title: Tracking and Quantifying Developmental Processes in C. elegans Using Open-source Tools.
abstract: Quantitatively capturing developmental processes is crucial to derive mechanistic models and key to identify and describe mutant phenotypes. Here protocols are presented for preparing embryos and adult C. elegans animals for short- and long-term time-lapse microscopy and methods for tracking and quantification of developmental processes. The methods presented are all based on C. elegans strains available from the Caenorhabditis Genetics Center and on open-source software that can be easily implemented in any laboratory independently of the microscopy system used. A reconstruction of a 3D cell-shape model using the modelling software IMOD, manual tracking of fluorescently-labeled subcellular structures using the multi-purpose image analysis program Endrov, and an analysis of cortical contractile flow using PIVlab (Time-Resolved Digital Particle Image Velocimetry Tool for MATLAB) are shown. It is discussed how these methods can also be deployed to quantitatively capture other developmental processes in different models, e.g., cell tracking and lineage tracing, tracking of vesicle flow.
authors.affiliation: Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, School of Medicine, Goethe University.
authors.forename: Priyanka
authors.initials: P
authors.lastname: Dutta
authors.affiliation: Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, School of Medicine, Goethe University.
authors.forename: Christina
authors.initials: C
authors.lastname: Lehmann
authors.affiliation: Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, School of Medicine, Goethe University.
authors.forename: Devang
authors.initials: D
authors.lastname: Odedra
authors.affiliation: Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, School of Medicine, Goethe University.
authors.forename: Deepika
authors.initials: D
authors.lastname: Singh
authors.affiliation: Buchmann Institute for Molecular Life Sciences and Institute of Biochemistry II, School of Medicine, Goethe University; Pohl@em.uni-frankfurt.de.
authors.forename: Christian
authors.initials: C
authors.lastname: Pohl
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000196:embryology / Q000254:growth & development*; D048430:Cell Shape / Q000502:physiology; D058948:Cell Tracking / Q000295:instrumentation / Q000379:methods*; D021621:Imaging, Three-Dimensional / Q000379:methods; D036641:Microscopy, Fluorescence, Multiphoton / Q000295:instrumentation / Q000379:methods*; D010641:Phenotype; D012984:Software; D013347:Subcellular Fractions / Q000502:physiology; D059008:Time-Lapse Imaging / Q000379:methods