[ome-users] Problem using LOCI to import .czi images

[Richard Lipkin]

Dear Melissa,

Thanks very much for the information. I installed the stitching plugins to
which you sent me the link. However, when I follow the procedure you
mentioned, I get an error that says "Exception: null / Could not initialise
stitching." In order to attempt to stitch the image, I unchecked "Compute
overlap," selected "Save computation time (but use more RAM)" (we have
192GB of RAM), and all other settings were defaults.

Are there any further pointers you could give me in order to avoid this
error?
Thanks very much again,

Richard

On Thu, Apr 12, 2012 at 2:57 PM, Melissa Linkert <
melissa at glencoesoftware.com> wrote:

> Hi Richard,
>
> > I am writing from Andrew Dwork's lab at Columbia University. I was very
> > pleased to see that your latest version of LOCI provides support for the
> > Carl Zeiss .czi imaging format. However, I have run into a minor snag
> while
> > importing images, and I was wondering whether you can provide some
> advice.
> >
> > I have some .czi images that each contain numerous stacks stitched
> together
> > in specific relationships to one another. When I run the LOCI bio-formats
> > importer, it gives me a choice of which of these stacks to open. It then
> > lets me choose which dimension gets which planes (Z, C, or T). Then it
> > opens the individual stacks flawlessly. My question is, is it possible to
> > have LOCI import these .czi files as one big image with the stitching
> > between the stacks preserved?
>
> Yes - there are two options for doing so.  To get a very rough stitched
> image, you can select the "Stitch tiles" option in the "Bio-Formats
> Import Options" window.  This will attempt to stitch the stacks back
> together based upon the stage positions, but it assumes 0% overlap
> (which more often than not is not the case).
>
> The much better solution is to use the stitching plugins developed by
> Stephan Preibisch:
>
> http://fiji.sc/wiki/index.php/Image_Stitching
>
> ...which will open the file for you (using Bio-Formats) and perform the
> stitching based upon the metadata in the file and some parameters that
> you specify.
>
> In this case, you probably want to use it by selecting
> "Plugins > Stitching > Grid/Collection stitching", then set the type to
> "Positions from file" and the order to "Defined by image metadata".
> You'll then be asked for the name of the file and some extra parameters,
> after which point the stitched image should just appear.
>
> Regards,
> -Melissa
>
> On Thu, Apr 12, 2012 at 09:53:03AM -0400, Richard Lipkin wrote:
> > Dear OME Users list,
> >
> > I am writing from Andrew Dwork's lab at Columbia University. I was very
> > pleased to see that your latest version of LOCI provides support for the
> > Carl Zeiss .czi imaging format. However, I have run into a minor snag
> while
> > importing images, and I was wondering whether you can provide some
> advice.
> >
> > I have some .czi images that each contain numerous stacks stitched
> together
> > in specific relationships to one another. When I run the LOCI bio-formats
> > importer, it gives me a choice of which of these stacks to open. It then
> > lets me choose which dimension gets which planes (Z, C, or T). Then it
> > opens the individual stacks flawlessly. My question is, is it possible to
> > have LOCI import these .czi files as one big image with the stitching
> > between the stacks preserved?
> >
> > Thank you very much for your assistance,
> >
> > Richard Lipkin
> > lipkinr at nyspi.columbia.edu
>
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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