Neuronal tracing for connectomic studies

Neuroinformatics

Volumn 9, Issue 2-3, 2011, Pages 159-166

  Lu, Ju ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Connectomics; Electron microscopy; Fluorescence microscopy; Image segmentation; Neuron tracing

Indexed keywords

ANIMAL; BRAIN MAPPING; COMPUTER PROGRAM; CYTOLOGY; ELECTRON MICROSCOPY; FLUORESCENCE MICROSCOPY; HUMAN; IMAGE PROCESSING; METHODOLOGY; NERVE TRACT; NEUROANATOMICAL TRACT TRACING; PHYSIOLOGY; REVIEW;

ANIMALS; BRAIN MAPPING; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, ELECTRON; MICROSCOPY, FLUORESCENCE; NEURAL PATHWAYS; NEUROANATOMICAL TRACT-TRACING TECHNIQUES; SOFTWARE DESIGN;

EID: 79958097484     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-011-9101-6     Document Type: Review

References (94)

1. KA Al-Kofahi S Lasek DH Szarowski CJ Pace G Nagy JN Turner, et al. 2002 Rapid automated three-dimensional tracing of neurons from confocal image stacks IEEE Transactions on Information Technology in Biomedicine 6 2 171 187 12075671 10.1109/TITB.2002.1006304 (Pubitemid 34799098)
2. Andres, B., Kothe, U., Helmstaedter, M., Denk, W., & Hamprecht, F. A. (2008). Segmentation of SBFSEM volume data of neural tissue by hierarchical classification. In G. Rigoll (Ed.), Pattern Recognition, 30th DAGM Symposium, Munich, Germany, June 10-13, 2008, Proceedings. Lecture Notes in Computer Science 5096 (pp. 142-152). Springer.
3. JR Anderson S Mohammed B Grimm BW Jones P Koshevoy T Tasdizen, et al. 2011 The Viking viewer for connectomics: scalable multi-user annotation and summarization of large volume data sets Journal of Microscopy 241 1 13 28 21118201 10.1111/j.1365-2818.2010.03402.x 1:STN:280:DC%2BC3M%2FisVGmtA%3D%3D
4. GA Ascoli DE Donohue M Halavi 2007 NeuroMorpho. Org: a central resource for neuronal morphologies The Journal of Neuroscience 27 35 9247 9251 17728438 10.1523/JNEUROSCI.2055-07.2007 1:CAS:528:DC%2BD2sXhtVaks7fF (Pubitemid 47358196)
5. Bas, E., & Erdogmus, D. (2011). Principal curves as skeletons of tubular objects: locally characterizing the structures of axons. Neuroinformatics. doi: 10.1007/s12021-011-9105-2.
6. E Betzig GH Patterson R Sougrat OW Lindwasser S Olenych JS Bonifacino, et al. 2006 Imaging intracellular fluorescent proteins at nanometer resolution Science 313 5793 1642 1645 16902090 10.1126/science.1127344 1:CAS:528: DC%2BD28XpsVOktL0%3D (Pubitemid 44414039)
7. BB Biswal M Mennes XN Zuo S Gohel C Kelly SM Smith, et al. 2010 Toward discovery science of human brain function Proceedings of the National Academy of Sciences of the United States of America 107 10 4734 4739 20176931 10.1073/pnas.0911855107 1:CAS:528:DC%2BC3cXjs1elsrk%3D
8. KL Briggman W Denk 2006 Towards neural circuit reconstruction with volume electron microscopy techniques Current Opinion in Neurobiology 16 5 562 570 16962767 10.1016/j.conb.2006.08.010 1:CAS:528:DC%2BD28XhtVagtrjM (Pubitemid 44466398)
9. Briggman, K. L., Helmstaedter, M., & Denk, W. (2011) Wiring specificity in the direction-selectivity circuit of the mammalian retina. Nature, in press.
10. PJ Broser R Schulte S Lang A Roth F Helmchen J Waters, et al. 2004 Nonlinear anisotropic diffusion filtering of three-dimensional image data from two-photon microscopy Journal of Biomedical Optics 9 6 1253 1264 15574067 10.1117/1.1806832 (Pubitemid 40168141)
11. HM Cai XY Xu J Lu JW Lichtman SP Yung STC Wong 2006 Repulsive force based snake model to segment and track neuronal axons in 3D microscopy image stacks Neuroimage 32 4 1608 1620 16861006 10.1016/j.neuroimage.2006.05.036 (Pubitemid 44332286)
12. HM Cai XY Xu J Lu J Lichtman SP Yung STC Wong 2008 Using nonlinear diffusion and mean shift to detect and connect cross-sections of axons in 3D optical microscopy images Medical Image Analysis 12 6 666 675 18440853 10.1016/j.media.2008.03.002
13. Cardona, A., Saalfeld, S., Preibisch, S., Schmid, B., Cheng, A., Pulokas, J., et al. (2010). An integrated micro- and macroarchitectural analysis of the Drosophila brain by computer-assisted serial section electron microscopy. PLoS Biology, 8(10).
14. Chothani, P., Mehta, V., & Stepanyants, A. (2011). Automated tracing of neurites from light microscopy stacks of images. Neuroinformatics. doi: 10.1007/s12021-011-9121-2.
15. AR Cohen B Roysam JN Turner 1994 Automated tracing and volume measurements of neurons from 3-D confocal fluorescence microscopy data Journal of Microscopy 173 103 114 8169949 1:STN:280:DyaK2c3itlKkuw%3D%3D (Pubitemid 24178629)
16. JA Conchello JW Lichtman 2005 Optical sectioning microscopy Nature Methods 2 12 920 931 16299477 10.1038/nmeth815 1:CAS:528:DC%2BD2MXht1aksr3K (Pubitemid 43108728)
17. H Cuntz F Forstner J Haag A Borst 2008 The morphological identity of insect dendrites PLoS Computational Biology 4 12 e1000251 19112481 10.1371/journal.pcbi.1000251
18. Cuntz, H., Forstner, F., Borst, A., & Hausser, M. (2010). One rule to grow them all: a general theory of neuronal branching and its practical application. PLoS Computational Biology, 6(8).
19. A Dani B Huang J Bergan C Dulac X Zhuang 2010 Superresolution imaging of chemical synapses in the brain Neuron 68 5 843 856 21144999 10.1016/j.neuron. 2010.11.021 1:CAS:528:DC%2BC3cXhsFGhu73I
20. J DeFelipe 2010 From the connectome to the synaptome: an epic love story Science 330 6008 1198 1201 21109663 10.1126/science.1193378 1:CAS:528: DC%2BC3cXhsVGrtr7I
21. W Denk H Horstmann 2004 Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure PLoS Biology 2 11 1900 1909 10.1371/journal.pbio.0020329 1:CAS:528:DC%2BD2cXhtVamsrvE (Pubitemid 40280487)
22. A Dima M Scholz K Obermayer 2002 Automatic segmentation and skeletonization of neurons from confocal microscopy images based on the 3-D wavelet transform IEEE Transactions on Image Processing 11 7 790 801 18244675 10.1109/TIP.2002.800888 (Pubitemid 34949983)
23. A Dima M Scholz K Obermayer 2003 Automatic three-dimensional graph construction of nerve cells from confocal microscopy Journal of Electronic Imaging 12 1 134 150 10.1117/1.1526102
24. G Feng RH Mellor M Bernstein C Keller-Peck QT Nguyen M Wallace, et al. 2000 Imaging neuronal subsets in transgenic mice expressing multiple spectral variants of GFP Neuron 28 1 41 51 11086982 10.1016/S0896-6273(00)00084-2 1:CAS:528:DC%2BD3cXnvVGlt7w%3D
25. JC Fiala 2005 Reconstruct: a free editor for serial section microscopy Journal of Microscopy 218 Pt 1 52 61 15817063 10.1111/j.1365-2818.2005.01466.x 1:STN:280:DC%2BD2M7osV2msQ%3D%3D (Pubitemid 40524168)
26. JT Frohn HF Knapp A Stemmer 2000 True optical resolution beyond the Rayleigh limit achieved by standing wave illumination Proceedings of the National Academy of Sciences of the United States of America 97 13 7232 7236 10840057 10.1073/pnas.130181797 1:CAS:528:DC%2BD3cXksVKitLc%3D (Pubitemid 30431446)
27. WB Gan J Grutzendler WT Wong RO Wong JW Lichtman 2000 Multicolor "DiOlistic" labeling of the nervous system using lipophilic dye combinations Neuron 27 2 219 225 10985343 10.1016/S0896-6273(00)00031-3 1:CAS:528:DC%2BD3cXmsVWmtrY%3D
28. MGL Gustafsson 2000 Surpassing the lateral resolution limit by a factor of two using structured illumination microscopy Journal of Microscopy 198 82 87 10810003 10.1046/j.1365-2818.2000.00710.x 1:CAS:528:DC%2BD3cXktVOgt7o%3D (Pubitemid 30316807)
29. MGL Gustafsson 2005 Nonlinear structured-illumination microscopy: wide-field fluorescence imaging with theoretically unlimited resolution Proceedings of the National Academy of Sciences of the United States of America 102 37 13081 13086 16141335 10.1073/pnas.0406877102 1:CAS:528:DC%2BD2MXhtVaqu7bK (Pubitemid 41324982)
30. X He E Kischell M Rioult TJ Holmes 1998 Three-dimensional thinning algorithm that peels the outmost layer with application to neuron tracing Journal of Computer-Assisted Microscopy 10 3 123 135 10.1023/A:1023437403657
31. 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 12901764 10.1017/S143192760303040X 1:CAS:528:DC%2BD3sXlvFaqtr4%3D
32. R Heintzmann MGL Gustafsson 2009 Subdiffraction resolution in continuous samples Nature Photonics 3 7 362 364 10.1038/nphoton.2009.102 1:CAS:528:DC%2BD1MXnvVagtLs%3D
33. R Heintzmann TM Jovin C Cremer 2002 Saturated patterned excitation microscopy - a concept for optical resolution improvement Journal of the Optical Society of America A 19 8 1599 1609 10.1364/JOSAA.19.001599
34. SW Hell 2007 Far-field optical nanoscopy Science 316 5828 1153 1158 17525330 10.1126/science.1137395 1:CAS:528:DC%2BD2sXls1KitL4%3D (Pubitemid 46877470)
35. F Helmchen W Denk 2005 Deep tissue two-photon microscopy Nature Methods 2 12 932 940 16299478 10.1038/nmeth818 1:CAS:528:DC%2BD2MXht1aksr3E (Pubitemid 43108729)
36. M Helmstaedter KL Briggman W Denk 2008 3D structural imaging of the brain with photons and electrons Current Opinion in Neurobiology 18 6 633 641 19361979 10.1016/j.conb.2009.03.005 1:CAS:528:DC%2BD1MXmtVKksL0%3D
37. ST Hess TPK Girirajan MD Mason 2006 Ultra-high resolution imaging by fluorescence photoactivation localization microscopy Biophysical Journal 91 11 4258 4272 16980368 10.1529/biophysj.106.091116 1:CAS:528:DC%2BD28Xht1Khur%2FN (Pubitemid 44887284)
38. V Jain HS Seung SC Turaga 2010 Machines that learn to segment images: a crucial technology for connectomics Current Opinion in Neurobiology 20 1 14 10.1016/j.conb.2010.07.004
39. WK Jeong J Beyer M Hadwiger R Blue C Law A Vazquez-Reina, et al. 2010 Ssecrett and NeuroTrace: interactive visualization and analysis tools for large-scale neuroscience data sets IEEE Computer Graphics and Applications 30 3 58 70 20650718 10.1109/MCG.2010.56
40. E Jurrus M Hardy T Tasdizen PT Fletcher P Koshevoy CB Chien, et al. 2009 Axon tracking in serial block-face scanning electron microscopy Medical Image Analysis 13 1 180 188 18617436 10.1016/j.media.2008.05.002
41. E Jurrus AR Paiva S Watanabe JR Anderson BW Jones RT Whitaker, et al. 2010 Detection of neuron membranes in electron microscopy images using a serial neural network architecture Medical Image Analysis 14 6 770 783 20598935 10.1016/j.media.2010.06.002
42. N Kasthuri JW Lichtman 2007 The rise of the 'projectome' Nature Methods 4 4 307 308 17396125 10.1038/nmeth0407-307 1:CAS:528:DC%2BD2sXkt1eqsro%3D (Pubitemid 46766971)
43. N Kasthuri K Hayworth J Lichtman N Erdman CA Ackerley 2007 New technique for ultra-thin serial brain section imaging using scanning electron microscopy Microscopy and Microanalysis 13 26 27 10.1017/S1431927607078002
44. G Knott H Marchman D Wall B Lich 2008 Serial section scanning electron microscopy of adult brain tissue using focused ion beam milling The Journal of Neuroscience 28 12 2959 2964 18353998 10.1523/JNEUROSCI.3189-07.2008 1:CAS:528:DC%2BD1cXjvFCjs7k%3D (Pubitemid 351442268)
45. Lee, P. C., Ching, Y. T., Chang, H. M., & Chiang, A. S. (2008). A semi-automatic method for neuron centerline extraction in confocal microscopic image stack. 5th IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI 2008) (pp. 959-962). Paris, France.
46. PC Lee HM Chang CY Lin AS Chiang YT Ching 2009 Constructing neuronal structure from 3D confocal microscopic images Journal of Medical and Biological Engineering 29 1 1 6 10.1007/978-0-387-79311-5-1
47. JW Lichtman JR Sanes 2008 Ome sweet ome: what can the genome tell us about the connectome? Current Opinion in Neurobiology 18 3 346 353 18801435 10.1016/j.conb.2008.08.010 1:CAS:528:DC%2BD1cXhtlSgsrzI
48. JW Lichtman J Livet JR Sanes 2008 A technicolour approach to the connectome Nature Reviews Neuroscience 9 6 417 422 18446160 10.1038/nrn2391 1:CAS:528:DC%2BD1cXmtVahurw%3D
49. J Livet TA Weissman H Kang RW Draft J Lu RA Bennis, et al. 2007 Transgenic strategies for combinatorial expression of fluorescent proteins in the nervous system Nature 450 7166 56 62 17972876 10.1038/nature06293 1:CAS:528:DC%2BD2sXht1CgtbnN (Pubitemid 350070576)
50. J Lu JC Fiala JW Lichtman 2009 Semi-automated reconstruction of neural processes from large numbers of fluorescence images PLoS ONE 4 5 e5655 19479070 10.1371/journal.pone.0005655
51. J Lu JC Tapia OL White JW Lichtman 2009 The interscutularis muscle connectome PLoS Biology 7 2 e32 19209956 10.1371/journal.pbio.1000032
52. Luisi, J., Narayanaswamy, A., Galbreath, Z., & Roysam, B. (2011). The FARSIGHT trace editor: an open source tool for 3-D inspection and efficient pattern analysis aided editing of automated neuronal reconstructions. Neuroinformatics. doi: 10.1007/s12021-011-9115-0.
53. ER Macagno V Lopresti C Levintha 1973 Structure and development of neuronal connections in isogenic organisms - variations and similarities in optic system of Daphnia magna Proceedings of the National Academy of Sciences of the United States of America 70 1 57 61 4509664 10.1073/pnas.70.1.57 1:STN:280:DyaE3s%2Fot1Ckuw%3D%3D
54. JH Macke N Maack R Gupta W Denk B Scholkopf A Borst 2008 Contour-propagation algorithms for semi-automated reconstruction of neural processes Journal of Neuroscience Methods 167 2 349 357 17870180 10.1016/j.jneumeth.2007.07.021 (Pubitemid 350235619)
55. D Mayerich J Keyser 2009 Hardware accelerated segmentation of complex volumetric filament networks IEEE Transactions on Visualization and Computer Graphics 15 4 670 681 19423890 10.1109/TVCG.2008.196
56. E Meijering 2010 Neuron tracing in perspective Cytometry. Part A 77 7 693 704 10.1002/cyto.a.20895
57. Y Mishchenko 2009 Automation of 3D reconstruction of neural tissue from large volume of conventional serial section transmission electron micrographs Journal of Neuroscience Methods 176 2 276 289 18834903 10.1016/j.jneumeth.2008. 09.006
58. Y Mishchenko T Hu J Spacek J Mendenhall KM Harris DB Chklovskii 2010 Ultrastructural analysis of hippocampal neuropil from the connectomics perspective Neuron 67 6 1009 1020 20869597 10.1016/j.neuron.2010.08.014 1:CAS:528:DC%2BC3cXht1WisrzP
59. DR Myatt SJ Nasuto 2008 Improved automatic midline tracing of neurites with Neuromantic BMC Neuroscience 9 Suppl 1 81 10.1186/1471-2202-9-S1-P81
60. UV Nagerl KI Willig B Hein SW Hell T Bonhoeffer 2008 Live-cell imaging of dendritic spines by STED microscopy Proceedings of the National Academy of Sciences of the United States of America 105 48 18982 18987 19028874 10.1073/pnas.0810028105 1:CAS:528:DC%2BD1cXhsV2rtbvF
61. Narayanaswamy, A., Wang, Y., & Roysam, B. (2011). 3-D image pre-processing algorithms for improved automated tracing of neuronal arbors. Neuroinformatics. doi: 10.1007/s12021-011-9116-z.
62. H Peng 2008 Bioimage informatics: a new area of engineering biology Bioinformatics 24 17 1827 1836 18603566 10.1093/bioinformatics/btn346 1:CAS:528:DC%2BD1cXhtVGlurrI
63. H Peng Z Ruan D Atasoy S Sternson 2010 Automatic reconstruction of 3D neuron structures using a graph-augmented deformable model Bioinformatics 26 12 i38 46 20529931 10.1093/bioinformatics/btq212 1:CAS:528:DC%2BC3cXnsVOksL0%3D
64. H Peng Z Ruan F Long JH Simpson EW Myers 2010 V3D enables real-time 3D visualization and quantitative analysis of large-scale biological image data sets Nature Biotechnology 28 4 348 353 20231818 10.1038/nbt.1612 1:CAS:528:DC%2BC3cXjt1Ogtb8%3D
65. Ramon y Cajal, S. (1995). Histology of the Nervous System of Man and Vertebrates. (trans.) Swanson N. and Swanson L., Oxford University Press.
66. A Rodriguez D Ehlenberger K Kelliher M Einstein SC Henderson JH Morrison, et al. 2003 Automated reconstruction of three-dimensional neuronal morphology from laser scanning microscopy images Methods 30 1 94 105 12695107 10.1016/S1046-2023(03)00011-2 1:CAS:528:DC%2BD3sXivV2mtbc%3D (Pubitemid 36410327)
67. A Rodriguez DB Ehlenberger PR Hof SL Wearne 2009 Three-dimensional neuron tracing by voxel scooping Journal of Neuroscience Methods 184 1 169 175 19632273 10.1016/j.jneumeth.2009.07.021
68. MJ Rust M Bates XW Zhuang 2006 Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM) Nature Methods 3 10 793 795 16896339 10.1038/nmeth929 1:CAS:528:DC%2BD28XpvVCmtLY%3D (Pubitemid 44445825)
69. Saetzler, K., McCanny, P., Rodriguez, E. P., Horstmann, H., Bruno, R. M., & Denk, W. (2009). A fuzzy algorithm to trace stained neurons in serial block-face scanning electron microscopy image series. 13th International Machine Vision and Image Processing Conference (IMVIP 2009) (pp. 162-167). Dublin, Ireland.
70. 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 15589093 10.1016/j.neuroimage.2004.06.047 (Pubitemid 40260352)
71. A Sharonov RM Hochstrasser 2006 Wide-field subdiffraction imaging by accumulated binding of diffusing probes Proceedings of the National Academy of Sciences of the United States of America 103 50 18911 18916 17142314 10.1073/pnas.0609643104 1:CAS:528:DC%2BD28XhtlChu77N (Pubitemid 350002802)
72. FS Sjöstrand 1958 Ultrastructure of retinal rod synapses of the guinea pig eye as revealed by 3-dimensional reconstructions from serial sections Journal of Ultrastructure Research 2 1 122 170 13631744 10.1016/S0022-5320(58) 90050-9
73. SJ Smith 2007 Circuit reconstruction tools today Current Opinion in Neurobiology 17 5 601 608 18082394 10.1016/j.conb.2007.11.004 1:CAS:528:DC%2BD1cXislKhug%3D%3D
74. O Sporns G Tononi R Kotter 2005 The human connectome: a structural description of the human brain PLoS Computational Biology 1 4 e42 16201007 10.1371/journal.pcbi.0010042
75. R Srinivasan X Zhou E Miller J Lu J Litchman STC Wong 2007 Automated axon tracking of 3D Confocal laser scanning microscopy images using guided Probabilistic region merging Neuroinformatics 5 3 189 203 17917130 10.1007/s12021-007-0013-4 (Pubitemid 350135988)
76. JR Swedlow IG Goldberg KW Eliceiri 2009 Bioimage informatics for experimental biology Annual Review of Biophysics 38 327 346 19416072 10.1146/annurev.biophys.050708.133641 1:CAS:528:DC%2BD1MXntlentb4%3D
77. SC Turaga JF Murray V Jain F Roth M Helmstaedter K Briggman, et al. 2010 Convolutional networks can learn to generate affinity graphs for image segmentation Neural Computation 22 2 511 538 19922289 10.1162/neco.2009.10-08- 881
78. Türetken, E., González, G., Blum, C., & Fua, P. (2011). Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors. Neuroinformatics. doi: 10.1007/s12021-011-9122-1.
79. Z Vasilkoski A Stepanyants 2009 Detection of the optimal neuron traces in confocal microscopy images Journal of Neuroscience Methods 178 1 197 204 19059434 10.1016/j.jneumeth.2008.11.008
80. Vazquez, L., Sapiro, G., & Randall, G. (1998). Segmenting neurons in electronic microscopy via geometric tracing. 1998 International Conference on Image Processing (ICIP'98) (vol. 3, pp. 814-818). Chicago, IL.
81. Wang, Y., Narayanaswamy, A., Tsai, C.-L., & Roysam, B. (2011). A broadly applicable 3-D neuron tracing method based on open-curve snake. Neuroinformatics. doi: 10.1007/s12021-011-9110-5.
82. S Ward N Thomson JG White S Brenner 1975 Electron microscopical reconstruction of the anterior sensory anatomy of the nematode Caenorhabditis elegans The Journal of Comparative Neurology 160 3 313 337 1112927 10.1002/cne.901600305 1:STN:280:DyaE2M%2FpsF2gsA%3D%3D
83. RW Ware V Lopresti 1975 3-dimensional reconstruction from serial sections International Review of Cytology 40 325 440 1097356 10.1016/S0074-7696(08) 60956-0 1:STN:280:DyaE2M3htVOisQ%3D%3D
84. 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 16344143 10.1016/j.neuroscience.2005.05.053 1:CAS:528:DC%2BD2MXhtlaiurvN (Pubitemid 41774717)
85. CM Weaver PR Hof SL Wearne WB Lindquist 2004 Automated algorithms for multiscale morphometry of neuronal dendrites Neural Computation 16 7 1353 1383 15165394 10.1162/089976604323057425 (Pubitemid 38740014)
86. JG White E Southgate JN Thomson S Brenner 1986 The structure of the nervous system of the nematode Caenorhabditis elegans Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences 314 1 340 10.1098/rstb.1986.0056
87. KI Willig RR Kellner R Medda B Hein S Jakobs SW Hell 2006 Nanoscale resolution in GFP-based microscopy Nature Methods 3 9 721 723 16896340 10.1038/nmeth922 1:CAS:528:DC%2BD28XosVOnsLo%3D (Pubitemid 44275740)
88. BA Wilt LD Burns ET Wei Ho KK Ghosh EA Mukamel MJ Schnitzer 2009 Advances in light microscopy for neuroscience Annual Review of Neuroscience 32 435 506 19555292 10.1146/annurev.neuro.051508.135540 1:CAS:528:DC%2BD1MXpsV2nu7Y%3D
89. CY Xu JL Prince 1998 Snakes, shapes, and gradient vector flow IEEE Transactions on Image Processing 7 3 359 369 18276256 10.1109/83.661186 1:STN:280:DC%2BD1c7hslKmtQ%3D%3D (Pubitemid 128745354)
90. XS Yuan JT Trachtenberg SM Potter B Roysam 2009 MDL constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images Neuroinformatics 7 4 213 232 20012509 10.1007/s12021-009-9057-y
91. PA Yushkevich J Piven HC Hazlett RG Smith S Ho JC Gee, et al. 2006 User-guided 3D active contour segmentation of anatomical structures: significantly improved efficiency and reliability Neuroimage 31 3 1116 1128 16545965 10.1016/j.neuroimage.2006.01.015 (Pubitemid 43851334)
92. Y Zhang X Zhou J Lu J Lichtman D Adjeroh ST Wong 2008 3D axon structure extraction and analysis in confocal fluorescence microscopy images Neural Computation 20 8 1899 1927 18336075 10.1162/neco.2008.05-07-519
93. Zhao, T., Xie, J., Amat, F., Clack, N., Ahammad, P., Peng, H., et al. (2011). Automated reconstruction of neuronal morphology based on local geometrical and global structural models. Neuroinformatics. doi: 10.1007/s12021-011-9120-3.
94. H Zong JS Espinosa HH Su MD Muzumdar L Luo 2005 Mosaic analysis with double markers in mice Cell 121 3 479 492 15882628 10.1016/j.cell.2005.02.012 1:CAS:528:DC%2BD2MXktlShsr0%3D (Pubitemid 40692306)