[ome-users] incorrect px dimension value read from .dm3 files

[Melissa Linkert]

Hi Nuno,

> Thanks for the reply. The units are in micrometers. if you go FIJI
> Image>Show Info... you get
> 
> root.ImageList.1.ImageData.Calibrations.Dimension.0.Scale = 0.014181178
> root.ImageList.1.ImageData.Calibrations.Dimension.0.Units = µm
> root.ImageList.1.ImageData.Calibrations.Dimension.1.Scale = 0.014181178
> root.ImageList.1.ImageData.Calibrations.Dimension.1.Units = µm
> 
> I acquired these images myself and these values above are correct
> (15 nm). Having pixel dimensions in the range of 0.02 nm in images
> taken from a SEM is as far as I know not even possible... Wouldn't
> it be 10x the resolution needed to see atoms?

You're absolutely correct - what Bio-Formats shows is off by a factor of
1000.  There is now a ticket for this on our issue tracking system:

http://trac.openmicroscopy.org.uk/ome/ticket/12154

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Regards,
-Melissa

On Tue, Apr 01, 2014 at 02:39:49PM +0100, Nuno Goncalo Dias wrote:
> Hi,
> 
> Thanks for the reply. The units are in micrometers. if you go FIJI
> Image>Show Info... you get
> 
> root.ImageList.1.ImageData.Calibrations.Dimension.0.Scale = 0.014181178
> root.ImageList.1.ImageData.Calibrations.Dimension.0.Units = µm
> root.ImageList.1.ImageData.Calibrations.Dimension.1.Scale = 0.014181178
> root.ImageList.1.ImageData.Calibrations.Dimension.1.Units = µm
> 
> I acquired these images myself and these values above are correct
> (15 nm). Having pixel dimensions in the range of 0.02 nm in images
> taken from a SEM is as far as I know not even possible... Wouldn't
> it be 10x the resolution needed to see atoms?
> 
> Thanks,
> Nuno.
> 
> On 31-03-2014 12:00, ome-users-request at lists.openmicroscopy.org.uk wrote:
> >I think the behaviour is correct, even though it might appear a little odd.
> >
> >Internally, the data model used by bioformats currently stores all
> >physical sizes in micrometres.  It appears that the file you uploaded is
> >using nanometres, so it was converted to ?m.  The original file uses a
> >physical x size of 0.01418117806315422nm and this is converted to
> >1.4181178063154221E-5?m.
> >
> >One thing we're currently working on is adding support for proper units
> >to bioformats, so that it will be able to store sizes at any scale.
> >Once this is done, there will be no conversion to micrometres since we
> >can store it directly as the nanometre value.
> >
> 
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