<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Hi Jonas,<br><br><br>On Dec 15, 2009, at 1:45 PM, Jonas Dorn wrote:<br><br><blockquote type="cite">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.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">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.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">I have the following questions:<br></blockquote><blockquote type="cite">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?<br></blockquote>There are no limitations, you should be able to do anything in Matlab you can do in the java interface.<br><blockquote type="cite">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?<br></blockquote>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:<br><br><a href="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/PixelsService.java</a><br><a href="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/PixelBuffer.java</a><br><a href="http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/romio/src/ome/io/nio/DeltaVision.java">http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/romio/src/ome/io/nio/DeltaVision.java</a><br><br><br><blockquote type="cite">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?<br></blockquote>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.<br><br><blockquote type="cite">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?<br></blockquote>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.<br><br><blockquote type="cite">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?<br></blockquote><blockquote type="cite"><br></blockquote>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:<br><br>creates and uploads roi to pytables<br><br><a href="http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/scripts/populateroi.py">http://trac.openmicroscopy.org.uk/omero/browser/trunk/components/tools/OmeroPy/scripts/populateroi.py</a><br><br>reads from pytables:<br><a href="http://trac.openmicroscopy.org.uk/shoola/browser/trunk/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java:371">http://trac.openmicroscopy.org.uk/shoola/browser/trunk/SRC/org/openmicroscopy/shoola/env/data/OMEROGateway.java:371</a><br><br>Hope this helps<br><br>Donald<br><br><blockquote type="cite">Thanks for all your help!<br></blockquote><blockquote type="cite">Jonas<br></blockquote><blockquote type="cite">_______________________________________________<br></blockquote><blockquote type="cite">ome-devel mailing list<br></blockquote><blockquote type="cite"><a href="mailto:ome-devel@lists.openmicroscopy.org.uk">ome-devel@lists.openmicroscopy.org.uk</a><br></blockquote><blockquote type="cite"><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br></blockquote><div><font class="Apple-style-span" color="#144FAE"><br></font></div></body></html>