[ome-devel] A few questions

[Zachary Pincus]

Hello,

I've got a few general questions about OME, to help me get my footing. 
(Sorry to spam the developer list if this isn't really appropriate 
traffic -- let me know.)

Also, since I know so little about the guts of the system, some of 
these might actually be feature requests, etc -- so let me know if 
that's the case and I'll enter them into the bug-tracker.

(1)  I quite like how each image can be associated with various 
features. Is there any way to associate an image with features that are 
themselves images? (e.g. the spots resulting from spot-finding or some 
such.) Or is the appropriate way to deal with this just by following an 
analysis chain backwards to find the "parent" image?

(2) At the moment, are there any tools for creating 5-D images from 
multiple lower-D image files? Clearly this can be done with the omeis 
API, but has this functionality been bundled up in a tool anywhere?

(3) Is there a UI for editing image metadata? After importing images, 
I'd love to add more metadata about the microscope, CCD, illumination, 
etc (i.e. everything supported by the OME XML interchange format) that 
are not present in the original image files/accessible to the import 
engine. (Corollary question: if so, can this be done in a batch-mode to 
multiple images at once?) Again, clearly the API can handle this -- I'm 
just wondering if this has been added/planned for the various UIs.

(4) How are units dealt with in OME? The schema specify things like 
"PixelSizeX" or "Wavelength" but the units don't seem to be specified. 
In general they are obvious for biological imaging (microns, 
nanometers) -- is that enough?

(5) I'm a bit unclear as to how one goes about asking for "all relevant 
information" about a feature from the database or the web UI. Let me 
provide an example -- After running "find spots," information about 
various features is generated and stored in several database tables: 
Signals, Extent, Location, Threshold, and Timepoint.

I know this because the "find spots" module specifically declares this. 
So if I want to find out the "Extent" associated with a given feature, 
I need to look at the appropriate "Module Execution" record in the web 
UI. Already something is strange -- why can't I look at the "Feature" 
record and see this information?

Perhaps this is just a UI issue, but the problem seems deeper: nowhere 
in the "Feature" record is any information about the tables in which 
the attributes of the feature are stored. Nor does there appear to be a 
backwards reference to the module execution that generated that 
feature, where you could find that information. (And what if a feature 
wasn't added by a module execution, but manually?)

So, given only a feature ID, how do you find all the attributes of that 
feature? It appears to my uninformed eye that you would need to trawl 
through the entire database and ask each table for all records with 
feature ID = whatever. Is there any unified mechanism for doing this 
(in SQL or the API)? Or am I missing something fundamental here?

(6) Finally, I'm wondering in what areas the APIs are just thin 
wrappers around the database, and in what areas there is a lot of logic 
in the code itself. This question is just to get me oriented to what 
the API does, and where...

Thanks for any help at all,

Zach Pincus


Department of Biochemistry and Program in Biomedical Informatics
Stanford University School of Medicine