[ome-users] Atomic force microscopy images

[Roger Leigh]

On 25/08/2013 00:41, Roger Leigh wrote:
> 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 for uploading some sample images.  I've taken a look, and
what's happening is that while Bio-Formats is reading the ImageJ scaling
metadata, it is not preserving the scale unit (nm), and is currently
discarding it.  Thus the scale value you have set is being treated as
the default (µm) rather than nm.

I've opened a ticket
(https://trac.openmicroscopy.org.uk/ome/ticket/11399) to track this
issue, and you should get copied on any changes to this ticket.


Regards,
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