[ome-devel] OMERO/Matlab

[dzmacdonald]

Hi Jonas,


On Dec 15, 2009, at 1:45 PM, Jonas Dorn wrote:

> 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?
There are no limitations, you should be able to do anything in Matlab  
you can do in the java interface.
> 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?
It is possible, the idea would be to create an image whose name is the  
path to the file, we then replace the RawPixelsStore contents so that  
it reads from the file referenced by the image directly. There is  
already code in place to read directly from deltavision files:

http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/romio/src/ome/io/nio/PixelsService.java
http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/romio/src/ome/io/nio/PixelBuffer.java
http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/romio/src/ome/io/nio/DeltaVision.java


> 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?
Yes, you can annotate roi. We also have started to have support for  
Pytables in OMERO which may be a more suitable solution for working  
with lots of table data where each row refers to an ROI.

> 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?
you can serch for terms inside files created by the protocol editor.  
Not sure what you want to do with graphs, are these images saved as  
png? if so then no.

> 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?
>
you could search for roi annotated using the structured annotations,  
or using the pytables api it would be much faster to select a subset  
of the table. I believe for the implementation your talking about the  
pytables api would be better. Examples of using the pytable api:

creates and uploads roi to pytables

http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/scripts/populateroi.py

reads from pytables:
http://trac.openmicroscopy.org.uk/shoola/browser/trunk/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java:371

Hope this helps

Donald

> Thanks for all your help!
> Jonas
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> ome-devel at lists.openmicroscopy.org.uk
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