[ome-users] LIF Metadata Issues Generated by LAS X

[Roger Leigh]

On 17/03/15 13:36, Amir Momen Roknabadi wrote:
> Hi!
>
> We are using a Leica SP8, running LAS X to generate multiple series.
> When we try to use bioformats in ImageJ or Matlab to read the files, the
> metadata does not get loaded properly. For example, in Matlab
> getPixelsTimeIncrement from OmeMetadata value is empty. It is the same
> in ImageJ. Is there anyway that we could fix this?

Dear Amir,

I've checked the LIF Reader used for this, and it does appear to
correctly support the TimeIncrement property on Pixels:

       if (tSteps[index] != null) {
         store.setPixelsTimeIncrement(new Time(tSteps[index], UNITS.S), i);
       }

When you load the image into ImageJ using the Bio-Formats importer, if
you tick the "Display OME-XML Metadata" box, is TimeIncrement visible
there on the Pixels element?  (If this is what you already checked,
please ignore this.)

If it's missing, it might be that we're not handling this with newer
versions of LAS X, or that your data is in a slightly different format
than the examples we've seen to date for this file format (for example),
and it would be useful to have a sample image to look at to determine
what's happening here.  If you could upload an example here so that we
can investigate further:

   http://qa.openmicroscopy.org.uk/qa/upload/

it would be very much appreciated.


Kind regards,
Roger Leigh

--
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