Help with registration please

[(s) Jodie Nicholls]

I have a pair of images which I am trying to bring into registration. I can't post the images to the list, but I am happy to email them to anyone who would like to try registering them.

There are lots of alternative methods to use for registration, and I have used several (Turboreg, Unwarpj, bUnwarpj). Within each method, there are several options for how to do the registration (rigid, affine, etc). I have tried many permutations, and I am not very happy with my results so far. When I animate the registered image stack, there is a huge amount of motion that is occurring between the two views. In other words, the registration is not good.

In principle, I think that it should be possible to do good registration with images such as mine, and I am asking for any help that you experts might give. There are many readily identifiable features in the images that could be used by an algorithm for registration. For example, in these images, there are lots of blood vessels that are plain to see but that jump around like crazy in the "registered" animation. There are clearly defined blobs that jump around as well.

I am sure that there are people on the list with lots of experience and wisdom related to registration. Please give me some advice about a good way to produce nicely registered image pairs for images with well-defined landmarks.

Thanks very much for any help.

[Carnë Draug]

Could you maybe post the images in http://picpaste.com/ so we get an
idea of what the images look like? A link for the first 2-3 images
would be nice (you can only post JP(E)G, PNG, GIF and BMP pictures
with a size up to 7 megabyte there). Or maybe open the stack and in
imageJ go to "Image > Stacks > Make montage..." and create one for the
first few frames. Then paste it in picpaste.

On 15 March 2011 14:28, (s) Jodie Nicholls
<[hidden email]> wrote:

> I have a pair of images which I am trying to bring into registration. I can't post the images to the list, but I am happy to email them to anyone who would like to try registering them.
>
> There are lots of alternative methods to use for registration, and I have used several (Turboreg, Unwarpj, bUnwarpj). Within each method, there are several options for how to do the registration (rigid, affine, etc). I have tried many permutations, and I am not very happy with my results so far. When I animate the registered image stack, there is a huge amount of motion that is occurring between the two views. In other words, the registration is not good.
>
> In principle, I think that it should be possible to do good registration with images such as mine, and I am asking for any help that you experts might give. There are many readily identifiable features in the images that could be used by an algorithm for registration. For example, in these images, there are lots of blood vessels that are plain to see but that jump around like crazy in the "registered" animation. There are clearly defined blobs that jump around as well.
>
> I am sure that there are people on the list with lots of experience and wisdom related to registration. Please give me some advice about a good way to produce nicely registered image pairs for images with well-defined landmarks.
>
> Thanks very much for any help.
>

[Carnë Draug]

Always make "reply to all", inclusive the ImageJ mailing list, so
everyone can see and try to help you.

2011/3/15 (s) Jodie Nicholls <[hidden email]>:

> Hello,
>
> Here are links to the two images i am trying to register and the registered image i created using bUnwarpj.
>
> I really appreciate any help you could give me.
>
> Thank you for your time.
>
> http://picpaste.com/AALtcc1-vHO3x2yo.png
> http://picpaste.com/AALtcc2-bPhCbrq8.png
> http://picpaste.com/AA_time_1_2_lt_cc_motion_bunwarp-7P4Xluji.gif
> ________________________________________
> From: [hidden email] [[hidden email]] On Behalf Of Carnë Draug [[hidden email]]
> Sent: 15 March 2011 15:10
> To: ImageJ Interest Group
> Cc: (s) Jodie Nicholls
> Subject: Re: Help with registration please
>
> Could you maybe post the images in http://picpaste.com/ so we get an
> idea of what the images look like? A link for the first 2-3 images
> would be nice (you can only post JP(E)G, PNG, GIF and BMP pictures
> with a size up to 7 megabyte there). Or maybe open the stack and in
> imageJ go to "Image > Stacks > Make montage..." and create one for the
> first few frames. Then paste it in picpaste.
>
> On 15 March 2011 14:28, (s) Jodie Nicholls
> <[hidden email]> wrote:
>> I have a pair of images which I am trying to bring into registration. I can't post the images to the list, but I am happy to email them to anyone who would like to try registering them.
>>
>> There are lots of alternative methods to use for registration, and I have used several (Turboreg, Unwarpj, bUnwarpj). Within each method, there are several options for how to do the registration (rigid, affine, etc). I have tried many permutations, and I am not very happy with my results so far. When I animate the registered image stack, there is a huge amount of motion that is occurring between the two views. In other words, the registration is not good.
>>
>> In principle, I think that it should be possible to do good registration with images such as mine, and I am asking for any help that you experts might give. There are many readily identifiable features in the images that could be used by an algorithm for registration. For example, in these images, there are lots of blood vessels that are plain to see but that jump around like crazy in the "registered" animation. There are clearly defined blobs that jump around as well.
>>
>> I am sure that there are people on the list with lots of experience and wisdom related to registration. Please give me some advice about a good way to produce nicely registered image pairs for images with well-defined landmarks.
>>
>> Thanks very much for any help.
>>
>

[(s) Jodie Nicholls]

Hello,

Here are links to the two images i am trying to register and the registered image i created using bUnwarpj.

I really appreciate any help.

Thank you for your time.

http://picpaste.com/AALtcc1-vHO3x2yo.png 
http://picpaste.com/AALtcc2-bPhCbrq8.png 
http://picpaste.com/AA_time_1_2_lt_cc_motion_bunwarp-7P4Xluji.gif
________________________________________
From: [hidden email] [[hidden email]] On Behalf Of Carnë Draug [[hidden email]]
Sent: 15 March 2011 15:10
To: ImageJ Interest Group
Cc: (s) Jodie Nicholls
Subject: Re: Help with registration please

Could you maybe post the images in http://picpaste.com/ so we get an
idea of what the images look like? A link for the first 2-3 images
would be nice (you can only post JP(E)G, PNG, GIF and BMP pictures
with a size up to 7 megabyte there). Or maybe open the stack and in
imageJ go to "Image > Stacks > Make montage..." and create one for the
first few frames. Then paste it in picpaste.

On 15 March 2011 14:28, (s) Jodie Nicholls
<[hidden email]> wrote:

> I have a pair of images which I am trying to bring into registration. I can't post the images to the list, but I am happy to email them to anyone who would like to try registering them.
>
> There are lots of alternative methods to use for registration, and I have used several (Turboreg, Unwarpj, bUnwarpj). Within each method, there are several options for how to do the registration (rigid, affine, etc). I have tried many permutations, and I am not very happy with my results so far. When I animate the registered image stack, there is a huge amount of motion that is occurring between the two views. In other words, the registration is not good.
>
> In principle, I think that it should be possible to do good registration with images such as mine, and I am asking for any help that you experts might give. There are many readily identifiable features in the images that could be used by an algorithm for registration. For example, in these images, there are lots of blood vessels that are plain to see but that jump around like crazy in the "registered" animation. There are clearly defined blobs that jump around as well.
>
> I am sure that there are people on the list with lots of experience and wisdom related to registration. Please give me some advice about a good way to produce nicely registered image pairs for images with well-defined landmarks.
>
> Thanks very much for any help.
>