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

[Stéphane Dallongeville]

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 
>>>>> <mailto: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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-- 
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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