[ome-users] dm4 imports with um scale instead of nm
Ralph Sperling
sperling.ralph at gmail.com
Mon Nov 4 06:26:51 GMT 2013
Dear all,
if there is good reason to stick with microns everywhere, nanometers
could be taken into account by just dividing the pixel size by 1000, I
guess this is exactly what Stephane suggested.
At the moment I am doing similar things with a macro - is there a way to
do custom adjustments automagically, e.g. always after importing .dm4
files? This would be a convenient solution for the moment.
Cheers, RAlph
On 30.10.2013 16:22, ome-users-request at lists.openmicroscopy.org.uk wrote:
>
> Message: 2
> Date: Wed, 30 Oct 2013 10:22:02 -0500
> From: Curtis Rueden <ctrueden at wisc.edu>
> To: St?phane Dallongeville <stephane.dallongeville at pasteur.fr>
> Cc: OME-users mailing list <ome-users at lists.openmicroscopy.org.uk>
> Subject: Re: [ome-users] dm4 imports with um scale instead of nm
> Message-ID:
> <CADN69y=Gx+qZ3+y2X-JKfsMw3YrwS_5AnHfY=U-0QwEL3gRVkg at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi St?phane, 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, St?phane 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 ?crit :
>>
>> 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
>> Unit? 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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