[ome-users] extract images from OMERO

[Jason Swedlow]

Hi Kees-

On 3 Apr 2009, at 17:51, Straatman, Dr K.R. wrote:

> Dear OMERO users,
>
> We have been testing OMERO Beta 3.x (the Computer Centre the server  
> side, I the user side) and the improvements I have seen on the  
> website for OMERO 4 are impressive but we had no time to test it yet.

OK-- if you have any problems installing and running, please do  
contact us.  We are on track for a 4.0.1 release later next week, to  
fix a few bugs.  Beta4 is substantial change and functionality  
upgrade, and a few bugs and simple missed things are to be expected.


> We are looking for an imaging storage and backup system and OMERO  
> can do many things I like. However, going through the function  
> descriptions on the website it is not clear for me how to export  
> data from OMERO to for example Imaris software, Huygens  
> deconvolution software or any other analysis package the users might  
> want to use.

This is critical functionality for us-- it's what we refer to the  
"whole workflow" or "getting in and out".  We've worked hard in Beta4  
to get as much metadata as possible into OMERO-- our extension of  
metadata support in a number of file formats and the integration of  
OMERO.editor into OMERO.insight are examples of this.  However, it's  
time to get data out of OMERO.  In Beta4, OMERO.insight creates a  
report-- a .xls file with thumbnails and annotations.  That's a start,  
and is by no means everything we have to do.  We are working hard on  
an ImageJ plug-in that supports OMERO-Beta4; more details on this will  
follow in the next week or so.  As OME-TIFF is now supported by many  
commercial imaging applications, we will also work to have OMERO  
export this format.  And finally, for presentation, we are exploring  
the creation of MPEGs from data stored in OMERO.


> I understand from an earlier email from Andrew Patterson, which also  
> has been posted on the list server, that a plugin for ImageJ is  
> being updated and I saw there is also support for MatLab. He also  
> mentioned OMERO.fs. Will this keep the full functionality of OMERO  
> or because the images are on a different location will lose  
> functionality?

I'm not sure what you mean by 'lose functionality'.  Initially,  
OMERO.fs is implemented as a dropbox for files, to enable automatic  
import.  As we move forward, we intend to use OMERO.fs to enable  
multiple data repositories.  Supporting all the different OS's and  
filesystems is no small feat, but we are trying.


> Before I can implement OMERO I have to be sure how to get images out  
> of OMERO, analyse them and put them back into OMERO, if possible  
> without too much fuss.

As you've seen, access via Matlab is currently supported.  As an  
example, we've provided support for Cellprofiler (http://www.cellprofiler.org 
), the data analysis tool released by Anne Carpenter's group at the  
Broad, via the OMERO Matlab gateway.  Bespoke applications, written in  
C++, Java, and Python can also access data within OMERO.  The  
functionality described above are the next we'll provide.

Hopefully, that helps.  The bad news-- we're not done.  The good  
news-- we are making steps towards everything you want.  It is  
possible that if you start using OMERO now in a limited way, you can  
follow along with the delivery of new functionality and help us define  
what you need.

Cheers,

Jason

>
> Thanks for your help
>
> Kees
>
>
> Dr. K.R. Straatman
> Senior Experimental Officer
> School of Biological Sciences
> http://www.le.ac.uk/biochem/microscopy/home.html
>
> Postal address:
> Department of Biochemistry
> Henry Wellcome Building
> University of Leicester
> Lancaster Rd.
> Leicester LE1 9HN
> UK
> tel.: + 44 (0)116 229 7085/252 2263
> fax: + 44 (0)116 229 7031
>
> Times Higher Education University of the Year 2008-9
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users



**************************
Wellcome Trust Centre for Gene Regulation & Expression
College of Life Sciences
MSI/WTB/JBC Complex
University of Dundee
Dow Street
Dundee  DD1 5EH
United Kingdom

phone (01382) 385819
Intl phone:  44 1382 385819
FAX   (01382) 388072
email: jason at lifesci.dundee.ac.uk

Lab Page: http://www.dundee.ac.uk/lifesciences/swedlow/
Open Microscopy Environment: http://openmicroscopy.org
**************************

The University of Dundee is a Scottish Registered Charity, No. SC015096.



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20090404/19407640/attachment.html>