[ome-users] General information request

[Jason Swedlow]

Bernd-

Ilya and Chris have filled in most of what you asked.  One more thing 
to keep in mind is that we have included a MatLab interface in the 
server system to allow a user to integrate MatLab-based analytics.  To 
our knowledge, this has not been used much yet-- any feedback from the 
community is much appreciated.

Cheers,

Jason

On 4 May 2005, at 21:19, Ilya Goldberg wrote:

>
> On May 4, 2005, at 2:51 PM, Bernd Jagla wrote:
>
>> Hi,
>>
>> I am setting up the IT infrastructure for an HTS/HCS lab that is 
>> using a HT
>> imaging system and have a couple of questions regarding OME and its
>> usability:
>> *	Is anyone using OME for HT imaging of cell based assays? If so,
>> could I get in contact with these people to exchange some experience?
>
> I can't comment on up-and-running HTS/HCS because we are only 
> preparing to do this in my group, and I know that others are further 
> along in using OME for their HCS efforts.  HCS is one of the reasons 
> OME came into this world, so this application is obviously a top 
> priority.
>
>> *	Can automation equipment be linked to OME?
>> *	Can I easily integrate such systems as ActivityBase, Genedata or
>> similar products?
>> *	Would OME try to replace such systems as ActivityBase or GeneData?
>
> Our goal is definitely not to supplant existing commercial software, 
> nor is it to replicate its functionality.  The goal is to provide an 
> open-source platform that can compliment commercial products and can 
> be quickly and locally adopted to specific imaging needs without 
> having to reinvent too many wheels.  We have done well in working with 
> industry to provide functionality that is complementary to what is 
> available in the commercial world.  So far this has consisted of 
> interoperating with image acquisition systems and other imaging 
> software by publishing a mutually agreed-upon file format and 
> supporting many existing image formats directly in OME.  As for HCS 
> formats specifically, we support the HTD format from UI's MetaMorph, 
> and one of our users has developed support for Beckman's IC100, which 
> will be included in the next software release.
> We have also demonstrated a high level of interoperability with other 
> independently-developed software projects (VisBio and ImageJ, thanks 
> to the LOCI group at Madison), so there is proof that a high level of 
> integration is possible beyond the mere sharing of common file 
> formats.  Work is in progress to explore mechanisms of integrating OME 
> with other structured data sources (i.e. federation with other 
> databases).  Some progress on this is expected before the end of the 
> summer.  We have no specific plans with regard to ActivityBase or 
> GeneData.
>
>
>> *	Are images stored inside the DB or as linked files? (I understood
>> from the web-page that they are inside the DB as blobs, but don't 
>> understand
>> why.)
>
> Images are not stored in the DB - only references to them.  I'm sorry 
> that this was not made more clear in the on-line documentation.  The 
> references maintained by the OME DB refer to IDs issued by OMEIS (The 
> OME Image Server) that is described in detail here:
> http://www.openmicroscopy.org/api/omeis/
> The Image server maintains original image files and a cache of the 
> pixels extracted from them.  This storage is done using regular files 
> in its own private section of the OS's file system.  Part of the 
> design philosophy of OMEIS is to provide storage infrastructure for 
> diskless, embedded or otherwise stripped-down acquisition systems.  
> There are a couple of efforts underway to use it in this manner.  It 
> would be an ideal "back-end" for a high-throughput acquisition system.
>
>>
>> I am very interested in participating actively in the project, but I 
>> first
>> need to understand how I could fit in.
>
> Very glad to have you.  You can contact me or Jason Swedlow off-list 
> if you want to discuss this further.
>
> -Ilya
>

NOTE NEW EMAIL ADDRESS: jason at lifesci.dundee.ac.uk
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