I'm trying to register some 16-bit microscope images. Following the example here: https://simpleelastix.readthedocs.io/NonRigidRegistration.html works quite well prior to background removal. On the other hand if I do background removal (setting background pixels to zero) and then try to register I end up with a mess of bright (>63k) pixels.
Figure one is before registration and figure 2 is the result after.
A quick fix would be for me to set a high threshold after registration to remove the hot pixels but I'm reluctant to do that since they range (somewhat) in value. I'm wondering if there's a more rigorous way to fix this?
I'm trying to register some 16-bit microscope images. Following the example here: https://simpleelastix.readthedocs.io/NonRigidRegistration.html works quite well prior to background removal. On the other hand if I do background removal (setting background pixels to zero) and then try to register I end up with a mess of bright (>63k) pixels.
Figure one is before registration and figure 2 is the result after.
A quick fix would be for me to set a high threshold after registration to remove the hot pixels but I'm reluctant to do that since they range (somewhat) in value. I'm wondering if there's a more rigorous way to fix this?
Thanks.
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