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

[Graham Klyne]

At 01:20 20/07/05 -0400, Ilya Goldberg wrote:

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

;-)   Hidden forces at work!


>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.

Sounds like scope for community contributions here.  Maybe a wiki?

>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.

If the dataset can provide defaults (you hinted at that possibility in 
another message), then I imagine a more complex i/f would be less 
problematic if the (hopefully) few per-image changes only take a couple of 
clicks.

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

I took that verbatim - I'd never heard of it before, either.  Maybe it's 
local lingo for something well-known, or specific to the microscope setup.

Google shows optivar as a drug!

Try again: Google for "optivar microscope" returns a number of hits, one of 
which suggests the optivar modifies the objective magnification (sounds a 
bit like a camera teleconverter to me):
   http://nature.berkeley.edu/pipermail/pgec/2005-June/000740.html

[later] I just spoke to the researchers, and they confirm an optivar is 
just an additional magnifier lense.

>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.

Ah, now I see.  A little.  In which case, I guess that the adjustable 
values don't really belong as part of the instrument description?

#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
>>
>>_______________________________________________
>>ome-users mailing list
>>ome-users at lists.openmicroscopy.org.uk
>>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users

---
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