[ome-users] OME-TIF Batch Export

[Christophe TREFOIS]

Hi Will,

Sure, that would be nice. Select a screen plate (in a dropdown) and then select wells, maybe I only want half the plate or 1 well or the whole plate.
After that, a batch export would occur, creating say 1 OME-TIF per Field (since you can have more than 1 Field) per Well.

It should obviously not kill the Server, however at least from our side, we will have a relatively strong infrastructure.

Is there anything known on a timeframe or anything we can do to help ?

--
Christophe
................................................................................

Dipl.-Ing. Christophe TREFOIS
PhD Student

Ing. Sys. Com. Dipl. EPF

[Description: cid:image001.jpg at 01CACC35.07191DE0]
Luxembourg Centre for Systems Biomedicine
UNIVERSITY OF LUXEMBOURG
CAMPUS LIMPERTSBERG
162a, avenue de la Faïencerie
L-1511 Luxembourg
T +352 46 66 44 6124
F +352 46 66 44 6949
www.lcsb.lu<http://www.uni.lu/>

From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
Sent: Wednesday, August 03, 2011 5:09 PM
To: Christophe TREFOIS
Cc: ome-users at lists.openmicroscopy.org.uk
Subject: Re: [ome-users] OME-TIF Batch Export

Hi Christophe,

The limitation on exporting OME-TIFF is really just the processing required on the server to generate the files, since this requires a lot of database traversing and moving data around.

We are currently experimenting with adding OME-TIFF support to the Batch_Image_Export script.
This should address the functionality you want, but it will need some assessment to see how the server holds up when batch exporting large numbers of images.

The other issue is that the script currently runs on Datasets of images (or Images identified by ID), but you'd presumably want to specify a Plate of Images?


  Will.


On 3 Aug 2011, at 16:00, Christophe TREFOIS wrote:


Dear Ome's (is that correct?),

I read on some forums that there is no batch export for OME-TIF and I also only found a batch export for PNG or JPG.

Is there a specific reason for that?
More specifically, does anyone of you have any experience with this?

We would like to use OMERO with HCS data (Opera). Mass Import AND Export therefor becomes a necessity.

Thanks for any help,

--
Christophe
................................................................................
Dipl.-Ing. Christophe TREFOIS
PhD Student
Ing. Sys. Com. Dipl. EPF

<image001.jpg>
Luxembourg Centre for Systems Biomedicine
UNIVERSITY OF LUXEMBOURG
CAMPUS LIMPERTSBERG
162a, avenue de la Faïencerie
L-1511 Luxembourg
T +352 46 66 44 6124
F +352 46 66 44 6949
www.lcsb.lu<http://www.uni.lu/>

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William Moore
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 386364
http://openmicroscopy.org





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