Re: problem with grid/collection stitching

Posted by Aryeh Weiss on Aug 24, 2016; 5:47pm
URL: http://imagej.273.s1.nabble.com/problem-with-grid-collection-stitching-tp5017105p5017108.html

Dear Jan,

Thank you for your reply.
I suspect that because my image are sparse, I need to reduce the
regression threshold. However, I still dont understand why it works when
I do 1/2 of the image at a time. When it works, even with the very low
regression threshold, it works very well. I examined many of the seams
which I thought would be troublesome, and the stitching was perfect.

So, I stitched the two halves separately, and these are the results:
Top half:
https://drive.google.com/file/d/0Bytu294eIohjUWZhY3JkZDJLQVk/view?usp=sharing
bottom half:
https://drive.google.com/file/d/0Bytu294eIohjSEZhejZ1ekRtSjA/view?usp=sharing

But I cannot get these two images to pairwise stitch, apparently because
of the black borders (my scope software staggers the fields when I
collect with overlap -- I wish I knew how to tell NIS elements not to do
that).

I thought checking "ignore zero" would help, and I set up ROIs in the
areas where I wanted the program to check, but still no success.

  Best regards
--aryeh


On 24/08/2016 10:57 AM, Jan Eglinger wrote:

> Dear Aryeh,
>
> I didn't have time to check out your images yet, but had some problems
> with misalignment in the past as well. See also this discussion on the
> ImageJ forum:
> http://forum.imagej.net/t/limit-the-tile-displacement-in-stitching/424?u=imagejan 
>
>
> If I understood correctly after looking at the source code, the
> max/avg displacement parameter defines how far each tile can deviate
> in the global optimization from its computed position in the pairwise
> alignment with each overlapping tile. That means if the pairwise
> alignment returned "wrong" values, the tile will get misaligned no
> matter what are its coordinates defined in the TileConfiguration.txt.
>
> Maybe Stephan Preibisch can comment more on that.
>
> Best regards,
> Jan
>
>
> On 24.08.2016 05:49, Aryeh Weiss wrote:
>> I am having trouble with stitching the following set of images (filename
>> defined positions):
>>
>> https://drive.google.com/file/d/0Bytu294eIohjUE5waC1EQUhfZE0/view?usp=sharing 
>>
>>
>> The above link is to a zip file that contains the 120 tiles that I am
>> trying to stich (nominally 10% overlap)
>>
>> With the default parameters, the following is obtained, with many
>> "misplaced" tiles
>> Here is a link to what I get.
>> https://drive.google.com/file/d/0Bytu294eIohjbzYwWG15bW5qWEk/view?usp=sharing 
>>
>>
>>
>> If I reduced the regression threshold to 0.02 (from 0.3), it is better,
>> but I still have the (1,1) tile misplaced:
>> https://drive.google.com/file/d/0Bytu294eIohjbDQ0N2VxVVVuUVE/view?usp=sharing 
>>
>>
>>
>> If I repeat with the smaller regression threshold, but I only stitch the
>> top half of the image, including the (1,1) tile, it works correctly.
>>
>> By eye it looks like I have enough  "structure" (marks, spots, etc) to
>> align. In any case, I dont see how it can get so misalligned, even when
>> I reduced the max/avg displacement.
>>
>> Is there something inherently wrong with  with my images? Is there a
>> better set of parameters which I can use to get it right.
>>
>> Thanks in advance for any help you can provide.
>>
>> --aryeh
>>
>

--
Aryeh Weiss
Faculty of Engineering
Bar Ilan University
Ramat Gan 52900 Israel

Ph:  972-3-5317638
FAX: [phone]

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