Stackreg zero padding issue

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Stackreg zero padding issue

Kolluri Kanti
 Hi,
I raised a similar question on image.sc forums
https://forum.image.sc/t/stackreg-zero-padding/35129

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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Re: Stackreg zero padding issue

Krs5
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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Re: Stackreg zero padding issue

Kolluri Kanti
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
>
> --
> ImageJ mailing list:
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7C831e301fc84c445082c808d7cb084732%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201108733821008&amp;sdata=cS26UDOYpo9wPNvhPRtmqM%2FS0CJizoHsI80q06FOpEg%3D&amp;reserved=0
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

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Re: Stackreg zero padding issue

Krs5
Other option might be https://github.com/ved-sharma/HyperStackReg

Best wishes
Kees

-----Original Message-----
From: ImageJ Interest Group <[hidden email]> On Behalf Of Kolluri Kanti
Sent: 19 March 2020 01:09
To: [hidden email]
Subject: Re: Stackreg zero padding issue

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
> (https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fbradbusse.net%2Fdownloads.html&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201774889186742&amp;sdata=GPwut3ZsoyQvOddRa%2Fzcu0f4oWh%2FLKxns9XGTsCu%2BN0%3D&amp;reserved=0) 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
> https://eur03.safelinks.protection.outlook.com/?url=www.le.ac.uk%2Fadv
> anced-imaging-facility&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7Cf12
> 313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7
> C1%7C637201774889186742&amp;sdata=agkkphBDVB5gp1cPhrPQsXpkb%2FHTgC1nXb
> 8vSA%2BhDls%3D&amp;reserved=0
>
>
> -----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%2Fforu
> m.image.sc%2Ft%2Fstackreg-zero-padding%2F35129&amp;data=02%7C01%7Ckrs5
> %40leicester.ac.uk%7Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b
> 0195ce8274afe853d9%7C0%7C1%7C637201774889186742&amp;sdata=qqWWQEVzUxHS
> vlVE2nY%2FJRchIPMTVEgZgJGbW79sXrQ%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
>
> --
> ImageJ mailing list:
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimage
> j.nih.gov%2Fij%2Flist.html&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7
> Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7
> C0%7C1%7C637201774889196740&amp;sdata=8DgFPBbuwjK2JS8nPwO3Bxyhml3sLorw
> J1YOZPcAhn4%3D&amp;reserved=0
>
> --
> ImageJ mailing list:
> https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimage
> j.nih.gov%2Fij%2Flist.html&amp;data=02%7C01%7Ckrs5%40leicester.ac.uk%7
> Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7
> C0%7C1%7C637201774889196740&amp;sdata=8DgFPBbuwjK2JS8nPwO3Bxyhml3sLorw
> J1YOZPcAhn4%3D&amp;reserved=0
>

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