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.
Key words
This is a preview of subscription content, log in via an institution.
Buying options
Tax calculation will be finalised at checkout
Purchases are for personal use only
Learn about institutional subscriptionsReferences
Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) Cell Profiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol 7(10):100
Rasband WS (1997) ImageJ. National Institutes of Health, Bethesda, MD, USA. Available from: http://imagej.nih.gov/ij/
Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O’Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE (2012) An image analysis toolbox for high-throughput C. elegans assays. Nat Methods 9(7):714–716
Jiang Y, Qi X, Chrenek MA, Gardner C, Boatright JH, Grossniklaus HE, Nickerson JM (2013) Functional principal component analysis reveals discriminating categories of retinal pigment epithelial morphology in mice. Invest Ophthalmol Vis Sci 54(12):7274–7283
Mussadiq Z, Laszlo B, Helyes L, Gyuricza C (2015) Evaluation and comparison of open source program solutions for automatic seed counting on digital images. Comput Electron Agric 117:194–199
Turner SR, Somerville CR (1997) Collapsed xylem phenotype of Arabidopsis identifies mutants deficient in cellulose deposition in the secondary cell wall. Plant Cell 9(5):689–701
Etchells JP, Mishra LS, Kumar M, Campbell L, Turner SR (2015) Wood formation in trees is increased by manipulating PXY-regulated cell division. Curr Biol 25:1050–1055
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2017 Springer Science+Business Media LLC
About this protocol
Cite this protocol
Campbell, L., Kumar, M., Turner, S. (2017). Using CellProfiler to Analyze and Quantify Vascular Morphology. In: de Lucas, M., Etchhells, J. (eds) Xylem. Methods in Molecular Biology, vol 1544. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6722-3_13
Download citation
DOI: https://doi.org/10.1007/978-1-4939-6722-3_13
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-6720-9
Online ISBN: 978-1-4939-6722-3
eBook Packages: Springer Protocols