title: Using CellProfiler to Analyze and Quantify Vascular Morphology.
abstract: Computational programs can be used in place of time-consuming, error-prone manual data collection. CellProfiler is a free, open source program that allows researchers to automate image analysis and collect large amounts of phenotypic data relatively easily. Here, we describe how to adapt CellProfiler to analyze cross sections of xylem tissue and use it to gather a variety of information on traits such as cell size, shape, and number. We provide step-by-step instructions to create a typical CellProfiler analysis pipeline, alongside explanations of important modules, options and parameters available to the user.
authors.affiliation: University of Manchester, Oxford Road, Manchester, UK.
authors.forename: Liam
authors.initials: L
authors.lastname: Campbell
authors.affiliation: University of Manchester, Oxford Road, Manchester, UK.
authors.forename: Manoj
authors.initials: M
authors.lastname: Kumar
authors.affiliation: University of Manchester, Oxford Road, Manchester, UK. Simon.Turner@manchester.ac.uk.
authors.forename: Simon
authors.initials: S
authors.lastname: Turner
mesh_terms: D002473:Cell Wall; D019295:Computational Biology / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D010641:Phenotype; D058526:Plant Vascular Bundle / Q000166:cytology*; D012984:Software; D052584:Xylem / Q000166:cytology
keywords: Bioinformatics; Cell wall; CellProfiler; Image analysis; Lumen; Xylem morphology