[ome-users] Atomic force microscopy images

[Lorenzo Lunelli]

Many  thanks for your help.

Regards, 
Lorenzo


On 26 Aug 2013, at 17:35 , Roger Leigh wrote:

> 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
> 
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