@INBOOK{IPB-2413, author = {Möller, B. and Zergiebel, L. and Bürstenbinder, K.}, title = {{Plant Cell Morphogenesis}}, year = {2019}, pages = {151-171}, chapter = {{Quantitative and Comparative Analysis of Global Patterns of (Microtubule) Cytoskeleton Organization with CytoskeletonAnalyzer2D}}, journal = {Methods Mol Biol}, editor = {Cvrčková, F. \& Žárský, V., eds.}, doi = {10.1007/978-1-4939-9469-4_10}, url = {https://dx.doi.org/10.1007/978-1-4939-9469-4_10}, volume = {1992}, abstract = {The microtubule cytoskeleton plays important roles in cell morphogenesis. To investigate the mechanisms of cytoskeletal organization, for example, during growth or development, in genetic studies, or in response to environmental stimuli, image analysis tools for quantitative assessment are needed. Here, we present a method for texture measure-based quantification and comparative analysis of global microtubule cytoskeleton patterns and subsequent visualization of output data. In contrast to other approaches that focus on the extraction of individual cytoskeletal fibers and analysis of their orientation relative to the growth axis, CytoskeletonAnalyzer2D quantifies cytoskeletal organization based on the analysis of local binary patterns. CytoskeletonAnalyzer2D thus is particularly well suited to study cytoskeletal organization in cells where individual fibers are difficult to extract or which lack a clearly defined growth axis, such as leaf epidermal pavement cells. The tool is available as ImageJ plugin and can be combined with publicly available software and tools, such as R and Cytoscape, to visualize similarity networks of cytoskeletal patterns.} }