Stackreg zero padding issue
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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 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C831e301fc84c445082c808d7cb084732%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201108733821008&sdata=Aqe5bVuIUzt1oXRLH4UgHgU4iQS1RvSd7m%2BXOn7v%2FzY%3D&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&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C831e301fc84c445082c808d7cb084732%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201108733821008&sdata=cS26UDOYpo9wPNvhPRtmqM%2FS0CJizoHsI80q06FOpEg%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
Re: Stackreg zero padding issue
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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&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C831e301fc84c445082c808d7cb084732%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201108733821008&sdata=Aqe5bVuIUzt1oXRLH4UgHgU4iQS1RvSd7m%2BXOn7v%2FzY%3D&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&data=02%7C01%7Ckrs5%40leicester.ac.uk%7C831e301fc84c445082c808d7cb084732%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201108733821008&sdata=cS26UDOYpo9wPNvhPRtmqM%2FS0CJizoHsI80q06FOpEg%3D&reserved=0 > > -- > ImageJ mailing list: http://imagej.nih.gov/ij/list.html > -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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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&data=02%7C01%7Ckrs5%40leicester.ac.uk%7Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201774889186742&sdata=GPwut3ZsoyQvOddRa%2Fzcu0f4oWh%2FLKxns9XGTsCu%2BN0%3D&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&data=02%7C01%7Ckrs5%40leicester.ac.uk%7Cf12 > 313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7 > C1%7C637201774889186742&sdata=agkkphBDVB5gp1cPhrPQsXpkb%2FHTgC1nXb > 8vSA%2BhDls%3D&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&data=02%7C01%7Ckrs5 > %40leicester.ac.uk%7Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b > 0195ce8274afe853d9%7C0%7C1%7C637201774889186742&sdata=qqWWQEVzUxHS > vlVE2nY%2FJRchIPMTVEgZgJGbW79sXrQ%3D&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&data=02%7C01%7Ckrs5%40leicester.ac.uk%7 > Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7 > C0%7C1%7C637201774889196740&sdata=8DgFPBbuwjK2JS8nPwO3Bxyhml3sLorw > J1YOZPcAhn4%3D&reserved=0 > > -- > ImageJ mailing list: > https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimage > j.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40leicester.ac.uk%7 > Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7 > C0%7C1%7C637201774889196740&sdata=8DgFPBbuwjK2JS8nPwO3Bxyhml3sLorw > J1YOZPcAhn4%3D&reserved=0 > -- ImageJ mailing list: https://eur03.safelinks.protection.outlook.com/?url=http%3A%2F%2Fimagej.nih.gov%2Fij%2Flist.html&data=02%7C01%7Ckrs5%40leicester.ac.uk%7Cf12313bf6d224451d3b808d7cba360de%7Caebecd6a31d44b0195ce8274afe853d9%7C0%7C1%7C637201774889196740&sdata=8DgFPBbuwjK2JS8nPwO3Bxyhml3sLorwJ1YOZPcAhn4%3D&reserved=0 -- ImageJ mailing list: http://imagej.nih.gov/ij/list.html |
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