Motion correction only succeeds with small ROI

[Christopher Snyder]

Good afternoon,

I'm using the HMM motion correction. What I find is that it fails to find a solution whenever my ROI is bigger than say 50x50 or so.

My hypothesis is that maybe the model fails when the motion in the region is not 'rigid enough'. With a wider field of view, I think it's possible that different parts of the image are moving in different directions and that it has trouble with that if all it can do is move entire rows up or down.

Alternate explanation is that the model struggles computationally with a 500x2000 image.

In your experience do you see performance drop offs with "large" images of this scale? Which hypothesis do you think is more likely?

Best,

Chris Snyder

[Patrick Kaifosh]

Hi Chris,

I think the first hypothesis is more plausible. Currently, our motion
correction is not designed to handle non-rigid warping within the field
of view. We have run the software on rather large field of views and
that has not been a problem.

Cheers,
PK

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