Journal Articles (Work, finish, publish*)

(2036-2040) (2031-2035) (2026-2030)

(2021-2025) (2016-2020) (2011-2015)

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

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

(2021 - 2025)

Biomechanics of a scanning sensorimotor system link contact forces to perception. R. Liu, K. Dekel, A. Fassihi-Zakeri, P. Yao, D. H. O'Connor, D. Kleinfeld^ and D. Golomb^, in final preparation.*
A red fluorescent genetically encoded biosensor for extracellular L-lactate. Y. Nasu^, Y. Kamijo, Ph. Mächler, N. Ness, C. Q. Vu, T. Kusakizako, Z. Ku, M. Boisvert, E. Grebenik, I. Miyazaki, R. Hashizume, H. Sato, R. Liu, Y. Hori, T. Tomita, G. Caraveo, M.-E. Paquet, M. Drobizhev, O. Nureki, S. Arai, M. Brancaccio, D. Kleinfeld and R. E. Campbell^, in final preparation.*
CellBoost: A pipeline for machine assisted annotation in neuroanatomy. K. Qian, B. Friedman, J. Takatoh, F. Wang, D. Kleinfeld and Y. Freund, bioRxiv https://doi.org/10.1101/2023.09.13.557658.
Spatiotemporal development of growth and death zones in expanding bacterial colonies driven by emergent nutrient dynamics. H. Kannan, P. Sun^, T. Çağlar, P. Yao, K. Sahu, D. Ge, B. R. Taylor, M. Warren, D. Kleinfeld, J. Dong^, B. Li^ and T. Hwa^, Nature Communications under revision.
Long-wavelength traveling waves of vasomotion modulate the perfusion of cortex. T. Broggini, J. Duckworth, X. Ji, R. Liu, X. Xia*, P. Machler, I. Shaked, L. P. Munting, S. Iyengar, M. Kotlikoff, S. J. van Veluw, M. Vergassola, G. Mishne and D. Kleinfeld, Neuron* (2024) in press.
A lone spike in blood glucose can enhance the thrombo-inflammatory response in cortical venules. I. Shaked, C. Foo, P. Machler, R. Liu, Y. Cui, X. Ji, T. Broggini, T. Kiminski, S. Jadhav, P. Sundd, M. Firer, A. Devor, B. Friedman^ and D. Kleinfeld^, Journal of Cerebral Blood Flow and Metabolism (2024) 44:252–271 (PMC10993879).	PDF (3.3 MB)
Supplementary figures and associated legends	PDF (0.6 MB)
Elephant trunks: Strength and dexterity from mini-fascicles. W. Olson, L. Zhang, D. H. O’Connor and D. Kleinfeld. Current Biology (2023) 33:R1186–R1207 (PMC11039408).	PDF (2.0 MB)
Dispatch on "Dense reconstruction of elephant trunk musculature" by L. L. Longren, E. Lennart, A. Shubitidze, O. Lieschnegg, D. Baum, J. A. Nyakatura, T. Hildebrandt and M. Brecht. Current Biology (2023) 33:4713–4720.	PDF (6.1 MB)
Vagal sensory neurons mediate the Bezold-Jarisch reflex and induce syncope. J. W. Lovelace, J. Ma, S. Yadav, K. Chhabria, H. Shen, Z. Pang, T. Qi, R. Sehgal, Y. Li, Y. Zhang, T. Bali, T. Vaissiere, S. Tan, G. Rumbaugh, L. Ye, D. Kleinfeld, C. Stringer and V. Augustine. Nature (2023) 623:387-396 (PMC10632149).	PDF (145.2 MB)
Nature News article "What causes fainting? Scientists finally have an answer." (1 November 2023) by Miryam Naddaf.	PDF (2.5 MB)
UC San Diego press release "What happens when we pass out? Researchers ID new brain and heart connections." (1 November 2023) appeared widely, including "EurekAlert! Science News" of the AAAS.	PDF (0.3 MB)
Construction and use of an adaptive optics two-photon microscope with direct wavefront sensing. P. Yao, R. Liu, T. Broggini, M. Thunemann and D. Kleinfeld, Nature Protocols (2023) 18:3722-3766 (PMC11033548).	PDF (6.8 MB)
Supplementary Data 1 (Assembly drawings)	ZIP (12.9 MB)
Supplementary Data 2 (Part drawings)	ZIP (9.5 MB)
Supplementary Data 3 (ZEMAX file)	ZIP (8.0 MB)
Supplementary Table 1 (Comprehensive parts list including current prices and vendor links)	XLSX (0.1 MB)
Supplementary Software (MATLAB Scripts)	ZIP (17.0 MB)
Journal cover based on article.
Low- and high-level coordination of orofacial motor actions. D. Kleinfeld, M. Deschênes, M. N. Economo, M. Elbaz, D. Golomb, S-M Liao, D. H. O'Connor and F. Wang, Current Opinion in Neurobiology. (2023) 83:e102784 (PMC11034851).	PDF (3.9 MB
A brainstem circuit for the expression of defensive facial reactions in rat. A. Callado-Pérez, M. Demers, A. Fassihi Zakeri, J. D. Moore, D. Kleinfeld^ and M. Deschênes^, Current Biology (2023) 18:4030-4035 (PMC11034846).	PDF (3.5 MB)
Supplementary figures and associated legends	PDF (13.4 MB)
Interchangeable role of motor cortex and reafference for the stable execution of an orofacial action. M. Elbaz^, M. Demers, D. Kleinfeld, C. Ethier and M. Deschênes^, Journal of Neuroscience (2023) 43:5521-5536 (PMC10376937).	PDF (5.4 MB)
Featured Research (15 August 2023)	PDF (0.2 MB)
Editorial Board of the Journal of Neuroscience Spotlight as one of ten publication that received the strongest reviews in 2023
Glutamate indicators with improved activation kinetics and localization for imaging synaptic transmission. A. Aggarwal, R. Liu, Y. Chen, A. J. Ralowicz, S. J. Bergerson, F. Tomaska, T. L. Hanson, P. J. Hasseman, D. Reep, G. Tsegaye, P. Yao, X. Ji, M. Kloos, D. Walpita, R. Patel, B. Mohar, P. W. Tilberg, The GENIE Project Team, L. L. Looger, J. S. Marvin, M. B. Hoppa, A. Konnerth, D. Kleinfeld, E. R. Schreiter and K. Podgorski, Nature Methods (2023) 20:925-934 (PMC10250197).	PDF (29.9 MB)
A change in behavioral state switches the pattern of motor output that underlies rhythmic head and orofacial movements. S.-M. Liao and D. Kleinfeld, Current Biology (2023) 33:1951-1966 (PMC10225163).	PDF (17.6 MB)
Supplementary figures and associated legends	PDF (12.4 MB)
Theory of hierarchically organized neuronal oscillator dynamics that mediate rodent rhythmic whisking. D. Golomb^, J. D. Moore, A. Fassihi, J. Takatoh, V. Prevosto, F. Wang and D. Kleinfeld^, Neuron (2022) 110:3833-3851. (PMC10248719)	PDF (5.0 MB)
Supplementary Information (Supplementary figures and Supplementary figure legends)	PDF (0.5 MB)
Datasets supporting this study, and associated "README" files, are available at https://doi.org/10.6076/D10K5P or can be downloaded here.	ZIP (21.2 MB)
The whisking oscillator circuit. J. Takatoh, V. Prevosto, P. M. Thompson, J. Lu, L. Chung, A. Harrahill, S. Li, S. Zhao, Z. He, D. Golomb, D. Kleinfeld and F. Wang, Nature (2022) 609:560–568 (PMC10038238).	PDF (41.2 MB)
MIT press release "‘How the brain generates rhythmic behavior" (31 August 2022) by Anne Trafton appeared in MIT News.	PDF (1.3 MB)
Probing neuropeptide volume transmission in vivo by simultaneous near-infrared light triggered release and optical sensing. H. Xiong, E. Lacin, H. Ouyang, A. Naik, X. Xu, C. Xie, J. Youn, K. Kumar, T. Kern, E. Aisenberg, D. Kircher, X. Li, J. A. Zasadzinski, C. Mateo, D. Kleinfeld, S. Hrabetova, P. A. Slesinger and Z. Qin, Angewandte Chemie (2022) e202206122 (PMC9388559).	PDF (6.7 MB)
A vibrissa pathway that activates the limbic system. M. Elbaz, A. Callado-Pérez, M. Demers, S. Zhao, C. Foo, D. Kleinfeld^ and M. Deschênes^, eLife (2022) 11:e72096 (PMC8830883).	PDF (16.8 MB)
Supplementary figures and associated legends	PDF (20.9 MB)
Datasets supporting this study, and high resolution images, are available at https://datadryad.org/stash/share/xz3Mt8XWrxuPjrZAoowsIswzcdQcgi8cdg2Wk_vfVHk.
The global configuration of visual stimuli alters co-fluctuations of cross-hemispheric human brain activity. S. Nasr, D. Kleinfeld and J. R. Polimeni, Journal of Neuroscience (2021) 41:9756-9766 (PMC8612647).	PDF (3.6 MB)
Contribution of animal models toward understanding resting state functional connectivity. P. Pais-Roldán, C. Mateo, W.-J. Pan, B. Acland, D. Kleinfeld, L. H. Snyder, X. Yu and S. Keilholz, NeuroImage (2021) 245:e118630 (PMC9031339). Special issue on "Advances in Mapping the Connectome".	PDF (3.3 MB)
Modulating the blood-brain barrier by light stimulation of molecular-targeted nanoparticles. X. Li, V. Vemireddy, Q. Cai, H. Xiong, P. Kang, X. Li, M. Giannotta, H. N. Hayenga, E. Pan, S. R. Sirsi, C. Mateo, D. Kleinfeld, C. Greene, M. Campbell, E. Dejana, R. Bachoo and Z. Qin. Nano Letters (2021) https://doi.org/10.1021/acs.nanolett.1c02996 (PMC8616836).	PDF (13.5 MB)
Assessment of single-vessel cerebral blood velocity by phase contrast fMRI. X. Chen, Y. Jiang, S. Choi, R. Pohmann, K. Scheffler, D. Kleinfeld and X. Yu, Public Library of Science: Biology (2021) 19:e3000923 (PMC8454982).	PDF (7.9 MB)
Reinforcement learning links spontaneous dopamine impulses to reward. C. Foo, A. Lozada, J. Aljadeff, Y. Li, J. W. Wang, P. A. Slesinger^ and D. Kleinfeld^, Current Biology (2021) 31:4111-4119 (PMC8605927).	PDF (2.2 MB)
Supplementary Information (Supplementary figures and Supplementary figure legends)	PDF (4.3 MB)
Datasets supporting this study, and an associated "read me" file, are available at https://datadryad.org/stash/share/He3oAHCTB6W0fUlaULv2i-WtySJu3LqkQJavqKsLBSo.
Code for the model is available at https://github.com/aljdf/DopamineTransients_Foo2021.
Highlighted in Kavli Foundation Neuroscience News on "The Neuroscience of Motivation" by Lindsay Borthwick.	PDF (1.3 MB)
Summarized in "Pleasurable Dopamine Impulses Can Be Controlled at Will, Mouse Studies Show" in Genetic Engineering and Biotechnology News, in "El cerebro puede ser entrenado para la felicidad" in Tendencias, and in both "Three Potential Ways to Train the Brain to Release Dopamine on Demand" and "Why Passion is Pessimism’s Best Antidote" in Psychology Today.	PDF (0.6 MB)
UC San Diego press release "‘Feel Good’ Brain Messenger Can Be Willfully Controlled, New Study Reveals" (23 July 2021) appeared in "EurekAlert! Science News" of the AAAS, "Michigan Psychological Association", "Florida News Times", "Science Daily", "Newsbeezer.com", "NeuroscienceNews.com", "Newsbeezer.com", "Times of San Diego", "MashupMD", "Jioforme.com", "SciTechDaily", "Min.News", "USA News Lab", "Burada Biliyorum", "USA News Wall", "Industrial Update", "Reddit", "New Zealand Online News", biotechniques, "Laboratory Equipment", "Futura Sciences News", "San Diego Biotech Networks", "Medpage Today", and "Medical Xpress", "Thrivous", "DaBigNewsUpdate", "Technilive", NigerDeltaConnect", and others.
Abortive intussusceptive angiogenesis causes multi-cavernous vascular malformations. W. Li, V. Tran, I. Shaked, B. Xue, T. Moore, R. Lightle, D. Kleinfeld, I. Awad and M. Ginsberg, eLIFE (2021) 10:e62155 (PMC8175082).	PDF (4.5 MB)
PIP₂ as the "coin of the realm" for neurovascular coupling. S. Earley and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (2021) 118:e2106308118 (PMC8166173). Commentary on "PIP₂ corrects cerebral blood flow deficits in small vessel disease by rescuing capillary Kir2.1 activity" by F. Dabertrand, O. F. Harraz, M. Koide, T. A. Longden, A. C. Rosehart, D. C. Hill-Eubanks, A. Joutel and M. T. Nelson, Proceedings of the National Academy of Sciences USA (2021) 118: e2025998118.	PDF (0.7 MB)
Constructing an adult orofacial premotor atlas in Allen Mouse CCF. J. Takatoh, J. H. Park, J. Lu, S. Li, P. M. Thompson, B.-X. Han, S. Zhao, D. Kleinfeld, B. Friedman and F. Wang, eLIFE* (2021) 10:e67291 (PMC8137149).	PDF (35.6 MB)
Mathematical synthesis of the cortical circulation for the whole mouse brain - part II: Microcirculatory closure. G. Hartung, S. Badr, S. Mihelic, A. Dunn, X. Cheng, S. Kura, D. A. Boas, D. Kleinfeld, A. Alaraj and A. Linninger, Microcirculation (2021) 00:e12687 (PMC8504684).	PDF (5.9 MB)
Specific populations of basal ganglia output neurons target distinct brain stem areas while collateralizing throughout the diencephalon. L. E. McElvain, Y. Chen, J. D. Moore, G. S. Brigidi, B. L. Bloodgood, B. K. Lim, R. M. Costa^ and D. Kleinfeld^, Neuron (2021) 109:1721–1738 (PMC8169061).	PDF (5.4 MB)
Supplementary Information (Supplementary figures and figure legends)	PDF (48.0 MB)
Preview "Basal ganglia reign through downstream control of motor centers in midbrain and brain stem while updating cortex with efference copy information" by S. Grillner and W. S. Thompson, Neuron (2021) 109:1587-1589.	PDF (0.5 MB)
Journal cover based on article.
Joint Columbia University and UC San Diego press release "New blueprint for brain connections reveals a wide range of central regulators" (6 April 2021) appeared in the "NINDS Grantees in the News" as well as in "Arabica Post", "Florida News Times", "Fox 5 San Diego", "India Educational Diary", "Medical Life Sciences News", "Microsoft News", "Neuroscience News, "Newsbreak", "NewsWise: News for Journalists", "Pulse", "Science Daily", "Science Direct", and "Times of San Diego".	PDF (2.1 MB)
Endothelial struts: A mechanism to generate large lumenized blood vessels de novo. B. Weijts, I. Shaked, M. Ginsberg, D. Kleinfeld, C. Robin and D. Traver, Nature Cell Biology (2021) 23:322–329 (PMC8500358).	PDF (13.5 MB)
A suite of neurophotonic tools to underpin fMRI signals with respect to internal brain states. P. Mächler, T. Broggini, C. Mateo, M. Thunemann, N. Fomin-Thunemann, P. R. Doran, I. Sencan, K. Kilic, M. Desjardins, H. Uhlirova, M. A. Yaseen, D. A. Boas, A. A. Linninger, M. Vergassola, X. Yu, L. D. Lewis, J. R. Polimeni, B. R. Rosen, S. Sakadžić, R. B. Buxton, M. Lauritzen, D. Kleinfeld and A. Devor, Current Opinion in Biomedical Engineering (2021) 18:e100273 (PMC8095678). Special issue on "Functional Brain Imaging".	PDF (2.2 MB)
Brain microvasculature has a common topology with local differences in geometry that match metabolic load. X. Ji, T. Ferreira, B. Friedman, R. Liu, H. Liechty, E. Bas, J. Chandrashekar and D. Kleinfeld, Neuron (2021) 109:1168-1187 (PMC8525211).	PDF (7.0 MB)
Supplementary Information (Supplementary figures, Supplementary figure legends, and Supplementary tables - except Table S3)	PDF (1.4 MB)
Supplementary Table S3.	XLSX (0.2 MB)
Supplementary movie: Local capillary length density.	AVI (45.1 MB)
Supplementary movie: Local capillary anisotropy.	AVI (46.4 MB)
Matlab code with ReadMe and updated Stitching; 22 Feb 2021. https://github.com/xiangjiph/VCRA	ZIP (4.7 MB)
Press release "Food for Thought: New Maps Reveal How Brains are Kept Nourished" (6 March 2021) appeared in the "NINDS Grantees in the News" as well as "Science Daily", "Neuroscience News and Research from Technology Networks", "Medical Press", "Medical, Life Sciences NEWS", "Ptch", Neuroscience News", Times of San Diego", "EurekAlert! Science News" of the AAAS, and "NewsWise: News for Journalists".	PDF (0.1 MB)
Data used for "Blue Brain Project" visualization.	PDF (1.2 MB)
Voxelized mesh-free simulation of cerebral oxygen perfusion elucidates hypoxia in aged mouse cortex. G. Hartung, S. Badr, M. Moeini, F. Lesage, D. Kleinfeld, A. Alaraj and A. Linninger, Public Library of Science: Computational Biology (2021) 17:e1008584 (PMC7842915).	PDF (5.2 MB)

(2016 - 2020)

Ultra-slow oscillations in fMRI and resting-state connectivity: Neuronal and vascular contributions and technical confounds. P. J. Drew, C. Mateo, K. Turner, X. Yu and D. Kleinfeld, Neuron (2020) 107:782-804 (PMC7886622). Perspective.	PDF (6.7 MB)
Supplementary material.	PDF (0.9 MB)
Cerebrospinal fluid influx drives acute ischemic tissue swelling. H. Mestre, T. Du, A. M. Sweeney, G. Liu, A. J. Samson, W. Peng, K. N. Mortensen, F. F. Staeger, P. Bork, L. Bashford, E. R. Toro, J. Tithof, D. H. Kelley, P. G. Hjorth, E. A. Martens, R. Mehta, O. Solis, P. Blinder, D. Kleinfeld, H. Hirase, Y. Morii^ and M. Nedergaard^, Science (2020) 367:eaax7171 (PMC7375109).	PDF (22.4 MB)
News release, titled "Brain drowns in its own fluid after a stroke" featured in "Science Daily", "IFL Science", "Knowridge Science Report", "New Altas", "Brain 8", "News Break", "BioWorld", and "EurekAlert! Science News" of the AAAS.	PDF (0.1 MB)
Orofacial movements involve parallel corticobulbar projections from motor cortex to trigeminal premotor nuclei. N. Mercer Lindsay, P. M. Knutsen, A. Lozada, D. Gibbs, H. J. Karten and D. Kleinfeld, Neuron (2019) 104:765-780 (PMC7962749).	PDF (50.9 MB)
Supplementary material.	PDF (12.0 MB)
Can one concurrently record electrical spikes from every neuron in a mammalian brain? D. Kleinfeld, L. Luan, P. P. Mitra, J. T. Robertson, R. Sarpeshkar, K. Shepard, C. Xie, and T. D. Harris, Neuron (2019) 103:1005-1015 (PMC6763354). Viewpoint.	PDF (3.8 MB)
Press release "Wired to Think" (23 September 2019) appeared in "Newswise: News for Journalists", "Technology.org", and other news outlets.	PDF (0.2 MB)
Prescient editorial titled "BRAIN Project Meets Physics" by Emily Underwood, Science (2014) 344:954-955.	PDF (0.2 MB)
Direct wavefront sensing enables functional imaging of infragranular axons and spines. R. Liu, Z. Li, J. S. Marvin and D. Kleinfeld, Nature Methods (2019) 16:615–618 (PMC6763395).	PDF (3.1 MB)
Supplementary figures.	PDF (35.4 MB)
Supplementary tables.	PDF (0.1 MB)
Supplementary movies and captions.	ZIP (260.8 MB)
Matlab code.	ZIP (0.1 MB)
Press release "Borrowing from Astronomy to Rob the Twinkle from Brain Imagery" (19 June 2019) appeared in "Newswise: News for Journalists", and other news outlets.	PDF (4.6 MB)
"Multiphoton Microscopy Points Imaging to New Depths" by Darryl McCoy and Marco Arrigoni in BioPhotonics (Jan/Feb 2020), Vol. 25, Issue 3, pp. 22-25.	PDF (0.4 MB)
Awake mouse imaging: From two-photon microscopy to blood-oxygen-level dependent functional magnetic resonance imaging. M. Desjardins, K. Kıvılcım; M. Thunemann, C. Mateo, D. Holland, C. G. L. Ferri, J. Cremonesi, B. Li, Q. Cheng, K. L. Weldy, P. A. Saisan, D. Kleinfeld, T. Komiyama, T. T. Liu, R. Bussel, E. C. Wong, M. Scadeng, A. K. Dunn, D. A. Boas, S. Sakadžić, J. B. Mandeville, R. B. Buxton, A. M. Dale and A. Devor, Biological Psychiatry: Cognitive Neuroscience and Neuroimaging (2019) 4:533-542 (PMC6556427). Special issue on "The bridging of scales: Techniques for translational neuroscience".	PDF (5.5 MB)
An active texture-based digital atlas enables automated mapping of structure and markers across brains. Y. Chen, L. E. McElvain, A. Tolpygo, D. Ferrant, B. Friedman, P. P. Mitra, H. J. Karten, Y. Freund* and D. Kleinfeld, Nature Methods* (2019) 16:314-350 (PMC6736610).	PDF (4.4 MB)
Supplementary material.	PDF (20.7 MB)
Brain capillary networks across species: A few simple organizational requirements are sufficient to reproduce both structure and function. A. F. Smith, V. Doyeux, M. Berg, M. Peyrounette, M. H. Javaherian, A. E. Larue, J. H. Slater, F. Lauwers, P. Blinder, P. S. Tsai, D. Kleinfeld, C. B Shaffer, N. Nishimura, Y. Davit and S. Lorthois, Frontiers in Physiology (2019) https://doi.org/10.3389/fphys.2019.00233 (PMC6444172).	PDF (12.7 MB)
Functional brainstem circuits for control of nose motion. A. Kurnikova, M. Deschênes and D. Kleinfeld, Journal of Neurophysiology (2019) 121:205–217 (PMC6383659).	PDF (5.1 MB)
Supplementary material.	PDF (4.4 MB)
Simulations of blood as a suspension predicts a depth dependent hematocrit in the circulation throughout the cerebral cortex. G. Hartung, C. Vesel, R. Morley, A. Alaraj, J. Sled, D. Kleinfeld and A. Linninger, Public Library of Science: Computational Biology (2018) 14:e1006549 (PMC6277127).	PDF (30.3 MB)
Comparing two classes of biological distribution systems using network analysis. L. Papadopoulos, P. Blinder, H. Ronellenfitsch, F. Klimm, E. Katifori, D. Kleinfeld and D. S. Bassett, Public Library of Science: Computational Biology (2018) 14:e1006428 (PMC6145589).	PDF (9.4 MB)
Circuits in the rodent brainstem that control whisking in concert with other orofacial motor actions. L. E. McElvain, B. Friedman, H. J. Karten, K. Svoboda, F. Wang, M. Deschênes and D. Kleinfeld, Neuroscience (2018) 368:152–170 (PMC5849401). Special issue on "Barrel cortex function".	PDF (3.9 MB)
Ultra-slow single-vessel BOLD and CBV-based fMRI spatiotemporal dynamics and their correlation with neuronal intracellular calcium signals. Y. He, M. Wang, X. Chen, R. Pohmann, J. R. Polimeni, K. Scheffler, B. R. Rosen, D. Kleinfeld and X. Yu, Neuron (2018) 97:925–939 (PMC5845844).	PDF (7.6 MB)
Entrainment of arteriole vasomotor fluctuations by neural activity is a basis of blood-oxygenation-level-dependent “resting-state” connectivity. C. Mateo, P. M. Knutsen, P. S. Tsai, A. Y. Shih and D. Kleinfeld, Neuron (2017) 96:936–948 (PMC5851777).	PDF (4.7 MB)
Supplementary material.	PDF (22.0 MB)
Tabulated data.	XLSX (12.3 MB)
Preview "Good vibrations: Resting-state functional connectivity reflects entrainment of vasomotion" by A. W. Chan and T. H. Murphy, Neuron (2017) 96:716-717.	PDF (0.2 MB)
Articles based on the UCSD press release "UC San Diego researchers solve mystery of oxygenation connections in the brain" appeared in "DeathRattleSports", "EcoDiario", "EurekAlert! Science News" of the AAAS, "homeAI", "MedicalXpress", "NSF 'News From the Field'", "Neuroscience News and Research", "NewswiseScience Daily", "ScienceNewsline", and "Topix".	PDF (0.5 MB)
The impact of vessel size, orientation and intravascular contribution on the neurovascular fingerprint of BOLD bSSFP fMRI. M. G. Báez-Yánez, P. Ehses, P. Mirkes, P. S. Tsai, D. Kleinfeld and K. Scheffler, NeuroImage (2017) 163:13–23 (PMC5857886).	PDF (4.8 MB)
Parallel inhibitory and excitatory trigemino-facial feedback circuitry for reflexive vibrissa movement. M.-A. Bellavance, J. Takatoh, J. Lu, M. Demers, D. Kleinfeld^, F. Wang^ and M. Deschênes^, Neuron (2017) 95:673–682 (PMC5845798).	PDF (4.8 MB)
Correction. Neuron (2017) 95:722-723.	PDF (0.3 MB)
Coordination of orofacial motor actions into exploratory behavior by rat. A. Kurnikova, J. D. Moore, S.-M. Liao, M. Deschênes and D. Kleinfeld, Current Biology (2017) 27:688–696 (PMC5653531).	PDF (4.0 MB)
Supplemental material.	PDF (2.6 MB)
Dispatch "Active sensing: The rat’s nose dances in step with whiskers, head, and breath" by K. S. Severson and D. H. O’Connor, Current Biology (2017) 27:R183-185.	PDF (0.6 MB)
Video abstract.	MP4 (82.8 MB)
Depth dependent flow and pressure characteristics in cortical microvascular networks. F. Schmid, P. S. Tsai, D. Kleinfeld, P. Jenny and B. Weber, Public Library of Science: Computational Biology (2017) 13:e1005392 (PMC5347440).	PDF (4.7 MB)
The capillary bed offers the largest hemodynamic resistance to the cortical blood supply. I. G. Gould, P. Tsai, D. Kleinfeld and A. Linninger, Journal of Cerebral Blood Flow & Metabolism (2017) 37:52–68 (PMC5363755).	PDF (2.0 MB)
Journal cover based on article.	JPEG (0.4 MB)
Precision mapping of vibrissa representation within murine primary somatosensory cortex. P. M. Knutsen, C. Mateo and D. Kleinfeld, Philosophical Transactions of the Royal Society B (2016) 371:20150351 (PMC5003853). Special issue on "Interpreting BOLD: A dialogue between basic and cognitive sciences".	PDF (1.1 MB)
Correction in Philosophical Transactions of the Royal Society B (2017) 372:20170002.	PDF (0.2 MB)
The roadmap for estimation of cell-type-specific neuronal activity from noninvasive measurements. H. Uhlirova, K. Kılıc, P. Tian, S. Sakadžić, L. Gagnon, M. Thunemann, M. Desjardins, P. A. Saisan, K. Nizar, M. A. Yasseen, D. J. Hagler, Jr., M. Vandenberghe, S. Djurovic, O. A. Andreassen, G. A. Silva, E. Masliah, D. Kleinfeld, S. Vinogradov, R. B. Buxton, G. T. Einevoll, D. A. Boas, A. M. Dale and A. Devor, Philosophical Transactions of the Royal Society B (2016) 371:20150356 (PMC5003857). Special issue on "Interpreting BOLD: A dialogue between basic and cognitive sciences".	PDF (2.1 MB)
Analysis of neuronal spike trains, deconstructed. Y. Aljadeff, B. J. Lansdell, A. L. Fairhall and D. Kleinfeld, Neuron (2016) 91:221-259 (PMC4970242). Primer.	PDF (8.1 MB)
Minor corrections.	PDF (0.1 MB)
A 3-star F1000Prime selection.	PDF (0.2 MB)
Cell type specificity of neurovascular coupling in cerebral cortex. H. Uhlirova, K. Kılıç, P. Tian, M. Thunemann, M. Desjardins, P. A. Saisan, S. Sakadžić, T. V. Ness, C. Mateo, Q. Cheng, K. L. Weldy, F. Razoux, M. Vandenberghe, J. A. Cremonesi, K. Nizar, V. B. Sridhar, T. C. Steed, M. Abashin, Y. Fainman, E. Masliah, S. Djurovic, O. A. Andreassen, G. A. Silva, D. A. Boas, D. Kleinfeld, R. B. Buxton, G. T. Einevoll, A. M. Dale and A. Devor, eLIFE (2016) 5:e14315 (PMC4933561).	PDF (7.2 MB)
Circuits in the ventral medulla that phase lock motoneurons for coordinated sniffing and whisking. M. Deschênes, A. Kurnikova, M. Elbaz and D. Kleinfeld, Neural Plasticity (2016) ID 7493048, 9 pages, http://dx.doi.org/10.1155/2016/7493048 (PMC4887653). Special issue on "Adaptation and plasticity of breathing during behavioral and cognitive tasks".	PDF (8.1 MB)
Construction of cell-based neurotransmitter fluorescently engineered reporters (CNiFERs) for optical detection of neurotransmitters in vivo. E. Lacin, A. Muller, M. Fernando, D. Kleinfeld and P. A. Slesinger, Journal of Visualized Experiments (2016) http://www.jove.com/video/53290 (PMC4939270).	PDF (1.5 MB)
Material list.	PDF (0.1 MB)
Featured in the article "Brain's chemical signals seen in real time" by D. Reardon, Nature News & Comment, 22 August 2016.	PDF (0.9 MB)
Featured in the American Chemical Society feed "Watching thoughts - and addiction - form in the brain", Science Daily, 22 August 2016. Further reproducd in Quartz,The Siasat Daily, India TV News, Gizmodo India, ZME Science, Free Press Journal, Science 2.0, EurekAlert, ABC Ciencia, and Quo.	PDF (0.8 MB)
Featured in the article "Mind aglow: Scientists watch thoughts form in the brain" by S. Chodosh, Scientific American, 24 August 2016.	PDF (0.9 MB)
Inhibition, not excitation, drives rhythmic whisking. M. Deschênes, J. Takatoh, A. Kurnikova, J.D. Moore, M. Demers, M Elbaz, T. Furuta, F. Wang and D. Kleinfeld, Neuron (2016) 90:374–387 (PMC4929009).	PDF (5.5 MB)
Supplementary information.	PDF (6.7 MB)
Preview "Inhibition patterns the whisking rhythm" by V. Sreenivasan and C.C.H. Petersen, Neuron (2016) 90:211-213.	PDF (0.4 MB)
Whisking, sniffing, and the hippocampal θ-rhythm: A tale of two oscillators D. Kleinfeld, M. Deschênes and N. Ulanovsky, Public Library of Science: Biology (2016) 14:e1002385 (PMC4758648). Primer on "Coherence between rat sensorimotor system and hippocampus is enhanced during tactile discrimination" by N. Grion, A. Akrami, Y. Zuo, F. Stella and M. E. Diamond, Public Library of Science: Biology (2016) 14:e1002384.	PDF (1.7 MB)

(2011 - 2015)

Vibrissa self-motion and touch are reliably encoded along the same somatosensory pathway from brainstem through thalamus. J. D. Moore, N. Mercer Lindsay, M. Deschênes* and D. Kleinfeld, Public Library of Science: Biology* (2015) 13:e1002253 (PMC4579082).	PDF (14.3 MB)
Ultra–large field-of-view two-photon laser scanning microscopy. P. S. Tsai, C. Mateo, J. J. Field, C. B. Schaffer, M. E. Anderson and D. Kleinfeld, Optics Express (2015) 123:13833-13847 (PMC4523368).	PDF (5.6 MB)
Selected by the editors-in-chief, Andrew Dunn and Anthony Durkin, for publication in the 4 August 2015, Volume 10, Issue 6 of Virtual Journal for Biomedical Optics
Highlighted in the Technology Feature "The real-time technicolour living brain" by A. Dance, Nature (2016) 539:315-318.	PDF (0.9 MB)
The brainstem oscillator for whisking and the case for breathing as the master clock for orofacial motor actions. D. Kleinfeld, J. D. Moore, F. Wang and M. Deschênes In Cold Spring Harbor Symposia on Quantitative Biology: Cognition, Volume 79, 2015, 79:29-39 (PMC4924579). Issue on "Cognition".	PDF (5.4 MB)
Juxtacellular monitoring and localization of single neurons within sub-cortical brain structures of alert, head-restrained rats. J. D. Moore, M. Deschênes and D. Kleinfeld, Journal of Visualized Experiments (2015) http://www.jove.com/video/51453 (PMC4541592).	PDF (3.3 MB)
Material list.	PDF (0.1 MB)
Deflection of a vibrissa leads to a gradient of strain across mechanoreceptors in the mystacial follicle. S. J. Whiteley. P. M. Knutsen, D. W. Matthews and D. Kleinfeld, Journal of Neurophysiology (2015) 114:138-145 (PMC4507969).	PDF (0.7 MB)
The musculature that drives active touch by vibrissae and nose in mice. S. Haidarliu, D. Kleinfeld, M. Deschênes & E. Ahissar, Anatomical Record (2015) 280:1347-1358 (PMC4930880).	PDF (1.8 MB)
Robust and fragile aspects of cortical blood flow in relation to the underlying angioarchitecture. A. Y. Shih, C. Rühlmann, P. Blinder, A. Devor, P. J. Drew. B. Friedman, P. M. Knutsen, P. D. Lyden, C. Mateo, L. Mellander N. Nishimura, C. B. Schaffer, P. S. Tsai and D. Kleinfeld, Microcirculation (2015) 22:204-218 (PMC4393797). Special issue on "Neurovascular coupling"	PDF (3.0 MB)
Fluorescently labeled peptide highlights degenerated facial nerve branches during surgery and improves functional outcome. T. Hussain, M. B. Mastrodimos, S. C. Raju, H. L. Glasgow, M. Whitney, B. Friedman, J. D. Moore, D. Kleinfeld, P. Steinbach, K. Messer, M. Pu, R. Y. Tsien and Q. T. Nguyen, Public Library of Science ONE (2015) journal.pone.0119600:1-13 (PMC4353702).	PDF (1.2 MB)
Feedback in the brainstem: An excitatory disynaptic pathway for control of whisking. D. W. Matthews, M. Deschênes, T. Furuta, J. D. Moore, F. Wang, H. J. Karten* and D. Kleinfeld, Journal of Comparative Neurology* (2015) 523:921-942 (PMC4329057).	PDF (6.1 MB)
Muscles involved in naris dilation and nose motion in rat. M. Deschênes, S. Haidarliu, M. Demers, J. D. Moore, D. Kleinfeld and E. Ahissar, Anatomical Record (2015) 298:546-553 (PMC4929008).	PDF (1.2 MB)
*Cell-based reporters reveal in vivo* dynamics of dopamine and norepinephrin release in murine cortex.** A. Muller, V. Joseph, P. A. Slesinger^ and D. Kleinfeld^, Nature Methods (2014) 11:1245-1252 (PMC4245316).	PDF (1.4 MB)
Supplementary material.	PDF (6.7 MB)
Featured in the article "Sensors shed light on levels of chemical messengers in mice" by M. Fessenden in the 12 November 2014 issue of Simons Foundation Autism Research Initiative News.	PDF (0.1 MB)
Articles based on the UCSD press release "Real-time read-out of neurchemical activity" appeared in Medical Xpress, News Medical, ZeeNews, eBioTrade, PsyPost, newKerala, Business Standard, Neuroscience News, Wn, Mangaloria, The Indian Journal, Driya News, Bright Surf, and Genetic Engineering & Biotechnology News.	PDF (0.2 MB)
"The author file: David Kleinfeld" by V. Marx, Nature Methods (2014) 11:1185.	PDF (0.2 MB)
How the brainstem controls orofacial behaviors comprised of rhythmic actions. J. D. Moore, D. Kleinfeld and F. Wang, Trends in Neuroscience (2014) 37:370-380 (PMC4100695).	PDF (2.7 MB)
Activation and measurement of free whisking in the lightly anesthetized rodent. J. D. Moore, M. Deschênes, A. Kurnikova and D. Kleinfeld, Nature Protocols (2014) 9:1792-1802 (PMC4934662) .	PDF (1.6 MB)
More than a rhythm of life: Breathing as a binder of orofacial sensation. D. Kleinfeld, M. Deschênes, F. Wang and J. D. Moore, Nature Neuroscience (2014) 17:647-551 (PMC4140942).	PDF (0.7 MB)
Mediation of muscular control of rhinarial motility in rats by the nasal cartilaginous skeleton. S. Haidarliu, D. Kleinfeld and E. Ahissar, Anatomical Record (2013) 296:1821-1832 (PMC4157211).	PDF (1.3 MB)
The challenge of connecting the dots in the B.R.A.I.N. A. Devor, P. A. Bandettini, D. A. Boas, J. M. Bower, R. B. Buxton, L. B. Cohen, A. M. Dale, G. T. Einevoll, P. T. Fox, M. A. Franchescini, K. J. Friston, J. G. Fujimoto, M. A. Geyer, J. H. Greenberg, E. Halgren, M. S. Hämäläinen, F. Helmchen, B. T. Hyman, A. Jasanoff, T. L. Jernigan, L. L. Judd, S.-G. Kim, D. Kleinfeld, N. J. Kopell, M. Kutas, K. K. Kwong, M. E. Larkum, E. H. Lo, P. J. Magistretti, J. B. Mandeville, E. Masliah, P. P. Mitra, W. C. Mobley, M. A. Moskowitz, A. Nimmerjahn, J. H. Reynolds, B. R. Rosen, B. M. Salzberg, C. B. Schaffer, G. A. Silva, P. T. C. So, N. C. Spitzer, R. B. Tootell, D. C. Van Essen, W. Vanduffel, S. A. Vinogradov, L. L. Wald, L. V. Wang, B. Weber and A. G. Yodh, Neuron (2013) 80:270-274 (PMC3864648).	PDF (0.1 MB)
All-optical osteotomy to create windows for transcranial imaging in mice. D. C. Jeong, P. S. Tsai and D. Kleinfeld, Optics Express (2013) 21:23160-23168 (PMC3971057).	PDF (3.4 MB)
Selected by the editors-in-chief, Andrew Dunn and Anthony Durkin, for publication in Virtual Journal for Biomedical Optics
ReaChR: A red-shifted variant of channelrhodopsin enables neuronal activation through the intact skull. J. Y. Lin, P. M. Knutsen, A. Muller, D. Kleinfeld and R. Y. Tsien, Nature Neuroscience (2013) 16:1499-1508 (PMC3793847).	PDF (2.0 MB)
Supplementary material.	PDF (4.2 MB)
A 2-star F1000Prime selection.	PDF (0.3 MB)
The cortical angiome: An interconnected vascular network with noncolumnar patterns of blood flow. P. Blinder, P. S. Tsai, J. P. Kaufhold, P. M. Knutsen, H. Suhl and D. Kleinfeld, Nature Neuroscience (2013) 16:889-897 (PMC4141079).	PDF (3.7 MB)
Vectorized data (.MAT and "read-me" files).	ZIP (232.9 MB)
A 2-star F1000Prime selection.	PDF (0.5 MB)
The Research Brief "Mouse brain circulatory system knows no bound?" appeared in the Alzheimer Research Forum.	PDF (0.3 MB)
Articles based on the UCSD press release "3-D map of blood vessels in cerebral cortex holds surprises" appeared in Africa-News, Association Alzheimer-Riese (Italy), Bio-Medicine, EurekAlert, Health Medicine Network, Journaux-Francais, MedicalPress (Spain), MyScience, News-Medical (France; Germany; Italy; Korea Poland; Russia; Spain), ScienceDaily, and ZeeNews.
The article "In Natural Networks, Strength in Loops" by Emily Singer, appeared in the Quanta Magazine.	PDF (1.0 MB)
The article "Nutrient Flow in the Brain is Controlled by Blood-Vessel Dilation, Reveals Network Model" by Martina Ribar Hestericova, appeared in Physics World.	PDF (0.6 MB)
Hierarchy of orofacial rhythms revealed through whisking and breathing. J. D. Moore, M. Deschênes, T. Furuta, D. Huber, M. C. Smear, M. Demers and D. Kleinfeld, Nature (2013) 469:53-57 (PMC4159559).	PDF (3.6 MB)
Supplementary material.	PDF (8.9 MB)
An 8-star F1000Prime selection.	PDF (0.3 MB)
The smallest stroke: Occlusion of one penetrating vessel leads to infarction and a cognitive deficit. A. Y. Shih, P. Blinder, P. S. Tsai, B. Friedman, G. Stanley, P. D. Lyden and D. Kleinfeld, Nature Neuroscience (2013) 16:55-63 (PMC3952571).	PDF (5.8 MB)
Supplementary material.	PDF (23.1 MB)
"Mini-stroke does mega-damage — Can Memantine help?" appeared in the Alzheimer Research Forum.	PDF (0.1 MB)
"Even the tiniest stroke can damage the brain" appeared in the New Scientist.	PDF (0.1 MB)
Articles based on the UCSD press release "Even the smallest possible stroke can damage brain tissue and impair cognitive function" appeared in Science 2.0, Pressetext, Doctor Tipster, Science Daily, redOrbit, Medical Daily, Medical Xpress, EurekAlert, Health.India, Hindustantimes, IANS live, and Barchester Healthcare.	PDF (0.1 MB)
Vectorization of optically sectioned brain microvasculature: Learning aids completion of vascular graphs by connecting gaps and deleting open-ended segments. J. P. Kaufhold, P. S. Tsai, P. Blinder and D. Kleinfeld, Medical Image Analysis (2012) 16:1241-1258 (PMC3443315).	PDF (4.0 MB)
Dorsorostral snout muscles in the rat subserve coordinated movement for whisking and sniffing. S. Haidarliu, D. Golomb, D. Kleinfeld and E. Ahissar, Anatomical Record (2012) 295:1181-1191 (PMC4153473).	PDF (2.9 MB)
Two-photon microscopy as a tool to study blood flow and neurovascular coupling in the rodent brain. A. Y. Shih, J. D. Driscoll, P. J. Drew, N. Nishimura, C. B. Schaffer and D. Kleinfeld, Journal of Cerebral Blood Flow and Metabolism (2012) 32:1277-1309 (PMC3390800).	PDF (2.7 MB)
Erratum (dosage), Journal of Cerebral Blood Flow and Metabolism (2013) 33:319.	PDF (0.1 MB)
Sniffing and whisking in rodents. M. Deschênes, J. D. Moore and D. Kleinfeld, Current Opinion in Neurobiology (2012) 22:243-250 (PMC4934665).	PDF (1.7 MB)
A polished and reinforced thinned skull window for long-term imaging and optical manipulation of the mouse cortex. A. Y. Shih, P. J. Drew, C. Mateo, P. S. Tsai and D. Kleinfeld, Journal of Visualized Experiments (2012) http://www.jove.com/video/3742 (PMC3460568).	PDF (0.7 MB)
High resolution video.	MOV (238.8 MB)
Prospect for feedback guided surgery with ultra-short pulsed laser light. D. C. Jeong, P. S. Tsai and D. Kleinfeld, Current Opinions in Neurobiology (2012) 22:24-33 (PMC3763077).	PDF (2.2 MB)
Differential multiphoton laser-scanning microscopy. J. J. Field, K. E. Sheetz, E. V. Chandler, E. E. Hoover, M. D. Young, S.-Y. Ding, A. W. Sylvester, D. Kleinfeld and J. A. Squier, IEEE Journal of Selected Topics in Quantum Electronics (2012) 18:14-28 (PMC4932844).	PDF (1.3 MB)
Large-scale automated histology in the pursuit of connectomes. D. Kleinfeld, A. Bharioke, P. Blinder, D. D. Bock, K. L. Briggman, D. B. Chklovskii, W. Denk, M. Helmstaedter, J. P. Kaufhold, W-C. A. Lee, H. S. Meyer, K. D. Micheva, M. Oberlaender, S. Prohaska, R. C. Reid, S. J. Smith, S. Takemura, P. S. Tsai and B. Sakmann, Journal of Neuroscience (2011) 31:16125-16138 (PMC3758571).	PDF (7.7 MB)
Neuronal basis for object location in the vibrissa scanning sensorimotor system. D. Kleinfeld and M. Deschênes. Neuron (2011) 72:455-468 (PMC3971931).	PDF (2.4 MB)
Hear David Kleinfeld interviewed by Senior Editor Katja Brose in a Cell PodCast on this work.	MP3 (9.9 MB)
Primary motor cortex reports efferent control of vibrissa position on multiple time scales. D. N. Hill, J. C. Curtis, J. D. Moore and D. Kleinfeld, Neuron (2011) 72:344–356 (PMC3717360).	PDF (2.1 MB)
Supplementary material.	PDF (4.5 MB)
Associated Preview "Movement, confusion, and orienting in frontal cortices" by M. Brecht, Neuron (2011) 71:193-195.	PDF (0.3 MB)
Photon counting, censor corrections, and lifetime imaging for improved detection in two-photon microscopy. J. D. Driscoll, A. Y. Shih, S. Iyengar, J. J. Field, G. A. White, J. A. Squire, G. Cauwenberghs and D. Kleinfeld, Journal of Neurophysiology (2011) 105:3106–3113 (PMC3118755).	PDF (1.6 MB)
Supplement on maximum likelihood estimate of counts	PDF (0.2 MB)
Supplement on firmware and hardware	PDF (0.3 MB)
Quality metrics to accompany spike sorting of extracellular signals. D. N. Hill, S. B. Mehta and D. Kleinfeld, Journal of Neuroscience (2011) 31:8699–8705 (PMC3123734).	PDF (1.2 MB)
Fluctuating and sensory-induced vasodynamics in rodent cortex extend arteriole capacity. P. J. Drew, A. Y. Shih and D. Kleinfeld, Proceedings of the National Academy of Sciences USA (2011) 108:8473-8478 (PMC3100929).	PDF (4.6 MB)
Supplementary material	PDF (4.5 MB)
A guide to delineate the logic of neurovascular signaling in the brain. D. Kleinfeld, P. Blinder, P. J. Drew, J. D. Driscoll, A. Muller, P. S. Tsai and A. Y. Shih, Frontiers in Neuroenergetics (2011) 3:1-9 (PMC3085135).	PDF (4.0 MB)
Characterizing ligand-gated ion channel receptors with genetically encoded Ca²⁺ sensors. J. G. Yamauchi, Á. Nemecz, Q.-T. Nguyen, A. Muller, L. F. Schroeder, T. T. Talley, J. Lindstrom, D. Kleinfeld and P. Taylor, Public Library of Science: ONE (2011) 6:e16519 (PMC3030600).	PDF (0.5 MB)

(2006 - 2010)

Chronic optical access through a polished and reinforced thinned skull. P. J. Drew, A. Y. Shih, J. D. Driscoll, P. M. Knutsen, P. Blinder, D. Davalos, K. Akassoglou, P. S. Tsai and D. Kleinfeld, Nature Methods (2010) 7:981-984 (PMC3204312).	PDF (3.7 MB)
Supplemental information	PDF (1.8 MB)
Journal cover based on article.	TIFF (0.4 MB)
Editorial titled "Brain Observations" Nature Methods (2010) 7:937.	PDF (0.1 MB)
Spatio-temporally focused femtosecond laser pulses for nonreciprocal writing in optically transparent materials. D. N. Vitek, E. Block, Y. Bellouard, D. E. Adams, S. Backus, D. Kleinfeld, C. G. Durfee and J. A. Squier, Optics Express (2010) 18:24673-24678 (PMC4157520).	PDF (3.2 MB)
Selected by the editor-in-chief, Gregory Faris, for publication in the Virtual Journal for Biomedical Optics
Automatic identification of fluorescently labeled brain cells for rapid functional imaging. I. Valmianski, A. Y. Shih, J. D. Driscoll, D. M. Matthews, Y. Freund and D. Kleinfeld, Journal of Neurophysiology (2010) 104:1803-1811 (PMC2944673).	PDF (3.5 MB)
Supplemental information.	PDF (1.1 MB)
Temporally focused femtosecond laser pulses for low numerical aperture micromachining through optically transparent materials. D. N. Vitek, D. E. Adams, A. Johnson, P. S. Tsai, S. Backus, C. G. Durfee, D. Kleinfeld and J. A. Squier, Optics Express (2010) 18:18086-18094 (PMC3408926).	PDF (1.8 MB)
Selected by the editor-in-chief, Gregory Faris, for publication in the Virtual Journal for Biomedical Optics
Topological basis for the robust distribution of blood to rodent neocortex. P. Blinder, A. Y. Shih, C. A. Rafie and D. Kleinfeld, Proceedings of the National Academy of Sciences USA (2010) 107:12670–12675 (PMC2906564).	PDF (2.6 MB)
Supplemental information.	PDF (1.0 MB)
Optimizing the fluorescent yield in two-photon laser scanning microscopy with dispersion compensation. J. J. Field, R. Carriles, K. E. Sheetz, E. E. Hoover, E. V. Chandler, S. Tillo, T. E. Hughes, A. W. Sylvester, D. Kleinfeld and J. A. Squier, Optics Express (2010) 18:13661-13672 (PMC4151303).	PDF (1.5 MB)
Selected by the editor-in-chief, Gregory Faris, for publication in the Virtual Journal for Biomedical Optics
An in vivo biosensor for neurotransmitter release and in situ receptor activity. Q.-T. Nguyen, L. F. Schroeder, M. Mank, A. Muller, P. W. Taylor, O. Griesbeck and D. Kleinfeld, Nature Neuroscience (2010) 13:127-132 (PMC3992257).	PDF (1.1 MB)
Supplemental information	PDF (0.6 MB)
Journal cover based on article.
A 1-star F1000Prime selection.
Featured in News and Views titled "Advancing neurochemical monitoring" by P A Garris, Nature Methods (2009) 7:106-107.	PDF (0.3 MB)
NIBIB Health and Education article titled "New Biosensors Shed Light on Brain Cell Cross-Talk"	PDF (10.3 MB)
News release, titled "New Biosensors Reveal Workings of Anti-Psychotic"	PDF (0.3 MB)
"Drugs in the Living Brain" featured in Science Daily, eurekalert.org, esciencenews.com, medicalnewstoday.com, machineslikeus.com, azonano.com, genengnews.com, news-medical.net, tumblr.com, bioportfolio.co.uk, physorg.com, genengnews.com, scienceblog.com, sciepedia.comlifesciencelog.com, newkerala.com, madeofstarstuff.tumblr.com, dailyindia.com, southasianews.com, healthcanal.com, sindhtoday.net, silobreaker.com, medicalonline.hu, scientistlive.com, sciencecentric.com, laboratoryequipment.com, thaindian.com, andhranews.net, surchur.com, and ebionews.com.	PDF (0.2 MB)
"Uncovering the Mystery of Anti-Psychotic Drugs in the Brain" featured in Ivanhoe Broadcast News.	PDF (0.2 MB)
"Biological cells reveal brain chemistry secrets" featured in BBC News.	PDF (0.1 MB)
"Researchers Design Cells to Help Determine Workings of Drugs" featured in Genetic Engineering and Biotechnology News.	PDF (0.1 MB)
Rapid determination of particle velocity from space-time images using the Radon transform. P. J. Drew, P. Blinder, G. Cauwenberghs, A. Y. Shih and D. Kleinfeld, Journal of Computational Neuroscience (2010) 29:5-11 (PMC4962871).	PDF (0.6 MB)
Enter the ratrix. B. Pesaran and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (2009) 106:19209-19210 (PMC2780815). Commentary on "Visually evoked activity in cortical cells imaged in freely moving animals" by J. Sawinski, D. J. Wallace, D. S. Greenberg, S. Grossmann, W. Denk and J. N. D. Kerr, Proceedings of the National Academy of Sciences USA (2009) 106:19557-19562.	PDF (0.3 MB)
Correlations of neuronal and microvascular densities in murine cortex revealed by direct counting and colocalization of nuclei and vessels. P. S. Tsai, J. P. Kaufhold, P. Blinder, B. Friedman, P. J. Drew, H. J. Karten, P. D. Lyden and D. Kleinfeld, Journal of Neuroscience (2009) 29:14553-14570 (PMC4972024).	PDF (6.4 MB)
Supplemental information.	PDF (0.7 MB)
Severe blood brain barrier disruption and surrounding tissue injury. B. Chen, B. Friedman, Q. Cheng, P. S. Tsai, E. Schim, D. Kleinfeld and P. D. Lyden, Stroke (2009) 40:e666-674 (PMC2819286).	PDF (1.4 MB)
Journal cover based on article.
The glial response is an essential component of hypoxia-induced erythropoiesis in mice. A. Weidemann, K. X. Knaup, C. A. Rafie, A. T. Boutin, C. Stockmann, N. Takeda, M. Scadeng, A. Y. Shih, V. H. Haase, M. C. Simon, D. Kleinfeld and R. S. Johnson, Journal of Clinical Investigations (2009) 119:3373-3383 (PMC2769183).	PDF (4.1 MB)
Supplemental information.	PDF (0.5 MB)
A proposal for a coordinated effort for the determination of brainwide neuroanatomical connectivity in model organisms at a mesoscopic scale. J. W. Bohland, C. Wu, H. Barbas, H. Bokil, H. T. Cline, P. J. Freed, R. J. Greenspan, S. N. Haber, M. Hawrylycz, D. G. Herrera, C. C. Hilgetag, Z. J. Huang, A. Jones, E. G. Jones, H. J. Karten, D. Kleinfeld, R. Kötter, H. A. Lester, J. M. Lin, S. Mikula, J. Panksepp, J. Safdieh, C. B. Saper, N. D. Schiff, B. W. Stillman, K. Svoboda, L. W. Swanson, A. W. Toga, J. D. Watson and P. P. Mitra, Public Library of Science: Computational Biology (2009) 5:e1000334 (PMC2655718).	PDF (0.6 MB)
Phase-to-rate transformations encode touch in cortical neurons of a scanning sensorimotor system. J. C. Curtis and D. Kleinfeld, Nature Neuroscience (2009) 12:492-501 (PMC2863011).	PDF (2.1 MB)
Supplemental information.	PDF (5.5 MB)
Associated News and Views "It's not you, it's me. Really" by G. B. Stanley, Nature Neuroscience (2009) 12:374-375.	PDF (0.2 MB)
Acute vascular disruption and Aquaporin 4 loss after stroke. B. Friedman, C. Schachtrup, P. S. Tsai, A. Y. Shih, K. Akassaglou, D. Kleinfeld and P. D. Lyden, Stroke (2009) 40:2182-2190 (PMC2753985).	PDF (1.1 MB)
Preliminary aspects of this work were the subject of a news release at the 2007 Society for Neuroscience Annual Meeting.
Plasma-mediated ablation: An optical tool for submicrometer surgery on neuronal and vascular systems. P. S. Tsai, P. Blinder, B. J. Migliori, J. Neev, Y. Jin, J. A. Squier and D. Kleinfeld, Current Opinion in Biotechnology (2009) 20:90-99 (PMC3123732).	PDF (1.2 MB)
Active dilation of penetrating arterioles restores red blood cell flux to penumbral neocortex after focal stroke. A. Y. Shih, B. Friedman, P. J. Drew, P. S. Tsai, P. D. Lyden and D. Kleinfeld, Journal of Cerebral Blood Flow and Metabolism (2009) 29:738-751 (PMC2893883).	PDF (0.7 MB)
Supplemental information.	PDF (2.6 MB)
News release, titled "Mesh-like Network Of Arteries Adjusts To Restore Blood Flow To Stroke-injured Brain " featured in Science Direct, United Press International, Post Chronicle, St. Louis Star, e! Science News, ScienceBlog, BioMedicine, PhysOrg.com, Science Codex, Big News Network, Machines Like Us, Lab Spaces, ScienceMode, Genetic Engneering and Biotechnology News, RxPG NEWS, NewsGuide.US, Science Centric, ZAMP Bionews, Eureka! Science News (Canada), KopalniaWiedzy (Poland), Insciences Organisation (Switzerland), Science Centric (Bulgaria), Medical News Today (UK), Newspost Online (India), Smash Hits (India), Hindu News (India), Fresh News (India), Frontline (India), Howrah News (India), Yahid News (India), SINDH TODAY (Pakistan), Thaindian.com (Thailand), NewsX (Asia).	PDF (0.2 MB)
Movie on "Two-photon Imaging of Blood Flow in the Pial Vasculature of Rat."	MOV (4.7 MB)
Stimulus-induced changes in blood flow and 2-deoxyglucose uptake dissociate in ipsilateral somatosensory cortex. A. Devor, E. M. C. Hillman, P. Tian, C. Waeber, I. C. Teng, L. Ruvinskaya, M. Shalinsky, H. Zhu, R. H. Haslinger, S. N. Narayanan, I. Ulbert, A. K. Dunn, E. H. Lo, B. R. Rosen, A. M. Dale, D. Kleinfeld and D. A. Boas, Journal of Neuroscience (2008) 28:14347-14357 (PMC2655308).	PDF (0.7 MB)
Selected for This Week in the Journal, December 31, 2008	PDF (0.1 MB)
"Research Highlight" in Nature Reviews Neuroscience (February 2009)	PDF (0.1 MB)
"Neuroimaging: Interpreting the signal" by Leonie Welberg in Nature Reviews Neuroscience (11 February 2009)	PDF (0.1 MB)
"Wiring and plumbing in the brain" by Jean Rossier in Frontiers in Human Neuroscience 3:1-2 (2009)	PDF (0.1 MB)
Advancing multifocal nonlinear microscopy: Development and application of a novel multibeam Yb:KGd(WO₄)₂ oscillator. K. E. Sheetz, E. E. Hoover, R. Carriles, D. Kleinfeld and J. A Squier, Optics Express (2008) 16:17574-15584.	PDF (0.3 MB)
Selected by the editor-in-chief, Gregory Faris, for publication in the Virtual Journal for Biomedical Optics.
Finding coherence in spontaneous oscillations. P. J. Drew, J. H. Duyn, E. Golanov and D. Kleinfeld, Nature Neuroscience (2008) 11:991-993. Commentary on "Interhemispheric correlations of slow spontaneous neuronal fluctuations revealed in human sensory cortex" by Y. Nir, R. Mukamel, I. Dinstein, E. Privman, M. Hare, L. Fisch, H. Gelbard-Sagiv, S. Kipervasser, F. Andelman, M. Y. Neufeld, U. Kramer, A. Arieli, I. Fried and R. Malach R. Nature Neuroscience (2008) 11:1100-1108.	PDF (0.7 MB)
Hear Patrick Drew, David Kleinfeld and Rafael Malach in "Brain waves: What they do and how to study them" by Kerri Smith, Nature NeuroPod, 27 March 2009, 15:40-22:40.	MP3 (11.5 MB)
Texture coding in the rat whisker system: Slip-stick versus differential resonance. J. Wolfe, D. N. Hill, S. Pahlavan, P. J. Drew, D. Kleinfeld and D. E. Feldman, Public Library of Science: Biology (2008) 6:1661-1677 (PMC2525689).	PDF (4.7 MB)
Associated Primer "Whisker-Mediated Texture Discrimination" by M. E. Diamond, M. von Heimendahl and E. Arabzadeh, Public Library of Science: Biology (2008) 6:1627-1630.	PDF (2.9 MB)
"Where" and "What" in the whisker sensorimotor system. M. E. Diamond, M. von Heimendahl, P. M. Knutsen, D. Kleinfeld and E. Ahissar, Nature Reviews of Neuroscience (2008) 9:601-612.	PDF (1.1 MB)
Journal cover based on article.
In vivo measurements of blood flow and glial cell function with two-photon laser scanning microscopy. F. Helmchen and D. Kleinfeld, Methods in Enzymology (2008) 444:231-254.	PDF (1.5 MB)
Biomechanics of the vibrissa motor plant in rat: Rhythmic whisking consists of triphasic neuromuscular activity. D. N. Hill, R. Bermejo, H. P. Zeigler and D. Kleinfeld, Journal of Neuroscience (2008) 28:3438-3455.	PDF (2.7 MB);
Simulation video	MPG (8.5 MB)
Wilder Penfield in the age of YouTube: Visualizing the sequential activation of sensorimotor areas across neocortex. D. Kleinfeld and J. Waters, Neuron (2007) 56:760-762. Commentary on "Spatiotemporal dynamics of cortical sensorimotor integration in behaving mice" by I. Ferezou, F. Haiss, L. J. Gentet, A. Aronoff, B. Weber and C. C. Petersen. Neuron (2007) 56:907-923.	PDF (0.2 MB)
Spherical aberration correction in nonlinear microscopy and optical ablation using a transparent deformable membrane. P. S. Tsai, B. Migliori, K. Campbell, T. Kim, Z. Kam, A. Groisman and D. Kleinfeld, Applied Physics Letters (2007) 91:191102.	PDF (0.7 MB)
Supplementary methods	PDF (0.4 MB)
News release, titled "An adjustable corrective lens for two-photon microscopy" by H. Hogan, featured in Biophotonics International.	PDF (0.5 MB)
Suppressed neuronal activity and concurrent arteriolar vasoconstriction may explain negative blood oxygenation level-dependent signal[s]. A. Devor, P. Tian, N. Nishimura, I. C. Teng, E. M. C. Hillman, S. N. Narayanan, I. Ulbert, D. A. Boas, D. Kleinfeld and A. M. Dale, Journal of Neuroscience (2007) 27:4452-4459 (PMC2680207).	PDF (0.4 MB)
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". A. Devor, A. Trevelyan and D. Kleinfeld, Journal of Neurophysiology (2007) 97:1880-1882.	PDF (0.1 MB)
Large two-photon absorptivity of hemoglobin in the infrared range of 780 - 880 nm. G. O. Clay, C. B. Schaffer and D. Kleinfeld, Journal of Chemical Physics (2007) 126:025102.	PDF (0.3 MB)
Active spatial perception in the vibrissa scanning sensorimotor system. S. B. Mehta, D. Whitmer, R. Figueroa, B. A. Williams and D. Kleinfeld, Public Library of Science: Biology (2007) 5:309-322 (PMC1769422).	PDF (2.5 MB)
Supplementary methods	PDF (4.3 MB)
Penetrating arterioles are a bottleneck in the perfusion of neocortex. N. Nishimura, C. S. Schaffer, B. Friedman, P. D. Lyden and D. Kleinfeld, Proceedings of the National Academy of Sciences USA (2007) 104:365-370 (PMC1765467).	PDF (4.1 MB)
Supplementary methods.	PDF (1.2 MB)
News release, titled "Bottleneck In Blood Supply Makes Brain Vulnerable To Strokes ", featured in Science Daily, Medical News Today, Newswise, HULIQ.com, PHYSORG.com, SpiritIndia.com, and MedIndia.com.	PDF (0.1 MB)
Active sensation: Insights from the rodent vibrissa sensorimotor system. D. Kleinfeld, E. Ahissar and M. E. Diamond. Current Opinions in Neurobiology (2006) 16:435-444.	PDF (0.2 MB)
Laser photoablation: A new biomedical tool. N. Nishimura, C. B. Schaffer, B. Friedman, P. S. Tsai, P. D. Lyden and D. Kleinfeld. SPIE Newsroom (2006)	PDF (0.2 MB)
Exploratory whisking by rat is not phase-locked to the hippocampal theta rhythm. R. W. Berg, D. Whitmer and D. Kleinfeld. Journal of Neuroscience (2006) 26:6518–6522.	PDF (0.5 MB)
Journal cover based on article.
A 1-star F1000Prime selection.
Seeing what the mouse sees with its vibrissae: A matter of behavioral state. J. C. Curtis and D. Kleinfeld. Neuron (2006) 50:524-526. Commentary on "Visualizing the cortical representation of whisker touch: Voltage-sensitive dye imaging in freely moving mice" by I. Ferezou, S. Bolea and C. C. Petersen. Neuron (2006) 50:617-629 (PMCID: PMC2863010).	PDF (0.2 MB)
MPScope: A versatile software suite for multiphoton microscopy. Q.-T. Nguyen, P. S. Tsai and D. Kleinfeld, Journal of Neuroscience Methods (2006) 156:351-359	PDF (0.6 MB)
Featured in "Research from University of California, Physics Department yields new data on neuroscience", Science Letter via Technology Marketing Corporation (2007)	PDF (0.3 MB)
Targeted insult to individual subsurface cortical blood vessels using ultrashort laser pulses: Three models of stroke. N. Nishimura, C. B. Schaffer, B. Friedman, P. S. Tsai, P. D. Lyden and D. Kleinfeld, Nature Methods (2006) 3:99-108	PDF (2.5 MB)
Supplemetary methods	PDF (1.3 MB)
Supplementary notes	PDF (0.1 MB)
Journal cover based on article (Jenny Groisman, artist).	PDF (0.3 MB)
News and Views titled "Different strokes for rodent folks"by R Flaumenhaft and E. H. Lo, Nature Methods (2006) 3:79-80	PDF (0.6 MB)
News release, titled "Stroke modeled with increased precision", featured in Science Daily	PDF (0.5 MB)
United Press International, Dementia.com, Psychiatry24x7.com, Hum-Molgen News Alert, WebIndia, Post Chronicle, Biocompare Life Science News, and Monsters & Critics News. Additionally featured in "New bane for the rat brain" by K. Heyman in ScienceNow (27 January 2006)	PDF (0.6 MB)
Laser lesions simulate microvessel stroke" by A. Burton in The Lancet 5:206	PDF (0.1 MB)
Neurological disorders - Making steps in stroke therapy" by S. Barton in Nature Reviews of Drug Discovery 5:187 and Nature Reviews of Neuroscience 7:173	PDF (0.1 MB)
Preliminary results featured in "Femtosecond laser pulses in biology: From microscopy to ablation and micromanipulation" by M. Arrigoni, Biophotonics International (June 2004) 48-51	PDF (0.7 MB)
Micro-scalpel offers unprecedented precision" by K. Schmidt, New Scientist (25 March 2005) 40-45.	PDF (1.1 MB)
Spectral mixing in nervous systems: Experimental evidence and biologically plausible circuits. D. Kleinfeld and S. B. Mehta. Progress of Theoretical Physics, Supplement (2006) 161:86-98. Special issue on "Oscillation, chaos and network dynamics in nonlinear science".	PDF (1.5 MB)
Two-photon imaging of cortical surface microvessels reveals a robust redistribution in blood flow after vascular occlusion. C. B. Schaffer, B. Friedman, N. Nishimura, L. F. Schroeder, P. S. Tsai, F. F. Ebner, P. D. Lyden and D. Kleinfeld. Public Library of Science: Biology (2006) 4:258-270 (PMC1324794).	PDF (4.6 MB)
Supplemental information	PDF (6.6 MB)
Supplemental video	MOV (7.2 MB)
Supplemental video caption	PDF (0.1 MB)
Synopsis titled "Redundancy in Cortical Surface Vessels Supports Persistent Blood Flow" by L. Gross, PLoS: Biology (2006) 2:e46	PDF (0.4 MB)
News release, titled “Laser technique sheds light on strokes”, featured in Science Daily, Medical News Today, YubaNet.com, What's New in Health, Innovations Report (Germany), PhysOrg.com, ProHealth.com, SLF Org News Center, WhatsNextNetwork.com, WebIndia, NewKerala.com, Science News, ProHealth.com, GlobalRPh.com, AlzheimerSupport.com, MedGadget.com, and OE Magazine (SPIE).	PDF (0.3 MB)
Additionally featured in “Brain's blood re-routes round clots“ by J. Marshall in the New Scientist (2006) no. 2534, a news brief by P. Daukantas in Optics & Photonics News (February 2006), and a news brief by D. Burgess in Photonics Spectra (February 2006).	PDF (0.1 MB)
Spectroscopy of third harmonic generation: Evidence for resonances in model compounds and ligated hemoglobin. G. O. Clay, A. C. Millard, C. B. Schaffer, J. Aus-der-Au, P. S. Tsai, J. A. Squier and D. Kleinfeld. Journal of the Optical Society of America B (2006) 23:932-950.	PDF (1.8 MB)
Selected by the editor-in-chief, Gregory Faris, for publication in the Virtual Journal for Biomedical Optics
Coding of stimulus frequency by latency in thalamic networks through the interplay of GABA_B-mediated feedback and stimulus shape. D. Golomb, E. Ahissar and D. Kleinfeld, Journal of Neurophysiology (2006) 95:1735-1750.	PDF (1.1 MB)

(2001 - 2005)

From art to engineering? The rise of in vivo mammalian electrophysiology through genetically targeted labeling and nonlinear imaging. D. Kleinfeld and O. Griesbeck. Public Library of Science: Biology (2005) 3:1685-1689.	PDF (0.6 MB)
Related material quoted in "Peering into the brain: New frontiers in neural imaging" by B. Patoine, Dana Foundation's Brain Work Neuroscience Newsletter (2005) 15:1-3.	PDF (0.3 MB)
A femtosecond laser-drilled capillary integrated into a microfluidic device. T. N. Kim, K. Campbell, A. Groisman, D. Kleinfeld and C. B. Schaffer. Applied Physics Letters (2005) 86:201106.	PDF (0.3 MB)
Featured in "Femtosecond laser brings 3-D to microfluidics" by R. Gaughan, Photonics Spectra (2005) August issue.	PDF (0.9 MB)
Activation of nucleus basalis facilitates cortical control of a brainstem motor program. R. W. Berg, B. Friedman, L. F. Schroeder and D. Kleinfeld. Journal of Neurophysiology (2005) 94:699-711.	PDF (3.9 MB)
Positive feedback in a brainstem tactile sensorimotor loop. Q.-T. Nguyen and D. Kleinfeld. Neuron (2005) 45:447-457.	PDF (0.7 MB)
Featured in "Preview: Navigating a sensorimotor loop" by E. E. Fanselow and B. W. Connors, Neuron (2005) 45:329-330.	PDF (0.1 MB)
News release “Rat Whiskers Give Clues to Blinking Disorder” featured at Healthday.com (HealthDayNews) and picked up by CommunityMemorial.com (Menomonee Falls, WI), Forbes.com, GoTriad.com, HealthCentral.com, HealthFinder.gov (US Dept. HHS), HealthScout.com, Health.Yahoo.com, HON.ch (Health on the Net), hvlib.Integris-Health.com (Oklahoma City, OK), LifeClinic.com, NewsTrove.com, NorthShoreLIJ.com (North Shore - Long Island Jewish Health System, NY), Reflector.com (The Daily Reflector), and WaukeshaMemorial.org. “Eye Disorder Clue from Rat Whiskers “ featured at Health24.com (South Africa).	PDF (0.1 MB)
“Rat Whisking May Provide Insight Into Debilitating Eye Disorder” featured at Innovations-Reports.com (Germany), NewsWise.com, ScienceDaily.com, UrekAlert.org (AAAS), and MediLexicon.com.	PDF (0.1 MB)
"A Hairy Clue About Blepharospam" featured in EyeOrbit (American Academy of Opthamology)	PDF (0.1 MB)
Goal-directed whisking behavior increases phase-locking between vibrissa movement and electrical activity in primary sensory cortex in rat. K. Ganguly and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (2004) 101:12348-12353.	PDF (0.6 MB)
Supplemental Material.	PDF (0.6 MB)
Beyond observation: Microscopy with ultrashort laser pulses to probe and manipulate cortical vasculature. G. O. Clay, N. Nishimura, C. B. Schaffer, P. S. Tsai and D. Kleinfeld. SPIE International Technical Group Newsletter, Optics in Information Systems (2004)15:4-5.	PDF (1.2 MB)
Current flow in vibrissa motor cortex can phase-lock with exploratory whisking in rat. K. F. Ahrens and D. Kleinfeld. Journal of Neurophysiology (2004) 92:1700-1707.	PDF (1.2 MB)
Featured in "What Makes Whiskers Shake? Focus on: Current Flow in Vibrissa Motor Cortex Can Phase-Lock With Exploratory Rhythmic Whisking in Rat'' by M. Brecht, Journal of Neurophysiology (2004) 92:1265-1266.	PDF (0.1 MB)
Ultrashort pulsed laser light: A cool tool for ultraprecise cutting of tissue and cells. P. S. Tsai, B. Friedman, J. A. Squier and D. Kleinfeld. Optics and Photonics News (2004) 15:24-29.	PDF (1.2 MB)
Selected by the editor-in-chief, Gregory Faris, for publication in the Virtual Journal for Biomedical Optics
Developmental regulation of active and passive membrane properties in rat vibrissa motoneurons. Q.-T. Nguyen, R. Wessel and D. Kleinfeld. Journal of Physiology (2004) 556:203-219.	PDF (0.9 MB)
Frisking the whiskers: Coding of patterned sensory input in the rat vibrissa system. S. B. Mehta and D. Kleinfeld. Neuron (2003) 41:181-184.	PDF (1.0 MB)
Reversing cerebellar long-term depression. V. Lev-Ram, S. B. Mehta, D. Kleinfeld and R. Y. Tsien. Proceedings of the National Academy of Sciences USA (2003) 100:15989-15993.	PDF (0.5 MB)
Featured in "Synaptic plasticity: Ups and downs of cerebellar plasticity" by S. Farley, Nature Reviews of Neuroscience 5:85 (2004).
Imaging reveals synaptic targets of a swim-terminating neuron in the leech CNS. A. Taylor, G. Cottrell, D. Kleinfeld and W. Kristan, Jr. Journal of Neuroscience (2003) 23:11402-11410.	PDF (0.5 MB)
Vibrissa movement elicited by rhythmic electrical microstimuation to motor cortex in the aroused rat mimics exploratory whisking. R. W. Berg and D. Kleinfeld. Journal of Neurophysiology (2003) 90:2950-2963.	PDF (1.3 MB)
All-optical histology using ultrashort laser pulses. P. S. Tsai, B. Friedman, A. I. Ifarraguerri, B. D. Thompson, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, J. A. Squier and D. Kleinfeld. Neuron (2003) 39:27-41.	PDF (0.9 MB)
Featured in "Femtosecond laser for cutting and imaging brain tissue" by P. Schewe, J. Riordon and B. Stein AIP Bulletin (Physics news update, 5 June 2003); "Lasers take 3D brain scans: Infrared light probes tissue a slice at a time" by G. Brumfiel, Nature (Science update, 10 June 2003); "Ultrafast lasers capture brain images", Photonics.com (Feature article, 2 July 2003); "Brain breakthrough", Fox 6 News (2 July 2003)	MOV (7.2 MB)
"Ultrafast lasers slice up high-quality brain tissue images", Space Daily (7 July 2003); "All-optical histology with femtosecond lasers" by S. Benka, Physics Today (Physics update, August 2003); "Ultrafast lasers enable all-optical histology" by D. Burgess, Photonics Spectra (August 2003); "All-optical histology using ultra-short laser pulses" by D. Boas, Photonics International (September 2003); "Mind-reader" by R. Smallridge, Nature Reviews - Molecular cell Biology (September 2003)	PDF (0.2 Mb)
"Newest imaging methods begin 'golden age' of seeing inside body", by R. Ehrenberg, The Dallas Morning News (October 2003)	PDF (0.2 MB)
"Slice of Life: Researchers develop new techniques to unveil the architecture of tissues", by K. Heyman , The Scientist (November 2003)	PDF (0.3 MB)
Unilateral vibrissa contact: Changes in amplitude but not the timing of vibrissa movement. R. H. S. Sachdev, R. W. Berg, G. Chompney, D. Kleinfeld and F. F. Ebner. Somatosensory and Motor Research (2003) 20:162-169.	PDF (0.2 MB)
Rhythmic whisking in rat: Retraction as well as protraction is under active muscular control. R. W. Berg and D. Kleinfeld. Journal of Neurophysiology (2003) 89:104-117.	PDF (0.8 MB)
Closed loop neuronal computations: Focus on vibrissa somatosensation in rat. E. Ahissar* and D. Kleinfeld. Cerebral Cortex* (2003) 13:53-62. Special issue on "Computation in cortical columns".	PDF (0.5 MB)
Spectral mixing of rhythmic neuronal signals in sensory cortex. K. F. Ahrens, H. Levine, H. Suhl and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (2002) 99:15176-15181.	PDF (0.4 MB)
Adaptive filtering of vibrissa input in motor cortex of rat. D. Kleinfeld, R. N. S. Sachdev, L. M. Merchant, M. R. Jarvis and F. F. Ebner. Neuron (2002) 34:1021-1034.	PDF (0.7 MB)
Featured in "How does the human brain regulate sensory information", Medical Device and Diagnostic Industry (R&D Digest, July 2002).
Coherent electrical activity between vibrissa sensory areas of cerebellum and neocortex is enhanced during free whisking. S. M. O'Connor, R. W. Berg and D. Kleinfeld. Journal of Neurophysiology (2002) 87:2137-2148.	PDF (1.3 MB)
Cortical imaging through the intact mouse skull using two-photon excitation laser scanning microscopy. E. J. Yoder and D. Kleinfeld. Microscopy Research and Technique (2002) 56:304-305.	PDF (0.3 MB)
Traveling electrical waves in cortex: Insights from phase dynamics and speculation on a computational role. G. B. Ermentrout* and D. Kleinfeld. Neuron* (2001) 29:33-44. Viewpoint.	PDF (1.0 MB)
Chattering and differential signal processing in identified motion-sensitive neurons of parallel visual pathways in the chick tectum. H. Luksch, H. J. Karten, D. Kleinfeld, and R. Wessel. Journal of Neuroscience (2001) 15:6440-6446.	PDF (0.3 MB)

(1996 - 2000)

Distributed and largely separate pools of neurons may drive two different components of the gill withdrawl reflex in Aplysia. M. Zochowski, L. B. Cohen, G. Fuhrmann and D. Kleinfeld. Journal of Neuroscience (2000) 20:8485-8492.	PDF (0.7 MB)
Direct evidence for local oscillatory current sources and intracortical phase gradients in turtle visual cortex. J. C. Prechtl, T. H. Bullock and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (2000) 97:877-882.	PDF (2.0 MB)
Dendritic Ca²⁺-activated K⁺ conductances regulate electrical signal propagation in an invertebrate neuron. R. Wessel, W. B. Kristan Jr. and D. Kleinfeld. Journal of Neuroscience (1999) 19:8319-8326.	PDF (0.3 MB)
Ultra-miniature headstage with 6-channel drive and vacuum-assisted micro-wire implantation for chronic recording from the neocortex. S. Venkatachalam, M. S. Fee and D. Kleinfeld. Journal of Neuroscience Methods (1999) 90:37-46.	PDF (0.9 MB)
Identification of neural circuits by imaging coherent electrical activity with FRET-based dyes. T. W. Cacciatore, P. D. Brodfueher, J. E. Gonzalez, T. Jiang, S. R. Adams, R. Y. Tsien, W. B. Kristan Jr. and D. Kleinfeld. Neuron (1999) 23:449-459.	PDF (0.4 MB)
Supralinear summation of synaptic inputs by an invertebrate neuron: Dendritic gain is mediated by an "inward rectifier" K⁺ current. R. Wessel, W. B. Kristan Jr. and D. Kleinfeld. Journal of Neuroscience (1999) 19:5875-5888.	PDF (0.6 MB)
Anatomical loops and their electrical dynamics in relation to whisking by rat. D. Kleinfeld, R. W. Berg and S. M. O'Connor. Somatosensory and Motor Research (1999) 16:69-88.	PDF (1.1 MB)
Fluctuations and stimulus-induced changes in blood flow observed in individual capillaries in layers 2 through 4 of rat neocortex. D. Kleinfeld, P. P. Mitra, F. Helmchen, and W. Denk. Proceedings of the National Academy of Sciences USA (1998) 95:15741-15746.	PDF (0.4 MB)
Correction in Proceedings of the National Academy of Sciences USA (1999) 96:8307c.	PDF (0.1 MB)
Featured in "Multiphoton microscopy" by E. Samuel, OPN Trends, supplement to Optics & Photonics News (2001) 1:12-15.
Reproduced in "Multiphoton Excitation Microscopy" (B.R. Masters, editor), 2003, SPIE Milestone Series of Selected Reprints, Bellingham, WA.
Charge displacements in interfacial layers containing reaction centers. P. Brzezinski, A. Messinger, Y. Blatt, A. Gopher and D. Kleinfeld. Journal of Membrane Biology (1998) 165:213-225.	PDF (0.2 MB)
Voltage-sensitive dyes for monitoring multineuronal activity in the intact central nervous system. J.-Y. Wu, Y.-W, Lam, C. X. Falk, L. B. Cohen, J. Fang, L. Loew, J. C. Prechtl, D. Kleinfeld and Y. Tsau. Histochemical Journal (1998) 30:169-187. Special issue on "Live cell imaging".	PDF (1.1 MB)
Central versus peripheral determinates of patterned spike activity in rat vibrissa cortex during whisking. M. S. Fee, P. P. Mitra and D. Kleinfeld. Journal of Neurophysiology (1997) 78:1144-1149.	PDF (1.9 MB)
Functional study of the rat cortical microcircuitry with voltage-sensitive dye imaging of neocortical slices. R. Yuste, D. W. Tank and D. Kleinfeld. Cerebral Cortex (1997) 7:546-558.	PDF (0.4 MB)
Visual stimuli induce waves of electrical activity in turtle cortex. J. C. Prechtl, L. B. Cohen, B. Pesaran, P. P. Mitra and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (1997) 94:7621-7626.	PDF (0.8 MB)
In vivo dendritic calcium dynamics in neocortical neurons. K. Svoboda, W. Denk, D. Kleinfeld and D. W. Tank. Nature (1997) 385:161-165.	PDF (1.4 MB)
Featured in "The year of the dendrite" by T.J. Sejnowski, Science (1997) 275:178-179.
Variability of extracellular spike waveforms of cortical neurons. M. S. Fee, P. P. Mitra and D. Kleinfeld. Journal of Neurophysiology (1996) 76:3823-3833.	PDF (3.2 MB)
Automatic sorting of multiple unit neuronal signals in the presence of anisotropic and non-Gaussian variability. M. S. Fee, P. P. Mitra and D. Kleinfeld. Journal of Neuroscience Methods (1996) 69:175:188	PDF (0.5 MB)
Erratum in Journal of Neuroscience Methods (1997) 71:233.	PDF (0.2 MB)
Distributed representation of vibrissa movement in the upper layers of somatosensory cortex revealed with voltage sensitive dyes. D. Kleinfeld and K. R. Delaney. Journal of Comparative Neurology (1996) 375:89-108	PDF (7.7 MB)
Erratum in Journal of Comparative Neurology (1997) 378:594.	PDF (0.1 MB)
Central and reflexive neuronal responses elicited by odor in a terrestrial mollusc. R. Gervais, D. Kleinfeld, K. R. Delaney, and A. Gelperin. Journal of Neurophysiology (1996) 76:1327-1339.	PDF (6.6 MB)
Oscillations and gaseous oxides in invertebrate olfaction. A. Gelperin, D. Kleinfeld, W. Denk and I. R. C. Cooke. Journal of Neurobiology (now Developmental Neurobiology) (1996) 30:110-122. Special issue on "Olfaction: What's new in the nose"	PDF (1.7 MB)

(1991 - 1995)

BDNF and NT-4/5 exert neurotrophic influences on injured adult spinal motor neurons. B. Friedman, D. Kleinfeld, N. Y. Ip, V. Verge, R. Moulton, P. Boland, E. Zlotchenko, R. M. Lindsay and L. Liu. Journal of Neuroscience (1995) 15:1044-1056.	PDF (3.7 MB)
On temporal codes and the spatiotemporal response of neurons in the lateral geniculate nucleus. D. Golomb, D. Kleinfeld, R. C. Reid, R. M. Shapley and B. I. Shraiman. Journal of Neurophysiology (1994) 72:2990-3003.	PDF (4.9 MB)
Anatomical and functional imaging of neurons and circuits using two photon laser scanning microscopy. W. Denk, K. R. Delaney, A. Gelperin, D. Kleinfeld, B. Strowbridge, D. W. Tank and R. Yuste. Journal of Neuroscience Methods (1994) 54:151-162. Special issue on "Imaging techniques in neurobiology".	PDF (1.7 MB)
Reproduced in "Multiphoton Excitation Microscopy" (B.R. Masters, editor), 2002, SPIE Milestone Series of Selected Reprints, Bellingham, WA.
Odors, oscillations and waves: Does it all compute? D.W. Tank, A. Gelperin and D. Kleinfeld. Science (1994) 265:1819-1820.	PDF (0.5 MB)
Dynamics of propagating waves in the olfactory network of a terrestrial mollusc: An electrical and optical study. D. Kleinfeld, K. R. Delaney, M. S. Fee, J. A. Flores, D.W. Tank and A. Gelperin. Journal of Neurophysiology (1994) 72:1402-1419.	PDF (2.9 MB)
Waves and stimulus-modulated dynamics in an oscillating olfactory network. K. R. Delaney, A. Gelperin, M. S. Fee, J. A. Flores, R. Gervais, D. W. Tank and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (1994) 91:669-673.	PDF (8.0 MB)
Stimulus dependent synchronization of neuronal assemblies. E. Grannan, D. Kleinfeld and H. Sompolinsky. Neural Computation (1993) 5:550-569.	PDF (1.1 MB)
Noninvasive detection of changes in membrane potential in cultured neurons via light-scattering. R. A. Stepnoski, A. LaPorta, F. Raccuia-Behling, G. E. Blonder, R. E. Slusher and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (1991) 88:9382-9386.	PDF (1.3 MB)
Featured in "Noninvasive Optical Spectroscopy and Imaging of Human Brain Function", by A. Villringer and B. Chance, Trends in Neuroscience (1997) 20:435-442.
Long-term optical recording of patterns of electrical activity in ensembles of cultured Aplysia neurons. T. D. Parsons, B. M. Salzberg, A. L. Obaid, F. Raccuia-Behling and D. Kleinfeld. Journal of Neurophysiology (1991) 66:316-333.	PDF (7.4 MB)
Journal cover based on article.
Cooperative dynamics in visual processing. H. Sompolinsky, D. Golomb and D. Kleinfeld. Physical Review A (1991) 43:6990-7011.	PDF (3.6 MB)

(1986 - 1990)

Comment on 'Physical mechanisms underlying neurite outgrowth: A quantitative analysis of neuronal shape'. D. Kleinfeld, F. Raccuia-Behling and G. E. Blonder. Physical Review Letters (1990) 65:3064.	PDF (0.2 MB)
Foreign connections are formed in vitro by Aplysia californica interneurone L10 and its in vivo followers and non-followers. D. Kleinfeld, T. D. Parsons, F. Raccuia-Behling, B. M. Salzberg and A. L. Obaid. Journal of Experimental Biology (1990) 154:237-255.	PDF (1.6 MB)
Journal cover based on article.
Global processing of visual stimuli in a neural network of coupled oscillators. H. Sompolinsky, D. Golomb and D. Kleinfeld. Proceedings of the National Academy of Sciences USA (1990) 87:7200-7204.	PDF (1.1 MB)
Reproduced in "Artificial neural networks: Oscillations, chaos, and sequence processing" (L. Wang and D.C. Alkon, editors), 1993, IEEE Computer Society Press, Los Alamitos, CA, pp. 70-74.
Circuits constructed from identified Aplysia neurons exhibit multiple patterns of persistent activity. D. Kleinfeld, F. Raccuia-Behling and H. J. Chiel. Biophysical Journal (1990) 57:697-715.	PDF (2.6 MB)
Journal cover based on article.
Optical recording of the electrical activity of synaptically interacting Aplysia neurons in culture using potentiometric probes. T. D. Parsons, D. Kleinfeld, F. Raccuia-Behling and B. M. Salzberg. Biophysical Journal (1989) 56:213-221.	PDF (1.3 MB)
Journal cover based on article.
Associative neural network models for the generation of temporal patterns: Theory and application to central pattern generators. D. Kleinfeld and H. Sompolinsky. Biophysical Journal (1988) 54:1039-1051	PDF (1.7 MB)
Reproduced in the anthology "Artificial neural networks: Oscillations, chaos, and sequence processing" (L. Wang and D.C. Alkon, editors), 1993, IEEE Computer Society Press, Los Alamitos, CA, pp. 56-69.
Controlled outgrowth of dissociated neurons on patterned substrates. D. Kleinfeld, K. R. Kahler and P. E. Hockberger. Journal of Neuroscience (1988) 8:4098-4120.	PDF (2.8 MB)
Featured in "A new form of organic gardening" by I. Amato, Science (1992) 258:1084.
"Unlearning" increases the storage capacity of content addressable memories. D. Kleinfeld and D. B. Pendergraft. Biophysical Journal (1987) 51:47-53.	PDF (0.7 MB)
Sequential state generation by model neural networks. D. Kleinfeld. Proceedings of the National Academy of Sciences USA (1986) 83:9469-9473.	PDF (1.1 MB)

(1981 - 1985)

Charge recombination kinetics as a probe of protonation of the primary acceptor in photosynthetic reaction centers. D. Kleinfeld, M. Y. Okamura and G. Feher. Biophysical Journal (1985) 48:849-852.	PDF (0.5 MB)
*Electron transfer in reaction centers from Rhodopseudomonas sphaeroides: II. Free energy and kinetic relations between the acceptors Q^-_AQ^-_B and Q_AQ_B^2-.* D. Kleinfeld, M. Y. Okamura and G. Feher. Biochimica et Biophysica Acta (1985) 809:291-310.	PDF (1.5 MB)
Electron-transfer kinetics in photosynthetic reaction centers cooled to cryogenic temperatures in the charge-separated state: Evidence for light-induced structural changes. D. Kleinfeld, M. Y. Okamura and G. Feher. Biochemistry (1984) 23:5780-5786.	PDF (1.3 MB)
Electron transfer in reaction centers from Rhodopseudomonas sphaeroides: I. Determination of the charge recombination pathway of DQ_AQ^-_B and free energy and kinetic relations between Q^-_AQ_B and Q_AQ^-_B. D. Kleinfeld, M. Y. Okamura and G. Feher. Biochimica et Biophysica Acta (1984) 766:126-140.	PDF (1.2 MB)
Damping of oscillations in the semiquinone absorption in reaction centers after successive flashes: Determination of the equilibrium between Q^-_AQ_B and Q_AQ^-_B. D. Kleinfeld, E. C. Abresch, M. Y. Okamura and G. Feher. Biochimica et Biophysica Acta (1984) 765:406-409.	PDF (0.3 MB)

Journal Articles (Work, finish, publish*)

*Michael Faraday (1791-1867)