http://imagej.273.s1.nabble.com/Problem-with-Grid-Collection-stitching-plugin-tp5005228p5005390.html
robust. I've written up a short description of how to do it:
> 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,