  PhysicalSizeY is correct.  It looks like they
should both be the value of PhysicalSizeY.

I have opened this ticket:
https://trac.openmicroscopy.org.uk/ome/ticket/12478 .


Regards,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096