Posted by
Kurt Thorn on
Oct 17, 2013; 9:01pm
URL: http://imagej.273.s1.nabble.com/Problem-with-Grid-Collection-stitching-plugin-tp5005228p5005231.html
On 10/17/2013 1:41 PM, Curtis Rueden wrote:
> Hi Kurt,
>
>> the final stitched image is composed of repeated copies of the first
>> image stack
> Grid/Collection stitching uses Bio-Formats to read the stage position
> information as well as the pixels. If you run File > Import > Bio-Formats
> and point it at your Micro-Manager .txt file, does it properly detect all
> your stage positions? Do they open correctly individually? If not, this is
> a Bio-Formats bug rather than a problem with the Stitching plugins.
>
> Regards,
> Curtis
I'm running grid/collection stitching with the Filename defined position
option, and pointing it to a folder of tif stacks with the naming
convention tumor_grid_animal04_2_MMStack_1-Pos_{xxx}_{yyy}.ome.tif and
the stitching plugin reports that it opens each stack separately, so I
think that's working OK? But perhaps it's a more subtle interaction
between BioFormats and the stitching plugin?
Thanks,
Kurt
>
> On Thu, Oct 17, 2013 at 3:31 PM, Kurt Thorn <
[hidden email]> wrote:
>
>> Hi All -
>>
>> I'm trying to stitch a set of Z-stacks acquired in Micro-Manager using the
>> Grid/Collection stitching plugin in Fiji. Everything seems to work OK
>> except that the final stitched image is composed of repeated copies of the
>> first image stack in the set rather than stitching the actual stacks at
>> each position. However, the positions of these copies look like they are
>> in the correct place for the locations of the actual tiles. Can anyone
>> provide insight as to what may be going wrong? I've attached the log file
>> and can provide more information as needed.
>>
>> Thanks,
>> Kurt
>>
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