Question about processing 2 images

[gbarash]

Hello!
I am new to ImageJ and have a question: I need to write a java program that
utilizes ImageJ API to automatically align two images that contain a matrix
of beads, and compare the beads in each corresponding image.
What's the best way to go about this? Calculate the bead positions as
particles and then loop through them in each image?
Align both images using the fiduciary marks on each and then loop through
both of them?
Can anyone point me in a direction on how to do that? I have looked through
the API's but have not seen anything that does something like that.
Many thanks!

Gilad.

[dscho]

Dear Gilad,

On Mon, 30 Jan 2012, Gilad Barash wrote:

> I am new to ImageJ and have a question: I need to write a java program that
> utilizes ImageJ API to automatically align two images that contain a matrix
> of beads, and compare the beads in each corresponding image.
> What's the best way to go about this? Calculate the bead positions as
> particles and then loop through them in each image?
> Align both images using the fiduciary marks on each and then loop through
> both of them?

It might come as a surprise to you that others did that already ;-) There
is the Plugins>Registration>Descriptor-based registration (2d/3d) plugin
by Stephan Preibisch, for example.

It is included in the Fiji distribution of ImageJ (http://fiji.sc/).

The source code can be found here:
http://fiji.sc/cgi-bin/gitweb.cgi?p=fiji.git;a=tree;f=src-plugins/Descriptor_based_registration;hb=refs/heads/master

Ciao,
Johannes