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

[Nuno Goncalo Dias]

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.
>