<div dir="ltr">Hi Stéphane, Melissa & everyone,<div><br></div><div>> <span style="font-family:arial,sans-serif;font-size:13px">just do values conversion when filling the metadata</span></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br>
</span></div><div>Indeed, Bio-Formats does do value conversion in many cases. However, it is a bit trickier when the unit is specified in the original file as a string, which in general is tougher for Bio-Formats 4.x to deal with.</div>
<div><br></div><div>However, ImgLib2 solves the problem with built-in support for unit conversions. Since SCIFIO leverages ImgLib2 and uses its meta API for axis calibrations, it is now feasible for SCIFIO Translators -- which e.g. standardize proprietary metadata to OME-XML -- to transparently convert dimensional units to the ones OME needs for the schema. So as Bio-Formats readers are ported to the SCIFIO infrastructure moving forward, these sorts of unit issues will become less common.</div>
<div><br></div><div>Regards,</div><div>Curtis</div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On Wed, Oct 30, 2013 at 4:38 AM, Stéphane Dallongeville <span dir="ltr"><<a href="mailto:stephane.dallongeville@pasteur.fr" target="_blank">stephane.dallongeville@pasteur.fr</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<div>Hi,<br>
<br>
Just an idea but can OME keep fixed unit depending the data type
(i.e. micron for pixel size, ms for time lapse...) and just do
values conversion when filling the metadata ? The idea of using
fixed unit (aside it's easier to deal with) is that it also
consumes less space in database to store them.<br>
<br>
Cheers,<br>
<br>
- Stephane<br>
<br>
Le 30/10/2013 10:29, Will Moore a écrit :<br>
</div><div><div class="h5">
<blockquote type="cite">Hi Ralph,
<div><br>
</div>
<div>Unfortunately the OME schema does not support variable units
for each attribute of the model. They are "hard coded" and for</div>
<div>pixel size it is microns. The ticket for adding support for
different units is <a href="https://trac.openmicroscopy.org.uk/ome/ticket/3741" target="_blank">https://trac.openmicroscopy.org.uk/ome/ticket/3741</a></div>
<div><br>
</div>
<div>Cheers,</div>
<div><br>
</div>
<div> Will.</div>
<div><br>
</div>
<div><br>
</div>
<div> The ticket for support of units<br>
<div>
<div>On 30 Oct 2013, at 06:50, Ralph Sperling wrote:</div>
<br>
<blockquote type="cite">
<div>Hi Melissa,<br>
<br>
thanks - I had again a look and it seems the .dm4 files
contain a field "Units=nm" (in ImageJ: Show Info).<br>
So I guess the importer could read this field out and set
the scale unit accordingly.<br>
Please let me know if I can help with anything.<br>
<br>
Cheers, Ralph<br>
<br>
On 10.10.2013 17:23, Melissa Linkert wrote:<br>
<blockquote type="cite">Hi Ralph,<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">thanks for pointing me to this
mailing list. I have uploaded the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">file but had to _rename_ it to
from 8.dm4 to 8.dm3 because .dm4<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">files were not enabled for
upload.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">The image opens fine with both
.dm4 or .dm3 suffixx. The field of<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">view or physical size is right
in terms of the numbers but not the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">unit. Microns are displayed but
it should be nanometers, as it is a<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">TEM image.<br>
</blockquote>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Thank you for uploading a sample
file. There is a ticket on our issue<br>
</blockquote>
<blockquote type="cite">tracking system to address this
(as you may have seen already):<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite"><a href="https://trac.openmicroscopy.org.uk/ome/ticket/11509" target="_blank">https://trac.openmicroscopy.org.uk/ome/ticket/11509</a><br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">You will receive an automated
email each time that ticket is updated; if<br>
</blockquote>
<blockquote type="cite">you prefer not to receive those
updates please let us know.<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">Regards,<br>
</blockquote>
<blockquote type="cite">-Melissa<br>
</blockquote>
<blockquote type="cite"><br>
</blockquote>
<blockquote type="cite">On Thu, Oct 03, 2013 at 11:00:29PM
+0200, Ralph Sperling wrote:<br>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Hi Melissa,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">thanks for pointing me to this
mailing list. I have uploaded the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">file but had to _rename_ it to
from 8.dm4 to 8.dm3 because .dm4<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">files were not enabled for
upload.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">The image opens fine with both
.dm4 or .dm3 suffixx. The field of<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">view or physical size is right
in terms of the numbers but not the<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">unit. Microns are displayed but
it should be nanometers, as it is a<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">TEM image.<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Thanks and best regards,<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">Ralph<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">On 01.10.2013 01:01, Melissa
Linkert wrote:<br>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Hi Ralph,<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">I am CC'ing the ome-users
mailing list<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">(<a href="http://www.openmicroscopy.org/site/community/mailing-lists" target="_blank">http://www.openmicroscopy.org/site/community/mailing-lists</a>),
as that is the<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">best place to for Bio-Formats
questions.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">I saw your post about
importing dm4 files and your kind offer about
contacting the developers in regard to issues (<a href="http://imagej.1557.x6.nabble.com/DM4-td5004215.html" target="_blank">http://imagej.1557.x6.nabble.com/DM4-td5004215.html</a>)
- here I have one:<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">The dm4 import seems to work
well, but the displayed scale of the image is um
instead of nm, as it should be. The actual numbers
are fine.<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Of course I would be happy
to provide sample images, or any other information
needed.<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Thank you for the bug report,
and for offering to send sample files. If<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">you could please send one file
that demonstrates the problem along with<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">the expected physical size of
the image, that would be very helpful.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Files can be uploaded to:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><a href="http://qa.openmicroscopy.org.uk/qa/upload/" target="_blank">http://qa.openmicroscopy.org.uk/qa/upload/</a><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Note that anything uploaded
there is not made publicly available; it<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">would only be available to OME
developers.<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Regards,<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">-Melissa<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">On Sat, Sep 28, 2013 at
04:11:39PM -0700, <a href="mailto:ralphspg@gmail.com" target="_blank">ralphspg@gmail.com</a>
wrote:<br>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Hi Melissa, I saw your post
about importing dm4 files and your kind offer
about contacting the developers in regard to
issues (<a href="http://imagej.1557.x6.nabble.com/DM4-td5004215.html" target="_blank">http://imagej.1557.x6.nabble.com/DM4-td5004215.html</a>)
- here I have one:<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">The dm4 import seems to work
well, but the displayed scale of the image is um
instead of nm, as it should be. The actual numbers
are fine.<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Of course I would be happy
to provide sample images, or any other information
needed.<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Cheers, RAlph<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">_____________________________________<br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">Sent from <a href="http://imagej.1557.x6.nabble.com" target="_blank">http://imagej.1557.x6.nabble.com</a><br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite">
<blockquote type="cite"><br>
</blockquote>
</blockquote>
</blockquote>
</blockquote>
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</blockquote>
</div>
<br>
</div>
<br>
<fieldset></fieldset>
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<br>
<br>
</div></div><span class="HOEnZb"><font color="#888888"><pre cols="72">--
Stephane Dallongeville
Unité d'Analyse d'Images Quantitative
CNRS URA 2582
Institut Pasteur
25 rue du Dr Roux - 75015 Paris - France
Tel: <a href="tel:%2B33%20%280%291%2045%2068%2087%2001" value="+33145688701" target="_blank">+33 (0)1 45 68 87 01</a>
Fax: <a href="tel:%2B33%20%280%291%2040%2061%2033%2030" value="+33140613330" target="_blank">+33 (0)1 40 61 33 30</a>
<a href="http://www.bioimageanalysis.org/" target="_blank">http://www.bioimageanalysis.org/</a></pre>
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