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Re: 3d registration across multiple stacks

Posted by aget on Apr 01, 2020; 6:00pm
URL: http://imagej.273.s1.nabble.com/3d-registration-across-multiple-stacks-tp5023110p5023142.html

Got it, will dig it more; but in the meantime, I found "Correct 3D drift"
plugin of ImageJ could do nice 4D registration, though it only addresses
translation at xy plane.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4166950/

On Wed, Apr 1, 2020 at 12:26 PM mike chapman <[hidden email]>
wrote:

> That is correct.  All of the visualizations that I make using Dream3D are
> done in Paraview.
>
> Mike
>
> > On Apr 1, 2020, at 12:06 PM, aget liang <[hidden email]> wrote:
> >
> > Thank you Mike, that's very helpful. I posted a question in the forum.
> Also
> > opened some examples, and realized that this software cannot visualize
> > output, right? so we have to use Paraview?
> >
> > On Wed, Apr 1, 2020 at 10:51 AM mike chapman <[hidden email]>
> > wrote:
> >
> >> There is a webinar introduction from a few years ago posted on youtube (
> >> https://www.youtube.com/watch?v=CIYC1nPWb-g <
> >> https://www.youtube.com/watch?v=CIYC1nPWb-g>) which would be a good
> place
> >> to start that highlights how to use the software (there is a demo of
> using
> >> the software in the second half).
> >>
> >> There are some example pipelines if you go under bookmarks>prebuilt
> >> pipelines>Examples inside the gui
> >>
> >> There is also a forum (
> >> https://groups.google.com/forum/#!forum/dream3d-users <
> >> https://groups.google.com/forum/#!forum/dream3d-users>) which may be
> >> useful.  Mike Jackson (the lead on the software) is very responsive on
> the
> >> forum.
> >>
> >> Mike
> >>
> >>> On Apr 1, 2020, at 10:32 AM, aget liang <[hidden email]> wrote:
> >>>
> >>> Thanks Mike, I have installed the Dream.3D, but found it hard to start
> >>> with. The tutorial does not tell much about its use. Any suggestions
> >> about
> >>> where to find learning materials? Thank you!
> >>>
> >>> On Tue, Mar 31, 2020 at 10:56 AM mike chapman <[hidden email]
> >> <mailto:[hidden email]>>
> >>> wrote:
> >>>
> >>>> For registering multiple 3D stacks, I use another free program called
> >>>> Dream.3D (http://dream3d.bluequartz.net <
> http://dream3d.bluequartz.net/>
> >> <http://dream3d.bluequartz.net/ <http://dream3d.bluequartz.net/>>).
> >>>> I haven’t had much luck trying to do these types of registrations
> >> inside of
> >>>> ImageJ.
> >>>>
> >>>> Mike
> >>>>
> >>>>> On Mar 30, 2020, at 2:43 PM, Yajie Liang <[hidden email]>
> wrote:
> >>>>>
> >>>>> Thanks Mike for your reply. I may not describe the problem clear. The
> >>>> question is to register one 3d stack to another 3d stack, instead of
> >>>> registering the slices in one stack. Also need to extract the
> >>>> transformation for each slice in a stack. Any idea any plugin for this
> >>>> purpose? Thanks!
> >>>>>
> >>>>> --
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> >>>>
> >>>>
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> >>>>
> >>>
> >>>
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> >
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