An automated pipeline for dendrite spine detection and tracking of 3D optical microscopy neuron images of in vivo mouse models

Neuroinformatics

Volumn 7, Issue 2, 2009, Pages 113-130

  Fan, Jing ^a,b   Zhou, Xiaobo ^c   Dy, Jennifer G ^b   Zhang, Yong ^a   Wong, Stephen T C ^a  

^a HOUSTON METHODIST HOSPITAL   (United States)

^b Northeastern University   (United States)

^c WEILL CORNELL MEDICAL COLLEGE   (United States)

Author keywords

Dendrite spine detection; In vivo image; Level set; Quantification; Tracking

Indexed keywords

ALGORITHM; ALZHEIMER DISEASE; ANIMAL; ARTICLE; DENDRITIC SPINE; DISEASE MODEL; IMAGE PROCESSING; METHODOLOGY; MOUSE; MULTIPHOTON MICROSCOPY; NERVE CELL; PATHOLOGY; STATISTICAL MODEL; THREE DIMENSIONAL IMAGING; TIME; ULTRASTRUCTURE;

ALGORITHMS; ALZHEIMER DISEASE; ANIMALS; DENDRITIC SPINES; DISEASE MODELS, ANIMAL; IMAGE PROCESSING, COMPUTER-ASSISTED; IMAGING, THREE-DIMENSIONAL; LIKELIHOOD FUNCTIONS; MICE; MICROSCOPY, FLUORESCENCE, MULTIPHOTON; NEURONS; TIME FACTORS;

EID: 67651236909     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-009-9047-0     Document Type: Article

References (25)

1. 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 6 171 187 10.1109/TITB.2002.1006304 12075671 10.1109/TITB.2002.1006304 (Pubitemid 34799098)
2. Bertsekas, D.P. (2000) Dynamic programming and optimal control, Vols. 1 & 2, 2nd ed. Athena Scientific.
3. P Besl N McKay 1992 A method for registration of 3-D shapes IEEE Transactions on Pattern Analysis and Machine Intelligence 14 239 256 10.1109/34.121791 10.1109/34.121791
4. JN Bourne KM Harris 2008 Balancing structure and function at hippocampal dendritic spines Annual Review of Neuroscience 31 47 67 10.1146/annurev.neuro. 31.060407.125646 18284372 10.1146/annurev.neuro.31.060407.125646 1:CAS:528:DC%2BD1cXpt12nsr4%3D
5. JE Bresenham 1965 Algorithm for computer control of a digital plotter IBM Syst. 4 25 30
6. S Carsten 1998 An unbiased detector of curvilinear structures IEEE Transactions on Pattern Analysis and Machine Intelligence 20 113 125 10.1109/34.659930 10.1109/34.659930
7. TF Chan L Vese 2001 Active contours without edges IEEE Transactions on Image Processing 10 266 277 10.1109/83.902291 18249617 10.1109/83.902291 1:STN:280:DC%2BD1c%2FptFeltA%3D%3D (Pubitemid 32254596)
8. J Cheng X Zhou E Miller MR Witt J Zhu BL Sabatini STC Wong 2007 A novel computational approach for automatic dendrite spines detection in two-photon laser scan microscopy Journal of Neuroscience Methods 165 122 134 10.1016/j.jneumeth.2007.05.020 17629570 10.1016/j.jneumeth.2007.05.020 (Pubitemid 47077498)
9. SF Gibson F Lanni 1991 Experimental test of an analytical model of aberration in an oil-immersion objective lens used in three-dimensional light microscopy J Opt Soc Am A 8 1601 1613 10.1364/JOSAA.8.001601 10.1364/JOSAA.8.001601 1:CAS:528:DyaK3MXms1Gmurc%3D
10. Hell, P., & Nesetril, J.(2004) Graphs and homeomorphisms. Oxford Lecture Series in Mathematics and its Applications 28. Oxford University Press.
11. JH Jang KS Hong 2002 Detection of curvilinear structures and reconstruction of their regions in gray-scale images Pattern Recognition 35 807 824 10.1016/S0031-3203(01) 00073-5 10.1016/S0031-3203(01)00073-5
12. Kay, S.M. (1993) Fundamentals of Statistical Signal Processing: Estimation Theory. Prentice Hall.
13. IYY Koh WB Lindquist K Zito EA Nimchinsky K Svoboda 2002 An image analysis algorithm for dendritic spines Neural Computation 14 1283 1310 10.1162/089976602753712945 12020447 10.1162/089976602753712945
14. Li, C., Kao, C. Y., Gore, J. C., & Ding, Z. (2007). Implicit active contour driven by local binary fitting energy. MN: IEEE Conf. Comput. Vis Pattern Recognition. Minneapolis, Mn, 2007.
15. A Mizrahi J Lu R Irving G Feng LC Katz 2006 In vivo imaging of juxtaglomerular neuron turnover in the mouse olfactory bulb Proceedings of the National Academy of Sciences of the United States of America 103 1912 1917 10.1073/pnas.0506297103 16446451 10.1073/pnas.0506297103 1:CAS:528: DC%2BD28XhslehtLc%3D (Pubitemid 43228792)
16. Mosaliganti, K.P., Janoos, F., Xu, X., Machiraju, R., Huang, K., & Wong, S.T.C.(2006) Temporal matching of dendritic spines in confocal Microscopy images of neuronal tissue sections. MICCAI 2006 Proceedings. Copenhagen, Denmark. 106-113.
17. N Otsu 1979 A threshold selection method from gray-level histogram IEEE Transactions on Systems, Man, and Cybernetics 9 62 66 10.1109/TSMC.1979.4310076 10.1109/TSMC.1979.4310076
18. Peters, A., Palay, S.L., & Webster, H.(1991) The fine structure of the nervous system: neurons and their supporting cells. Oxford University Press.
19. M Segal 2005 Dendritic spines and long-term plasticity Nature Reviews. Neuroscience 6 277 284 10.1038/nrn1649 15803159 10.1038/nrn1649 1:CAS:528:DC%2BD2MXivVartr4%3D (Pubitemid 40469982)
20. TL Spires-Jones M Meyer-Luehmann JD Osetek PB Jones EA Stern BJ Bacskai BT Hyman 2007 Impaired spine stability underlies plaque-related spine loss in an Alzheimer's disease mouse model American Journal of Pathology 171 1304 1311 10.2353/ajpath.2007.070055 17717139 10.2353/ajpath.2007.070055 1:CAS:528:DC%2BD2sXht1SmtrzL (Pubitemid 47582903)
21. TL Spires M Meyer-Luehmann EA Stern PJ McLean J Skoch PT Nguyen BJ Bacskai BT Hyman 2005 Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy The Journal of Neuroscience 25 7278 7287 10.1523/JNEUROSCI.1879-05. 2005 16079410 10.1523/JNEUROSCI.1879-05.2005 1:CAS:528:DC%2BD2MXnvVWgt7s%3D (Pubitemid 41113944)
22. G Xiong X Zhou A Degterev L Ji STC Wong 2006 Automated neurite labeling and analysis in fluorescence microscopy images Cytometry Part A. 69A 494 505 10.1002/cyto.a.20296 (Pubitemid 44651336)
23. X Yang H Li X Zhou 2006 Nuclei segmentation using marker-controlled watershed, tracking using mean-shift and Kalman filter in time-lapse microscopy IEEE Trans. on Circuits and Systems I. 53 2405 2414 10.1109/TCSI.2006.884469 10.1109/TCSI.2006.884469 (Pubitemid 44829051)
24. Y Zhang X Zhou R Witt B Sabatini D Adjeroh STC Wong 2007 Dendritic spine detection using curvilinear structure detection and LDA classifier NeuroImage 36 346 360 10.1016/j.neuroimage.2007.02.044 17448688 10.1016/j.neuroimage.2007.02. 044 (Pubitemid 46722687)
25. Zhou, W., Li, H., & Zhou, X. (2008). 3D Dendrite Reconstruction and Spine Identification. MICCAI. New York, NY, 2008.