Shift / transform individual images in an image-stack

[LuriFax]

Dear List,

My main objective is to align a stack of images so that one structure stays in the same ROI over the entire series. I want this done for extraction of mean intensity values for use in quantitative analysis. I have managed to track the structure and generated x-y coordinates from it.

I want to shift / transform individual images in an image-stack based on x-y coordinates from a .txt-file.
Is this possible, and how can I do it the easiest way? (I am NOT a programmer and have almost no experience, so I need everything in detail)

Maybe something like this:
transform image1 : X-value, Y-value (ie. -1, 2)
then goto next image in stack
transform image2: X-value, Y-value (ie. -2, 3)
loop and stop when all images in stack have been transformed.

The txt-file has two columns: the first number X-value; the second number Y-value: like "-1,2" and so on (but can be altered in any way if that is an issue).
The stacks range from 100-5000 images, by the way.


Alternatively: (I do not know if this is something that exist as already available ImageJ- macro or -plugins)

- An animated ROI, so that I can "key-frame" it and then do the intensity-extraction in one run.


I would really appreciate a solution or some input to solve my problem. Thanks in advance!



Sincerely,

Luri-fax

[Katie Matho]

Dear Luri-fax,
Did you ever solve this problem of aligning a stack of images so that a given structure stays in the same ROI throughout the stack?
Thanks a lot
Katie

LuriFax wrote

Dear List,

My main objective is to align a stack of images so that one structure stays in the same ROI over the entire series. I want this done for extraction of mean intensity values for use in quantitative analysis. I have managed to track the structure and generated x-y coordinates from it.

I want to shift / transform individual images in an image-stack based on x-y coordinates from a .txt-file.
Is this possible, and how can I do it the easiest way? (I am NOT a programmer and have almost no experience, so I need everything in detail)

Maybe something like this:
transform image1 : X-value, Y-value (ie. -1, 2)
then goto next image in stack
transform image2: X-value, Y-value (ie. -2, 3)
loop and stop when all images in stack have been transformed.

The txt-file has two columns: the first number X-value; the second number Y-value: like "-1,2" and so on (but can be altered in any way if that is an issue).
The stacks range from 100-5000 images, by the way.


Alternatively: (I do not know if this is something that exist as already available ImageJ- macro or -plugins)

- An animated ROI, so that I can "key-frame" it and then do the intensity-extraction in one run.


I would really appreciate a solution or some input to solve my problem. Thanks in advance!



Sincerely,

Luri-fax