title: An interacting multiple model filter-based autofocus strategy for confocal time-lapse microscopy.
abstract: Gene expression and other cellular processes are stochastic, thus their study requires observing multiple events in multiple cells. Therefore, confocal microscopy cell imaging has recently gained much interest. In time-lapse imaging, adjustments are needed at short intervals to compensate for focus drift. There are several automated methods for this purpose. In general, before acquiring higher resolution images, software-based autofocus algorithms require a set of low-resolution images along the z-axis to determine the plane for which a predefined focusing function is maximized. These algorithms require 10-100 z-slices each time, and there is no fixed number or upper limit of required z-slices that ensures optimal focusing. The higher is this number, the stronger is photo bleaching, hampering the feasibility of long-time series measurements. We propose a new focusing strategy in time-lapse imaging. The algorithm relies on the nature and predictability of the focus drift. We first show that the focus drift curve is predictable within a small error bound in standard experimental setups. We, then, exploit the interacting multiple model filter algorithm to predict the drift at time, t, based on the measurement at time t-1. This allows a drastic reduction of the number of required z-slices for focus drift correction, largely overcoming the problem of photo bleaching. In addition, we propose a new set of functions for focusing in time-lapse imaging, derived from preexisting ones. We demonstrate the method's efficiency in time-lapse imaging of Escherichia coli cells expressing MS2d-GFP tagged RNA molecules.
authors.affiliation: Computational Systems Biology Research Group, Department of Signal Processing, Tampere University of Technology, Finland.
authors.forename: S
authors.initials: S
authors.lastname: Chowdhury
authors.forename: M
authors.initials: M
authors.lastname: Kandhavelu
authors.forename: O
authors.initials: O
authors.lastname: Yli-Harja
authors.forename: A S
authors.initials: AS
authors.lastname: Ribeiro
mesh_terms: D000465:Algorithms; D004926:Escherichia coli; D018613:Microscopy, Confocal / Q000379:methods*; D012984:Software; D059008:Time-Lapse Imaging / Q000379:methods*