[ome-devel] Fwd: experience with OME

[Jason Swedlow]

Forwarding to list.

Comments from OME devs, and/or from community?

Cheers,

Jason

Begin forwarded message:

> From: Michael Riffle <mriffle at u.washington.edu>
> Date: 10 September 2009 21:41:04 BST
> To: jason at lifesci.dundee.ac.uk
> Subject: experience with OME
>
> Jason,
>
> My name is Mike Riffle and I work with Trisha Davis over here in  
> Seattle, handling the informatics endeavors for the Yeast Resource  
> Center.  As you already know, we've developed a large database of  
> fluorescence microscopy images (YRC Public Image Repository, http://images.yeastrc.org/) 
> , for which I've implemented support for disseminating the data as  
> fully-valid OME TIFF files.  Trisha forwarded some email to me (from  
> you) regarding this web site and suggested that I send you some  
> feedback about OME and my experience getting it set up in our site.   
> I know how hard feedback can be to come by, and I'm more than happy  
> to oblige.
>
> I spent a /lot /of time going over the ample documentation the OME  
> project provides on their websites, and I know that I've barely  
> scratched the surface of all that OME has to offer.  My goal was  
> relatively simple:  I wanted to distribute the 500,000+ TIFF images  
> and accompanying experimental metadata as OME TIFFs in our public  
> image database.  The idea being that users who download these data  
> will be able to plug them directly into software that supports the  
> OME format specifications.
>
> Accomplishing this task, however, was not entirely trivial.  As you  
> know, the XML specification for OME-XML is very extensive.  While  
> documentation does exist, I did have some challenges figuring out  
> how our metadata should be mapped onto the elements present in the  
> XML specification.  I don't know if the documentation was intended  
> for people doing what I was doing, but expanding the documentation  
> to more generally describe what is meant by each element (from a  
> high-level light microscopy POV) could potentially be beneficial to  
> developers.  Also, a high level description or diagram of the data  
> model in terms of items present in most light microscopy  
> experiments, and where these common elements should go in the XML  
> would be great.  For example, given 4 emissions/excitation  
> wavelength channels and 6 z-sections of each channel, this is how  
> that data should be organized in an XML file.
>
> Once I figured out where I thought the metadata should appear in the  
> XML, I set about using the bio-formats Java library to assemble OME  
> TIFFs from my TIFF image data and metadata.  I found the bio-formats  
> library to be great and the documentation very helpful.  While it's  
> obvious some of the documentation exists as "stubs", it got the job  
> done.  I did have some questions about how to do certain things and  
> used the mailing list.  Curtis Rueden responded promptly and helped  
> guide me through my problems and I got everything working.   I was  
> definitely impressed by his promptness and eagerness to help.
>
> However, as it turns out, the bio-formats Java library doesn't  
> produce OME-TIFFs that pass validation using the OME-XML validation  
> tool at http://validator.openmicroscopy.org.uk/.  I talked to Curtis  
> and this is a known problem.  I was a bit worried about producing  
> "invalid" OME-TIFFs for distribution in our site, so I went ahead  
> and ended up writing my own code from scratch to produce valid OME- 
> TIFFs.  This required me to become even more intimately familiar  
> with the XML specification and all of its particular requirements  
> (such as the fact that it strictly enforces the order of the XML  
> elements in the OME-XML portion of the OME-TIFF file).
>
> Our site is now producing OME-TIFFs that pass validation at the OME  
> validator and include all of our experimental metadata, so I'm quite  
> pleased.  This certainly wouldn't have been possible without all of  
> the great documentation and the help of the OME staff.  Overall, it  
> was probably a bit more complicated than it needed to be, but it was  
> a fine experience and I learned a lot about the OME tools and file  
> specification.
>
> Another suggestion I have is regarding the possibility of adding in  
> support for describing the experiments biologically--particularly  
> relating to describing the tagged proteins, protein tags or dyes  
> used and possibly the ability to include some manual curation from  
> controlled vocabularies, such as the Gene Ontology.  I ended up  
> using user-defined elements to include these types of descriptive  
> elements in the OME-TIFF files.  I didn't see any official way to  
> include this information, and it definitely seems like information  
> relevant to the data being viewed.
>
> Again, it was a positive experience and I look forward to learning  
> more about OME and how we can make our data play well with your  
> tools.  If you are ever looking for feedback or for anyone to help  
> contribute to the cause, please don't hesitate to ask.  I would love  
> to be involved.
>
> Cheers,
> Mike
>
> -- 
> Michael Riffle
> Research Consultant, Informatics
> Yeast Resource Center & UW Proteomics Resource
> University of Washington, Seattle
>



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