[ome-users] dm4 imports with um scale instead of nm

Curtis Rueden ctrueden at wisc.edu
Wed Oct 30 15:22:02 GMT 2013 

Hi Stéphane, Melissa & everyone,

> just do values conversion when filling the metadata

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.

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.

Regards,
Curtis


On Wed, Oct 30, 2013 at 4:38 AM, Stéphane Dallongeville <
stephane.dallongeville at pasteur.fr> wrote:

>  Hi,
>
> 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.
>
> Cheers,
>
> - Stephane
>
> Le 30/10/2013 10:29, Will Moore a écrit :
>
> Hi Ralph,
>
>  Unfortunately the OME schema does not support variable units for each
> attribute of the model. They are "hard coded" and for
> pixel size it is microns. The ticket for adding support for different
> units is https://trac.openmicroscopy.org.uk/ome/ticket/3741
>
>  Cheers,
>
>     Will.
>
>
>   The ticket for support of units
>  On 30 Oct 2013, at 06:50, Ralph Sperling wrote:
>
>  Hi Melissa,
>
> thanks - I had again a look and it seems the .dm4 files contain a field
> "Units=nm" (in ImageJ: Show Info).
> So I guess the importer could read this field out and set the scale unit
> accordingly.
> Please let me know if I can help with anything.
>
> Cheers,   Ralph
>
> On 10.10.2013 17:23, Melissa Linkert wrote:
>
> Hi Ralph,
>
>
>  thanks for pointing me to this mailing list. I have uploaded the
>
>  file but had to _rename_ it to from 8.dm4 to 8.dm3 because .dm4
>
>  files were not enabled for upload.
>
>
>   The image opens fine with both .dm4 or .dm3 suffixx. The field of
>
>  view or physical size is right in terms of the numbers but not the
>
>  unit. Microns are displayed but it should be nanometers, as it is a
>
>  TEM image.
>
>
>  Thank you for uploading a sample file.  There is a ticket on our issue
>
> tracking system to address this (as you may have seen already):
>
>
>  https://trac.openmicroscopy.org.uk/ome/ticket/11509
>
>
>  You will receive an automated email each time that ticket is updated; if
>
> you prefer not to receive those updates please let us know.
>
>
>  Regards,
>
> -Melissa
>
>
>  On Thu, Oct 03, 2013 at 11:00:29PM +0200, Ralph Sperling wrote:
>
>  Hi Melissa,
>
>
>   thanks for pointing me to this mailing list. I have uploaded the
>
>  file but had to _rename_ it to from 8.dm4 to 8.dm3 because .dm4
>
>  files were not enabled for upload.
>
>
>   The image opens fine with both .dm4 or .dm3 suffixx. The field of
>
>  view or physical size is right in terms of the numbers but not the
>
>  unit. Microns are displayed but it should be nanometers, as it is a
>
>  TEM image.
>
>
>   Thanks and best regards,
>
>
>   Ralph
>
>
>   On 01.10.2013 01:01, Melissa Linkert wrote:
>
>   Hi Ralph,
>
>
>    I am CC'ing the ome-users mailing list
>
>   (http://www.openmicroscopy.org/site/community/mailing-lists), as that
> is the
>
>   best place to for Bio-Formats questions.
>
>
>    I saw your post about importing dm4 files and your kind offer about
> contacting the developers in regard to issues (
> http://imagej.1557.x6.nabble.com/DM4-td5004215.html) - here I have one:
>
>    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.
>
>    Of course I would be happy to provide sample images, or any other
> information needed.
>
>
>    Thank you for the bug report, and for offering to send sample files.
>  If
>
>   you could please send one file that demonstrates the problem along with
>
>   the expected physical size of the image, that would be very helpful.
>
>   Files can be uploaded to:
>
>
>    http://qa.openmicroscopy.org.uk/qa/upload/
>
>
>    Note that anything uploaded there is not made publicly available; it
>
>   would only be available to OME developers.
>
>
>    Regards,
>
>   -Melissa
>
>
>    On Sat, Sep 28, 2013 at 04:11:39PM -0700, ralphspg at gmail.com wrote:
>
>    Hi Melissa, I saw your post about importing dm4 files and your kind
> offer about contacting the developers in regard to issues (
> http://imagej.1557.x6.nabble.com/DM4-td5004215.html) - here I have one:
>
>    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.
>
>    Of course I would be happy to provide sample images, or any other
> information needed.
>
>    Cheers,   RAlph
>
>
>
>     _____________________________________
>
>    Sent from http://imagej.1557.x6.nabble.com
>
>
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>
>
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>
>
> --
> Stephane Dallongeville
> Unité d'Analyse d'Images Quantitative
> CNRS URA 2582
> Institut Pasteur
> 25 rue du Dr Roux - 75015 Paris - France
>
> Tel: +33 (0)1 45 68 87 01
> Fax: +33 (0)1 40 61 33 30
> http://www.bioimageanalysis.org/
>
>
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