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

[Melissa Linkert]

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

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