Book Chapters

(2021-2025) (2016-2020) (2011-2016)

(2006-2010) (2001-2005) (1996-2000)

(1991-1995) (1986-1990) (1981-1985)

(2021 - 2025)

Chapter 18: Sensory Coding. T. Sharpee and D. Kleinfeld. In Principles in Neural Science, seventh edition; T. D. Albright and X. Wang, section eds.; E. Kandel, ed., 2024, McGraw Hill
The vibrissa sensorimotor system of rodents: A view from sensory thalamus. M. Deschênes and D. Kleinfeld. In The Thalamus. M. Halassa, ed. 2021, Oxford University Press.	PDF (0.4 Mb)

CNiFERs: Cell-based biosensors with nanoMolar sensitivity to in vivo changes in neuromodulation.
D. Kircher, E. Lacin, D. Kleinfeld and P. A. Slesinger In Compendium of In Vivo Monitoring in Real-Time Molecular Neuroscience, Volume 3: Probing Brain Function, Disease and Injury with Enhanced Optical and Electochemical Sensors. G. S. Wilson and A. C. Michael, eds., 2020, World Scientific Press, 2:19-32.

PDF (1.2 Mb)

(2011 - 2015)

The central pattern generator for rhythmic whisking. D. Kleinfeld, M. Deschênes and J. D. Moore In Sensorimotor Integration in the Whisker System, P. Krieger and A. Groh, eds., 2015, Springer, 7:1-17.	PDF (3.9 Mb)
Imaging vasodynamics in the awake mouse brain with two-photon microscopy. A. Y. Shih, P. J. Drew and D. Kleinfeld. In Neurovascular Coupling Methods, M. Zhao, H. Ma and T. H. Schwartz, eds, NEUROMETHODS series, Volume 88, W. Walz, series eds., 2014, Springer Science + Business Media, NY, 4:55-73.	PDF (1.2 Mb)
Two-photon microscopy to measure blood flow and concurrent brain cell activity. A. Y. Shih, J. D. Driscoll, M. J. Pesavento and D. Kleinfeld. In Optical Imaging of Cortical Dynamics, B. Weber and F. Helmchen, eds., 2013, Elsevier, NY, 16:273-290.	PDF (1.8 Mb)
Optically induced occlusion of single blood vessels in neocortex. A. Y. Shih, N. Nishimura, J. Nguyen, B. Friedman, P. D. Lyden, C. B. Schaffer and D. Kleinfeld. In Imaging in Neuroscience: A Laboratory Manual (Book 2), F. Helmchen and A. Konnerth, editors, R. Yuste, series editor, 2011, Cold Spring Harbor Laboratory Press, NY, 85:939-948.	PDF (1.1 Mb)
Two-photon imaging of blood flow in rat cortex. J. D. Driscoll, A. Y. Shih, P. J. Drew, I. Valmianski, G. Cauwenberghs and D. Kleinfeld. In Imaging in Neuroscience: A Laboratory Manual (Book 2), F. Helmchen and A. Konnerth, editors, R. Yuste, series editor, 2011, Cold Spring Harbor Laboratory Press, NY, 84:927-938.	PDF (1.7 Mb)
All-optical, in situ histology of brain tissue with femtosecond laser pulses. P. S. Tsai, P. Blinder, J. D. Squire and D. Kleinfeld. In Imaging in Neuroscience: A Laboratory Manual (Book 2), F. Helmchen and A. Konnerth, editors, R. Yuste, series editor, 2011, Cold Spring Harbor Laboratory Press, NY, Chapter 45, 437-446.	PDF (0.7 Mb)
Interferometric detection of action potentials in vitro. A. LaPorta and D. Kleinfeld. In Imaging in Neuroscience: A Laboratory Manual (Book 2), F. Helmchen and A. Konnerth, editors, R. Yuste, series editor, 2011, Cold Spring Harbor Laboratory Press, NY 20:195-200.	PDF (0.5 Mb)
Spectral methods for functional brain imaging. D. Kleinfeld and P. P. Mitra. In Imaging: A Laboratory Manual (Book 1) R. Yuste, editor and series editor, 2011, Cold Spring Harbor Laboratory Press, NY, Chapter 12, 143-158.	PDF (5.3 Mb)
Movie of raw calcium dynamics in figure 4A	AVI (11.5 Mb)
Movie of denoised calcium dynamics in figure 4B	AVI (11.5 Mb)

(2006 - 2010)

Monitoring integrated activity of individual neurons using FRET-based voltage-sensitive dyes. K. L. Briggman, W. B. Kristan, J. E. Gonsalez, D. Kleinfeld and R. Y. Tsien. In Membrane Potential Imaging in the Nervous System: Methods and Applications (M. Canepari and D. Zecevic, editors), 2010, Springer Press, Chapter 6. 61-70.	PDF (2.2 Mb)
Two-photon laser scanning microscopy as a tool to study cortical vasodynamics under normal and ischemic conditions. A. Devor, A. Y. Shih, P. S. Tsai, P. Blinder, P. Tian, I. C. Teng and D. Kleinfeld. In Imaging the Brain with Optical Methods, A. Roe, editor, 2009, Springer Press, 11:245-262.	PDF (0.6 Mb)
In vivo two-photon laser scanning microscopy with concurrent plasma-mediated ablation: Principles and hardware realization. P. S. Tsai and D. Kleinfeld. In Methods for In Vivo Optical Imaging, Second Edition, R. Frostig, editor, 2009, CRC Press, 3:59-115 (http://www.ncbi.nlm.nih.gov/books/NBK20231/).	PDF (7.1 Mb)
MPScope 2.0: A computer system for two-photon laser scanning microscopy with concurrent plasma-mediated ablation and electrophysiology. Q.-T. Nguyen, J. Driscoll, E. M. Dolnick and D. Kleinfeld. In Methods for In Vivo Optical Imaging, Second Edition, R. Frostig, editor, 2009, CRC Press, 4:117-142 (http://www.ncbi.nlm.nih.gov/books/NBK20235/).	PDF (1.6 Mb)
Computational intelligence in electrophysiology: Trends and open problems. C. Gunay, T. G. Smolinski, W. W. Lytton, T. M. Morse, P. Gleeson, S. Crook, V. Steuber, A. Silver, H. Voicu, P. Andrews, H. Bokil, H. Maniar, C. Loader, S. Mehta, D. Kleinfeld, D. Thomson, P. P. Mitra, G. Aaron and J.-M. Fellous. In Applications of Computational Intelligence in Biology, Current Trends and Open Problems, T. G. Smolinski, M. G. Milanova and A.-E. Hassanien, editors, 2008, Studies in Computational Intelligence, Springer 112:325-359 (2008).	PDF (9.1 Mb)
Application of spectral methods to representative data sets in electrophysiology and functional neuroimaging. D. Kleinfeld. In Syllabus for Society for Neuroscience Short Course III on "Neural Signal Processing: Quantitative Analysis of Neural Activity", 2008, Society for Neuroscience. 3:21-34	PDF (1.0 Mb)
Full Syllabus	PDF (3.7 Mb)
Presentation	PDF (34.4 Mb)
Targeted occlusion to surface and deep vessels in neocortex via linear and nonlinear optical absorption. D. Kleinfeld, B. Friedman, P. D. Lyden and A. Y. Shih. In Animal Models of Acute Neurological Injuries, J. Chen, Z. Xu, X.-M. Xu and J. Zhang, editors, 2008, Contemporary Neuroscience Series, The Humana Press, 14:169-185.	PDF (2.1 Mb)
Vibrissa movement, sensation and sensorimotor control. D. Kleinfeld. In The New Encyclopedia of Neuroscience, L. Squire, editor-in-chief, T. Albright, F. Bloom, F. Gage, N. Spitzer, senior editors, 2008, Elsevier.	PDF (2.3 Mb)
Pioneering applications of two-photon microscopy to mammalian neurophysiology: Seven case studies. Q.-T. Nguyen, G. O. Clay, N. Nishimura, C. B. Schaffer, L. F. Schroeder, P. S. Tsai and D. Kleinfeld. In Nonlinear Optical Microscopy Techniques and Applications (B. Masters and P. So, editors), 2008, Oxford Press, 28:715-734.	PDF (1.4 Mb)
Spike Sorting. D. N. Hill, D. Kleinfeld and S. B. Mehta. In Observed Brain Dynamics by P. P. Mitra and H. Bokil, 2007, Oxford Press, 9:257-270.	PDF (1.8 Mb)

(2001 - 2005)

Spectral analysis for dynamical imaging data. B. Pesarian, A. Sornborger, N. Nishimura, D. Kleinfeld and P.P. Mitra. In Imaging in Neuroscience and Development: A Laboratory Manual (R. Yuste and A. Konnerth, editors), 2005, Cold Spring Harbor Laboratory Press, NY, 57:439-444.	PDF (1.2 Mb)
All-optical, in situ histology of neuronal tissue with femtosecond laser pulses. P. S. Tsai, B. Friedman, C. B. Schaffer, J. A. Squier and D. Kleinfeld. In Imaging in Neuroscience and Development: A Laboratory Manual (R. Yuste and A. Konnerth, editors), 2005, Cold Spring Harbor Laboratory Press, NY, 102:815-826	PDF (1.6 Mb)
Two-photon imaging of cortical microcirculation. D. Kleinfeld and W. Denk. In Imaging in Neuroscience and Development: A Laboratory Manual (R. Yuste and A. Konnerth, editors), 2005, Cold Spring Harbor Laboratory Press, NY, 93:701-705.	PDF (0.5 Mb)
Interferometric detection of action potentials in vitro. A. LaPorta and D. Kleinfeld. In Imaging in Neuroscience and Development: A Laboratory Manual (R. Yuste and A. Konnerth, editors), 2005, Cold Spring Harbor Laboratory Press, NY, 72:539-543.	PDF (0.3 Mb)
Reproduced with updated references In Imaging in Neuroscience: A Laboratory Manual (Book 2), F. Helmchen and A. Konnerth, editors, R. Yuste, series editor, 2011, Cold Spring Harbor Laboratory Press, NY, Chapter 20, 195-199.	PDF (0.6 Mb)
Detection of action potentials in vitro by changes in refractive index. D. Kleinfeld and A. LaPorta. In Light Scattering Imaging of Neural Tissue Function (D. M. Rector and J. S. George, editors), 2005, Humana Press, in press.	PDF (0.4 Mb)
Cortical blood flow through individual capillaries in rat vibrissa S1 cortex: Stimulus induced changes in flow are comparable to the underlying fluctuations in flow. D. Kleinfeld. In Brain Activation and Cerebral Blood Flow Control (M. Tomita, editor), 2002, Excerpta Medica, International Congress Series 1235, Elsevier Science.	PDF (1.3 Mb)
Principles, design and construction of a two photon scanning microscope for in vitro and in vivo studies. P. S. Tsai, N. Nishimura, E. J. Yoder, A. White, E. Dolnick and D. Kleinfeld. In Methods for In Vivo Optical Imaging (R. Frostig, editor), 2002, CRC Press, pp. 113-171.	PDF (2.5 Mb)

(1996 - 2000)

Two-photon imaging of neocortical microcirculation. D. Kleinfeld and W. Denk. In Imaging Neurons: A Laboratory Manual (R. Yuste, F. Lanni, and A. Konnerth, editors), 1999, Cold Spring Harbor Laboratory Press, NY, pp. 23.1-23.15.	PDF (1.3 Mb)
Analysis of dynamic optical imaging data. P. P. Mitra, B. Pesaran, and D. Kleinfeld. In Imaging Neurons: A Laboratory Manual (R. Yuste, F. Lanni, and A. Konnerth, editors), 1999, Cold Spring Harbor Laboratory Press, NY, pp. 9.1-9.9.	PDF (0.8 Mb)

(1991 - 1995)

Phase coherence and computation in a neural network of coupled oscillators. H. Sompolinsky, D. Golomb and D. Kleinfeld. In Nonlinear Dynamics and Neuronal Networks (H. G. Schuster, editor), 1991, VCH, Weinheim, pp. 113-130.	PDF (1.1 Mb)
Small nervous systems and neural network models. D. Kleinfeld, H. J. Chiel and H. Sompolinsky. In Nonlinear Dynamics and Neuronal Networks (H. G. Schuster, editor), 1991, VCH, Weinheim, pp. 77-109.	PDF (2.0 Mb)

(1986 - 1990)

Associative network models for central pattern generators.
D. Kleinfeld and H. Sompolinsky. In Methods in Neuronal Modeling: From Synapses to Networks (C. Koch and I. Segev, editors), 1989, MIT Press, Cambridge, MA, pp. 195-246.

PDF (6.0 Mb)

Electron transfer reactions in bacterial photosynthesis: Charge recombination kinetics as a structure probe.
G. Feher, M. Y. Okamura and D. Kleinfeld. In Protein Structure: Molecular and Electronic Reactivity (R. Austin, B. Chance and H. Frauenfelder, editors), 1987, Springer-Verlag, New York, NY, pp. 399-421. Reproduced in "Biological Physics" (E.V. Mielczarek, E. Greenbaum, and R.S. Knox, editors), 1993, American Institute of Physics, New York, NY, pp. 388-410.

PDF (1.7 Mb)

(1981 - 1985)

Quinone binding sites in reaction centers from photosynthetic bacteria.
M. Y. Okamura, R. J. Debus, D. Kleinfeld and G. Feher. In Function of Quinones in Energy Conserving Systems (B. L. Trumpower, editor), 1982, Academic Press, New York, NY, pp. 299-317.

PDF (1.3 Mb)