<div>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.</div>
<div><br></div><div>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.</div>
<div><br></div><div>I have the following questions:</div><div>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?</div>
<div>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?</div>
<div>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?</div>
<div>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?</div>
<div>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?</div><div><br></div><div>Thanks for all your help!</div><div>Jonas</div>