[ome-users] OME: Putting it all together (take 1)

[Graham Klyne]

Now that I'm getting an inkling of how OME ticks, this message outlines my 
emerging plan for configuring OME to serve our requirements for image 
collection and annotation.


1. Requirements

We want to capture images of in situ hybridization in Drosophila testes 
with the following information for each image:

(1) Date/time/user
(2) Strain of drosophila (wild type or identified mutant).
     Maybe two or more strains in an image.
(3) Gene identifier (target of hybridization probes)
(4) Slide identification (a unique identifier is required so that images 
from the same slide can be compared;  for practical considerations, the 
slide preparation date and strain labels will be incorporated in the 
identification string.
(5) Developmental stages at which gene expression is observed (from an 
controlled vocabulary to be defined)
(6) Microscope magnification - objective (4x, 10x, 20x, 40x)
(7) Microscope magnification - optivar (1, 1.25, 1.6, 2)

Other external information will be cross-referenced later via gene 
identifier and/or strain identifier.

Several images of at least two different strains are captured for each 
slide prepared.


2. Operating hardware/software environment.

- Olympus [BX50(?)] microscope with JVC 3CCD video camera
- KY-link image acquisition software running on Windows
- OME running on same host in VMware environment, but could be remote.

The plan is to grab images into a designated file system area using 
KY-link, and immediately import them into OME and annotate (with 
information noted above) them using a Windows Web browser.


3. Proposed organization

All datasets to be organized under a single project.

Each experimenter to have a separate OME login, so that experimenter 
information can be captured automatically by OME.  (Are there any pitfalls 
here if experimenters want to search across other's datasets?)

Each dataset to contain images from a single slide.  Thus, the dataset 
description can contain information about the slide identifier.  (It might 
also be handy to include the gene name/identifier that is common to all 
images from a slide, but categories don't seem to apply to datasets, so 
that may not be an option).  The choice of one dataset per slide seems to 
be operationally convenient.  (There may be requirements to add further 
images from a given slide at a later date; does OME prevent this? I vaguely 
remember reading something that suggested it might).

Each image to be annotated with:
- gene identifier (if this can't be "inherited" from the dataset in some way).
- strain identifiers (as categories would be neat, but the mutual exclusion 
is a problem.  I might be able to use a category for the "main" strain, and 
annotations for additional strains.
- objective and optivar magnification details to be entered as instrument 
details if possible, or as a separate custom annotation using a new 
semantic type.
- developmental stages showing expression to be drawn from a fixed 
vocabulary (based on GO).  Each possible stage to be a CategoryGroup, each 
with Categories corresponding to Yes/No.  Thus any combination of 
development stages can be captured and used as basis for grouping.

This approach seems to require making several separate classification 
annotations, which might be a bit inconvenient.  An alternative would be to 
create a new semantic type and a new data entry template to gather all the 
required information on a single screen per image.

...

Does this outline proposal expose any fundamental oversights I may have 
concerning the way OME works?  Thanks again for any insights.

#g


---
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