I was wondering if there is a way to register a z-stack in the specific case of sample 'wobble'. I've just started with some OpenSPIM data sets, and in some cases I suffer from a small jiggling between z frames as the wobble of the low melting point agarose shakes back and forth with the stage steps. I know this is something to optimized, with stage movement settings and agarose concentrations, but I hoped to get the data as nice as possible even in cases when the above doesn't go to plan.
I need to register the stack and wondered which plugins might work best. I've played with the test bead stacks I've acquired, but not with the real, more challenging, potential low signal, data sets. However, in practice, the majority of the data should have beads around the sample to assist with this registration (on the off-chance, does anybody know if the SPIM registration (now in Multiview Reconstruction) take this into account?).
My thoughts on the requirements/directions:
- only a small translation (or other simple non-elastic transformation required)
- might there be a way to deconvolve the below z data with an offset PSF before correlating the images?
- wobble would likely be periodic with an average displacement close to zero (one hopes)
- if data is spare on some z levels, but the above and below z sections follow a somewhat well behaved periodic jiggle, maybe an assumed displacement could be assigned.
Thanks in advance for your time thinking on this.
This e-mail message (including any attachments) is for the sole use of
the intended recipient(s) and may contain confidential and privileged
information. If the reader of this message is not the intended
recipient, you are hereby notified that any dissemination, distribution
or copying of this message (including any attachments) is strictly
If you have received this message in error, please contact
the sender by reply e-mail message and destroy all copies of the
original message (including attachments).