Nonuniform temporal alignment of slice sequences for four-dimensional imaging of cyclically deforming embryonic structures

The temporal alignment of nongated slice-sequences acquired at different axial positions in the living embryonic zebrafish heart permits the reconstruction of dynamic, three-dimensional data. This approach overcomes the current acquisition-speed limitation of confocal microscopes for real-time three-dimensional imaging of fast processes. Current synchronization methods align and uniformly scale the data in time, but do not compensate for slight variations in the heart rhythm that occur within a heartbeat. Therefore, they impose constraints on the admissible data quality. Here, we derive a nonuniform registration procedure based on the minimization of the absolute value of the intensity difference between adjacent slice-sequence pairs. The method compensates for temporal intra-sample variations and allows the processing of a wider range of data to build functional, dynamic models of the beating embryonic heart. We show reconstructions from data acquired in living, fluorescent zebrafish embryos