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David Kleinfeld

Title(s)Researcher, Physics
SchoolAcademic Aff
Phone858-822-0342
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    Collapse Research 
    Collapse Research Activities and Funding
    Reverse Engineering the Brain Stem Circuits that Govern Exploratory Behavior
    NIH/NINDS U19NS107466Sep 15, 2018 - May 31, 2023
    Role: Principal Investigator
    Resilient versus fragile aspects of blood flow in the mammalian brain
    NIH/NINDS R35NS097265Dec 1, 2016 - Nov 30, 2024
    Role: Principal Investigator
    Resting state connectivity: Biophysical basis for and improved fMRI measurements
    NIH/NIMH R01MH111438Sep 16, 2016 - Jun 30, 2021
    Role: Principal Investigator
    Realization of Optical Cell-based Reporters for in vivo Detection of Neuropeptides
    NIH/NIMH R01MH111499Sep 9, 2016 - Jun 30, 2019
    Role: Principal Investigator
    Ultra-large field two-photon microscope to image transcortical brain dynamics
    NIH/NIMH R21MH108503May 1, 2015 - Jan 31, 2017
    Role: Principal Investigator
    Optogenetic mapping of synaptic activity and control of intracellular signaling
    NIH/NINDS U01NS090590Sep 30, 2014 - Jul 31, 2017
    Role: Principal Investigator
    Revealing the connectivity and functionality of brain stem circuits
    NIH/NINDS U01NS090595Sep 30, 2014 - Jul 31, 2017
    Role: Principal Investigator
    Defining the Logic of Neurovascular Signaling in the Brain
    NIH/NINDS DP1NS082097Sep 30, 2010 - Jul 31, 2015
    Role: Principal Investigator
    Defining the Logic of Neurovascular Signaling in the Brain
    NIH DP1OD006831Sep 30, 2010 - Jul 31, 2015
    Role: Principal Investigator
    CNiFERs Cell-based Neurotransmitter Fluorescent Engineered Reporters
    NIH/NIDA R01DA029706Jul 1, 2010 - Apr 30, 2015
    Role: Principal Investigator
    Neuronal Signaling, Network Topology, and Blood Flow Dynamics in Cortex
    NIH/NIMH R01MH085499Sep 1, 2008 - Jun 30, 2012
    Role: Principal Investigator
    Sentinel cells that report neural and neurovascular signaling
    NIH/NIDA R21DA024206Sep 20, 2007 - Aug 31, 2010
    Role: Principal Investigator
    Multi-scale mapping of 3D spatial-temporal cortical hemodynamics at the level of
    NIH/NINDS R21NS059832Jul 1, 2007 - May 31, 2010
    Role: Principal Investigator
    Sensorimotor Loops in Vibrissa Somatosensation
    NIH/NINDS R01NS058668Mar 1, 2007 - Apr 30, 2018
    Role: Principal Investigator
    Femtosecond Light to Manipulate Neurons and Vasculature
    NIH/NCRR R21RR021907Sep 15, 2005 - Jul 31, 2009
    Role: Principal Investigator
    All-Optical Histology for 3-D Cortical Reconstructions
    NIH/NIMH R21MH072570Feb 1, 2005 - Jan 31, 2008
    Role: Principal Investigator
    Manipulating Neural Tissue with Ultra-Short Laser Pulses
    NIH/NIBIB R01EB003832May 1, 2004 - Aug 31, 2015
    Role: Principal Investigator
    DEEP MULTI-PHOTON IMAGING OF BRAIN STRUCTURE &FUNCTION
    NIH/NINDS R01NS041096Sep 21, 2000 - Aug 31, 2004
    Role: Principal Investigator
    OPTICAL IMAGER FOR ELECTRICAL DYNAMICS IN CORTEX
    NIH/NCRR R21RR013419May 15, 2000 - Apr 30, 2003
    Role: Principal Investigator
    MOTOR MODULATION OF SENSORY INPUT IN RAT VIBRISSA CORTEX
    NIH/NIMH R01MH059867May 1, 2000 - Apr 30, 2005
    Role: Principal Investigator
    WORK GROUP ON NEURONAL DYNAMICS
    NIH/NIMH R13MH057000Jul 25, 1997 - Jun 30, 2002
    Role: Principal Investigator

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
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    1. Liu R, Li Z, Marvin JS, Kleinfeld D. Direct wavefront sensing enables functional imaging of infragranular axons and spines. Nat Methods. 2019 Jun 17. PMID: 31209383.
      View in: PubMed
    2. Smith AF, Doyeux V, Berg M, Peyrounette M, Haft-Javaherian M, Larue AE, Slater JH, Lauwers F, Blinder P, Tsai P, Kleinfeld D, Schaffer CB, Nishimura N, Davit Y, Lorthois S. Brain Capillary Networks Across Species: A few Simple Organizational Requirements Are Sufficient to Reproduce Both Structure and Function. Front Physiol. 2019; 10:233. PMID: 30971935.
      View in: PubMed
    3. Chen Y, McElvain LE, Tolpygo AS, Ferrante D, Friedman B, Mitra PP, Karten HJ, Freund Y, Kleinfeld D. An active texture-based digital atlas enables automated mapping of structures and markers across brains. Nat Methods. 2019 04; 16(4):341-350. PMID: 30858600.
      View in: PubMed
    4. Desjardins M, Kiliç K, Thunemann M, Mateo C, Holland D, Ferri CGL, Cremonesi JA, Li B, Cheng Q, Weldy KL, Saisan PA, Kleinfeld D, Komiyama T, Liu TT, Bussell R, Wong EC, Scadeng M, Dunn AK, Boas DA, Sakadžic S, Mandeville JB, Buxton RB, Dale AM, Devor A. Awake Mouse Imaging: From Two-Photon Microscopy to Blood Oxygen-Level Dependent Functional Magnetic Resonance Imaging. Biol Psychiatry Cogn Neurosci Neuroimaging. 2018 Dec 12. PMID: 30691968.
      View in: PubMed
    5. Kurnikova A, Deschênes M, Kleinfeld D. Functional brain stem circuits for control of nose motion. J Neurophysiol. 2019 Jan 01; 121(1):205-217. PMID: 30461370.
      View in: PubMed
    6. Hartung G, Vesel C, Morley R, Alaraj A, Sled J, Kleinfeld D, Linninger A. Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex. PLoS Comput Biol. 2018 11; 14(11):e1006549. PMID: 30452440.
      View in: PubMed
    7. Papadopoulos L, Blinder P, Ronellenfitsch H, Klimm F, Katifori E, Kleinfeld D, Bassett DS. Comparing two classes of biological distribution systems using network analysis. PLoS Comput Biol. 2018 09; 14(9):e1006428. PMID: 30192745.
      View in: PubMed
    8. He Y, Wang M, Chen X, Pohmann R, Polimeni JR, Scheffler K, Rosen BR, Kleinfeld D, Yu X. Ultra-Slow Single-Vessel BOLD and CBV-Based fMRI Spatiotemporal Dynamics and Their Correlation with Neuronal Intracellular Calcium Signals. Neuron. 2018 Feb 21; 97(4):925-939.e5. PMID: 29398359.
      View in: PubMed
    9. Mateo C, Knutsen PM, Tsai PS, Shih AY, Kleinfeld D. Entrainment of Arteriole Vasomotor Fluctuations by Neural Activity Is a Basis of Blood-Oxygenation-Level-Dependent "Resting-State" Connectivity. Neuron. 2017 Nov 15; 96(4):936-948.e3. PMID: 29107517.
      View in: PubMed
    10. Báez-Yánez MG, Ehses P, Mirkes C, Tsai PS, Kleinfeld D, Scheffler K. The impact of vessel size, orientation and intravascular contribution on the neurovascular fingerprint of BOLD bSSFP fMRI. Neuroimage. 2017 12; 163:13-23. PMID: 28890417.
      View in: PubMed
    11. McElvain LE, Friedman B, Karten HJ, Svoboda K, Wang F, Deschênes M, Kleinfeld D. Circuits in the rodent brainstem that control whisking in concert with other orofacial motor actions. Neuroscience. 2018 Jan 01; 368:152-170. PMID: 28843993.
      View in: PubMed
    12. Bellavance MA, Takatoh J, Lu J, Demers M, Kleinfeld D, Wang F, Deschênes M. Parallel Inhibitory and Excitatory Trigemino-Facial Feedback Circuitry for Reflexive Vibrissa Movement. Neuron. 2017 Aug 02; 95(3):722-723. PMID: 28772127.
      View in: PubMed
    13. Bellavance MA, Takatoh J, Lu J, Demers M, Kleinfeld D, Wang F, Deschênes M. Parallel Inhibitory and Excitatory Trigemino-Facial Feedback Circuitry for Reflexive Vibrissa Movement. Neuron. 2017 Aug 02; 95(3):673-682.e4. PMID: 28735746.
      View in: PubMed
    14. Knutsen PM, Mateo C, Kleinfeld D. Correction to 'Precision mapping of the vibrissa representation within murine primary somatosensory cortex'. Philos Trans R Soc Lond B Biol Sci. 2017 Apr 19; 372(1718). PMID: 28242742.
      View in: PubMed
    15. Kurnikova A, Moore JD, Liao SM, Deschênes M, Kleinfeld D. Coordination of Orofacial Motor Actions into Exploratory Behavior by Rat. Curr Biol. 2017 Mar 06; 27(5):688-696. PMID: 28216320.
      View in: PubMed
    16. Schmid F, Tsai PS, Kleinfeld D, Jenny P, Weber B. Depth-dependent flow and pressure characteristics in cortical microvascular networks. PLoS Comput Biol. 2017 02; 13(2):e1005392. PMID: 28196095.
      View in: PubMed
    17. Gould IG, Tsai P, Kleinfeld D, Linninger A. The capillary bed offers the largest hemodynamic resistance to the cortical blood supply. J Cereb Blood Flow Metab. 2017 01; 37(1):52-68. PMID: 27780904.
      View in: PubMed
    18. Uhlirova H, Kiliç K, Tian P, Sakadžic S, Gagnon L, Thunemann M, Desjardins M, Saisan PA, Nizar K, Yaseen MA, Hagler DJ, Vandenberghe M, Djurovic S, Andreassen OA, Silva GA, Masliah E, Kleinfeld D, Vinogradov S, Buxton RB, Einevoll GT, Boas DA, Dale AM, Devor A. The roadmap for estimation of cell-type-specific neuronal activity from non-invasive measurements. Philos Trans R Soc Lond B Biol Sci. 2016 10 05; 371(1705). PMID: 27574309.
      View in: PubMed
    19. Knutsen PM, Mateo C, Kleinfeld D. Precision mapping of the vibrissa representation within murine primary somatosensory cortex. Philos Trans R Soc Lond B Biol Sci. 2016 10 05; 371(1705). PMID: 27574305.
      View in: PubMed
    20. Kleinfeld D. Roger Tsien 1952-2016. Nat Neurosci. 2016 09 27; 19(10):1269-70. PMID: 27669983.
      View in: PubMed
    21. Aljadeff J, Lansdell BJ, Fairhall AL, Kleinfeld D. Analysis of Neuronal Spike Trains, Deconstructed. Neuron. 2016 07 20; 91(2):221-59. PMID: 27477016.
      View in: PubMed
    22. Uhlirova H, Kiliç K, Tian P, Thunemann M, Desjardins M, Saisan PA, Sakadžic S, Ness TV, Mateo C, Cheng Q, Weldy KL, Razoux F, Vandenberghe M, Cremonesi JA, Ferri CG, Nizar K, Sridhar VB, Steed TC, Abashin M, Fainman Y, Masliah E, Djurovic S, Andreassen OA, Silva GA, Boas DA, Kleinfeld D, Buxton RB, Einevoll GT, Dale AM, Devor A. Cell type specificity of neurovascular coupling in cerebral cortex. Elife. 2016 05 31; 5. PMID: 27244241; PMCID: PMC4933561.
      View in: PubMed, PubMed Central
    23. Deschênes M, Kurnikova A, Elbaz M, Kleinfeld D. Circuits in the Ventral Medulla That Phase-Lock Motoneurons for Coordinated Sniffing and Whisking. Neural Plast. 2016; 2016:7493048. PMID: 27293905; PMCID: PMC4887653.
      View in: PubMed, PubMed Central
    24. Lacin E, Muller A, Fernando M, Kleinfeld D, Slesinger PA. Construction of Cell-based Neurotransmitter Fluorescent Engineered Reporters (CNiFERs) for Optical Detection of Neurotransmitters In Vivo. J Vis Exp. 2016 May 12; (111). PMID: 27214050.
      View in: PubMed
    25. Deschênes M, Takatoh J, Kurnikova A, Moore JD, Demers M, Elbaz M, Furuta T, Wang F, Kleinfeld D. Inhibition, Not Excitation, Drives Rhythmic Whisking. Neuron. 2016 04 20; 90(2):374-87. PMID: 27041498; PMCID: PMC4929009 [Available on 03/20/17].
      View in: PubMed, PubMed Central
    26. Akassoglou K, Agalliu D, Chang CJ, Davalos D, Grutzendler J, Hillman EM, Khakh BS, Kleinfeld D, McGavern DB, Nelson SJ, Zlokovic BV. Neurovascular and Immuno-Imaging: From Mechanisms to Therapies. Proceedings of the Inaugural Symposium. Front Neurosci. 2016; 10:46. PMID: 26941593; PMCID: PMC4761864.
      View in: PubMed, PubMed Central
    27. Kleinfeld D, Deschênes M, Ulanovsky N. Whisking, Sniffing, and the Hippocampal ?-Rhythm: A Tale of Two Oscillators. PLoS Biol. 2016 Feb; 14(2):e1002385. PMID: 26890361.
      View in: PubMed
    28. Moore JD, Mercer Lindsay N, Deschênes M, Kleinfeld D. Vibrissa Self-Motion and Touch Are Reliably Encoded along the Same Somatosensory Pathway from Brainstem through Thalamus. PLoS Biol. 2015; 13(9):e1002253. PMID: 26393890.
      View in: PubMed
    29. Tsai PS, Mateo C, Field JJ, Schaffer CB, Anderson ME, Kleinfeld D. Ultra-large field-of-view two-photon microscopy. Opt Express. 2015 Jun 01; 23(11):13833-47. PMID: 26072755; PMCID: PMC4523368.
      View in: PubMed, PubMed Central
    30. Moore JD, Deschênes M, Kleinfeld D. Juxtacellular Monitoring and Localization of Single Neurons within Sub-cortical Brain Structures of Alert, Head-restrained Rats. J Vis Exp. 2015 Apr 27; (98). PMID: 25938559.
      View in: PubMed
    31. Kleinfeld D, Moore JD, Wang F, Deschênes M. The Brainstem Oscillator for Whisking and the Case for Breathing as the Master Clock for Orofacial Motor Actions. Cold Spring Harb Symp Quant Biol. 2014; 79:29-39. PMID: 25876629; PMCID: PMC4924579.
      View in: PubMed, PubMed Central
    32. Whiteley SJ, Knutsen PM, Matthews DW, Kleinfeld D. Deflection of a vibrissa leads to a gradient of strain across mechanoreceptors in a mystacial follicle. J Neurophysiol. 2015 Jul; 114(1):138-45. PMID: 25855692.
      View in: PubMed
    33. Shih AY, Rühlmann C, Blinder P, Devor A, Drew PJ, Friedman B, Knutsen PM, Lyden PD, Mateo C, Mellander L, Nishimura N, Schaffer CB, Tsai PS, Kleinfeld D. Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture. Microcirculation. 2015 Apr; 22(3):204-218. PMID: 25705966; PMCID: PMC4393797.
      View in: PubMed, PubMed Central
    34. Hussain T, Mastrodimos MB, Raju SC, Glasgow HL, Whitney M, Friedman B, Moore JD, Kleinfeld D, Steinbach P, Messer K, Pu M, Tsien RY, Nguyen QT. Fluorescently labeled peptide increases identification of degenerated facial nerve branches during surgery and improves functional outcome. PLoS One. 2015; 10(3):e0119600. PMID: 25751149; PMCID: PMC4353702.
      View in: PubMed, PubMed Central
    35. Matthews DW, Deschênes M, Furuta T, Moore JD, Wang F, Karten HJ, Kleinfeld D. Feedback in the brainstem: an excitatory disynaptic pathway for control of whisking. J Comp Neurol. 2015 Apr 15; 523(6):921-42. PMID: 25503925; PMCID: PMC4329057.
      View in: PubMed, PubMed Central
    36. Briggman KL, Kristan WB, González JE, Kleinfeld D, Tsien RY. Monitoring Integrated Activity of Individual Neurons Using FRET-Based Voltage-Sensitive Dyes. Adv Exp Med Biol. 2015; 859:149-69. PMID: 26238052.
      View in: PubMed
    37. Haidarliu S, Kleinfeld D, Deschênes M, Ahissar E. The Musculature That Drives Active Touch by Vibrissae and Nose in Mice. Anat Rec (Hoboken). 2015 Jul; 298(7):1347-58. PMID: 25408106; PMCID: PMC4930880.
      View in: PubMed, PubMed Central
    38. Muller A, Joseph V, Slesinger PA, Kleinfeld D. Cell-based reporters reveal in vivo dynamics of dopamine and norepinephrine release in murine cortex. Nat Methods. 2014 Dec; 11(12):1245-52. PMID: 25344639; PMCID: PMC4245316.
      View in: PubMed, PubMed Central
    39. Deschênes M, Haidarliu S, Demers M, Moore J, Kleinfeld D, Ahissar E. Muscles involved in naris dilation and nose motion in rat. Anat Rec (Hoboken). 2015 Mar; 298(3):546-53. PMID: 25257748; PMCID: PMC4929008.
      View in: PubMed, PubMed Central
    40. Moore JD, Deschênes M, Kurnikova A, Kleinfeld D. Activation and measurement of free whisking in the lightly anesthetized rodent. Nat Protoc. 2014 Aug; 9(8):1792-802. PMID: 24992095; PMCID: PMC4934662.
      View in: PubMed, PubMed Central
    41. Moore JD, Kleinfeld D, Wang F. How the brainstem controls orofacial behaviors comprised of rhythmic actions. Trends Neurosci. 2014 Jul; 37(7):370-80. PMID: 24890196; PMCID: PMC4100695.
      View in: PubMed, PubMed Central
    42. Kleinfeld D, Deschênes M, Wang F, Moore JD. More than a rhythm of life: breathing as a binder of orofacial sensation. Nat Neurosci. 2014 May; 17(5):647-51. PMID: 24762718; PMCID: PMC4140942.
      View in: PubMed, PubMed Central
    43. Kleinfeld D, Mitra PP. Spectral methods for functional brain imaging. Cold Spring Harb Protoc. 2014 Mar 01; 2014(3):248-62. PMID: 24591695.
      View in: PubMed
    44. Shih AY, Nishimura N, Nguyen J, Friedman B, Lyden PD, Schaffer CB, Kleinfeld D. Optically induced occlusion of single blood vessels in rodent neocortex. Cold Spring Harb Protoc. 2013 Dec 01; 2013(12):1153-60. PMID: 24298038.
      View in: PubMed
    45. Haidarliu S, Kleinfeld D, Ahissar E. Mediation of muscular control of rhinarial motility in rats by the nasal cartilaginous skeleton. Anat Rec (Hoboken). 2013 Dec; 296(12):1821-32. PMID: 24249396; PMCID: PMC4157211.
      View in: PubMed, PubMed Central
    46. Devor A, Bandettini PA, Boas DA, Bower JM, Buxton RB, Cohen LB, Dale AM, Einevoll GT, Fox PT, Franceschini MA, Friston KJ, Fujimoto JG, Geyer MA, Greenberg JH, Halgren E, Hämäläinen MS, Helmchen F, Hyman BT, Jasanoff A, Jernigan TL, Judd LL, Kim SG, Kleinfeld D, Kopell NJ, Kutas M, Kwong KK, Larkum ME, Lo EH, Magistretti PJ, Mandeville JB, Masliah E, Mitra PP, Mobley WC, Moskowitz MA, Nimmerjahn A, Reynolds JH, Rosen BR, Salzberg BM, Schaffer CB, Silva GA, So PT, Spitzer NC, Tootell RB, Van Essen DC, Vanduffel W, Vinogradov SA, Wald LL, Wang LV, Weber B, Yodh AG. The challenge of connecting the dots in the B.R.A.I.N. Neuron. 2013 Oct 16; 80(2):270-4. PMID: 24139032.
      View in: PubMed
    47. Jeong DC, Tsai PS, Kleinfeld D. All-optical osteotomy to create windows for transcranial imaging in mice. Opt Express. 2013 Oct 07; 21(20):23160-8. PMID: 24104230.
      View in: PubMed
    48. Lin JY, Knutsen PM, Muller A, Kleinfeld D, Tsien RY. ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation. Nat Neurosci. 2013 Oct; 16(10):1499-508. PMID: 23995068; PMCID: PMC3793847.
      View in: PubMed, PubMed Central
    49. Driscoll JD, Shih AY, Drew PJ, Cauwenberghs G, Kleinfeld D. Two-photon imaging of blood flow in the rat cortex. Cold Spring Harb Protoc. 2013 Aug 01; 2013(8):759-67. PMID: 23906919.
      View in: PubMed
    50. Blinder P, Tsai PS, Kaufhold JP, Knutsen PM, Suhl H, Kleinfeld D. The cortical angiome: an interconnected vascular network with noncolumnar patterns of blood flow. Nat Neurosci. 2013 Jul; 16(7):889-97. PMID: 23749145.
      View in: PubMed
    51. Moore JD, Deschênes M, Furuta T, Huber D, Smear MC, Demers M, Kleinfeld D. Hierarchy of orofacial rhythms revealed through whisking and breathing. Nature. 2013 May 09; 497(7448):205-10. PMID: 23624373; PMCID: PMC4159559.
      View in: PubMed, PubMed Central
    52. Tsai PS, Blinder P, Squier JA, Kleinfeld D. All-optical in situ histology of brain tissue with femtosecond laser pulses. Cold Spring Harb Protoc. 2013 Apr 01; 2013(4):327-34. PMID: 23547156.
      View in: PubMed
    53. Shih AY, Blinder P, Tsai PS, Friedman B, Stanley G, Lyden PD, Kleinfeld D. The smallest stroke: occlusion of one penetrating vessel leads to infarction and a cognitive deficit. Nat Neurosci. 2013 Jan; 16(1):55-63. PMID: 23242312; PMCID: PMC3952571.
      View in: PubMed, PubMed Central
    54. Kaufhold JP, Tsai PS, Blinder P, Kleinfeld D. Vectorization of optically sectioned brain microvasculature: learning aids completion of vascular graphs by connecting gaps and deleting open-ended segments. Med Image Anal. 2012 Aug; 16(6):1241-58. PMID: 22854035; PMCID: PMC3443315.
      View in: PubMed, PubMed Central
    55. Haidarliu S, Golomb D, Kleinfeld D, Ahissar E. Dorsorostral snout muscles in the rat subserve coordinated movement for whisking and sniffing. Anat Rec (Hoboken). 2012 Jul; 295(7):1181-91. PMID: 22641389; PMCID: PMC4153473.
      View in: PubMed, PubMed Central
    56. Shih AY, Mateo C, Drew PJ, Tsai PS, Kleinfeld D. A polished and reinforced thinned-skull window for long-term imaging of the mouse brain. J Vis Exp. 2012 Mar 07; (61). PMID: 22433225; PMCID: PMC3460568.
      View in: PubMed, PubMed Central
    57. LaPorta A, Kleinfeld D. Interferometric detection of action potentials. Cold Spring Harb Protoc. 2012 Mar 01; 2012(3):307-11. PMID: 22383643.
      View in: PubMed
    58. Shih AY, Driscoll JD, Drew PJ, Nishimura N, Schaffer CB, Kleinfeld D. Two-photon microscopy as a tool to study blood flow and neurovascular coupling in the rodent brain. J Cereb Blood Flow Metab. 2012 Jul; 32(7):1277-309. PMID: 22293983; PMCID: PMC3390800.
      View in: PubMed, PubMed Central
    59. Deschênes M, Moore J, Kleinfeld D. Sniffing and whisking in rodents. Curr Opin Neurobiol. 2012 Apr; 22(2):243-50. PMID: 22177596.
      View in: PubMed
    60. Jeong DC, Tsai PS, Kleinfeld D. Prospect for feedback guided surgery with ultra-short pulsed laser light. Curr Opin Neurobiol. 2012 Feb; 22(1):24-33. PMID: 22088392; PMCID: PMC3763077.
      View in: PubMed, PubMed Central
    61. Kleinfeld D, Bharioke A, Blinder P, Bock DD, Briggman KL, Chklovskii DB, Denk W, Helmstaedter M, Kaufhold JP, Lee WC, Meyer HS, Micheva KD, Oberlaender M, Prohaska S, Reid RC, Smith SJ, Takemura S, Tsai PS, Sakmann B. Large-scale automated histology in the pursuit of connectomes. J Neurosci. 2011 Nov 09; 31(45):16125-38. PMID: 22072665; PMCID: PMC3758571.
      View in: PubMed, PubMed Central
    62. Kleinfeld D, Deschênes M. Neuronal basis for object location in the vibrissa scanning sensorimotor system. Neuron. 2011 Nov 03; 72(3):455-68. PMID: 22078505; PMCID: PMC3971931.
      View in: PubMed, PubMed Central
    63. Hill DN, Curtis JC, Moore JD, Kleinfeld D. Primary motor cortex reports efferent control of vibrissa motion on multiple timescales. Neuron. 2011 Oct 20; 72(2):344-56. PMID: 22017992.
      View in: PubMed
    64. Hill DN, Mehta SB, Kleinfeld D. Quality metrics to accompany spike sorting of extracellular signals. J Neurosci. 2011 Jun 15; 31(24):8699-705. PMID: 21677152; PMCID: PMC3123734.
      View in: PubMed, PubMed Central
    65. Drew PJ, Shih AY, Kleinfeld D. Fluctuating and sensory-induced vasodynamics in rodent cortex extend arteriole capacity. Proc Natl Acad Sci U S A. 2011 May 17; 108(20):8473-8. PMID: 21536897; PMCID: PMC3100929.
      View in: PubMed, PubMed Central
    66. Kleinfeld D, Blinder P, Drew PJ, Driscoll JD, Muller A, Tsai PS, Shih AY. A guide to delineate the logic of neurovascular signaling in the brain. Front Neuroenergetics. 2011; 3:1. PMID: 21559095; PMCID: PMC3085135.
      View in: PubMed, PubMed Central
    67. Driscoll JD, Shih AY, Iyengar S, Field JJ, White GA, Squier JA, Cauwenberghs G, Kleinfeld D. Photon counting, censor corrections, and lifetime imaging for improved detection in two-photon microscopy. J Neurophysiol. 2011 Jun; 105(6):3106-13. PMID: 21471395.
      View in: PubMed
    68. Yamauchi JG, Nemecz Á, Nguyen QT, Muller A, Schroeder LF, Talley TT, Lindstrom J, Kleinfeld D, Taylor P. Characterizing ligand-gated ion channel receptors with genetically encoded Ca2++ sensors. PLoS One. 2011 Jan 28; 6(1):e16519. PMID: 21305050; PMCID: PMC3030600.
      View in: PubMed, PubMed Central
    69. Vitek DN, Block E, Bellouard Y, Adams DE, Backus S, Kleinfeld D, Durfee CG, Squier JA. Spatio-temporally focused femtosecond laser pulses for nonreciprocal writing in optically transparent materials. Opt Express. 2010 Nov 22; 18(24):24673-8. PMID: 21164813; PMCID: PMC4157520.
      View in: PubMed, PubMed Central
    70. Field JJ, Sheetz KE, Chandler EV, Hoover EE, Young MD, Ding SY, Sylvester AW, Kleinfeld D, Squier JA. Differential Multiphoton Laser Scanning Microscopy. IEEE J Sel Top Quantum Electron. 2012 Jan-Feb; 18(1):14-28. PMID: 27390511.
      View in: PubMed
    71. Drew PJ, Shih AY, Driscoll JD, Knutsen PM, Blinder P, Davalos D, Akassoglou K, Tsai PS, Kleinfeld D. Chronic optical access through a polished and reinforced thinned skull. Nat Methods. 2010 Dec; 7(12):981-4. PMID: 20966916; PMCID: PMC3204312.
      View in: PubMed, PubMed Central
    72. Vitek DN, Adams DE, Johnson A, Tsai PS, Backus S, Durfee CG, Kleinfeld D, Squier JA. Temporally focused femtosecond laser pulses for low numerical aperture micromachining through optically transparent materials. Opt Express. 2010 Aug 16; 18(17):18086-94. PMID: 20721196; PMCID: PMC3408926.
      View in: PubMed, PubMed Central
    73. Valmianski I, Shih AY, Driscoll JD, Matthews DW, Freund Y, Kleinfeld D. Automatic identification of fluorescently labeled brain cells for rapid functional imaging. J Neurophysiol. 2010 Sep; 104(3):1803-11. PMID: 20610792; PMCID: PMC2944673.
      View in: PubMed, PubMed Central
    74. Blinder P, Shih AY, Rafie C, Kleinfeld D. Topological basis for the robust distribution of blood to rodent neocortex. Proc Natl Acad Sci U S A. 2010 Jul 13; 107(28):12670-5. PMID: 20616030; PMCID: PMC2906564.
      View in: PubMed, PubMed Central
    75. Field JJ, Carriles R, Sheetz KE, Chandler EV, Hoover EE, Tillo SE, Hughes TE, Sylvester AW, Kleinfeld D, Squier JA. Optimizing the fluorescent yield in two-photon laser scanning microscopy with dispersion compensation. Opt Express. 2010 Jun 21; 18(13):13661-72. PMID: 20588500; PMCID: PMC4151303.
      View in: PubMed, PubMed Central
    76. Nguyen QT, Schroeder LF, Mank M, Muller A, Taylor P, Griesbeck O, Kleinfeld D. An in vivo biosensor for neurotransmitter release and in situ receptor activity. Nat Neurosci. 2010 Jan; 13(1):127-132. PMID: 20010818; PMCID: PMC3992257.
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    77. Tsai PS, Kaufhold JP, Blinder P, Friedman B, Drew PJ, Karten HJ, Lyden PD, Kleinfeld D. Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels. J Neurosci. 2009 Nov 18; 29(46):14553-70. PMID: 19923289; PMCID: PMC4972024.
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    78. Pesaran B, Kleinfeld D. Enter the ratrix. Proc Natl Acad Sci U S A. 2009 Nov 17; 106(46):19209-10. PMID: 19906991; PMCID: PMC2780815.
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    79. Chen B, Friedman B, Cheng Q, Tsai P, Schim E, Kleinfeld D, Lyden PD. Severe blood-brain barrier disruption and surrounding tissue injury. Stroke. 2009 Dec; 40(12):e666-74. PMID: 19893002; PMCID: PMC2819286.
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    80. Weidemann A, Kerdiles YM, Knaup KX, Rafie CA, Boutin AT, Stockmann C, Takeda N, Scadeng M, Shih AY, Haase VH, Simon MC, Kleinfeld D, Johnson RS. The glial cell response is an essential component of hypoxia-induced erythropoiesis in mice. J Clin Invest. 2009 Nov; 119(11):3373-83. PMID: 19809162.
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    81. Drew PJ, Blinder P, Cauwenberghs G, Shih AY, Kleinfeld D. Rapid determination of particle velocity from space-time images using the Radon transform. J Comput Neurosci. 2010 Aug; 29(1-2):5-11. PMID: 19459038; PMCID: PMC4962871.
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    82. Friedman B, Schachtrup C, Tsai PS, Shih AY, Akassoglou K, Kleinfeld D, Lyden PD. Acute vascular disruption and aquaporin 4 loss after stroke. Stroke. 2009 Jun; 40(6):2182-90. PMID: 19372455; PMCID: PMC2753985.
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    83. Bohland JW, Wu C, Barbas H, Bokil H, Bota M, Breiter HC, Cline HT, Doyle JC, Freed PJ, Greenspan RJ, Haber SN, Hawrylycz M, Herrera DG, Hilgetag CC, Huang ZJ, Jones A, Jones EG, Karten HJ, Kleinfeld D, Kötter R, Lester HA, Lin JM, Mensh BD, Mikula S, Panksepp J, Price JL, Safdieh J, Saper CB, Schiff ND, Schmahmann JD, Stillman BW, Svoboda K, Swanson LW, Toga AW, Van Essen DC, Watson JD, Mitra PP. A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. PLoS Comput Biol. 2009 Mar; 5(3):e1000334. PMID: 19325892; PMCID: PMC2655718.
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    84. Curtis JC, Kleinfeld D. Phase-to-rate transformations encode touch in cortical neurons of a scanning sensorimotor system. Nat Neurosci. 2009 Apr; 12(4):492-501. PMID: 19270688; PMCID: PMC2863011.
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    85. Tsai PS, Blinder P, Migliori BJ, Neev J, Jin Y, Squier JA, Kleinfeld D. Plasma-mediated ablation: an optical tool for submicrometer surgery on neuronal and vascular systems. Curr Opin Biotechnol. 2009 Feb; 20(1):90-9. PMID: 19269159; PMCID: PMC3123732.
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    86. Shih AY, Friedman B, Drew PJ, Tsai PS, Lyden PD, Kleinfeld D. Active dilation of penetrating arterioles restores red blood cell flux to penumbral neocortex after focal stroke. J Cereb Blood Flow Metab. 2009 Apr; 29(4):738-51. PMID: 19174826; PMCID: PMC2893883.
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    87. Devor A, Hillman EM, Tian P, Waeber C, Teng IC, Ruvinskaya L, Shalinsky MH, Zhu H, Haslinger RH, Narayanan SN, Ulbert I, Dunn AK, Lo EH, Rosen BR, Dale AM, Kleinfeld D, Boas DA. Stimulus-induced changes in blood flow and 2-deoxyglucose uptake dissociate in ipsilateral somatosensory cortex. J Neurosci. 2008 Dec 31; 28(53):14347-57. PMID: 19118167; PMCID: PMC2655308.
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    88. Sheetz KE, Hoover EE, Carriles R, Kleinfeld D, Squier JA. Advancing multifocal nonlinear microscopy: development and application of a novel multibeam Yb:KGd(WO4)2 oscillator. Opt Express. 2008 Oct 27; 16(22):17574-84. PMID: 18958037.
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    89. Drew PJ, Duyn JH, Golanov E, Kleinfeld D. Finding coherence in spontaneous oscillations. Nat Neurosci. 2008 Sep; 11(9):991-3. PMID: 18725901.
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    90. Wolfe J, Hill DN, Pahlavan S, Drew PJ, Kleinfeld D, Feldman DE. Texture coding in the rat whisker system: slip-stick versus differential resonance. PLoS Biol. 2008 Aug 26; 6(8):e215. PMID: 18752354; PMCID: PMC2525689.
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    91. Diamond ME, von Heimendahl M, Knutsen PM, Kleinfeld D, Ahissar E. 'Where' and 'what' in the whisker sensorimotor system. Nat Rev Neurosci. 2008 Aug; 9(8):601-12. PMID: 18641667.
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    92. Hill DN, Bermejo R, Zeigler HP, Kleinfeld D. Biomechanics of the vibrissa motor plant in rat: rhythmic whisking consists of triphasic neuromuscular activity. J Neurosci. 2008 Mar 26; 28(13):3438-55. PMID: 18367610.
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    93. Helmchen F, Kleinfeld D. Chapter 10. In vivo measurements of blood flow and glial cell function with two-photon laser-scanning microscopy. Methods Enzymol. 2008; 444:231-54. PMID: 19007667.
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    94. Kleinfeld D, Waters J. Wilder Penfield in the age of YouTube: visualizing the sequential activation of sensorimotor areas across neocortex. Neuron. 2007 Dec 06; 56(5):760-2. PMID: 18054853.
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    95. Devor A, Tian P, Nishimura N, Teng IC, Hillman EM, Narayanan SN, Ulbert I, Boas DA, Kleinfeld D, Dale AM. Suppressed neuronal activity and concurrent arteriolar vasoconstriction may explain negative blood oxygenation level-dependent signal. J Neurosci. 2007 Apr 18; 27(16):4452-9. PMID: 17442830; PMCID: PMC2680207.
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    96. Mehta SB, Whitmer D, Figueroa R, Williams BA, Kleinfeld D. Active spatial perception in the vibrissa scanning sensorimotor system. PLoS Biol. 2007 Feb; 5(2):e15. PMID: 17227143; PMCID: PMC1769422.
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    97. Clay GO, Schaffer CB, Kleinfeld D. Large two-photon absorptivity of hemoglobin in the infrared range of 780-880 nm. J Chem Phys. 2007 Jan 14; 126(2):025102. PMID: 17228976.
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    98. Devor A, Trevelyan A, Kleinfeld D. Is there a common origin to surround-inhibition as seen through electrical activity versus hemodynamic changes? Focus on "Duration-dependent response in SI to vibrotactile stimulation in squirrel monkey". J Neurophysiol. 2007 Mar; 97(3):1880-2. PMID: 17215499.
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    99. Nishimura N, Schaffer CB, Friedman B, Lyden PD, Kleinfeld D. Penetrating arterioles are a bottleneck in the perfusion of neocortex. Proc Natl Acad Sci U S A. 2007 Jan 02; 104(1):365-70. PMID: 17190804; PMCID: PMC1765467.
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    100. Kleinfeld D, Ahissar E, Diamond ME. Active sensation: insights from the rodent vibrissa sensorimotor system. Curr Opin Neurobiol. 2006 Aug; 16(4):435-44. PMID: 16837190.
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    101. Berg RW, Whitmer D, Kleinfeld D. Exploratory whisking by rat is not phase locked to the hippocampal theta rhythm. J Neurosci. 2006 Jun 14; 26(24):6518-22. PMID: 16775139.
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    102. Curtis JC, Kleinfeld D. Seeing what the mouse sees with its vibrissae: a matter of behavioral state. Neuron. 2006 May 18; 50(4):524-6. PMID: 16701202; PMCID: PMC2863010.
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    103. Nguyen QT, Tsai PS, Kleinfeld D. MPScope: a versatile software suite for multiphoton microscopy. J Neurosci Methods. 2006 Sep 30; 156(1-2):351-9. PMID: 16621010.
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    104. Nishimura N, Schaffer CB, Friedman B, Tsai PS, Lyden PD, Kleinfeld D. Targeted insult to subsurface cortical blood vessels using ultrashort laser pulses: three models of stroke. Nat Methods. 2006 Feb; 3(2):99-108. PMID: 16432519.
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    105. Kleinfeld D. Science is an adventure, not a battle. Nature. 2006 Jan 05; 439(7072):18. PMID: 16397477.
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    106. Schaffer CB, Friedman B, Nishimura N, Schroeder LF, Tsai PS, Ebner FF, Lyden PD, Kleinfeld D. Two-photon imaging of cortical surface microvessels reveals a robust redistribution in blood flow after vascular occlusion. PLoS Biol. 2006 Feb; 4(2):e22. PMID: 16379497; PMCID: PMC1324794.
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    107. Golomb D, Ahissar E, Kleinfeld D. Coding of stimulus frequency by latency in thalamic networks through the interplay of GABAB-mediated feedback and stimulus shape. J Neurophysiol. 2006 Mar; 95(3):1735-50. PMID: 16267113.
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    108. Kleinfeld D, Griesbeck O. From art to engineering? The rise of in vivo mammalian electrophysiology via genetically targeted labeling and nonlinear imaging. PLoS Biol. 2005 Oct; 3(10):e355. PMID: 16207078; PMCID: PMC1250306.
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    109. Berg RW, Friedman B, Schroeder LF, Kleinfeld D. Activation of nucleus basalis facilitates cortical control of a brain stem motor program. J Neurophysiol. 2005 Jul; 94(1):699-711. PMID: 15728764.
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    110. Nguyen QT, Kleinfeld D. Positive feedback in a brainstem tactile sensorimotor loop. Neuron. 2005 Feb 03; 45(3):447-57. PMID: 15694330.
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    111. Ganguly K, Kleinfeld D. Goal-directed whisking increases phase-locking between vibrissa movement and electrical activity in primary sensory cortex in rat. Proc Natl Acad Sci U S A. 2004 Aug 17; 101(33):12348-53. PMID: 15297618; PMCID: PMC514478.
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    112. Ahrens KF, Kleinfeld D. Current flow in vibrissa motor cortex can phase-lock with exploratory rhythmic whisking in rat. J Neurophysiol. 2004 Sep; 92(3):1700-7. PMID: 15331651.
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    113. Nguyen QT, Wessel R, Kleinfeld D. Developmental regulation of active and passive membrane properties in rat vibrissa motoneurones. J Physiol. 2004 Apr 01; 556(Pt 1):203-19. PMID: 14766934; PMCID: PMC1664878.
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    114. Mehta SB, Kleinfeld D. Frisking the whiskers: patterned sensory input in the rat vibrissa system. Neuron. 2004 Jan 22; 41(2):181-4. PMID: 14741099.
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    115. Lev-Ram V, Mehta SB, Kleinfeld D, Tsien RY. Reversing cerebellar long-term depression. Proc Natl Acad Sci U S A. 2003 Dec 23; 100(26):15989-93. PMID: 14671315; PMCID: PMC307680.
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    116. Taylor AL, Cottrell GW, Kleinfeld D, Kristan WB. Imaging reveals synaptic targets of a swim-terminating neuron in the leech CNS. J Neurosci. 2003 Dec 10; 23(36):11402-10. PMID: 14673004.
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    117. Berg RW, Kleinfeld D. Vibrissa movement elicited by rhythmic electrical microstimulation to motor cortex in the aroused rat mimics exploratory whisking. J Neurophysiol. 2003 Nov; 90(5):2950-63. PMID: 12904336.
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    118. Tsai PS, Friedman B, Ifarraguerri AI, Thompson BD, Lev-Ram V, Schaffer CB, Xiong Q, Tsien RY, Squier JA, Kleinfeld D. All-optical histology using ultrashort laser pulses. Neuron. 2003 Jul 03; 39(1):27-41. PMID: 12848930.
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    119. Sachdev RN, Berg RW, Champney G, Kleinfeld D, Ebner FF. Unilateral vibrissa contact: changes in amplitude but not timing of rhythmic whisking. Somatosens Mot Res. 2003; 20(2):163-9. PMID: 12850826.
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    120. Ahissar E, Kleinfeld D. Closed-loop neuronal computations: focus on vibrissa somatosensation in rat. Cereb Cortex. 2003 Jan; 13(1):53-62. PMID: 12466215.
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    121. Berg RW, Kleinfeld D. Rhythmic whisking by rat: retraction as well as protraction of the vibrissae is under active muscular control. J Neurophysiol. 2003 Jan; 89(1):104-17. PMID: 12522163.
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    122. Ahrens KF, Levine H, Suhl H, Kleinfeld D. Spectral mixing of rhythmic neuronal signals in sensory cortex. Proc Natl Acad Sci U S A. 2002 Nov 12; 99(23):15176-81. PMID: 12403828; PMCID: PMC137563.
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    123. Kleinfeld D, Sachdev RN, Merchant LM, Jarvis MR, Ebner FF. Adaptive filtering of vibrissa input in motor cortex of rat. Neuron. 2002 Jun 13; 34(6):1021-34. PMID: 12086648.
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    124. O'Connor SM, Berg RW, Kleinfeld D. Coherent electrical activity between vibrissa sensory areas of cerebellum and neocortex is enhanced during free whisking. J Neurophysiol. 2002 Apr; 87(4):2137-48. PMID: 11929931.
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    125. Yoder EJ, Kleinfeld D. Cortical imaging through the intact mouse skull using two-photon excitation laser scanning microscopy. Microsc Res Tech. 2002 Feb 15; 56(4):304-5. PMID: 11877806.
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