[ome-users] incorrect px dimension value read from .dm3 files

[Roger Leigh]

On 28/03/14 17:06, Nuno Goncalo Dias wrote:

Hi Nuno,

> I submitted a file to http://qa.openmicroscopy.org.uk/qa/feedback/8007/
> with a comment explaining the problem. Do I also need to ask for help in
> this mailing list or uploading with a comment is enough?

So long as your email address is on the QA upload so we can respond,
that is sufficient.  However, asking here does mean that anyone else
having a similar problem can also benefit from the answer, and others
may also be able to help and provide additional advice, so asking here
is certainly preferred.

> The problem is that the OME plugin in FIJI was reading pixel dimensions
> correctly from files such as the one I uploaded but now the value comes
> out 3 extra decimal places lower.

I think the behaviour is correct, even though it might appear a little odd.

Internally, the data model used by bioformats currently stores all
physical sizes in micrometres.  It appears that the file you uploaded is
using nanometres, so it was converted to µm.  The original file uses a
physical x size of 0.01418117806315422nm and this is converted to
1.4181178063154221E-5µm.

One thing we're currently working on is adding support for proper units
to bioformats, so that it will be able to store sizes at any scale.
Once this is done, there will be no conversion to micrometres since we
can store it directly as the nanometre value.


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