Abstract

A dendritic spine is a small membranous protrusion from a neuron's dendrite that typically receives input from a single synapse of an axon. Recent research shows that the morphological changes of dendritic spines have a close relationship with some specific diseases. The distribution of different dendritic spine phenotypes is a key indicator of such changes. Therefore, it is necessary to classify detected spines with different phenotypes online. Since the dendritic spines have complex three dimensional (3D) structures, current neuron morphological analysis approaches cannot classify the dendritic spines accurately with limited features. In this paper, we propose a novel semi-supervised learning approach in order to perform the online morphological classification of dendritic spines. Spines are detected by a new approach based on wavelet transform in the 3D space. A small training data set is chosen from the detected spines, which has the spines labeled by the neurobiologists. The remaining spines are then classified online by the semi-supervised learning (SSL) approach. Experimental results show that our method can quickly and accurately analyze neuron images with modest human intervention.

© 2014 Optical Society of America

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  1. S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
    [CrossRef] [PubMed]
  2. T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
    [CrossRef] [PubMed]
  3. D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).
  4. J. B. Pawley, Handbook of Biological Confocal Microscopy. 3rd ed., Springer, 988 (2006).
  5. E. A. Nimchinsky, B. L. Sabatini, and K. Svoboda, “Structure and function of dendritic spines,” Annu. Rev. Physiol.64(1), 313–353 (2002).
    [CrossRef] [PubMed]
  6. Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
    [CrossRef] [PubMed]
  7. J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
    [CrossRef] [PubMed]
  8. W. Bai, L. Ji, J. Cheng, and S.T.C. Wong, “Automated dendritic spine analysis in two-photon laser scanning microscopy images,” Cytometry A71(10), 9 (2007).
    [PubMed]
  9. F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
    [CrossRef] [PubMed]
  10. A. Rodriguez, D. L. Dickstein, P. R. Hof, and S. L. Wearne, “Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images,” PLOS one, 3(4), e1997 (2008).
  11. A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, “Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images,” Nat. Protoc.1(4), 2152–2161 (2006).
    [CrossRef] [PubMed]
  12. M. Matsuzaki, G. C. Ellis-Davies, and H. Kasai, “Three-dimensional mapping of unitary synaptic connections by two-photon macro photolysis of caged glutamate,” J. Neurophysiol.99(3), 1535–1544 (2008).
    [CrossRef] [PubMed]
  13. R. Yuste and W. Denk, “Dendritic spines as basic functional units of neuronal integration,” Nature375(6533), 682–684 (1995).
    [CrossRef] [PubMed]
  14. K. Svoboda and R. Yasuda, “Principles of two-photon excitation microscopy and its applications to neuroscience,” Neuron50(6), 823–839 (2006).
    [CrossRef] [PubMed]
  15. Q. Li, X. B. Zhou, Z. Deng, M. Baron, M. A. Teylan, Y. Kim, and S. T. C. Wong, A Novel Surface-based Geometric Approach for 3D Dendritic Spine Detection from Multi-phonton Excitation Microscopy Images, in The Sixth IEEE International Symposium on Biomedical Imaging. IEEE: Boston, MA, U.S. (2009).
  16. H. Hering and M. Sheng, “Dendritic spines: structure, dynamics and regulation,” Nat. Rev. Neurosci.2(12), 880–888 (2001).
    [CrossRef] [PubMed]
  17. Y. Hayashi and A. K. Majewska, “Dendritic spine geometry: functional implication and regulation,” Neuron46(4), 529–532 (2005).
    [CrossRef] [PubMed]
  18. O. Chapelle and A. Zien, Semi-Supervised Learning (Cambridge: MIT Press 2006).
  19. D. Zhou, T. N. Lal, J. Weston, and B. Scholkopf, Learning with Local and Global Consistency. Advances in Neural Information Processing Systems, 16, 321–8 (2004).
  20. P. E. Greenwood, A Guide to Chi-Squared Testing, 280 (John Wiley & Sons, 1996).
  21. A. Tashiro and R. Yuste, “Structure and molecular organization of dendritic spines,” Histol. Histopathol.18(2), 617–634 (2003).
    [PubMed]
  22. J. Shawe-Taylor and N. Crisianini, Support Vector Machines and Other Kernel-Based Learning Methods (Cambridge, UK: Cambridge University Press 2000).

2009

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
[CrossRef] [PubMed]

2008

A. Rodriguez, D. L. Dickstein, P. R. Hof, and S. L. Wearne, “Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images,” PLOS one, 3(4), e1997 (2008).

M. Matsuzaki, G. C. Ellis-Davies, and H. Kasai, “Three-dimensional mapping of unitary synaptic connections by two-photon macro photolysis of caged glutamate,” J. Neurophysiol.99(3), 1535–1544 (2008).
[CrossRef] [PubMed]

2007

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

W. Bai, L. Ji, J. Cheng, and S.T.C. Wong, “Automated dendritic spine analysis in two-photon laser scanning microscopy images,” Cytometry A71(10), 9 (2007).
[PubMed]

2006

A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, “Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images,” Nat. Protoc.1(4), 2152–2161 (2006).
[CrossRef] [PubMed]

K. Svoboda and R. Yasuda, “Principles of two-photon excitation microscopy and its applications to neuroscience,” Neuron50(6), 823–839 (2006).
[CrossRef] [PubMed]

2005

Y. Hayashi and A. K. Majewska, “Dendritic spine geometry: functional implication and regulation,” Neuron46(4), 529–532 (2005).
[CrossRef] [PubMed]

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

2003

A. Tashiro and R. Yuste, “Structure and molecular organization of dendritic spines,” Histol. Histopathol.18(2), 617–634 (2003).
[PubMed]

2002

E. A. Nimchinsky, B. L. Sabatini, and K. Svoboda, “Structure and function of dendritic spines,” Annu. Rev. Physiol.64(1), 313–353 (2002).
[CrossRef] [PubMed]

2001

H. Hering and M. Sheng, “Dendritic spines: structure, dynamics and regulation,” Nat. Rev. Neurosci.2(12), 880–888 (2001).
[CrossRef] [PubMed]

1999

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

1995

R. Yuste and W. Denk, “Dendritic spines as basic functional units of neuronal integration,” Nature375(6533), 682–684 (1995).
[CrossRef] [PubMed]

Adjeroh, D.

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

Alonso-Nanclares, L.

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Bacskai, B. J.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Bai, W.

W. Bai, L. Ji, J. Cheng, and S.T.C. Wong, “Automated dendritic spine analysis in two-photon laser scanning microscopy images,” Cytometry A71(10), 9 (2007).
[PubMed]

Cheng, J.

W. Bai, L. Ji, J. Cheng, and S.T.C. Wong, “Automated dendritic spine analysis in two-photon laser scanning microscopy images,” Cytometry A71(10), 9 (2007).
[PubMed]

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

DeFelipe, J.

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Denk, W.

R. Yuste and W. Denk, “Dendritic spines as basic functional units of neuronal integration,” Nature375(6533), 682–684 (1995).
[CrossRef] [PubMed]

Dickstein, D. L.

A. Rodriguez, D. L. Dickstein, P. R. Hof, and S. L. Wearne, “Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images,” PLOS one, 3(4), e1997 (2008).

Diehl, T.

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

Ehlenberger, D. B.

A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, “Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images,” Nat. Protoc.1(4), 2152–2161 (2006).
[CrossRef] [PubMed]

Ellis-Davies, G. C.

M. Matsuzaki, G. C. Ellis-Davies, and H. Kasai, “Three-dimensional mapping of unitary synaptic connections by two-photon macro photolysis of caged glutamate,” J. Neurophysiol.99(3), 1535–1544 (2008).
[CrossRef] [PubMed]

Fernaud-Espinosa, I.

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Ferrer, I.

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Gonzalez-Soriano, J.

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Hartley, D. M.

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

Hayashi, Y.

Y. Hayashi and A. K. Majewska, “Dendritic spine geometry: functional implication and regulation,” Neuron46(4), 529–532 (2005).
[CrossRef] [PubMed]

Hering, H.

H. Hering and M. Sheng, “Dendritic spines: structure, dynamics and regulation,” Nat. Rev. Neurosci.2(12), 880–888 (2001).
[CrossRef] [PubMed]

Hof, P. R.

A. Rodriguez, D. L. Dickstein, P. R. Hof, and S. L. Wearne, “Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images,” PLOS one, 3(4), e1997 (2008).

A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, “Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images,” Nat. Protoc.1(4), 2152–2161 (2006).
[CrossRef] [PubMed]

Huang, K.

F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
[CrossRef] [PubMed]

Hyman, B. T.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Janoos, F.

F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
[CrossRef] [PubMed]

Ji, L.

W. Bai, L. Ji, J. Cheng, and S.T.C. Wong, “Automated dendritic spine analysis in two-photon laser scanning microscopy images,” Cytometry A71(10), 9 (2007).
[PubMed]

Kasai, H.

M. Matsuzaki, G. C. Ellis-Davies, and H. Kasai, “Three-dimensional mapping of unitary synaptic connections by two-photon macro photolysis of caged glutamate,” J. Neurophysiol.99(3), 1535–1544 (2008).
[CrossRef] [PubMed]

Knafo, S.

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Machiraju, R.

F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
[CrossRef] [PubMed]

Majewska, A. K.

Y. Hayashi and A. K. Majewska, “Dendritic spine geometry: functional implication and regulation,” Neuron46(4), 529–532 (2005).
[CrossRef] [PubMed]

Matsuzaki, M.

M. Matsuzaki, G. C. Ellis-Davies, and H. Kasai, “Three-dimensional mapping of unitary synaptic connections by two-photon macro photolysis of caged glutamate,” J. Neurophysiol.99(3), 1535–1544 (2008).
[CrossRef] [PubMed]

McLean, P. J.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Merino-Serrais, P.

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Meyer-Luehmann, M.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Miller, E.

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

Nguyen, P. T.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Nimchinsky, E. A.

E. A. Nimchinsky, B. L. Sabatini, and K. Svoboda, “Structure and function of dendritic spines,” Annu. Rev. Physiol.64(1), 313–353 (2002).
[CrossRef] [PubMed]

Rodriguez, A.

A. Rodriguez, D. L. Dickstein, P. R. Hof, and S. L. Wearne, “Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images,” PLOS one, 3(4), e1997 (2008).

A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, “Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images,” Nat. Protoc.1(4), 2152–2161 (2006).
[CrossRef] [PubMed]

Sabatini, B. L.

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

E. A. Nimchinsky, B. L. Sabatini, and K. Svoboda, “Structure and function of dendritic spines,” Annu. Rev. Physiol.64(1), 313–353 (2002).
[CrossRef] [PubMed]

Selkoe, D. J.

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

Sheng, M.

H. Hering and M. Sheng, “Dendritic spines: structure, dynamics and regulation,” Nat. Rev. Neurosci.2(12), 880–888 (2001).
[CrossRef] [PubMed]

Skoch, J.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Spires, T. L.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Stern, E. A.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

Svoboda, K.

K. Svoboda and R. Yasuda, “Principles of two-photon excitation microscopy and its applications to neuroscience,” Neuron50(6), 823–839 (2006).
[CrossRef] [PubMed]

E. A. Nimchinsky, B. L. Sabatini, and K. Svoboda, “Structure and function of dendritic spines,” Annu. Rev. Physiol.64(1), 313–353 (2002).
[CrossRef] [PubMed]

Tashiro, A.

A. Tashiro and R. Yuste, “Structure and molecular organization of dendritic spines,” Histol. Histopathol.18(2), 617–634 (2003).
[PubMed]

Teplow, D. B.

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

Vasquez, S.

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

Vassilev, P.M.

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

Wearne, S. L.

A. Rodriguez, D. L. Dickstein, P. R. Hof, and S. L. Wearne, “Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images,” PLOS one, 3(4), e1997 (2008).

A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, “Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images,” Nat. Protoc.1(4), 2152–2161 (2006).
[CrossRef] [PubMed]

Witt, R. M.

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

Wong, S. T.

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

Wong, S. T. C.

F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
[CrossRef] [PubMed]

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

Wong, S.T.C.

W. Bai, L. Ji, J. Cheng, and S.T.C. Wong, “Automated dendritic spine analysis in two-photon laser scanning microscopy images,” Cytometry A71(10), 9 (2007).
[PubMed]

Xu, X.

F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
[CrossRef] [PubMed]

Yasuda, R.

K. Svoboda and R. Yasuda, “Principles of two-photon excitation microscopy and its applications to neuroscience,” Neuron50(6), 823–839 (2006).
[CrossRef] [PubMed]

Ye, C. P.

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

Yuste, R.

A. Tashiro and R. Yuste, “Structure and molecular organization of dendritic spines,” Histol. Histopathol.18(2), 617–634 (2003).
[PubMed]

R. Yuste and W. Denk, “Dendritic spines as basic functional units of neuronal integration,” Nature375(6533), 682–684 (1995).
[CrossRef] [PubMed]

Zhang, Y.

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

Zhou, X.

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

Zhu, J.

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

Annu. Rev. Physiol.

E. A. Nimchinsky, B. L. Sabatini, and K. Svoboda, “Structure and function of dendritic spines,” Annu. Rev. Physiol.64(1), 313–353 (2002).
[CrossRef] [PubMed]

Cereb. Cortex

S. Knafo, L. Alonso-Nanclares, J. Gonzalez-Soriano, P. Merino-Serrais, I. Fernaud-Espinosa, I. Ferrer, and J. DeFelipe, “Widespread changes in dendritic spines in a model of Alzheimer’s disease,” Cereb. Cortex19(3), 586–592 (2009).
[CrossRef] [PubMed]

Cytometry A

W. Bai, L. Ji, J. Cheng, and S.T.C. Wong, “Automated dendritic spine analysis in two-photon laser scanning microscopy images,” Cytometry A71(10), 9 (2007).
[PubMed]

Histol. Histopathol.

A. Tashiro and R. Yuste, “Structure and molecular organization of dendritic spines,” Histol. Histopathol.18(2), 617–634 (2003).
[PubMed]

J. Neurophysiol.

M. Matsuzaki, G. C. Ellis-Davies, and H. Kasai, “Three-dimensional mapping of unitary synaptic connections by two-photon macro photolysis of caged glutamate,” J. Neurophysiol.99(3), 1535–1544 (2008).
[CrossRef] [PubMed]

J. Neurosci.

T. L. Spires, M. Meyer-Luehmann, E. A. Stern, P. J. McLean, J. Skoch, P. T. Nguyen, B. J. Bacskai, and B. T. Hyman, “Dendritic spine abnormalities in amyloid precursor protein transgenic mice demonstrated by gene transfer and intravital multiphoton microscopy,” J. Neurosci.25(31), 7278–7287 (2005).
[CrossRef] [PubMed]

J. Neurosci. Methods

D. M. Hartley, C. P. Ye, T. Diehl, S. Vasquez, P.M. Vassilev, D. B. Teplow, and D. J. Selkoe, “Protofibrillar Intermediates of amyloid beta-protein induce acute electrophysiological changes and progressive neurotoxicity in cortical neurons,” J. Neurosci. Methods19(20), 9 (1999).

J. Cheng, E. Miller, R. M. Witt, J. Zhu, B. L. Sabatini, and S. T. C. Wong, “A novel computational approach for automated dendrite spines detection in two-photon laser scan microscopy,” J. Neurosci. Methods165(1), 13 (2007).
[CrossRef] [PubMed]

Med. Image Anal.

F. Janoos, X. Xu, R. Machiraju, K. Huang, and S. T. C. Wong, “Robust 3D reconstruction and identification of dendritic spines from optical microscopy imaging,” Med. Image Anal.13(1), 167–179 (2009).
[CrossRef] [PubMed]

Nat. Protoc.

A. Rodriguez, D. B. Ehlenberger, P. R. Hof, and S. L. Wearne, “Rayburst sampling, an algorithm for automated three-dimensional shape analysis from laser scanning microscopy images,” Nat. Protoc.1(4), 2152–2161 (2006).
[CrossRef] [PubMed]

Nat. Rev. Neurosci.

H. Hering and M. Sheng, “Dendritic spines: structure, dynamics and regulation,” Nat. Rev. Neurosci.2(12), 880–888 (2001).
[CrossRef] [PubMed]

Nature

R. Yuste and W. Denk, “Dendritic spines as basic functional units of neuronal integration,” Nature375(6533), 682–684 (1995).
[CrossRef] [PubMed]

Neuroimage

Y. Zhang, X. Zhou, R. M. Witt, B. L. Sabatini, D. Adjeroh, and S. T. Wong, “Dendritic spine detection using curvilinear structure detector and LDA classifier,” Neuroimage36(2), 346–360 (2007).
[CrossRef] [PubMed]

Neuron

K. Svoboda and R. Yasuda, “Principles of two-photon excitation microscopy and its applications to neuroscience,” Neuron50(6), 823–839 (2006).
[CrossRef] [PubMed]

Y. Hayashi and A. K. Majewska, “Dendritic spine geometry: functional implication and regulation,” Neuron46(4), 529–532 (2005).
[CrossRef] [PubMed]

PLOS one

A. Rodriguez, D. L. Dickstein, P. R. Hof, and S. L. Wearne, “Automated three-dimensional detection and shape classification of dendritic spines from fluorescence microscopy images,” PLOS one, 3(4), e1997 (2008).

Other

J. B. Pawley, Handbook of Biological Confocal Microscopy. 3rd ed., Springer, 988 (2006).

O. Chapelle and A. Zien, Semi-Supervised Learning (Cambridge: MIT Press 2006).

D. Zhou, T. N. Lal, J. Weston, and B. Scholkopf, Learning with Local and Global Consistency. Advances in Neural Information Processing Systems, 16, 321–8 (2004).

P. E. Greenwood, A Guide to Chi-Squared Testing, 280 (John Wiley & Sons, 1996).

Q. Li, X. B. Zhou, Z. Deng, M. Baron, M. A. Teylan, Y. Kim, and S. T. C. Wong, A Novel Surface-based Geometric Approach for 3D Dendritic Spine Detection from Multi-phonton Excitation Microscopy Images, in The Sixth IEEE International Symposium on Biomedical Imaging. IEEE: Boston, MA, U.S. (2009).

J. Shawe-Taylor and N. Crisianini, Support Vector Machines and Other Kernel-Based Learning Methods (Cambridge, UK: Cambridge University Press 2000).

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Figures (6)

Fig. 1
Fig. 1

Flowchart of the dendritic spine morphological analysis

Fig. 2
Fig. 2

Illustration of casting rays sampling. (a) Casting rays inside the dendrite, the green line and the red line represent the longest and shortest diameters casting inside the neuron. (b) Blue circles represent the estimated dendrite with casting rays diameters in different areas while the red curve represents the estimated center line of the dendrite. A magnified figure can be seen in (c).

Fig. 3
Fig. 3

Determination of the segmenting position.

Fig. 4
Fig. 4

Spine detection results after wavelet transform. (a) The original intensity map of each section, (b) The wavelet response map of each section. The sections are along a spine, and have 2 microns at intervals.

Fig. 5
Fig. 5

Examples of the predefined phenotypes, mushroom, thin, and stubby.

Fig.6
Fig.6

Error rates for morphological classification of dendritic spines. X coordinate denotes the portion of training samples in each class and Y coordinate shows the error rate for classification. The line marked with triangles denotes results classified into 3 categories and the line with circles denotes results obtained by the second classification of the phenotypes into 2 categories

Tables (3)

Tables Icon

Table 1 Comparison of spine detection results on the whole dataset

Tables Icon

Table 2 Average and std. deviation of features in morphological classification of dendritic spines. The unit of length is micron (µm), and the unit of angle is degree

Tables Icon

Table 3 Classification performance for the sample datasets of [10]. The size for the training dataset is set to 10% samples in each class

Equations (1)

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W ij =exp( c k x i / x j 2 2 σ 2 )=exp( k=1 d c k | x ik / x jk | 2 2 σ 2 )

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