Re: align and contatenate two stacks

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Re: align and contatenate two stacks

Xuefeng Liu
Hi, I took two stack images from two physically consecutive brain slices,
and I would like to align the two stacks and concatenate them into a new
stack images. What plugins should I use?
    I imagine the easiest algorithm is to align the last image of the first
stack to the first image of the second stack (like Align Image by ling ROI)
, and align one stack to the other using such offset information, but I
just don't know if such a plugin exists to tackle this problem.
     As an example, I uploaded two stacks ( stack 1 and stack 2, only two
sections for each stack as an example, sorry about the small size due to
email limit and hope attachment could go through.), so my aim is to align
and concatenate the two stacks.

Thanks for your help.


On Mon, Jan 6, 2014 at 12:28 PM, Xuefeng Liu <[hidden email]> wrote:

> Hi, I took two stack images from two physically consecutive brain slices,
> and I would like to align the two stacks and concatenate them into a new
> stack images. What plugins should I use?
>     I imagine the easiest algorithm is to align the last image of the
> first stack to the first image of the second stack (like Align Image by
> ling ROI) , and align one stack to the other using such offset information,
> but I just don't know if such a plugin exists to tackle this problem.
>      As an example, I uploaded two stacks ( stack 1 and stack 2, only two
> sections for each stack as an example, hope attachment could go through.),
> so my aim is to align and concatenate the two stacks.
>
> Thanks for your help.
>
> Xuefeng
>
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stack1.tif (439K) Download Attachment
stack2.tif (382K) Download Attachment
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Re: align and contatenate two stacks

Nikolay
I would split stack's to images and combine them to one stack, then
apply *StackReg
<http://bigwww.epfl.ch/thevenaz/stackreg/> *plugin for align.


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Best regards
Rogoshchenkov Nikolay


On Mon, Jan 6, 2014 at 2:01 PM, Xuefeng Liu <[hidden email]> wrote:

> Hi, I took two stack images from two physically consecutive brain slices,
> and I would like to align the two stacks and concatenate them into a new
> stack images. What plugins should I use?
>     I imagine the easiest algorithm is to align the last image of the first
> stack to the first image of the second stack (like Align Image by ling ROI)
> , and align one stack to the other using such offset information, but I
> just don't know if such a plugin exists to tackle this problem.
>      As an example, I uploaded two stacks ( stack 1 and stack 2, only two
> sections for each stack as an example, sorry about the small size due to
> email limit and hope attachment could go through.), so my aim is to align
> and concatenate the two stacks.
>
> Thanks for your help.
>
>
> On Mon, Jan 6, 2014 at 12:28 PM, Xuefeng Liu <[hidden email]> wrote:
>
> > Hi, I took two stack images from two physically consecutive brain slices,
> > and I would like to align the two stacks and concatenate them into a new
> > stack images. What plugins should I use?
> >     I imagine the easiest algorithm is to align the last image of the
> > first stack to the first image of the second stack (like Align Image by
> > ling ROI) , and align one stack to the other using such offset
> information,
> > but I just don't know if such a plugin exists to tackle this problem.
> >      As an example, I uploaded two stacks ( stack 1 and stack 2, only two
> > sections for each stack as an example, hope attachment could go
> through.),
> > so my aim is to align and concatenate the two stacks.
> >
> > Thanks for your help.
> >
> > Xuefeng
> >
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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ImageJ mailing list: http://imagej.nih.gov/ij/list.html
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Re: align and contatenate two stacks

L'assegnista
In reply to this post by Xuefeng Liu
TrackEM2 can do the work,  take a look at the Fiji web site.

Federico.

Sent from my HTC

----- Reply message -----
From: "Xuefeng Liu" <[hidden email]>
To: <[hidden email]>
Subject: align and contatenate two stacks
Date: Mon, Jan 6, 2014 20:01


Hi, I took two stack images from two physically consecutive brain slices,
and I would like to align the two stacks and concatenate them into a new
stack images. What plugins should I use?
    I imagine the easiest algorithm is to align the last image of the first
stack to the first image of the second stack (like Align Image by ling ROI)
, and align one stack to the other using such offset information, but I
just don't know if such a plugin exists to tackle this problem.
     As an example, I uploaded two stacks ( stack 1 and stack 2, only two
sections for each stack as an example, sorry about the small size due to
email limit and hope attachment could go through.), so my aim is to align
and concatenate the two stacks.

Thanks for your help.


On Mon, Jan 6, 2014 at 12:28 PM, Xuefeng Liu <[hidden email]> wrote:

> Hi, I took two stack images from two physically consecutive brain slices,
> and I would like to align the two stacks and concatenate them into a new
> stack images. What plugins should I use?
>     I imagine the easiest algorithm is to align the last image of the
> first stack to the first image of the second stack (like Align Image by
> ling ROI) , and align one stack to the other using such offset information,
> but I just don't know if such a plugin exists to tackle this problem.
>      As an example, I uploaded two stacks ( stack 1 and stack 2, only two
> sections for each stack as an example, hope attachment could go through.),
> so my aim is to align and concatenate the two stacks.
>
> Thanks for your help.
>
> Xuefeng
>

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


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