[ome-users] which commercial software vendors or microscopy hardware vendors are supporting OME today (December 5, 2008) ? What are the benefits people are getting?

[Jason Swedlow]

Hi Rich-

Interesting questions....thanks for this.

On 6 Dec 2008, at 02:45, Lysakowski, Rich wrote:

>
> Dear Colleagues,
>
> Which commercial software vendors or microscopy hardware vendors are
> supporting OME today??  (December 5, 2008)
>

Here are the ones we know about.

http://www.openmicroscopy.org/site/about/partners

If we are missing any, please let us know.

> At a company I am working for, we are specifying purchase of a  
> software
> product right now, so we want to know if it is realistic to put in OME
> support as a requirement for purchasing.

It depends on what you mean-- and you have to decide this.  Do you  
mean they have write OME-TIFF (probably through a "Save As..."  
mechanism)?  Use an OME API?  Incorporate OME software (e.g., OMERO or  
Bio-Formats)?

>
> My initial thinking -- until I learn more -- is that OME needs to be a
> primary requirement for all imaging software and hardware/software
> purchases in life sciences research (where image data handling is
> crucial).

That is certainly our goal, but our efforts are focussed on delivering  
great specs, tools, and docs.  The community has to make the decision  
about whether it is a requirement or not.  BTW, we define the  
community as including users, developers, vendors, publishers, and  
funders.  Your posting here is helpful, but maybe also consider other  
microscopy lists and the HCS list?

>
> To make widespread OME adoption happen, buyers must mandate OME as a
> condition of all purchases (from today forward).  Products with
> equivalent functionality for imaging application that don't support  
> OME
> should be passed over.
>

We'd certainly be happy to see customers in academic, biotech, and  
biopharma labs demanding this.  But, you must remember that OME's  
specs and tools are still developing.  We have made great progress,  
but there are still things missing.  An example is our support for HCS  
data-- it is still developing.  But we can progress rapidly where we  
have guidance from vendors and users, where we get authoritative input  
on what should and should not be available, sample data sets, etc.


> How important do you consider imaging informatics to your future  
> imaging
> research?  Microscopes have evolved so much, to where the  
> differentiator
> is often not the microscope, but the image data handling capabilities
> and your ability to use the image and annotation data for your  
> intended
> purpose.

"Imaging" is a VERY broad field.  The binary data structures (the  
"Pixels" in OME) are very similar (but not always, e.g. FLIM)  but  
there is a vast range of metadata that must be supported.  This  
differs alot between different imaging modalities.  That is why we  
haven't following the "minimal set" approaches that have been popular  
elsewhere.

>
> Based on over 20 years working for the buyer side of the lab software
> industry, if people do not mandate standards, vendors do NOT invest,  
> and
> you stay caught in the old "Catch 22".

You are correct-- these decisions will be mandated by the customers.

>
> Without OME (or some proprietary and open equivalent) image  
> informatics
> or analytics will be constrained unnecessarily, especially for image
> collections and repositories with images from different microscopes.
>
> Imaging Scientists lose analytical capabilities you didn't know you
> could have.  (Sometimes... ignorance is bliss... but not in Science.
> ;^))
>
> What have been your experiences at imaging conferences and trade  
> shows?
>
>
> Are vendors showing significant applications and benefits of OME in
> their shipping products?
>
> Are there good industrial applications papers being presented that  
> show
> its capabilities and benefits?
>
> Has OME made it to mainstream in industrial companies yet?
>
> Thank you for your answers...

Alot of big questions there.....

Anecdotally, I can tell you that most of the imaging companies have  
been very supportive of our efforts.  They see the value of defined  
data and API specifications for themselves and their customers.  
However, the fact is that the the OME strategy is rather new in  
biological imaging (although open source/commercial partnerships and  
open standards efforts are well-developed in other domains).  As  
mentioned above, a number of companies are supporting the OME-XML or  
OME-TIFF  file formats and we have received alot of informal advice,  
input, and formal letters of support from many of the commercial  
companies (the letters should not be dismissed-- very very important  
for funding, without which, the whole thing stops).  Most recently,  
PerkinElmer has begun releasing a customised version of OMERO software  
alongside their Opera (TM) HCS system that allows customers to use  
open-source OMERO clients (http://las.perkinelmer.com/Imaging/Products/HCS/Columbus.htm 
) and the Journal of Cell Biology has released the JCB Dataviewer that  
uses OME technology  to enable visualization of original data  
associated with publications (http://jcb.rupress.org/cgi/content/full/jcb.200811132 
).

To quote you, "Has OME made it...?".  Not yet, but it is certainly  
happening, and we are very excited about the recent developments. But,  
you are correct-- OME becomes a community standard when the community  
decides it will be.  We are working as hard as we can to develop the  
tools to meet that challenge, but it is for the community to decide  
if  our tech meets that challenge.  We always appreciate any feedback/ 
criticism/comments (and we love positive feedback too!).

Thanks for your comments, and as always, thanks for your support.

Cheers,

Jason

>

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