[ome-devel] Zeiss 710

[Rubén Muñoz]

Hi Curtis and Will, 

I haven been using OMERO recently, but make efforts in having our OME.TIF in good shape, including SPW. This will permit us to migrate across imaging platforms.
The problem with some ome.tif (generated by scripting or by companies) is that multi-file and SPW capabilities can be missing.
The same way that OMERO has a solution for this, we though in having a file-based command-line tool. 

I consider the ImageJ plugins and macros a temporal solution, because actually they can be slow for our throughput. 
Therefore tried this with bfconvert, even when appending to existing OME.TIF is not supported yet.

However wIth the latest revision of bioformats 7034 when I output the bfconvert to the same file consecutively, the file is always getting bigger in size.

Is appending to OME.TIF a work in progress or is there a bug there?

Thanks for the help, best regards,

Rubén

On Sep 30, 2010, at 3:27 PM, Curtis Rueden wrote:

> Hi Rubén,
> 
> I believe similar functionality exists in ImageJ but don't know the details?
> 
> In ImageJ, you can use the Bio-Formats Importer with the "Concatenate series when compatible" option to stitch together the 48 series, as long as they all have the same dimensional extents.
> 
> -Curtis
> 
> On Thu, Sep 30, 2010 at 5:22 AM, Will Moore <will at lifesci.dundee.ac.uk> wrote:
> Hi Ruben,
> 
> 
> On 30 Sep 2010, at 10:38, Rubén Muñoz wrote:
> 
> I have asked the author of these images. She produced the data using a Zeiss macro that actually doesn't perform series, but many different single images, renamed independently.
> I have nothing to add to this thread. It is not an issue. Never mind about that dataset, I am not sure how I will convert them, but bioformats should not do it directly.
> 
> However... Can one add the corresponding independent series to one OME.TIF file creating a new multiT set?
> 
> 
> There is a script in OMERO to stitch multiple images into a single image with more dimensions (which you could then export). This would duplicate the data. See:
> http://cvs.openmicroscopy.org.uk/snapshots/movies/omero-4-2/mov/Scripting1.mov
> The script has evolved a bit since then to auto recognise images by name. See:
> http://trac.openmicroscopy.org.uk/shoola/wiki/UtilScripts#CombineImages
> 
> You could edit the script itself to tailor it to your requirements if necessary.
> 
> I believe similar functionality exists in ImageJ but don't know the details?
> 
>  Cheers,
> 
>    Will.
> 
> 
> Thanks for the discussion.
> 
> Rubén
> 
> 
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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
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> 
> 
> 
> 
> 
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