REFEREED PUBLICATIONS 32. A.F. Smith, V. Doyeux, M. Berg, M. Pyrounette, M. Haft-Javaherian, A.E. Larue, J.H. Slater, F. Lauwers, P. Blinder, P. S. Tsai, D. Kleinfeld, C.B. Schaffer, N. Nishimura,          Y. Davit, and S. Lorthois, Brain Capillary Networks Across Species: A few Simple Organizational Requirements Are Sufficient to Reproduce Both Structure and                 Function. Frontiers in Physiology (2019) 10:3389. 31. M. G. Baez-Yanez, P. Ehses, P. Mirkes, P. S. Tsai, D. Kleinfeld and K. Scheffler, The impact of vessel size, orientation and intravascular contribution on the           neurovascular fingerprint of BOLD bSSFP fMRI. NeuroImage (2017) 163:13-23 30.  C. I. Mateo, P. M. Knutsen, P. S. Tsai, A. Y. Shih and D. Kleinfeld, Entrainment of arteriole vasomotor fluctuations by neuronal activity: A basis of blood oxygen level           dependent "resting state" connectivity across cortex. Neuron (2017) 20(3):406-416 29.  K.Kisler, A. R. Nelson, S. V. Rege, A. Ramanathan, Y. Wang, A. Ahuja, D. Lazic, P. S. Tsai, Z. Zhao, Y. Zhou, D. A. Boas, S. Sakadzic & B. V. Zlokovic, Pericyte degeneration leads to           neurovascular uncoupling and limits oxygen supply to brain. Nature Neuroscience (2017) 28.  F. Schmid, P. S. Tsai, D. Kleinfeld, P. Jenny and B. Weber, Depth dependent flow and pressure characteristics in cortical microvascular networks. Public Library of Science: Computational               Biology (2017) 13:e1005392. 27.  I. Gould, P. S. Tsai, D. Kleinfeld and A. Linninger, The capillary bed offers the largest hemodynamic resistance to the cortical blood supply. Journal of Cerebral Blood Flow & Metabolism           (2017) 37:52-68. 26.  P. S. Tsai, C. Mateo, J.J. Field, C.B. Schaffer, M.E. Anderson & D. Kleinfeld, Ultra-large field-of-view two-photon microscopy. Optics Express (2015) 23: 13833-13847 25.  A.Y. Shih, C. Ruehlmann, 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, Robust           and Fragile Aspects of Cortical Blood Flow in Relation to the Underlying Angioarchitecture. Microcirculation (2015) 22:204-218 24.  D. C. Jeong, P. S. Tsai and D. Kleinfeld, All-optical osteotomy to create windows for transcranial imaging in mice. Optics Express 21:23160-23168 (2013). 23.  P. Blinder*, P. S. Tsai*, J. P. Kaufhold, P. M. Knutsen, H. Suhl and D. Kleinfeld, The cortical angiome: An interconnected vascular network with noncolumnar           patterns of blood flow. Nature Neuroscience 16:889-897 (2013). 22.  A. Y. Shih, P. Blinder, P. S. Tsai, B. Friedman, G. Stanley, P. D. Lyden and D. Kleinfeld,The smallest stroke: Occlusion of one penetrating vessel leads to           infarction and a cognitive deficit. Nature Neuroscience  16:55-63 (2013). 21.  J. P. Kaufhold, P. S. Tsai, P. Blinder and D. Kleinfeld, Vectorization of optically sectioned brain microvasculature: Learning aids completion of vascular graphs           by connecting gaps and deleting open-ended segments, Medical Image Analysis (2012). 20.  A. Y. Shih, P. J. Drew, C. Mateo, P. S. Tsai and D. Kleinfeld, A polished and reinforced thinned skull window for long-term imaging and optical manipulation of           the mouse cortex,. Journal of Visualized Neuroscience, http://www.jove.com/video/3742, (2011). 19.  D.C. Jeong, P. S. Tsai and D. Kleinfeld, Prospect for feedback guided surgery with ultra-short pulsed laser light, Current Opinions in Neurobiology, 22:24-33,           (2011). 18.  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, Large-scale automated histology in the pursuit of           connectomes. Journal of Neuroscience 31:16125-16138, (2011). 17.  D. Kleinfeld, P. Blinder, P. J. Drew, J. D. Driscoll, A. Muller, P. S. Tsai and A. Y. Shih, A guide to delineate the logic of neurovascular signaling in the brain.           Frontiers in Neuroenergetics, 3:1-9 (2010). 16.  P. J. Drew, A. Y. Shih, P. Knutsen, D. Davalos, P. Blinder, K. Akassoglou,  P. S. Tsai and D. Kleinfeld, Chronic imaging and optical manipulation of cortical cells           and microvessels through a large-area polished and reinforced thinned-skull. Nature Methods.,981-984, (2010). 15.  D. N. Vitek, D. E. Adams, A. Johnson, P. S. Tsai, S. Backus, C. G. Durfee, D. Kleinfeld and J. A. Squier, Temporally focused femtosecond laser pulses for low           numerical aperture micromachining through optically transparent materials. Optics Express 18:18086-18094, (2010). 14.  B. Chen, B. Friedman, Q. Cheng, P. S. Tsai, E. Schim, D. Kleinfeld, and P. D. Lyden, Severe blood-brain barrier disruption and surronding tissue injury, Stroke,           40, E666-E674 (2009). 13.  P. S. Tsai, J. Kaufhold, P. Blinder, B. Friedman, P.J. Drew, H.J. Karten, P. D. Lyden and D. Kleinfeld, Correlations of neuronal and microvascular densisties in           murine cortex revealed by direct counting and colocalization of nuclei and vessels, Journal of Neuroscience, 29(46) 14553-14570 (2009). 12.  P. S. Tsai, P. Blinder, B. J. Migliori, J. Neev, Y. Jin, J. A. Squier and D. Kleinfeld, Plasma-mediated ablation: An optical tool for submicrometer surgery on           neuronal and vascular systems. Current Opinion in Biotechnology, 20(1), 90-99 (2009). 11.  B. Friedman, C. Schachtrup, P. S. Tsai, A. Y. Shih, J. Nordberg, K. Akassoglou, D. Kleinfeld and P. D. Lyden, Acute vascular disruption and Aquaporin 4 loss           after stroke, Stroke, 40(6), 2182-2190, (2009). 10.  A. Shih, B. Friedman, P. Drew, P. S. Tsai, P. Lyden, and D.Kleinfeld, Active dilation of penetrating arterioles restores red blood cell flux to penumbral neocortex           after focal stroke, Journal of Cerebral Blood Flow and Metabolism, 29, 738-751. (2009). 9.    P. S. Tsai, B. Migliori, K. Campbell, T. N. Kim, Z. Kam, A. Groisman, and D. Kleinfeld, Spherical aberration correction in nonlinear microscopy and optical           ablation using a transparent deformable membrane, Applied Physics Letters, 91(19), 191102 (2007). 8.    Q. T. Nguyen, P. S. Tsai, D. Kleinfeld, MPScope: A versatile software suite for multiphoton microscopy, Journal of Neuroscience Methods, 156 (1-2), 351-359           (2006). 7.    G. O. Clay, A. C. Millard, C. B. Schaffer, J. Aus-der-Au, P. S. Tsai, J. A. Squier, and D. Kleinfeld, Spectroscopy of third harmonic generation: Evidence for           resonances in model compounds and ligated hemoglobin, Journal of the Optical Society of America B, 23 932 (2006). 6.    N. Nishimura, C. B. Schaffer, B. Friedman, P. S. Tsai, P. D. Lyden, and D. Kleinfeld, Targeted insult to individual subsurface cortical blood vessels using           ultrashort laser pulses: Three models of stroke. Nature Methods, 3, 99 (2006). 5.    C. B. Schaffer, B. Friedman, N. Nishimura, L. F. Schroeder, P. S. Tsai, F. F. Ebner, P. D. Lyden, and D. Kleinfeld, Two-photon imaging of cortical surface           microvessels reveals a robust redistribution in blood flow after vascular occlusion, Public Library of Science Biology, 4 (2), e22 (2006). 4.    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, All-Optical           Histology Using Ultrashort Laser Pulses, Neuron, 39, 27 (2003). 3.    J. A. Davis, P. S. Tsai, D.M. Cottrell, T. Sonehara, J. Amako, Transmission Variations in Liquid Crystal Spatial Light Modulators Caused by Interference and              Diffraction Effects. Optical Engineering, 38, 1051 (1999). 2.    J. A. Davis, P. S. Tsai, K.G. D’Neilly, Simple Technique for Determining the Extraordinary Axis Direction for Twisted-Nematic Liquid Crystal Spatial Light           Modulators, Optical Engineering, 38, 929 (1999). 1.    J. A. Davis, I. Moreno, P. S. Tsai, Polarization Eigenstates for Twisted-Nematic Liquid-Crystal Displays, Applied Optics, 37, 937 (1998).