<div dir="ltr">Dear Roger,<div><br></div><div>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.</div><div><br></div><div>Thank you.</div><div><br></div><div>Best,</div><div>Amir</div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature">--<br>Amir Momen Roknabadi,<br><a href="mailto:amirr@princeton.edu" target="_blank">amirr@princeton.edu</a><br><a href="mailto:amroknabadi@gmail.com" target="_blank">amroknabadi@gmail.com</a><br></div></div>
<br><div class="gmail_quote">On Wed, Mar 18, 2015 at 6:20 AM, Roger Leigh <span dir="ltr"><<a href="mailto:rleigh@dundee.ac.uk" target="_blank">rleigh@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><span class="">On 17/03/15 13:36, Amir Momen Roknabadi wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi!<br>
<br>
We are using a Leica SP8, running LAS X to generate multiple series.<br>
When we try to use bioformats in ImageJ or Matlab to read the files, the<br>
metadata does not get loaded properly. For example, in Matlab<br>
getPixelsTimeIncrement from OmeMetadata value is empty. It is the same<br>
in ImageJ. Is there anyway that we could fix this?<br>
</blockquote>
<br></span>
Dear Amir,<br>
<br>
I've checked the LIF Reader used for this, and it does appear to<br>
correctly support the TimeIncrement property on Pixels:<br>
<br>
if (tSteps[index] != null) {<br>
store.setPixelsTimeIncrement(<u></u>new Time(tSteps[index], UNITS.S), i);<br>
}<br>
<br>
When you load the image into ImageJ using the Bio-Formats importer, if<br>
you tick the "Display OME-XML Metadata" box, is TimeIncrement visible<br>
there on the Pixels element? (If this is what you already checked,<br>
please ignore this.)<br>
<br>
If it's missing, it might be that we're not handling this with newer<br>
versions of LAS X, or that your data is in a slightly different format<br>
than the examples we've seen to date for this file format (for example),<br>
and it would be useful to have a sample image to look at to determine<br>
what's happening here. If you could upload an example here so that we<br>
can investigate further:<br>
<br>
<a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.<u></u>uk/qa/upload/</a><br>
<br>
it would be very much appreciated.<br>
<br>
<br>
Kind regards,<br>
Roger Leigh<br>
<br>
--<br>
Dr Roger Leigh -- Open Microscopy Environment<br>
Wellcome Trust Centre for Gene Regulation and Expression,<br>
College of Life Sciences, University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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</blockquote></div><br></div>