Three-dimensional neuron tracing by voxel scooping

Journal of Neuroscience Methods

Volumn 184, Issue 1, 2009, Pages 169-175

  Rodriguez, Alfredo ^a   Ehlenberger, Douglas B ^a   Hof, Patrick R ^a   Wearne, Susan L ^a  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

Author keywords

Centerline extraction; Image analysis; Medial axis; Neuron tracing

Indexed keywords

ALGORITHM; ANIMAL CELL; ARTICLE; CELL STRUCTURE; CLUSTER ANALYSIS; COMPUTER; CONFOCAL MICROSCOPY; CONTROLLED STUDY; IMAGE ANALYSIS; IMAGE PROCESSING; MALE; MATHEMATICAL ANALYSIS; NERVE CELL; NONHUMAN; PRIORITY JOURNAL; RHESUS MONKEY; SURFACE PROPERTY; THREE DIMENSIONAL IMAGING;

ALGORITHMS; ANIMALS; AUTOMATION; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; MACACA FASCICULARIS; MALE; MICROSCOPY, CONFOCAL; MODELS, NEUROLOGICAL; NEURONS; PREFRONTAL CORTEX; PYRAMIDAL CELLS;

EID: 70349257180     PISSN: 01650270     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jneumeth.2009.07.021     Document Type: Article

References (30)

1. Al-Kofahi K.A., Lasek S., Szarowski D.H., Pace C.J., Nagy G., Turner J.N., et al. Rapid automated three-dimensional tracing of neurons from confocal image stacks. IEEE Transactions on Information Technology in Biomedicine 6 (2002) 171-187
2. Al-Kofahi K.A., Can A., Lasek S., Szarowski D.H., Dowell-Mesfin N., Shain W., et al. Median-based robust algorithms for tracing neurons from noisy confocal microscope images. IEEE Transactions on Information Technology in Biomedicine 7 (2003) 302-317
3. Al-Kofahi Y., Dowell-Mesfin N., Pace C., Shain W., Turner J.N., and Roysam B. Improved detection of branching points in algorithms for automated neuron tracing from 3D confocal images. Cytometry Part A 73 (2008) 36-43
4. Blum H. A transformation for extracting new descriptors of shape. In: Wathen-Dunn W. (Ed). Models for the perception of speech and visual forms (1967), MIT Press, Cambridge 362-380
5. Borgefors G., Ingela Nyström I., and Sanniti di Baja G. Computing skeletons in three dimensions. Pattern Recognition 32 (1999) 1225-1236
6. Bower J.M., and Beeman D. The book of GENESIS: exploring realistic neural models with the GEneral Neural SImulation System (1998), TELOS/Springer-Verlag, New York
7. Dickstein D.L., Kabaso D., Rocher A.B., Luebke J.I., Wearne S.L., and Hof P.R. Changes in the structural complexity of the aged brain. Aging Cell 6 (2007) 275-284
8. Duan H., Wearne S.L., Morrison J.H., and Hof P.R. Quantitative analysis of the dendritic morphology of corticocortical projection neurons in the macaque monkey association cortex. Neuroscience 114 (2002) 349-359
9. Duan H., Wearne S.L., Rocher A.B., Macedo A., Morrison J.H., and Hof P.R. Age-related morphologic alterations in dendrites and spine densities of corticocortically projecting neurons in macaque monkeys. Cerebral Cortex 13 (2003) 950-961
10. He W., Hamilton T.A., Cohen A.R., Holmes T.J., Pace C., Szarowski D.H., et al. Automated three-dimensional tracing of neurons in confocal and brightfield images. Microscopy and Microanalysis 9 (2003) 296-310
11. Hines M.L., and Carnevale N.T. NEURON: a tool for neuroscientists. Neuroscientist 7 (2001) 123-135
12. Koh I.Y., Lindquist W.B., Zito K., Nimchinsky E.A., and Svoboda K. An image analysis algorithm for dendritic spines. Neural Computation 14 (2002) 1283-1310
13. Kabaso D., Coskren P.J., Henry B.I., Hof P.R., and Wearne S.L. The electrotonic structure of pyramidal neurons contributing to prefrontal cortical circuits in macaque monkeys is significantly altered in aging. Cerebral Cortex (2009) 10.1093/cercor/bhn242
14. Lee T.-C., Kashyap R.L., and Chu C.-N. Building skeleton models via 3-D medial surface/axis thinning algorithms. CVGIP: graph. Models Image Processing 56 (1994) 462-478
15. Luebke J.I., Chang Y.-M., Moore T.L., and Rosene D.L. Normal aging results in decreased synaptic excitation and increased synaptic inhibition of layer 2/3 pyramidal cells in the monkey prefrontal cortex. Neuroscience 125 (2004) 277-288
16. Myatt D.R., Nasuto S.J., and Maybank S.J. Towards the automatic reconstruction of dendritic trees using particle filters. Nonlinear Statistical Signal Processing Workshop 2006 (2006) 193-196
17. Pham D.L., Xu C., and Prince J.L. Current methods in medical image segmentation. Annual Review of Biomedical Engineering 2 (2000) 315-337
18. Radley J.J., Rocher A.B., Rodriguez A., Ehlenberger D.B., Damman M., McEwen B.S., et al. Repeated stress alters dendritic spine morphology in the rat medial prefrontal cortex. The Journal of Comparative Neurology 507 (2008) 1141-1150
19. Ridler T.W., and Calvard S. Picture thresholding using an iterative selection method. IEEE Transaction on Systems, Man, and Cybernetics 8 (1978) 630-632
20. Rocher A.B., Kinson M.S., and Luebke J.I. Significant structural but not physiological changes in cortical neurons of 12-month-old Tg2576 mice. Neurobiology of Disease 32 (2008) 309-318
21. Rodriguez A., Ehlenberger D., Kelliher K.T., Einstein M., Henderson S.C., Morrison J.H., et al. Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images. Methods 30 (2003) 94-105
22. Rodriguez A., Ehlenberger D.B., Hof P.R., and Wearne S.L. Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images. Nature Protocols 1 (2006) 2152-2161
23. Rodriguez A., Ehlenberger D.B., Dickstein D.L., Hof P.R., and Wearne S.L. Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images. PLoS ONE 3 4 (2008) e1997 10.1371/journal.pone.0001997
24. Santamaría-Pang A., Colbert C.M., Saggau P., and Kakadiaris I.A. Automatic centerline extraction of irregular tubular structures using probability volumes from multiphoton imaging. Proceedings of the Medical Image Computing and Computer-Assisted Intervention, vol. 4792 (2007) 486-494
25. Schmitt S., Evers J.F., Duch C., Scholz M., and Obermayer K. New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks. Neuroimage 23 (2004) 1283-1298
26. Scorcioni R., and Ascoli G.A. Algorithmic extraction of morphological statistics from electronic archives of neuroanatomy. In: Mira J., and Prieto A. (Eds). Lecture notes in computer science (2001), Springer-Verlag, Berlin 30-37
27. Storn R., and Price K. Differential evolution-a simple evolution strategy for fast optimization. Dr. Dobb's Journal 22 (1997) 18-24 and 78
28. Streekstra G.J., and van Pelt J. Analysis of tubular structures in three-dimensional confocal images. Network 13 (2002) 381-395
29. Wearne S.L., Rodriguez A., Ehlenberger D.B., Rocher A.B., Henderson S.C., and Hof P.R. New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales. Neuroscience 136 (2005) 661-680
30. Weaver C.M., and Wearne S.L. Neuronal firing sensitivity to morphologic and active membrane parameters. PLoS Computational Biology 4 1 (2008) e11 10.1371/journal.pcbi.0040011