title: Temporal ordering and registration of images in studies of developmental dynamics.
abstract: Progress of development is commonly reconstructed from imaging snapshots of chemical or mechanical processes in fixed tissues. As a first step in these reconstructions, snapshots must be spatially registered and ordered in time. Currently, image registration and ordering are often done manually, requiring a significant amount of expertise with a specific system. However, as the sizes of imaging data sets grow, these tasks become increasingly difficult, especially when the images are noisy and the developmental changes being examined are subtle. To address these challenges, we present an automated approach to simultaneously register and temporally order imaging data sets. The approach is based on vector diffusion maps, a manifold learning technique that does not require a priori knowledge of image features or a parametric model of the developmental dynamics. We illustrate this approach by registering and ordering data from imaging studies of pattern formation and morphogenesis in three model systems. We also provide software to aid in the application of our methodology to other experimental data sets.
authors.affiliation: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA These authors contributed equally to this work.
authors.forename: Carmeline J
authors.initials: CJ
authors.lastname: Dsilva
authors.affiliation: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA These authors contributed equally to this work.
authors.forename: Bomyi
authors.initials: B
authors.lastname: Lim
authors.affiliation: School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA.
authors.forename: Hang
authors.initials: H
authors.lastname: Lu
authors.affiliation: Department of Mathematics, Princeton University, Princeton, NJ 08544, USA Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USA.
authors.forename: Amit
authors.initials: A
authors.lastname: Singer
authors.affiliation: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA Program in Applied and Computational Mathematics, Princeton University, Princeton, NJ 08544, USA yannis@princeton.edu stas@princeton.edu.
authors.forename: Ioannis G
authors.initials: IG
authors.lastname: Kevrekidis
authors.affiliation: Department of Chemical and Biological Engineering, Princeton University, Princeton, NJ 08544, USA Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08544, USA yannis@princeton.edu stas@princeton.edu.
authors.forename: Stanislav Y
authors.initials: SY
authors.lastname: Shvartsman
mesh_terms: D000818:Animals; D001185:Artificial Intelligence; D019295:Computational Biology / Q000379:methods*; D066264:Datasets as Topic; D004330:Drosophila / Q000196:embryology; D047108:Embryonic Development / Q000502:physiology*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D012984:Software; D015027:Zebrafish / Q000502:physiology
keywords: Drosophila; Image registration; Temporal ordering; Vector diffusion maps; Zebrafish
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