[ome-users] General information request

[Ilya Goldberg]

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

>
>
>
> Thank you very much for your kind help.
>
>
>
> Bernd
>
> Bernd Jagla, PhD
> Associate Research Scientist
> Columbia University
> 1150 St. Nicholas Avenue
> Russ Berrie Medical Pavilion, Room 520
> New York, NY 10032
> Tel: 212 - 851 5560 x16
> Fax: 212 - 851 5570
> e-mail: baj2107 at columbia.edu
>
>
>
>
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