Hyperstack registration

[David Hovis]

Hello all,

I have a hyperstack (2-channels, 130 z-slices, 256x256 pixels).  I have two issues with the data that I need to address.  

1) There was drift during the experiment and there are small translations between most z-slices
2) There was one larger jump during the experiment.


If I only operate on one channel, StackReg does a good job of removing the slow drift, but doesn't handle the larger jump (~30-50 pixels).  

I would also like the second channel to be shifted the same as the first channel, but not separately registered.  

So my two questions are:
1) Is there a good way to manually shift all the slices after the jump so StackReg can do its job?
2) Is there a way to then do the exact same shifts on a parallel stack (or another channel in a hyperstack)?

Thanks,

--David

[Stephan Preibisch]

Hi David,

did you try the "Plugins > Registration > Descriptor-based series registration (3d+t)" which is included in Fiji, it might be able to do the job automatically. It can handle arbitrary jumps and usually aligns long time series reliably. It supports 3d-translation, 3d-rigid and 3d-affine (in 2d also 2d-similarity and 2d-perspective). It uses local features in the image stack to achieve that. I did not have time to write the documentation yet, it uses a similar algorithm as the SPIM registration but uses the image content itself instead of beads: http://fiji.sc/wiki/index.php/SPIM_Registration

Nice greetings,
Stephan

On Feb 24, 2012, at 15:06 , David Hovis wrote:

> Hello all,
>
> I have a hyperstack (2-channels, 130 z-slices, 256x256 pixels).  I have two issues with the data that I need to address.  
>
> 1) There was drift during the experiment and there are small translations between most z-slices
> 2) There was one larger jump during the experiment.
>
>
> If I only operate on one channel, StackReg does a good job of removing the slow drift, but doesn't handle the larger jump (~30-50 pixels).  
>
> I would also like the second channel to be shifted the same as the first channel, but not separately registered.  
>
> So my two questions are:
> 1) Is there a good way to manually shift all the slices after the jump so StackReg can do its job?
> 2) Is there a way to then do the exact same shifts on a parallel stack (or another channel in a hyperstack)?
>
> Thanks,
>
> --David

... [show rest of quote]

[John Kielkopf]

You could try the Image Stabilizer plugin.  It will log  translations and
apply the same ones again when requested:

http://www.cs.cmu.edu/~kangli/code/Image_Stabilizer.html

On Fri, Feb 24, 2012 at 10:06 AM, David Hovis <[hidden email]> wrote:

> Hello all,
>
> I have a hyperstack (2-channels, 130 z-slices, 256x256 pixels).  I have
> two issues with the data that I need to address.
>
> 1) There was drift during the experiment and there are small translations
> between most z-slices
> 2) There was one larger jump during the experiment.
>
>
> If I only operate on one channel, StackReg does a good job of removing the
> slow drift, but doesn't handle the larger jump (~30-50 pixels).
>
> I would also like the second channel to be shifted the same as the first
> channel, but not separately registered.
>
> So my two questions are:
> 1) Is there a good way to manually shift all the slices after the jump so
> StackReg can do its job?
> 2) Is there a way to then do the exact same shifts on a parallel stack (or
> another channel in a hyperstack)?
>
> Thanks,
>
> --David
>

... [show rest of quote]

--
John Kielkopf
Professor of Physics and Astronomy
University of Louisville
Louisville, KY 40292
Tel:[phone]
Fax:[phone]

[Brad Busse]

A few years ago I modified StackReg to do just what David wants:
http://www.stanford.edu/~bbusse/work/downloads.html

Using two simpler alignment steps (one rigid body, the second affine) often handles shifts that a single pass can't.  Failing that, if you manually correct the jump in TurboReg and save the transformation, the MultiStackReg jar includes a utility for splicing it into a larger transformation file (Compress Matrices).

For more complicated alignment problems such as nonlinear warping, we had the best luck with Fiji's Register/Transform Virtual Stack Slices plugins.

Hope it helps!


----- Original Message -----
From: "John Kielkopf" <[hidden email]>
To: [hidden email]
Sent: Friday, February 24, 2012 11:03:23 AM
Subject: Re: Hyperstack registration

You could try the Image Stabilizer plugin.  It will log  translations and
apply the same ones again when requested:

http://www.cs.cmu.edu/~kangli/code/Image_Stabilizer.html

On Fri, Feb 24, 2012 at 10:06 AM, David Hovis <[hidden email]> wrote:

> Hello all,
>
> I have a hyperstack (2-channels, 130 z-slices, 256x256 pixels).  I have
> two issues with the data that I need to address.
>
> 1) There was drift during the experiment and there are small translations
> between most z-slices
> 2) There was one larger jump during the experiment.
>
>
> If I only operate on one channel, StackReg does a good job of removing the
> slow drift, but doesn't handle the larger jump (~30-50 pixels).
>
> I would also like the second channel to be shifted the same as the first
> channel, but not separately registered.
>
> So my two questions are:
> 1) Is there a good way to manually shift all the slices after the jump so
> StackReg can do its job?
> 2) Is there a way to then do the exact same shifts on a parallel stack (or
> another channel in a hyperstack)?
>
> Thanks,
>
> --David
>

... [show rest of quote]

--
John Kielkopf
Professor of Physics and Astronomy
University of Louisville
Louisville, KY 40292
Tel:[phone]
Fax:[phone]

[TTian]

Hi David,

Have you solved your problem? Actually I posted this because I met a problem when proceeded StackReg. I opened my images, and clicked StackReg, but no reaction or processing. I could not find the cause so I wonder maybe you can help me? Sorry for my liberty.

Thanks!
Tian  

[Kenneth R Sloan]

I believe so.  We seem to have settled on SIFT.

My issue was primarily a question of registering images from different frequencies, as opposed to different depths.  That seems to work - but I’m not actively involved in it these days.
My other stack registration application is more traditional - many slices in Z, all imaged the same way.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On Jun 5, 2015, at 15:00 , TTian <[hidden email]> wrote:
>
> Hi David,
>
> Have you solved your problem? Actually I posted this because I met a problem
> when proceeded StackReg. I opened my images, and clicked StackReg, but no
> reaction or processing. I could not find the cause so I wonder maybe you can
> help me? Sorry for my liberty.
>
> Thanks!
> Tian  
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Hyperstack-registration-tp4503024p5013056.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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

[TTian]

Hi Kenneth,

Thanks for your help. Actually I also tried SPIM , but was always told " no features". Anyway, thanks so much.

Regards
Tian

2015年6月5日 下午4:05于 "Kenneth R Sloan [via ImageJ]" <[hidden email]>写道：

I believe so.  We seem to have settled on SIFT.

My issue was primarily a question of registering images from different frequencies, as opposed to different depths.  That seems to work - but I’m not actively involved in it these days.
My other stack registration application is more traditional - many slices in Z, all imaged the same way.

--
Kenneth Sloan
[hidden email]
Vision is the art of seeing what is invisible to others.

> On Jun 5, 2015, at 15:00 , TTian <[hidden email]> wrote:
>
> Hi David,
>
> Have you solved your problem? Actually I posted this because I met a problem
> when proceeded StackReg. I opened my images, and clicked StackReg, but no
> reaction or processing. I could not find the cause so I wonder maybe you can
> help me? Sorry for my liberty.
>
> Thanks!
> Tian  
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Hyperstack-registration-tp4503024p5013056.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

... [show rest of quote]

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

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... [show rest of quote]