[ome-users] TEM montage metadata in .dm3 files

[William Moore]

Hi Nuno,

 Sorry I didn't respond to your last question - I'd assumed that someone else from the list who knew about that would reply.
Only just noticed that you hadn't replied to one-users!

To check Bio-formats version number in Fiji, go to:

 Help -> About Plugins -> Bio-Formats plugins…


 Hope that helps,

   Will.



On 29 May 2014, at 13:30, Nuno Goncalo Dias <ngdias at ibmc.up.pt> wrote:

> Hello,
> 
> Thank you for the follow-up. I'm using Python at the moment.
> 
> 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. 
> 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?
> 
> Thanks,
> Nuno.
> 
> On 27-05-2014 13:31, William Moore wrote:
>> Hi Nuno,
>> 
>>  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?
>> 
>> Do you want Python? Java?
>> 
>> You can find a Python example of reading the Original Metadata key-value pairs at
>> https://github.com/openmicroscopy/openmicroscopy/blob/develop/examples/Training/python/Metadata.py#L111
>> 
>> Cheers,
>> 
>>   Will.
>> 
>> 
>> On 8 Apr 2014, at 00:46, Melissa Linkert <melissa at glencoesoftware.com> wrote:
>> 
>>> Hi Nuno,
>>> 
>>>> I submitted a Gatan file
>>>> http://qa.openmicroscopy.org.uk/qa/feedback/8024/
>>> 
>>> Thank you for the report.
>>> 
>>>> acquired in montage mode using a TEM. This file has metadata
>>>> information about the montage size and overlap, as read in FIJI:
>>>> 
>>>> root.ImageList.1.ImageTags.Montage.Acquisition.Number of X Steps = 7
>>>> root.ImageList.1.ImageTags.Montage.Acquisition.Number of Y Steps = 8
>>>> root.ImageList.1.ImageTags.Montage.Acquisition.Overlap between
>>>> images (%) = 14.999999
>>>> 
>>>> And this is what I get from OME now:
>>>> 
>>>> Number of X Steps 8.388608E7
>>>> Number of Y Steps 1.34217728E8
>>>> Overlap between images (%) 14.999999046325684
>>>> 
>>>> The number of X and Y steps is clearly wrong; the overlap is 15% and
>>>> there really is no need/point in having that many decimal places.
>>> 
>>> The step count issue is now ticketed here:
>>> 
>>> http://trac.openmicroscopy.org.uk/ome/ticket/12182
>>> 
>>> The overlap value is what is stored in the file; Bio-Formats does not
>>> perform rounding or truncation of decimal values.
>>> 
>>>> There might be other information in this file that is not included
>>>> in your current data model, but these 3 items are all I need at the
>>>> moment. You're welcome to go through the rest of the metadata and
>>>> add more fields to the model, of course.
>>> 
>>> Adding the tiling fields to the OME-XML model is ticketed here:
>>> 
>>> http://trac.openmicroscopy.org.uk/ome/ticket/6250
>>> 
>>>> I'd like to receive updates on this issue, particularly when a fix
>>>> becomes implemented. At that time, it would be nice to see a code
>>>> example for reading these values.
>>> 
>>> You have been CC'd on all of the above-mentioned tickets, and so you
>>> will receive an automated email each time one of the tickets changes.
>>> 
>>> Regards,
>>> -Melissa
>>> 
>>> On Thu, Apr 03, 2014 at 07:01:48PM +0100, Nuno Goncalo Dias wrote:
>>>> Hi,
>>>> 
>>>> I submitted a Gatan file
>>>> http://qa.openmicroscopy.org.uk/qa/feedback/8024/
>>>> 
>>>> acquired in montage mode using a TEM. This file has metadata
>>>> information about the montage size and overlap, as read in FIJI:
>>>> 
>>>> root.ImageList.1.ImageTags.Montage.Acquisition.Number of X Steps = 7
>>>> root.ImageList.1.ImageTags.Montage.Acquisition.Number of Y Steps = 8
>>>> root.ImageList.1.ImageTags.Montage.Acquisition.Overlap between
>>>> images (%) = 14.999999
>>>> 
>>>> And this is what I get from OME now:
>>>> 
>>>> Number of X Steps 8.388608E7
>>>> Number of Y Steps 1.34217728E8
>>>> Overlap between images (%) 14.999999046325684
>>>> 
>>>> The number of X and Y steps is clearly wrong; the overlap is 15% and
>>>> there really is no need/point in having that many decimal places.
>>>> 
>>>> There might be other information in this file that is not included
>>>> in your current data model, but these 3 items are all I need at the
>>>> moment. You're welcome to go through the rest of the metadata and
>>>> add more fields to the model, of course.
>>>> 
>>>> I'd like to receive updates on this issue, particularly when a fix
>>>> becomes implemented. At that time, it would be nice to see a code
>>>> example for reading these values.
>>>> 
>>>> Thank you,
>>>> Nuno.
>>>> 
>>>> 
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>> 
> 
> -- 
> 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
> http://www.ibmc.up.pt/index.php?id=364

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