A distance-field based automatic neuron tracing method

BMC Bioinformatics

Volumn 14, Issue , 2013, Pages

  Yang, Jinzhu ^a,b   Gonzalez Bellido, Paloma T ^b,c   Peng, Hanchuan ^b,d  

^a NORTHEASTERN UNIVERSITY   (China)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c MARINE BIOLOGICAL LABORATORY   (United States)

^d ALLEN INSTITUTE FOR BRAIN SCIENCE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANISOTROPIC FILTERING; AUTOMATED THRESHOLDING; DIGITAL RECONSTRUCTION; DISTANCE TRANSFORMS; LASER MICROSCOPY; MICROSCOPIC IMAGE; NEURON MORPHOLOGIES; NEURON STRUCTURE;

IMAGE RECONSTRUCTION; MORPHOLOGY; PIXELS; THREE DIMENSIONAL; THREE DIMENSIONAL COMPUTER GRAPHICS;

NEURONS;

ANISOPTERA (DRAGONFLIES);

ALGORITHM; ANIMAL; ANISOTROPY; ARTICLE; CONFOCAL MICROSCOPY; CYTOLOGY; METHODOLOGY; NERVE CELL; NEURITE; ODONATA; THREE DIMENSIONAL IMAGING; ULTRASTRUCTURE;

ALGORITHMS; ANIMALS; ANISOTROPY; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, CONFOCAL; NEURITES; NEURONS; ODONATA;

EID: 84874805074     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-14-93     Document Type: Article

References (31)

1. Peng H. V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets. Nature Biotechnol 2010, 28:348-353.
2. Peng H. Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model. Bioinformatics 2010a, 26:i38-i46.
3. Li A. Micro-optical sectioning tomography to obtain a high-resolution atlas of the mouse brain. Science 2010, 330:1404-1408. 10.1126/science.1191776, 21051596.
4. Peng H. BrainAligner: 3D registration atlases of Drosophila brains. Nat Method 2011, 8(6):493-498.
5. Lee T-C. Building skeleton models via 3-D medial surface/axis thinning algorithms. CVGIP: graph. Model Image Process 1994, 56:462-78.
6. Palagyi K. A 3D 6-subiteration thinning algorithm for extracting medial lines. Pattern Recognit Lett 1998, 19:613-27.
7. Borgefors G. Computing skeletons in three dimensions. Pattern Recognition 1999, 32:1225-36.
8. Al-Kofahi KA. Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Trans Inf Technol Biomed 2002, 6:171-87. 10.1109/TITB.2002.1006304, 12075671.
9. Streekstra GJ. Analysis of tubular structures in three-dimensional confocal images. Network 2002, 13:381-95. 10.1088/0954-898X/13/3/308, 12222820.
10. Schmitt S. New methods for the computer assisted 3-D reconstruction of neurons from confocal image stacks. NeuroImage 2004, 23:1283-98. 10.1016/j.neuroimage.2004.06.047, 15589093.
11. Santamaría-Pang A. Automatic centerline extraction of irregular tubular structures using probability volumes from multiphoton imaging. Proc Med Image Comput Comput-Assist Interv 2007, 4792:486-94.
12. Myatt DR. Towards the automatic reconstruction of dendritic trees using particle filters. Nonlinear Stat Signal Process Workshop 2006, 2006:193-6.
13. Evers JF. Progress in functional neuroanatomy: precise automatic geometric reconstruction of neuronal morphology from confocal image stacks. J Neurophysiol 2005, 93(4):2331-2342.
14. Meijering E. Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images. Cytometry A 2004, 58(2):167-76.
15. Weaver CM. Automated Algorithms for Multiscale Morphometry of Neuronal Dendrites. Neural Computation 2004, 16(7):1353-1383. 10.1162/089976604323057425, 15165394.
16. Wearne S. New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience 2005, 136:661-680. 10.1016/j.neuroscience.2005.05.053, 16344143.
17. Zhao T. Automated reconstruction of neuronal morphology based on local geometrical and global structural models. Neuroinformatics 2011, 9(2-3):247-61. 3104133, 21547564.
18. Zhang Y. (2008) 3D axon structure extraction and analysis in confocal fluorescence microscopy images. Neural Comput 2008, 20:1899-1927. 10.1162/neco.2008.05-07-519, 2587013, 18336075.
19. Xie J. Automatic neuron tracing in volumetric microscopy images with anisotropic path searching. Med Image Comput Comput-Assist Interv - MICCAI 2010 PT II 2010, 6362:472-479.
20. Peng H. Automatic 3D neuron tracing using all-path pruning. Bioinformatics 2011, 28:i239-i247.
21. Donohue DE. Automated reconstruction of neuronal morphology: an overview. Brain Res Rev 2011, 67(1-2):94-102. 3086984, 21118703.
22. Cannon RC. An on-line archive of reconstructed hippocampal neurons. J Neurosci Methods 1998, 1998(84):49-54.
23. Sato Y. 3D multi-scale line filter for segmentation and visualization of curvilinear structure in medical images. Med Image Analysis 1998, 2(2):143-168.
24. Descoteaux M. A multi-scale geometric flow for segmenting vasculature in MRI. Comput Vis Mathematical Method Med Biomed Image Analysis Lecture Notes Comput Sci 2004, 3117:169-180.
25. Yuan Y. Multi-scale model-based vessel enhancement using local line integrals. 30th Annu Int IEEE EMBS Conf Vancouver 2008, 2008:2225-8.
26. Borgefors G. (1986) Distance transformations on digital images. Comput Vis Graph Image Process 1986, 34:344-371.
27. Peng H. Proof-editing is the bottleneck of 3D neuron reconstruction: the problem and solutions. Neuroinformatics 2011, 9:2-3. 103-105.
28. Rodriguez A. Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser-scanning microscopy images. Nat Protoc 2006, 1(4):2156-2161.
29. Gonzalez-Bellido P. Eight pairs of descending visual neurons in the dragonfly give wing motor centers accurate population vector of prey direction. PNAS 2012, In press.
30. Huynh-Thu Q. Scope of validity of PSNR in image/video quality assessment. Electron Lett 2008, 44(13):800-801.
31. Jefferis G. Comprehensive maps of Drosophila higher olfactory centers: Spatially segregated fruit and pheromone representation. Cell 2007, 128(6):1187-1203. 10.1016/j.cell.2007.01.040, 1885945, 17382886.