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