[ome-devel] OMERO/Matlab

[Jonas Dorn]

At ASCB, I have talked a little bit with Donald and Jean-Marie, and they
suggested I follow up with a more complete explanation by email to the
mailing list for additional comments. As I looked over the OMERO
documentation, I realized that I also have some additional questions.

For my project, I measure protein intensity levels at centromeres during the
cell cycle. For each condition, I run 2-3 experiments. In each experiment, I
acquire ~30 movies, and each movie is a 3D+t data set that contains multiple
(~20) cells. I perform image analysis in Matlab using my own classes and
functions, and I would like to start using OMERO to organize the images and
the results.

I have the following questions:
1. I would like to populate and query the database from within Matlab as
much as possible, though I like the possibility to browse the data using
OMERO. What are the limitations of the Matlab plugin?
2. I cannot afford data duplication at the moment. How is it possible to use
OMERO without data duplication? Jean-Marie and Donald suggested that I store
the file name instead of the image in the 'image' field of the database. How
feasible is that?
3. It seems like the lowest hierarchy in the database are images. In my data
structure, the lowest hierarchy is cells. I do have (overlapping) ROIs for
each cell, and I notice that OMERO supports ROIs. Is it thus possible to
have ROIs as lowest hierarchy in OMERO that can be tagged/annotated
individually?
4. To describe the data in a user-friendly manner, I would like to annotate
each cell (and possibly each movie, experiment and condition) with some
parameters, as well as a few graphs and possibly a collage of a few movie
snapshots. I would like the parameters to be searchable, and it looks like
the protocol editor would allow me to define multiple
parameterName:parameterValue pairs. Is that searchable? Also, is it possible
to browse through the graphs, if they're provided as, say, .png?
5. Assume I want to run an analysis in Matlab on a subset of 'good' cells.
How would I access the list of 'good' cells from Matlab?

Thanks for all your help!
Jonas
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