[ome-users] Schema for instrument/magnification - how to use?

[Ilya Goldberg]

Its like you're listening in to our lab-meetings, Graham.

There is no UI targeted at Instrument annotation.  The data-model is  
there, but there is no easy to use UI for it.  The general ST  
annotation mechanism is not really adequate unless you are intimately  
familiar with the instrument datamodel as expressed with STs.   
Unfortunately, the instrument model is somewhat complex, so the general  
UI is not the greatest.  What can I tell you?  We're working on it.

Actually it was hoped (for those listening in) that instrument  
manufacturers would play some sort of role in this.  Its their  
instrument design after-all.  It would not be very difficult for them  
to ship an OME XML file that fully describes the instruments they sell  
you.  But alas, many scientists will probably need to describe the same  
instruments dozens of times before we get computer-parseable instrument  
descriptions from the manufacturers.  But I digress.

Given an instrument description (which is probably easier to do in XML  
than in the Web UI, BTW), the idea is to have a series of drop-down  
menus to adjust settings for a particular image or group of images.  We  
fully realize that if there are more than three or four clicks involved  
(hopefully its not just one or two), no one would ever do it, so we're  
trying to come up with a UI that takes this into account.


On Jul 19, 2005, at 3:42 PM, Graham Klyne wrote:

> I'm looking through the XML scema for "instrument" in OME [1].  I see  
> there is an element for the objective lens, with a magnification  
> factor value.
>
> The researchers here also use, and wish to record, an "optivar"  with  
> possible magnification values of 1, 1.25, 1.6, 2.  Am I overlooking a  
> schema element for this?

Nobody's ever mentioned an optivar before.  Is that something we all  
overlooked?



>
> I'm also a bit puzzled by the user interface for adding information  
> about the instrument:  it seems the instrument annotation can be  
> attached to a dataset in the UI (even though it is used in the  
> top-level <OME> element in the XML schema description).  The drop-down  
> list shown on the dataset display provides only two options, but if I  
> select "create" anyway, a further drop-down list with many more  
> options is provided.  Selecting instrument, I get a form for entering  
> microscope type, srial number, etc., but there is no option there for  
> entering objective data.  It feels to me as if there is a disconnect  
> between the schema and the interface, but I'm not seeing any logic for  
> this.
>
> Having created some description of the instrument, and clicked "create  
> instrument", there is no indication that any information has been  
> attached to the dataset.  I fear I'm getting completely lost and  
> confused by the user interface here.

The instrument and its components are global objects.  The fact that  
you were looking at a dataset doesn't matter - they are never  
associated with a dataset.  You can certainly use the search interface  
to convince yourself that its there.

-Ilya


>
> #g
> --
>
> [1]  
> http://cvs.openmicroscopy.org.uk/horde/chora/co.php?f=/OME/src/xml/ 
> OME/Core/Instrument.ome
>
>
>
> ---
> Graham Klyne
> Image Bioinformatics Research Group (http://www.bioimage.org/)
> Department of Zoology, University of Oxford
> South Parks Road, Oxford OX1 3PS, UK
> E-mail: <Graham.Klyne at zoo.ox.ac.uk>
> Direct phone: +44-(0)1865-281991
> Departmental fax: +44-(0)1865-310447
>
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