[ome-users] Atomic force microscopy images

[Roger Leigh]

On 25/08/13 00:01, Lorenzo Lunelli wrote:
> Hi,
>
> I would like to use  an Omero server as  central repository for my Atomic force microscopy images, sending the images (previously converted to TIFF) to Omero via the ImageJ plugin.
> It works, but there is an annoying issue with the lateral scale of the images.
> I prefer to obtain distances in nanometers, so I calibrated accordingly the images in ImageJ. However, once transferred to Omero the pixel unit seems to be interpreted as micrometers. I tried to set the units in ImageJ as "nm" or "nanometers", but without success.
> The only way I have found  to circumvent the problem so far is to calibrate the images in ImageJ using micrometers as units, but considered that most AFM images are sized in the nanometric range it is a bit annoying to get all the measurements in microns .
> What is the right way to use nanometers in Omero ?

Internally, the OME data model uses µm as its unit for scaling factors.
  We are currently working to make this work with other units.
However, if your image is using nm, we should be storing this as nm/1000
so that the scaling is correctly preserved.  If you're seeing nm units
treated as though they are µm this is probably a bug in the file
format-specific reader.

If you could possibly upload a sample image using
http://qa.openmicroscopy.org.uk/qa/upload/
then we can take a look at this in more detail.


Many thanks,
Roger

--
Dr Roger Leigh -- Open Microscopy Environment
Wellcome Trust Centre for Gene Regulation and Expression,
College of Life Sciences, University of Dundee, Dow Street,
Dundee DD1 5EH Scotland UK   Tel: (01382) 386364

The University of Dundee is a registered Scottish Charity, No: SC015096