Re: Stackreg zero padding issue

Posted by Kolluri Kanti on Mar 19, 2020; 1:09am
URL: http://imagej.273.s1.nabble.com/Stackreg-zero-padding-issue-tp5023046p5023066.html

Thanks for the reply.
I did use 'Multistackreg' rigid registration, after selecting one of the
channels,say ch1 (usually the brighter channel) as reference and the other
channel,ch2 as 'align to first stack'. Strangely,images of the second
channel are grossly misaligned.


On Wed, Mar 18, 2020 at 5:06 PM Straatman, Kees (Dr.) <[hidden email]>
wrote:

> Dear Kolluri,
>
> Would MultiStackReg (http://bradbusse.net/downloads.html) solve the
> problem?
>
> Best wishes
>
> Kees
>
>
> Dr Ir K.R. Straatman
> Senior Experimental Officer
> Advanced Imaging Facility
> Centre for Core Biotechnology Services
> University of Leicester
> www.le.ac.uk/advanced-imaging-facility
>
>
> -----Original Message-----
> From: ImageJ Interest Group <[hidden email]> On Behalf Of Kolluri
> Kanti
> Sent: 18 March 2020 05:54
> To: [hidden email]
> Subject: Stackreg zero padding issue
>
>  Hi,
> I raised a similar question on image.sc forums
>
> https://eur03.safelinks.protection.outlook.com/?url=https%3A%2F%2Fforum.image.sc%2Ft%2Fstackreg-zero-padding%2F35129&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7C831e301fc84c445082c808d7cb084732%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201108733821008&amp;sdata=Aqe5bVuIUzt1oXRLH4UgHgU4iQS1RvSd7m%2BXOn7v%2FzY%3D&amp;reserved=0
>
> We use Stackreg to align an image stack and try to apply the
> transformation matrices obtained to another channel of the same image
> stack. We do rigid registration of the image stack and stackreg does great.
> However, it also does zero padding of some of the images in the stack. Now,
> when we apply the transformation matrices (localTransform) obtained from
> StackReg to another channel of the same stack, this zero padding does not
> happen and so although the transformation matrices are applied, the 2 image
> stacks are not aligned well.
>
> Any idea how to resolve this issue?
>
> Thanks
>
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