title: Network analysis of time-lapse microscopy recordings.
abstract: Multicellular organisms rely on intercellular communication to regulate important cellular processes critical to life. To further our understanding of those processes there is a need to scrutinize dynamical signaling events and their functions in both cells and organisms. Here, we report a method and provide MATLAB code that analyzes time-lapse microscopy recordings to identify and characterize network structures within large cell populations, such as interconnected neurons. The approach is demonstrated using intracellular calcium (Ca(2+)) recordings in neural progenitors and cardiac myocytes, but could be applied to a wide variety of biosensors employed in diverse cell types and organisms. In this method, network structures are analyzed by applying cross-correlation signal processing and graph theory to single-cell recordings. The goal of the analysis is to determine if the single cell activity constitutes a network of interconnected cells and to decipher the properties of this network. The method can be applied in many fields of biology in which biosensors are used to monitor signaling events in living cells. Analyzing intercellular communication in cell ensembles can reveal essential network structures that provide important biological insights.
authors.affiliation: Unit of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm, Sweden.
authors.forename: Erik
authors.initials: E
authors.lastname: Smedler
authors.affiliation: Department of Chemical and Systems Biology, School of Medicine, Stanford University Stanford, CA, USA.
authors.forename: Seth
authors.initials: S
authors.lastname: Malmersjö
authors.affiliation: Unit of Molecular Neurobiology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet Stockholm, Sweden.
authors.forename: Per
authors.initials: P
authors.lastname: Uhlén
mesh_terms: D000818:Animals; D002118:Calcium / Q000378:metabolism; D002450:Cell Communication / Q000502:physiology*; D002478:Cells, Cultured; D004622:Embryo, Mammalian; D045604:Extracellular Fluid / Q000378:metabolism; D051379:Mice; D008853:Microscopy; D008959:Models, Neurological; D009415:Nerve Net / Q000502:physiology*; D058953:Neural Stem Cells / Q000502:physiology; D009474:Neurons / Q000502:physiology*; D012984:Software; D013223:Statistics as Topic; D013997:Time Factors; D059008:Time-Lapse Imaging / Q000295:instrumentation / Q000379:methods
chemical_list: D002118:Calcium
keywords: calcium signaling; cross correlation; graph theory; networks; neural networks; scale-free; small-world