Thanks for your replies, Michael and Donald.<div><br></div><div>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.</div>
<div><br></div><div>I think I should try and clarify some more what I'd like my workflow to look like:</div><div><br></div><div>Image analysis</div><div>- Find experiments or images that have not been analyzed yet (calling the database from Matlab)</div>
<div>- 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)</div><div>- Run analysis in Matlab</div>
<div>- 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?)</div><div>- 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. </div>
<div>- Attach graphs to ROIs.</div><div>- Attach path to analysis files to images.</div><div><br></div><div>Data browsing</div><div>- In Omero.insight, find images/ROIs with certain characteristics</div><div>- Look through attached graphs</div>
<div>- Improve/Extend annotation, e.g. to classify ROIs according to phenotype.</div><div><br></div><div>Data analysis</div><div>- Find images with completed analysis/annotation with specific characteristics by querying database (calling the database from Matlab or from insight)</div>
<div>- Run statistical comparisons between sets, display group averages/distributions using Matlab scripts, run more involved analysis in Matlab.</div><div><br></div><div>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.</div>
<div><br></div><div>To this end, I need to</div><div>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?). </div>
<div>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).</div>
<div>Donald, for my project all images are deltavision files already, so it looks like your idea should be no problem to implement.</div><div>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?</div>
<div>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?</div>
<div>4. A way to query these annotations from Matlab or from OMERO.insight.</div><div>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.</div>
<div><br></div><div>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?</div><div><br></div><div>Sorry for the wall of text and thanks for your insights!</div>
<div><br></div><div>Jonas</div>