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

[Curtis Rueden]

Hi Richard,


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?
>

Your best bet is to seek help on the fiji-users list, since the Stitching
plugins are part of Fiji.

I have CCed that list, in hopes that someone can help you out.

Regards,
Curtis


On Mon, Apr 16, 2012 at 8:29 AM, Richard Lipkin
<lipkinr at nyspi.columbia.edu>wrote:

> 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
>>
>> > _______________________________________________
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>> > ome-users at lists.openmicroscopy.org.uk
>> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
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