[ome-users] Z Stack Time Series Rebuilding

[Will Moore]

Hi Todd,

The ability to combine several single-plane images into a single image  
in OMERO is supported by one of the scripts that was shipped with  
OMERO 4.2 as part of the new scripting service.
A movie that introduces the scripting service and demonstrates that  
script can be seen here
http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-2/mov/Scripting1.mov

Actually, the movie is a little out of date already, and the script  
has been extended to recognise the Z and T indexes in the image names.  
This will be useful to you if all the images are named appropriately,  
E.g. image_Z08_T24.tiff.

Instructions on the latest version of the script are here http://trac.openmicroscopy.org.uk/shoola/wiki/UtilScripts#CombineImages
If your naming convention is not supported, or you need any other help  
with the script, let us know.

  Cheers,

   Will.



On 19 Jul 2010, at 23:38, Todd H. Stokes wrote:

>
> Hello,
>
> I have a large dataset (~2000 images) stored as TIFF images. These  
> images represent ~80 time points and a Z stack of size 15. As I  
> imported these images, there wasn't the proper meta-data in the  
> directory for OMERO to interpret these images as one big stack, so  
> each one has a separate record now.
>
> Is there a way for me (as the data administrator) to merge these  
> files into one record on the server, which can be browsed using the  
> Z-slider and the time slider?
> If not, is there a tool you can recommend that can merge these files  
> so that OMERO will import them properly?
>
> BTW, I upgraded to version 4.2 today with no problems!
>
> Thanks!
> Todd
> _______________________________________________
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> ome-users at lists.openmicroscopy.org.uk
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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.uk