Posted by
ctrueden on
Oct 18, 2013; 7:16pm
URL: http://imagej.273.s1.nabble.com/Problem-with-Grid-Collection-stitching-plugin-tp5005228p5005247.html
Hi Kurt,
> 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?
What happens if you select "Positions from file" for the Type, and "Defined
by image metadata" for the Order?
I will also reiterate my previous question:
> If you run File > Import > Bio-Formats and point it at your
> Micro-Manager .txt file, does it properly detect all your stage
> positions?
Regards,
Curtis
On Thu, Oct 17, 2013 at 4:01 PM, Kurt Thorn <
[hidden email]> wrote:
> 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
>>>
>>> --
>>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.****html<
http://imagej.nih.gov/ij/list.**html>
>>> <
http://imagej.nih.gov/**ij/list.html<
http://imagej.nih.gov/ij/list.html>
>>> >
>>>
>>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.**html<
http://imagej.nih.gov/ij/list.html>
>>
>>
>>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.**html<
http://imagej.nih.gov/ij/list.html>
>
--
ImageJ mailing list:
http://imagej.nih.gov/ij/list.html