Posted by
Peter Blankenheim on
Oct 30, 2013; 9:36pm
URL: http://imagej.273.s1.nabble.com/Problem-with-Grid-Collection-stitching-plugin-tp5005228p5005389.html
I have not used stacks or batches, but when I use filename defined positions for stitching in imageJ or Fiji, y is placed before x. Also it is just one y or x for the number, even if it is multidigit.
Peter
AMT
On Friday, October 18, 2013 6:58 PM, Kurt Thorn <
[hidden email]> wrote:
Hi Curtis -
On 10/18/2013 12:16 PM, Curtis Rueden wrote:
> 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?
This loads and stitches the images properly.
>
> 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?
If I point it to the first ome.tif file, it brings up a dialog asking
for the positions I want to open. If I point it to the first
metadata.txt file, I get an error: Unknown file format.
Thanks for your help!
Kurt
> 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
>>>>
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