ImageJ plugins for directional analysis in images
Written by Daniel Sage at the Biomedical Image Group (BIG), EPFL, Switzerland
The aim is to characterize the orientation and isotropy properties of a region of interest (ROI) in an image, based on the evaluation of the gradient structure tensor in a local neighborhood. The theoretical background is fully described in this PDF document. The software OrientationJ automates the orientation analysis. It is a series of Java plugins for ImageJ. OrientationJ has four functionalities: performing a visual representation of the orientation of a image, creation of a vector field map, plotting the distribution of orientations, and detection of keypoints (Harris Corner). OrientationJ has also others tools: the manual measurement of the orientation and coherency in a ROI, the computation of the dominant orientation, the alignment of images based on the gradient structure tensor and some test images (chirp).
- Reference on the method: Z. Püspöki, M. Storath, D. Sage, M. Unser, Transforms and Operators for Directional Bioimage Analysis: A Survey Advances in Anatomy, Embryology and Cell Biology, vol. 219, Focus on Bio-Image Informatics, Springer International Publishing, ch. 3, pp. 69-93, May 21, 2016.
- Reference on the angular distribution: R. Rezakhaniha, A. Agianniotis, J.T.C. Schrauwen, A. Griffa, D. Sage, C.V.C. Bouten, F.N. van de Vosse, M. Unser, N. Stergiopulos, Experimental Investigation of Collagen Waviness and Orientation in the Arterial Adventitia Using Confocal Laser Scanning Microscopy Biomechanics and Modeling in Mechanobiology, vol. 11, no. 3-4, pp. 461-473, 2012.
- Reference on the local measurements: E. Fonck, G.G. Feigl, J. Fasel, D. Sage, M. Unser, D.A. Rüfenacht, N. Stergiopulos, Effect of Aging on Elastin Functionality in Human Cerebral Arteries Stroke, vol. 40, no. 7, pp. 2552-2556, July 2009.