When the studied motion is periodic, such as for a beating heart, it is possible to acquire successive sets of two dimensional plus time data slice-sequences at increasing depths over at least one time period which are later rearranged to recover a three dimensional time sequence. Since gating signals are either unavailable or cumbersome to acquire in microscopic organisms, the invention is a method for reconstructing volumes based solely on the information contained in the image sequences. The central part of the algorithm is a least-squares minimization of an objective criterion that depends on the similarity between the data from neighboring depths. Owing to a wavelet-based multiresolution approach, the method is robust to common confocal microscopy artifacts. The method is validated on both simulated data and in-vivo measurements.