Registering a whole data set with beads on only one time point

[BarthD]

Hi, I would like to know if it was possible to register all the time points based on the registration parameters obtained with only one time point with beads (when I image on SPIM, I image beads once and then my sample, that has no kind of interest points that could be used for registration).
I initially thought it was impossible but this sentence on the description page of the plugin makes me doubt: "A reference time point that is individually registered first can serve as basis for all other time points. This kind of alignment usually only works with external landmarks like fluorescent beads."
Thanks,
Barth

[StephanPreibisch]

Hi @BarthD,

That is doable and kind of straight forward. The easiest way is to extend your time series by one time point, which is the bead acquisition (maybe just save as TIFFs and import and resave to HDF5). You then register the bead timepoint, save & close BigStitcher/MultiviewReconstruction. You then go to Plugins > Multiview Reconstruction > Batch Processing > Tools > Duplicate Transformations. You then select the XML you just saved and duplicate from one timepoint to other timepoints, selecting the bead timepoint as source. That updates the XML which you can then open again in the interactive application.

I still suggest to maybe run an ICP on each timepoint independently to maybe improve the registration. Also time series stabilization might be necessary.

Please let me know how this goes.