Re: questions about grid stitching

Posted by ctrueden on Aug 10, 2016; 7:14pm
URL: http://imagej.273.s1.nabble.com/questions-about-grid-stitching-tp5016991p5016994.html

Hi Aryeh,

> I would like the stitching to be done only in the xy directions, but not
in Z.

Did you try this?
http://imagej.net/Image_Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z

> Second - when I select "downsample tiles", the stitching does
> something strange. It puts all of my grid of tiles in on row.

Sounds like a bug. You can file an issue here:
   https://github.com/fiji/Stitching/issues

It would be helpful to list the settings you used which produced the
problem.

Sorry to say I might not have time to investigate the issue right away.

Regards,
Curtis

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Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
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On Wed, Aug 10, 2016 at 1:54 PM, Aryeh Weiss <[hidden email]> wrote:

> I have two questions about this plugin:
>
> First - I have a set of XYZ stacks that I am stitching.
>
> I would like the stitching to be done only in the xy directions, but not
> in Z. That is, even if the stitcher thinks that a stack should be shifted
> in Z, I do not want that to happen. I though that selecting the "Ignore Z-
> stage position" would do this, but it turns out that even with that option
> stacks are shifted in the Z direction.
>
> Is there a way to prevent this. I have the ROIs in the ROI manager, but I
> do not want to write my own fusion program to fuse the stacks.
>
> Second - when I select "downsample tiles", the stitching does something
> strange. It puts all of my grid of tiles in on row. When I do nto
> down-sample, with all else the same, it works as expected. Do I
> misunderstand what the downsample option does? I was trying ot use it to
> same space on a really large stitched image.
>
> Tnx in advance for your help,
>
> --aryeh
>
> --
> Aryeh Weiss
> Faculty of Engineering
> Bar Ilan University
> Ramat Gan 52900 Israel
>
> Ph:  972-3-5317638
> FAX: [phone]
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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