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

[William Moore]

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.
>> 
>> 
>> _______________________________________________
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>> ome-users at lists.openmicroscopy.org.uk
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