<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Nuno,<div><br></div><div> Sorry I didn't respond to your last question - I'd assumed that someone else from the list who knew about that would reply.</div><div>Only just noticed that you hadn't replied to one-users!</div><div><br></div><div>To check Bio-formats version number in Fiji, go to:</div><div><br></div><div> Help -> About Plugins -> Bio-Formats plugins…</div><div><br></div><div><br></div><div> Hope that helps,</div><div><br></div><div> Will.</div><div><br></div><div><br></div><div><br><div><div>On 29 May 2014, at 13:30, Nuno Goncalo Dias <<a href="mailto:ngdias@ibmc.up.pt">ngdias@ibmc.up.pt</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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Hello,<br>
<br>
Thank you for the follow-up. I'm using Python at the moment.<br>
<br>
I had a quick look at the link and the loop for printing all the
metadata key pairs is very useful and gives me the information I
need. <br>
I will give it a try soon; I'm not finding a way to check
Bio-formats version number in FIJI menu options... do I have to
check the version number in the .jar plugin filename?<br>
<br>
Thanks,<br>
Nuno.<br>
<br>
<div class="moz-cite-prefix">On 27-05-2014 13:31, William Moore
wrote:<br>
</div>
<blockquote cite="mid:9886470D-603E-4D54-9797-87B3AD1B5DE4@lifesci.dundee.ac.uk" type="cite">
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Hi Nuno,
<div><br>
</div>
<div> Now that this issue is fixed, and 5.0.2 will be released
soon, you wanted to know how to access the "Original Metadata"
via code?</div>
<div><br>
</div>
<div>Do you want Python? Java?</div>
<div><br>
</div>
<div>You can find a Python example of reading the Original
Metadata key-value pairs at</div>
<div><a moz-do-not-send="true" href="https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Metadata.py#L111">https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Metadata.py#L111</a></div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div> Will.</div>
<div><br>
</div>
<div><br>
<div>
<div>On 8 Apr 2014, at 00:46, Melissa Linkert <<a moz-do-not-send="true" href="mailto:melissa@glencoesoftware.com">melissa@glencoesoftware.com</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">Hi Nuno,<br>
<br>
<blockquote type="cite">I submitted a Gatan file<br>
<a moz-do-not-send="true" href="http://qa.openmicroscopy.org.uk/qa/feedback/8024/">http://qa.openmicroscopy.org.uk/qa/feedback/8024/</a><br>
</blockquote>
<br>
Thank you for the report.<br>
<br>
<blockquote type="cite">acquired in montage mode using a
TEM. This file has metadata<br>
information about the montage size and overlap, as read in
FIJI:<br>
<br>
root.ImageList.1.ImageTags.Montage.Acquisition.Number of X
Steps = 7<br>
root.ImageList.1.ImageTags.Montage.Acquisition.Number of Y
Steps = 8<br>
root.ImageList.1.ImageTags.Montage.Acquisition.Overlap
between<br>
images (%) = 14.999999<br>
<br>
And this is what I get from OME now:<br>
<br>
Number of X Steps<span class="Apple-tab-span" style="white-space:pre"> </span>8.388608E7<br>
Number of Y Steps<span class="Apple-tab-span" style="white-space:pre"> </span>1.34217728E8<br>
Overlap between images (%)<span class="Apple-tab-span" style="white-space:pre"> </span>14.999999046325684<br>
<br>
The number of X and Y steps is clearly wrong; the overlap
is 15% and<br>
there really is no need/point in having that many decimal
places.<br>
</blockquote>
<br>
The step count issue is now ticketed here:<br>
<br>
<a moz-do-not-send="true" href="http://trac.openmicroscopy.org.uk/ome/ticket/12182">http://trac.openmicroscopy.org.uk/ome/ticket/12182</a><br>
<br>
The overlap value is what is stored in the file; Bio-Formats
does not<br>
perform rounding or truncation of decimal values.<br>
<br>
<blockquote type="cite">There might be other information in
this file that is not included<br>
in your current data model, but these 3 items are all I
need at the<br>
moment. You're welcome to go through the rest of the
metadata and<br>
add more fields to the model, of course.<br>
</blockquote>
<br>
Adding the tiling fields to the OME-XML model is ticketed
here:<br>
<br>
<a class="moz-txt-link-freetext" href="http://trac.openmicroscopy.org.uk/ome/ticket/6250">http://trac.openmicroscopy.org.uk/ome/ticket/6250</a><br>
<br>
<blockquote type="cite">I'd like to receive updates on this
issue, particularly when a fix<br>
becomes implemented. At that time, it would be nice to see
a code<br>
example for reading these values.<br>
</blockquote>
<br>
You have been CC'd on all of the above-mentioned tickets,
and so you<br>
will receive an automated email each time one of the tickets
changes.<br>
<br>
Regards,<br>
-Melissa<br>
<br>
On Thu, Apr 03, 2014 at 07:01:48PM +0100, Nuno Goncalo Dias
wrote:<br>
<blockquote type="cite">Hi,<br>
<br>
I submitted a Gatan file<br>
<a class="moz-txt-link-freetext" href="http://qa.openmicroscopy.org.uk/qa/feedback/8024/">http://qa.openmicroscopy.org.uk/qa/feedback/8024/</a><br>
<br>
acquired in montage mode using a TEM. This file has
metadata<br>
information about the montage size and overlap, as read in
FIJI:<br>
<br>
root.ImageList.1.ImageTags.Montage.Acquisition.Number of X
Steps = 7<br>
root.ImageList.1.ImageTags.Montage.Acquisition.Number of Y
Steps = 8<br>
root.ImageList.1.ImageTags.Montage.Acquisition.Overlap
between<br>
images (%) = 14.999999<br>
<br>
And this is what I get from OME now:<br>
<br>
Number of X Steps<span class="Apple-tab-span" style="white-space:pre"> </span>8.388608E7<br>
Number of Y Steps<span class="Apple-tab-span" style="white-space:pre"> </span>1.34217728E8<br>
Overlap between images (%)<span class="Apple-tab-span" style="white-space:pre"> </span>14.999999046325684<br>
<br>
The number of X and Y steps is clearly wrong; the overlap
is 15% and<br>
there really is no need/point in having that many decimal
places.<br>
<br>
There might be other information in this file that is not
included<br>
in your current data model, but these 3 items are all I
need at the<br>
moment. You're welcome to go through the rest of the
metadata and<br>
add more fields to the model, of course.<br>
<br>
I'd like to receive updates on this issue, particularly
when a fix<br>
becomes implemented. At that time, it would be nice to see
a code<br>
example for reading these values.<br>
<br>
Thank you,<br>
Nuno.<br>
<br>
<br>
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</div>
<br>
</div>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Nuno Gonçalo Dias
PhD student
GCB - Glial Cell Biology Group
IBMC - Institute for Molecular and Cell Biology
Tel. +351 226 074 900 Ext.1550
Fax +351 226 099 157
<a class="moz-txt-link-freetext" href="http://www.ibmc.up.pt/index.php?id=364">http://www.ibmc.up.pt/index.php?id=364</a></pre>
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