Data Visualization of Fibril Orientation Tian Zhang Cosgrove Lab - PowerPoint PPT Presentation

Data Visualization of Fibril Orientation Tian Zhang Cosgrove Lab 10/27/2016

Goal: Quantify the orientation of fibrillar features Application: Comparing orientation of features between wild type and mutant; Analyzing reorientation/movement of features. Toolbox: SOAX OrientationJ LOCO (Lindeboom et al. Science 342, 2013; David Ehrhardt Group @ Stanford) Microfilament Analyzer (Jacques et al. Plant J. 74 , 2013; Kris Vissenberg Group @ University of Antwerp)

1) Open SOAX so-ware; 2) Open an image (remove scale) 3) Set parameters SOAX 4) Ini>alize snakes (‘Process’) 5) Deform snakes (‘Process’, will take a long >me…) 6) Save snake files (you can reload these snakes later) 7) ‘Analysis’ - > Compute spherical orienta>on

8) ‘View’ - > Color snakes by Arithmuzal ang SOAX

OrientationJ (fast) 1) Open an image 2) Run ‘Orienta>on 3) Set parameters window, Hue, S Brightness) 4) Run 5) You can save th generated imag orienta>on info