Registration Recomendations

FIJI | Plugins | Registration | has 15++ options to choose from.
There are also some external sites that look promising e.g.


http://bigwww.epfl.ch/thevenaz/stackreg/


http://www.cs.cmu.edu/~kangli/code/Image_Stabilizer.html (Initially I have experimented with this. And copied the two *.CLASS files into C:\ProgramsLocal\FIJI\plugins then restart FIJI. Then run Image stabilizer, this made things actually worse.)
Then I tried FIJI |Registration | Elastic | Elastic Stack Alignment (With the default values it fails with lots of errors in the console window. ”2 data points are not enough to solve the Model, at least 3 data points required.”) nothing is captured in the macro recorder.
I have noticeable stage jitter in a stack (600 slices 16-bit per color 4 MP images) and would like a method that also allows for slight rotation and some swelling of the specimen during the time lapse. Unfortunately there is very little contrast in my images, so it may be difficult to find enough information to do a full elastic affine registration.
What would be a good starting point, eventually this should run robustly from a macro without further user interaction.
Any advice from the experienced users would be appreciated.

If you have have a sequence of 2D images with small linear transformations between them, you should give a try to the Register Virtual Stack Slices plugin. To know which parameters to use, play around with a couple of images in the Extract SIFT Correspondences plugin. If you have problems finding the right parameters, please post here some images so we can help you.

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