FibrilTool, an ImageJ plug-in to quantify fibrillar structures in raw microscopy images.
Cell biology heavily relies on the behavior of fibrillar structures, such as the cytoskeleton, yet the analysis of their behavior in tissues often remains qualitative. Image analysis tools have been developed to quantify this behavior, but they often involve an image pre-processing stage that may bias the output and/or they require specific software. Here we describe FibrilTool, an ImageJ plug-in based on the concept of nematic tensor, which can provide a quantitative description of the anisotropy of fiber arrays and their average orientation in cells, directly from raw images obtained by any form of microscopy. FibrilTool has been validated on microtubules, actin and cellulose microfibrils, but it may also help analyze other fibrillar structures, such as collagen, or the texture of various materials. The tool is ImageJ-based, and it is therefore freely accessible to the scientific community and does not require specific computational setup. The tool provides the average orientation and anisotropy of fiber arrays in a given region of interest (ROI) in a few seconds.
1] Laboratoire de Reproduction et Développement des Plantes, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Ecole Normale Supérieure de Lyon (ENS), Université de Lyon, Lyon, France. [2] Laboratoire Joliot Curie, CNRS, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France.
Arezki
A
Boudaoud
Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland.
Agata
A
Burian
Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland.
Dorota
D
Borowska-Wykręt
1] Laboratoire de Reproduction et Développement des Plantes, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Ecole Normale Supérieure de Lyon (ENS), Université de Lyon, Lyon, France. [2] Institut Jean-Pierre Bourgin, UMR1318 INRA-AgroParisTech, Centre de Versailles, Versailles, France.
Magalie
M
Uyttewaal
August Chełkowski Institute of Physics, University of Silesia, Katowice, Poland.
Roman
R
Wrzalik
Department of Biophysics and Morphogenesis of Plants, University of Silesia, Katowice, Poland.
Dorota
D
Kwiatkowska
1] Laboratoire de Reproduction et Développement des Plantes, Institut National de la Recherche Agronomique (INRA), Centre National de la Recherche Scientifique (CNRS), Ecole Normale Supérieure de Lyon (ENS), Université de Lyon, Lyon, France. [2] Laboratoire Joliot Curie, CNRS, ENS Lyon, Université Claude Bernard Lyon 1, Université de Lyon, Lyon, France.
Olivier
0000000169066620
O
Hamant
D000199:Actins / Q000648:ultrastructure; D002477:Cells / Q000648:ultrastructure*; D002482:Cellulose / Q000648:ultrastructure; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D008853:Microscopy / Q000379:methods*; D008870:Microtubules / Q000648:ultrastructure; D008962:Models, Theoretical; D012984:Software
D000199:Actins; D002482:Cellulose