Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images

For the investigation of the molecular mechanisms involved in neurite outgrowth and differentiation, accurate and reproducible segmentation and quantification of neuronal processes are a prerequisite. To facilitate this task, we developed a semiautomatic neurite tracing technique. This article describes the design and validation of the technique.

[1]  Alejandro F. Frangi,et al.  3D MRA coronary axis determination using a minimum cost path approach , 2002, Magnetic resonance in medicine.

[2]  R Marsault,et al.  Overexpression of neuronal Sec1 enhances axonal branching in hippocampal neurons , 2002, Neuroscience.

[3]  Edward H. Adelson,et al.  The Design and Use of Steerable Filters , 1991, IEEE Trans. Pattern Anal. Mach. Intell..

[4]  M. Unser,et al.  Interpolation Revisited , 2000, IEEE Trans. Medical Imaging.

[5]  Alejandro F. Frangi,et al.  Model-based quantitation of 3-D magnetic resonance angiographic images , 1999, IEEE Transactions on Medical Imaging.

[6]  Audra E. Kosh,et al.  Linear Algebra and its Applications , 1992 .

[7]  Max A. Viergever,et al.  Quantitative evaluation of convolution-based methods for medical image interpolation , 2001, Medical Image Anal..

[8]  Douglas G. Altman,et al.  Practical statistics for medical research , 1990 .

[9]  David M. Jacobowitz,et al.  A Method for the Rapid Analysis of Neuronal Proportions and Neurite Morphology in Primary Cultures , 1998, Experimental Neurology.

[10]  Hong Shen,et al.  Rapid automated tracing and feature extraction from retinal fundus images using direct exploratory algorithms , 1999, IEEE Transactions on Information Technology in Biomedicine.

[11]  J. Bilsland,et al.  A rapid method for semi-quantitative analysis of neurite outgrowth from chick DRG explants using image analysis , 1999, Journal of Neuroscience Methods.

[12]  William A. Barrett,et al.  Interactive live-wire boundary extraction , 1997, Medical Image Anal..

[13]  Clifford Stein,et al.  Introduction to Algorithms, 2nd edition. , 2001 .

[14]  Jayaram K. Udupa,et al.  User-Steered Image Segmentation Paradigms: Live Wire and Live Lane , 1998, Graph. Model. Image Process..

[15]  Jieun Kim,et al.  Automatic morphometric analysis of neural cells , 1998 .

[16]  A W Smeulders,et al.  The homing cursor: a tool for three-dimensional chromosome analysis. , 1993, Cytometry.

[17]  M. Unser,et al.  Interpolation revisited [medical images application] , 2000, IEEE Transactions on Medical Imaging.

[18]  Thomas H. Cormen,et al.  Introduction to algorithms [2nd ed.] , 2001 .

[19]  Arnold W. M. Smeulders,et al.  A Minimum Cost Approach for Segmenting Networks of Lines , 2001, International Journal of Computer Vision.

[20]  Khalid A. Al-Kofahi,et al.  Rapid automated three-dimensional tracing of neurons from confocal image stacks , 2002, IEEE Transactions on Information Technology in Biomedicine.

[21]  Joseph J. Capowski,et al.  Computer Techniques in Neuroanatomy , 1989, Springer US.

[22]  W. Brent Lindquist,et al.  An algorithm for neurite outgrowth reconstruction , 2003, Journal of Neuroscience Methods.

[23]  Tony Lindeberg,et al.  Scale-Space Theory in Computer Vision , 1993, Lecture Notes in Computer Science.

[24]  C. Agner,et al.  The Neuron: Cell and Molecular Biology, 3rd Edition , 2002 .

[25]  Guido Gerig,et al.  Three-dimensional multi-scale line filter for segmentation and visualization of curvilinear structures in medical images , 1998, Medical Image Anal..

[26]  Anca Dima,et al.  Automatic segmentation and skeletonization of neurons from confocal microscopy images based on the 3-D wavelet transform , 2002, IEEE Trans. Image Process..

[27]  William A. Barrett,et al.  Interactive Segmentation with Intelligent Scissors , 1998, Graph. Model. Image Process..

[28]  Jayaram K. Udupa,et al.  An ultra-fast user-steered image segmentation paradigm: live wire on the fly , 2000, IEEE Transactions on Medical Imaging.

[29]  B. Spruijt,et al.  Quantitation of the growth‐associated protein B‐50/GAP‐43 and neurite outgrowth in PC12 cells , 1991, Journal of neuroscience research.

[30]  Arne Møller,et al.  A quantitative method for morphometric analysis in neuronal cell culture: unbiased estimation of neuron area and number of branch points , 1995, Journal of Neuroscience Methods.

[31]  Arne Møller,et al.  A simple procedure for quantification of neurite outgrowth based on stereological principles , 2000, Journal of Neuroscience Methods.

[32]  C. Blackstone The Neuron: Cell and Molecular Biology , 2003 .