Posted by
Tom Zhou on
Mar 27, 2015; 6:01pm
URL: http://imagej.273.s1.nabble.com/How-to-perform-3D-stitching-with-the-new-stitching-plugin-tp5012025p5012217.html
Hi Curtis,
Thanks for your reply. Unfortunately I cannot post my data due to lab
policy. But I can describe the problem in details:
My data is a set of brain scan images that consists of 60 (6*10) tiles in
each z-slice. As a trial, I performed stitching on 5 z-slices only.
I noticed the following inconsistency in the results:
-> In slice z=50, the edge of the brain has a "jump." The tiles are not
perfectly aligned.
-> In slice z=51, the jump is almost unnoticeable. The edge is very
continuous.
-> In slice z=52, the jump is again obvious, just like the slice z=50.
The problem is that when we construct a 3D model with these stitched
images, there will be an inconsistency while moving along the z direction.
At first the edge of brain has a jump, then it is smooth in the next slice,
then the jump is back. I would like to see a more smooth change across Z.
Thank you again for your help!
Thanks,
Tom
On Tue, Mar 24, 2015 at 11:55 AM, Curtis Rueden <
[hidden email]> wrote:
> Hi Tom,
>
> > I can only specify x and y ranges, but not z.
>
> The Stitching plugins do try to adjust 3D stacks along Z so that things
> align better, unless you follow the instructions on the wiki to disable
> that [1].
>
> If you are seeing otherwise, perhaps you could post a small dataset
> illustrating the issue, together with a description of what happens, vs.
> what you would like to happen.
>
> Regards,
> Curtis
>
> [1]
http://fiji.sc/Stitching#I_want_to_ignore_the_movement_of_tiles_in_Z>
> On Tue, Mar 17, 2015 at 6:00 PM, Tom Zhou <
[hidden email]> wrote:
>
> > Hi,
> >
> > I had a problem when trying to do 3D stitching with the grid/collection
> > stitching plugin in Fiji. I can only specify x and y ranges, but not z. I
> > noticed that there is an z option in the "deprecated" version of the
> > plugin.
> >
> > Should I make a stack with tiles with same x and y positions, then stitch
> > these stacks in order to do 3D stitching? How do I make sure that
> alignment
> > is computed across the z-slices?
> >
> > Thank you for your help!!
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
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