[ome-devel] Zeiss 710

[Melissa Linkert]

Hi Rubén,

> Therefore tried this with bfconvert, even when appending to existing OME.TIF is not supported yet.

Appending to existing OME-TIFF files is, in theory, supported.  However,
the MetadataRetrieve object used by OMETiffWriter must be correctly set
up, which unfortunately will not happen by repeatedly calling
bfconvert.

> 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.

Yes, I see the same behavior.  It is ticketed here:

http://dev.loci.wisc.edu/trac/software/ticket/578

And, as usual, you have been CC'd.  I am a bit curious though: why run
bfconvert repeatedly with the same output file?  Are you trying to
convert multiple datasets to a single OME-TIFF file?  If I know the use
case, then maybe there is a work-around until the above ticket is closed.

Regards,
-Melissa

On Tue, Oct 05, 2010 at 11:29:36AM +0200, Rubén Muñoz wrote:
> 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
> > http://openmicroscopy.org.uk
> > 
> > 
> > 
> > 
> > 
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> 

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