[ome-devel] OMERO/Matlab

[Jonas Dorn]

Thanks for your replies, Michael and Donald.

I have finally managed to find the OmeroMatlab documentation on the site,
and I am currently trying to install omero.server on my laptop so that I can
test some examples. However, looking over the examples on the ome page, I
noticed that they are mostly concerned with reading images from the
database. This is not what I need most.

I think I should try and clarify some more what I'd like my workflow to look
like:

Image analysis
- Find experiments or images that have not been analyzed yet (calling the
database from Matlab)
- Pass filenames of images to Matlab (I have implemented my own readers in
Matlab to read the pixels directly from disk, which is most likely faster
than accessing images via the database interface)
- Run analysis in Matlab
- Attach ROIs to images as soon as they become available in the analysis
(ROIs should be stored in the database so that I can access them from
multiple computers, correct?)
- Annotate ROIs and images as soon as the information becomes available in
the analysis. This annotation includes status of the analysis (when has what
analysis step been executed), but also some results, for example loading
speed.
- Attach graphs to ROIs.
- Attach path to analysis files to images.

Data browsing
- In Omero.insight, find images/ROIs with certain characteristics
- Look through attached graphs
- Improve/Extend annotation, e.g. to classify ROIs according to phenotype.

Data analysis
- Find images with completed analysis/annotation with specific
characteristics by querying database (calling the database from Matlab or
from insight)
- Run statistical comparisons between sets, display group
averages/distributions using Matlab scripts, run more involved analysis in
Matlab.

In short, I would like to use OMERO not so much to be able to interact with
the image data, but to have an easy way of accessing subsets of my data with
specific properties, be it analysis results or processing history.

To this end, I need to
1. Populate the database with references to images - all that OMERO needs to
store is the location of the raw image file. The pixels themselves should
not be imported into the database, because I have barely enough space for
one copy of my data, thus an import that copies data into OME-TIFF is not
feasible (Michael, does this answer your question?).
I do not plan to touch the raw data file at all, thus I would have no
problems accepting that the raw data becomes read-only upon import. Also, I
do not plan to move the data (again, there are not that many shares with
enough space on the server).
Donald, for my project all images are deltavision files already, so it looks
like your idea should be no problem to implement.
2. A way to attach ROIs to the images. I currently store ROIs as a fixed
rectangle plus, for each time point, a mask within the rectangle. I guess
that OMERO does not accept arbitrarily shaped ROIs (maybe I just didn't
quite understand the documentation, sorry). I think it should be fine to
just pass the rectangle to OMERO. However, are ROIs allowed to overlap?
3. A way to attach processing information and (scalar) analysis results to
ROIs and images. I was first looking at StructuredAnnotations, but it is, of
course, a problem if their values are immutable - I need to change their
value at least once. Ideally, I could annotate the data in a form of
'parameterName': parameterValue, though it seems like misusing the protocol
editor for this may be the only way to get this to work - can I set the
'experimental parameters' from Matlab?. Tables also look like a good
possibility, though I would prefer not to mix processing information and
analysis results in the same table. Is thus possible to attach multiple
tables to ROIs? Also, is a table editable in OMERO.insight?
4. A way to query these annotations from Matlab or from OMERO.insight.
5. A way to browse attached figures in OMERO.insight (so that I can use the
information presented by the graphs to manually annotate the ROIs.

Can I do all this with the current version of OMERO? What would I need to
change? Could you help me with general examples on how to accomplish these
steps from Matlab?

Sorry for the wall of text and thanks for your insights!

Jonas
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