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

[Amir Momen Roknabadi]

Dear Roger,

I have tried ImageJ. TimeIncrement is empty in the OME-XML metadata in
ImageJ as well. I uploaded a file named: "P2P-MS2-lacZ.lif" in the OMERO.qa
system. I really appreciate your help.

Thank you.

Best,
Amir

--
Amir Momen Roknabadi,
amirr at princeton.edu
amroknabadi at gmail.com

On Wed, Mar 18, 2015 at 6:20 AM, Roger Leigh <rleigh at dundee.ac.uk> wrote:

> 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
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