MDL constrained 3-d grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images

Neuroinformatics

Volumn 7, Issue 4, 2009, Pages 213-232

  Yuan, Xiaosong ^a   Trachtenberg, Joshua T ^b   Potter, Steve M ^c   Roysam, Badrinath ^a  

^a RENSSELAER POLYTECHNIC INSTITUTE   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c GEORGIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

3 D microscopy; 3 D morphology; Dendritic spines; Graph theory; Grayscale 3 D skeletonization; Minimum description length

Indexed keywords

ACCESS TO INFORMATION; ALGORITHM; ARTICLE; AUTOMATION; COLOR; COMPUTER PROGRAM; CONFOCAL MICROSCOPY; CYTOLOGY; DENDRITE; DENDRITIC SPINE; EVALUATION; FACTUAL DATABASE; FLUORESCENCE; LABORATORY DIAGNOSIS; METHODOLOGY; MULTIPHOTON MICROSCOPY; NERVE CELL; THREE DIMENSIONAL IMAGING;

ACCESS TO INFORMATION; ALGORITHMS; AUTOMATION; COLOR; DATABASES, FACTUAL; DENDRITES; DENDRITIC SPINES; FALSE NEGATIVE REACTIONS; FLUORESCENCE; IMAGING, THREE-DIMENSIONAL; MICROSCOPY, CONFOCAL; MICROSCOPY, FLUORESCENCE, MULTIPHOTON; NEURONS; SOFTWARE; SOFTWARE DESIGN;

EID: 75149149751     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-009-9057-y     Document Type: Article

References (84)

1. Abdul-Karim, M. A. (2005). Automated parameter selection for segmentation of tube-like biological structures using optimization algorithm and MDL. 2005 Ph.D. dissertation, Rensselaer Polytechnic Institute, Troy, NY 12180.
2. MA Abdul-Karim K Al-Kofahi EB Brown RK Jain B Roysam 2003 Automated tracing and change analysis of angiogenic vasculature from in vivo multiphoton confocal image time series Microvascular Research 66 2 113 125 10.1016/S0026-2862(03)00039-6 12935769 (Pubitemid 36962873)
3. MA Abdul-Karim B Roysam NM Dowell-Mesfin A Jeromin M Yuksel S Kalyanaraman 2005 Automatic selection of parameters for vessel/neurite segmentation algorithms IEEE Transactions on Image Processing 14 9 1338 1350 10.1109/TIP.2005.852462 16190469 (Pubitemid 41430896)
4. KA Al-Kofahi A Can S Lasek DH Szarowski N Dowell-Mesfin W Shain JN Turner B Roysam 2003 Median-based robust algorithms for tracing neurons from noisy confocal microscope images IEEE Transactions on Information Technology in Biomedicine 7 4 302 317 10.1109/TITB.2003.816564 15000357
5. Y Al-Kofahi N Dowell-Mesfin C Pace W Shain JN Turner B Roysam 2008 Improved detection of branching points in algorithms for automated neuron tracing from 3-D confocal images Cytometry A 73 1 36 43 18067123
6. KA Al-Kofahi S Lasek DH Szarowski CJ Pace G Nagy JN Turner B Roysam 2002 Rapid automated three-dimensional tracing of neurons from confocal image stacks IEEE Transactions on Information Technology in Biomedicine 6 2 171 187 10.1109/TITB.2002.1006304 12075671 (Pubitemid 34799098)
7. W Bai X Zhou L Ji J Cheng ST Wong 2007 Automatic dendritic spine analysis in two-photon laser scanning microscopy images Cytometry A 71 10 818 826 17654649
8. A Barron J Rissanen B Yu 1998 The minimum description length principle in coding and modeling IEEE Transactions on Information Theory 44 6 2743 2760 10.1109/18.720554
9. Blake, A., & Zisserman, A. (1987). Visual reconstruction. Cambridge: MIT.
10. Bondy, J. A., & Murty, U. S. R. (1976). Graph theory with applications. New York: Elsevier Science.
11. C Bouman K Sauer 1993 A generalized Gaussian image model for edge-preserving MAP estimation IEEE Transactions on Image Processing 2 3 296 310 10.1109/83.236536 1:STN:280:DC%2BD1c7js12isw%3D%3D 18296219 (Pubitemid 23697158)
12. H Cai X Xu J Lu JW Lichtman SP Yung ST Wong 2006 Repulsive force based snake model to segment and track neuronal axons in 3-D microscopy image stacks Neuroimage 32 4 1608 1620 10.1016/j.neuroimage.2006.05.036 16861006 (Pubitemid 44332286)
13. SRY Cajal 1888 Estructura de los centros nervioso de las aves Rev Trim Hitol norm Pat 1 1 10
14. SRY Cajal 1891 Sur la structure de l'ecorce cerebrale de quelques mammiferes Cellule 7 123 176
15. A Can H Shen JN Turner HL Tanenbaum B Roysam 1999 Rapid automated tracing and feature extraction from live high-resolution retinal fundus images using direct exploratory algorithms IEEE Transactions on Information Technology in Biomedicine 3 2 125 138 10.1109/4233.767088 1:STN:280:DC%2BD3c7osVCjug%3D%3D 10719494
16. Capowski, J. J. (ed). (1989). Computer techniques in neuroanatomy. New York: Plenum.
17. K Carlsson P Wallen L Brodin 1989 Three-dimensional imaging of neurons by confocal fluorescence microscopy Journal de Microscopie 155 Pt 1 15 26 1:STN:280:DyaL1Mzmt1CntA%3D%3D
18. RM Cesar Jr LF Costa 1999 Semi-automated dendrogram generation for neural shape analysis Journal of Neuroscience Methods 93 121 131 10.1016/S0165- 0270(99)00120-X 10634497
19. TJ Cham R Cipolla 1999 Automated B-Spline curve representation incorporating MDL and error-minimizing control point insertion strategies IEEE Transactions on Pattern analysis and Machine Intelligence 21 1 49 53 10.1109/34.745733
20. J Cheng X Zhou E Miller RM Witt J Zhu BL Sabatini ST Wong 2007a A novel computational approach for automatic dendrite spines detection in two-photon laser scan microscopy Journal of Neuroscience Methods 165 1 122 134 10.1016/j.jneumeth.2007.05.020 (Pubitemid 47077498)
21. Cheng, J., Zhou, X., Sabatini, B. L., & Wong, S. T. (2007b). NeuronIQ: a novel computational approach for automatic dendrite splines detection and analysis. IEEE/NIH Life Science Systems and Applications Workshop (LISSA 2007) pp. 168-71.
22. AR Cohen B Roysam JN Turner 1994 Automated tracing and volume measurements of neurons from 3-D confocal fluorescence microscopy data Journal de Microscopie 173 Pt 2 103 114 1:STN:280:DyaK2c3itlKkuw%3D%3D
23. Cormen, T. H., Leiserson, C. E., Rivest, R. L., & Stein, C. (2001). Introduction to algorithms (2nd ed., pp. 595-601). Cambridge: MIT.
24. ND Cornea D Silver X Yuan R Balasubramanian 2005 Computing hierarchical curve-skeletons of 3-D objects The Visual Computer 21 11 945 955 10.1007/s00371-005-0308-0 (Pubitemid 41456003)
25. LF Costa ET Manoel F Faucereau J Chelly J van Pelt G Ramakers 2002 Shape analysis framework for neuromorphometry Network 13 3 283 310 10.1088/0954-898X/13/3/303
26. Dierckx, P. (1993). Curve and surface fitting with splines. Oxford: Clarendon.
27. NM Dowell-Mesfin MA Abdul-Karim AM Turner S Schanz HG Craighead B Roysam JN Turner W Shain 2004 Topographically modified surfaces affect orientation and growth of hippocampal neurons Journal of Neural Engineering 1 2 78 90 10.1088/1741-2560/1/2/003 1:STN:280:DC%2BD2M3jvFGhuw%3D%3D 15876626 (Pubitemid 41079661)
28. AX Falcao LF Costa BS da Cunha 2002 Multiscale skeletons by image foresting transform and its application to neuromorphometry Pattern Recognition 35 7 1571 1582 10.1016/S0031-3203(01)00148-0 (Pubitemid 34440054)
29. AF Frangi WJ Niessen RM Hoogeveen TV Walsum MA Viergever 1999 Model-based quantitation of 3-D magnetic resonance angiographic images IEEE Transactions on Medical Imaging 18 10 946 956 10.1109/42.811279 1:STN:280: DC%2BD3c%2Fpt1GktA%3D%3D 10628954 (Pubitemid 32211110)
30. AF Frangi WJ Niessen KL Vincken MA Viergever 1998 Multiscale vessel enhancement filtering Medical Image Computing and Computer-Assisted Intervention 1496 130 137
31. EM Glaser M Tagamets NT McMullen H Van der Loos 1983 The image-combining computer microscope-an interactive instrument for morphometry of the nervous system Journal of Neuroscience Methods 8 1 17 32 10.1016/0165-0270(83)90048-1 1:STN:280:DyaL3s3mvF2rtQ%3D%3D 6688280
32. Globus, A., Levit, C., & Lasinski, T. (1991) A tool for visualizing the topology of three-dimensional vector fields. IEEE Visualization, 33-40
33. Grunwald, P., Myung, J., & Pitt, M. (2004). Advances in minimum description length: Theory and applications. Cambridge: MIT Press.
34. A Guéziec N Ayache 1994 Smoothing and matching of 3-D space curves International Journal of Computer Vision 12 1 79 104 10.1007/BF01420985
35. AT Gulledge BM Kampa GJ Stuart 2005 Synaptic integration in dendritic trees Journal of Neurobiology 64 75 90 10.1002/neu.20144 1:CAS:528: DC%2BD2MXlslyhu70%3D 15884003 (Pubitemid 40847432)
36. W He TA Hamilton AR Cohen TJ Holmes C Pace DH Szarowski JN Turner B Roysam 2003 Automated three-dimensional tracing of neurons in confocal and brightfield images Microscopy and Microanalysis 9 4 296 310 10.1017/ S143192760303040X 1:CAS:528:DC%2BD3sXlvFaqtr4%3D 12901764
37. Herzog, A., Krell, G., Michaelis, B., Wang, J., Zuschratter, W., & Braun, K. (1997). Restoration of three-dimensional quasi-binary images from confocal microscopy and its application to dendritic trees. BiOS. San Jose, 8-14.
38. Holmes, T. J., Bhattacharyya, S., Cooper, J. A., Hanzel, D., Krishnamurthi, V., Lin, W., et al. (1995). Light microscopic images reconstructed by maximum likelihood deconvolution. In J. Pawley (Ed.), Handbook of confocal microscopy. New York: Plenum.
39. F Janoos B Nouansengsy X Xu R MacHiraju STC Wong 2008 Classification and uncertainty visualization of dendritic spines from optical microscopy imaging Computer Graphics Forum 27 3 879 886 10.1111/j.1467-8659.2008.01220.x
40. P Kalus TJ Muller W Zuschratter D Senitz 2000 The dendritic architecture of prefrontal pyramidal neurons in schizophrenic patients NeuroReport 11 16 3621 3625 10.1097/00001756-200011090-00044 1:STN:280:DC%2BD3MzgtleitA%3D%3D 11095531
41. C Kirbas F Quek 2004 A review of vessel extraction techniques and algorithms ACM Computing Surveys 36 2 81 121 10.1145/1031120.1031121 (Pubitemid 43891429)
42. IY Koh WB Lindquist K Zito EA Nimchinsky K Svoboda 2002 An image analysis algorithm for dendritic spines Neural Computation 14 6 1283 1310 10.1162/089976602753712945 12020447
43. YG Leclerc 1989 Constructing simple stable descriptions for image partitioning International Journal of Computer Vision 3 1 73 102 10.1007/BF00054839
44. Lippman, J., & Dunaevsky, A. (2005). Dendritic spine morphogenesis and plasticity. Journal of Neurobiology, 64(1), 47-57.
45. Lolive, D., Barbot, N., & Boeffard, O. (2006). Melodic contour estimation with B-spline models using a MDL criterion. Proceedings of the 11th International Conference on Speech and Computer (SPECOM) (pp. 333-338). Saint Petersburg, Russia
46. M London M Hausser 2005 Dendritic computation Annual Review of Neuroscience 28 503 532 10.1146/annurev.neuro.28.061604.135703 1:CAS:528:DC%2BD2MXosVegtbo%3D 16033324 (Pubitemid 41098913)
47. BE Losavio Y Liang A Santamaria-Pang IA Kakadiaris CM Colbert P Saggau 2008 Live neuron morphology automatically reconstructed from multiphoton and confocal imaging data Journal of Neurophysiology 100 2422 2429 10.1152/jn.90627.2008 18701753
48. F Lu E Milios 1994 Optimal spline fitting to planar shape Signal Processing 37 129 140 10.1016/0165-1684(94)90171-6
49. M Matsuzaki 2007 Factors critical for the plasticity of dendritic spines and memory storage Neuroscience Research 57 1 9 10.1016/j.neures.2006.09.017 17070951 (Pubitemid 46073252)
50. E Meijering M Jacob JC Sarria Pl Steiner H Hirling M Unser 2004 Design and validation of a tool for neurite tracing and analysis in fluorescence microscopy images Cytometry 58A 2 167 176 10.1002/cyto.a.20022 (Pubitemid 38509178)
51. BW Mel 1994 Information-processing in dendritic trees Neural Computation 6 1031 1085 10.1162/neco.1994.6.6.1031
52. MI Miller B Roysam KR Smith JA O'Sullivan 1991 Representing and computing regular languages on massively parallel networks IEEE Transactions on Neural Networks 2 1 56 72 10.1109/72.80291 1:STN:280:DC%2BD1c7hslOmsA%3D%3D 18276351
53. Pawley, J. B. (2006). Handbook of biological confocal microscopy (3rd ed.) Springer.
54. P Perona J Malik 1990 Scale-space and edge detection using anisotropic diffusion IEEE Transactions on Pattern Analysis and Machine Intelligence 12 7 629 639 10.1109/34.56205 (Pubitemid 20726016)
55. SM Potter 1996 Vital imaging: two photons are better than one Current Biology 6 12 1595 1598 10.1016/S0960-9822(02)70782-3 1:CAS:528: DyaK28XnsFKjtrg%3D 8994823
56. Potter, S. M. (2005). Two-photon microscopy for 4D imaging of living neurons. In R. Yuste & A. Konnerth (Eds.), Imaging in neuroscience and development: A laboratory manual (pp. 59-70). Cold Spring Harbor: Cold Spring Harbor Laboratory.
57. J Rissanen 1978 Modeling by shortest data description Automatica 14 5 465 471 10.1016/0005-1098(78)90005-5 (Pubitemid 9397141)
58. A Rodriguez DB Ehlenberger PR Hof SL Wearne 2006 Rayburst sampling. An algorithm for automated three-dimensional shape analysis from laser scanning microscopy images National Protocol 1 4 2152 2161 10.1038/nprot.2006.313 1:CAS:528:DC%2BD2sXhtFagtrvL (Pubitemid 46773338)
59. A Rodriguez D Ehlenberger K Kelliher M Einstein SC Henderson JH Morrison PR Hof SL Wearne 2003 Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images Methods 30 1 94 105 10.1016/S1046-2023(03)00011-2 1:CAS:528:DC%2BD3sXivV2mtbc%3D 12695107 (Pubitemid 36410327)
60. Rogers, D. F. (1998). Procedural elements for computer graphics. Boston: McGraw-Hill.
61. JD Rolston DA Wagenaar SM Potter 2007 Precisely timed spatiotemporal patterns of neural activity in dissociated cortical cultures Neuroscience 148 1 294 303 10.1016/j.neuroscience.2007.05.025 1:CAS:528:DC%2BD2sXovFOrtLY%3D 17614210 (Pubitemid 47211621)
62. Satou, K., Aoki, Y., Mataga, N., Hensh, T. K., & Taki, K. (2005). Automatic analysis for neuron by confocal laser scanning microscope. Optomechatronic Machine Vision, Proceedings of SPIE, 6051.
63. S Schmitt JF Evers C Duch M Scholz K Obermayer 2004 New methods for the computer-assisted 3-D reconstruction of neurons from confocal image stacks Neuroimage 23 4 1283 1298 10.1016/j.neuroimage.2004.06.047 15589093 (Pubitemid 40260352)
64. Schroeder, W., Martin, K., & Lorensen, B. (1998). The visualization toolkit: An object oriented approach to 3-D graphics. Printice-Hall Inc.
65. Schumaker, L. L. (1981). Spine functions: Basic theory. New York: Wiley.
66. Scorcioni, R., Polavaram, S., & Ascoli, G. A. (2008). L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Nature Protocols, 3(5), 866-876.
67. R Srinivasan X Zhou E Miller J Lu J Litchman ST Wong 2007 Automated axon tracking of 3-D confocal laser scanning microscopy images using guided probabilistic region merging Neuroinformatics 5 3 189 203 10.1007/s12021-007- 0013-4 17917130 (Pubitemid 350135988)
68. Theisel, H., & Weinkauf, T. (2002). Vector field metrics based on distance measures of first order critical points. Journal of WSCG, 10(3).
69. JT Trachtenberg BE Chen GW Knott G Feng JR Sanes E Welker K Svoboda 2002 Long-term in vivo imaging of experience-dependent synaptic plasticity in adult cortex Nature 420 6917 788 794 10.1038/nature01273 1:CAS:528: DC%2BD38XpsFygtLw%3D 12490942 (Pubitemid 36019621)
70. JN Turner DH Szarowski KL Smith M Marko A Leith JW Swann 1991 Confocal microscopy and three-dimensional reconstruction of electrophysiologically identified neurons in thick brain slices Journal of Electron Microscopy Technique 18 1 11 23 10.1002/jemt.1060180104 1:STN:280:DyaK3M3nslyjtw%3D%3D 2056347
71. JN Turner DH Szarowski TJ Turner H Ancin WC Lin B Roysam TJ Holmes 1994 Three-dimensional imaging and image analysis of hippocampal neurons: confocal and digitally enhanced wide field microscopy Microscopy Research and Technique 29 4 269 278 10.1002/jemt.1070290403 1:STN:280:DyaK2M7ktlKgtg%3D%3D 7841499 (Pubitemid 24329584)
72. JA Tyrrell E di Tomaso D Fuja R Tong K Kozak RK Jain B Roysam 2007 Robust 3-D modeling of vasculature imagery using superellipsoids IEEE Transactions on Medical Imaging 26 2 223 237 10.1109/TMI.2006.889722 17304736 (Pubitemid 46362765)
73. JA Tyrrell V Mahadevan RT Tong EB Brown RK Jain B Roysam 2005 A 2-D/3-D model-based method to quantify the complexity of microvasculature imaged by in vivo multiphoton microscopy Microvascular Research 70 3 165 178 10.1016/j.mvr.2005.08.005 16239015 (Pubitemid 41586470)
74. Vliet, L. J. V. (1993). Grey-scale measurements in multi-dimensional digitized images. Ph.D. Thesis of the Pattern Recognition Group, Delft University of Technology, The Netherlands.
75. SL Wearne A Rodriguez DB Ehlenberger AB Rocher SC Henderson PR Hof 2005 New techniques for imaging, digitization and analysis of three-dimensional neural morphology on multiple scales Neuroscience 136 3 661 680 10.1016/j.neuroscience.2005.05.053 1:CAS:528:DC%2BD2MXhtlaiurvN 16344143 (Pubitemid 41774717)
76. CM Weaver PR Hof SL Wearne WB Lindquist 2004 Automated algorithms for multiscale morphometry of neuronal dendrites Neural Computation 16 7 1353 1383 10.1162/089976604323057425 15165394 (Pubitemid 38740014)
77. CC Wu JF Reilly WG Young JH Morrison FE Bloom 2004 High-throughput morphometric analysis of individual neurons Cerebral Cortex 14 5 543 554 10.1093/cercor/bhh016 15054070 (Pubitemid 38579655)
78. G Xiong X Zhou A Degterev L Ji ST Wong 2006 Automated neurite labeling and analysis in fluorescence microscopy images Cytometry A 69 6 494 505 16680708
79. X Xu ST Wong 2006 Optical microscopic image processing of dendritic spines morphology IEEE Signal Processing Magazine 23 4 132 135 10.1109/MSP.2006.1657828 (Pubitemid 44111514)
80. Yu, Z., & Bajaj, C. (2004). A segmentation-free approach for skeletonization of gray-scale images via anisotropic vector diffusion. Computer Vision and Pattern Recognition, CVPR. Proceedings of the 2004 IEEE Computer Society Conference on, 1, 415-20.
81. R Yuste T Bonhoeffer 2001 Morphological changes in dendritic spines associated with long-term synaptic plasticity Annual Review of Neuroscience 24 1071 1089 10.1146/annurev.neuro.24.1.1071 1:CAS:528:DC%2BD3MXls1Shsbw%3D 11520928 (Pubitemid 32695254)
82. Y Zhang X Zhou A Degterev M Lipinski D Adjeroh J Yuan ST Wong 2007 A novel tracing algorithm for high throughput imaging screening of neuron-based assays Journal of Neuroscience Methods 160 1 149 162 10.1016/j.jneumeth.2006.07. 028 16987551 (Pubitemid 46137998)
83. Zhang, Y., Zhou, X., Witt, R. M., Sabatini, B. L., Adjeroh, D., & Wong, S. T. (2007b). Automated spine detection using curvilinear structure detector and LDA Classifier. Biomedical Imaging: From Nano to Macro, ISBI. 4th IEEE International Symposium on, pp. 528-531. (Pubitemid 350141142)
84. Y Zhang X Zhou RM Witt BL Sabatini D Adjeroh ST Wong 2007 Dendritic spine detection using curvilinear structure detector and LDA classifier Neuroimage 36 2 346 360 10.1016/j.neuroimage.2007.02.044 17448688 (Pubitemid 46722687)