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

[Melissa Linkert]

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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