4Dia: A tool for automated 4D microscope image alignment

Abstract

Recent advances in microscopy enable three-dimensional live imaging at a high resolution. Long-term live imaging of a multicellular organism requires immobilization of the organism under stable physiological conditions. Despite proper immobilization, challenges remain within live imaging data analysis due to other intrinsic and extrinsic dynamics, which can result in misalignments of an image series over time. 4Dia, an ImageJ/Fiji macro script, aligns 3D timelapse images through Z-stacks as well as over time using any user selected channel. 4Dia can be used for essentially any tissue sample with no limit on the size of Z-stack or the number of timepoints.