How to perform 3D stitching with the new stitching plugin

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How to perform 3D stitching with the new stitching plugin

Tom Zhou
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!!

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Re: How to perform 3D stitching with the new stitching plugin

ctrueden
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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Re: How to perform 3D stitching with the new stitching plugin

Tom Zhou
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
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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