[ome-users] OME-TIF Batch Export

[Will Moore]

Hi Christophe,

You are correct, only Dataset or Image are supported.
I'll look into supporting Screen or Plate export: http://trac.openmicroscopy.org.uk/ome/ticket/6401

  Cheers,

    Will.


On 3 Aug 2011, at 17:58, Christophe TREFOIS wrote:

> Hi Will,
>
> Ok I will try the script. Thank you.
>
> Am I correct to assume that Screen export is not yet implemented  
> then ? So only images from projects are currently exportable?
> Not even as “alpha” ?
>
> This just so I don’t rip out my hear when trying the script ^^
>
> Kind Regards,
>
> ................................................................................
> 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
>
> From: Will Moore [mailto:will at lifesci.dundee.ac.uk]
> Sent: Wednesday, August 03, 2011 6:05 PM
> To: Christophe TREFOIS
> Cc: ome-users at lists.openmicroscopy.org.uk
> Subject: Re: [ome-users] OME-TIF Batch Export
>
> Hi Christophe,
>
> The OME-TIFF support in Batch_Image_Export.py should be in the next  
> release. This will be later this year, but we haven't set a target  
> date yet.
>
> You should be able to download the latest script and give it a go  
> (click on 'raw' at the top of this page):
> http://git.openmicroscopy.org/?p=ome.git;a=blob;f=components/tools/OmeroPy/scripts/omero/export_scripts/Batch_Image_Export.py;h=1df7b714586ea3c7ff6bfde17332bd1832c783b7;hb=develop
>
> Some warnings:
>  - This has not been thoroughly tested yet, although it seems to  
> work for me.
>  - This has only been tested on the latest development server,  
> although it "should" work on 4.3.1
>
> Try it in a "test" environment! Upload the script as a new script  
> (don't replace your existing Batch_Image_Export).
> More info on using scripts etc. http://trac.openmicroscopy.org.uk/ome/wiki/OmeroScripts
>
> Let us know how this works for you, performance etc.
>
> Cheers,
>
>  Will.
>
>
> On 3 Aug 2011, at 16:32, Christophe TREFOIS wrote:
>
>
> 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
>
> <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
>
> 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
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
> 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
>
>
>
>
>
>
> 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
>
>
>
>
>

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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