Proceedings

(2016 - 2020)

The active atlas: Combining 3D anatomical models with texture detectors.
Y. Chen, L. McElvain, A. Tolpygo, D. Ferrante, H. Karten, P. Mitra, D. Kleinfeld & Y. Freund. In Prooceedings of the Medical Image Computing and Computer Assisted Intervention Society, in press (2017).
Small blood vessels: Big health problems? Scientific recommendations of the National Institutes of Health Workshop.
F. Bosetti, Z. S. Galis, M. S. Bynoe, M. Charette, M. J. Cipolla, G. J. Del Zoppo, D. Gould, T. S. Hatsukami, T. L. Jones, J. I. Koenig, G. A. Lutty, C. Maric-Bilkan, T. Stevens, H. E. Tolunay and W. Koroshetz on behalf of Workshop participants. Journal of the American Heart Association 5:e004389 (2016).
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Collaborators: D. Agalliu, D. A. Antonetti, M. Boehm, C. E. Brooks, K. M. Caron, W. Chilian, M. J. Daemen, R. D'Amato, T. P. Davis, A. Ergul, J. E. Faber, A. R. Gomez, P. Grayson, I. Grumbach, J. Grutzendler, C. Gu, D. Gutterman, J. Hallenbeck, I. Herman, J. Humphrey, C. Iadecola, E. W. Inscho, D. Kleinfeld, E. H. Lo, J. A. Lopez, S. Macknik, A. Malik, T. N. Mayadas, D. McGavern, G. A. Meininger, V. M. Miller, M.Nedergaard, M. Nelson, S. Peirce-Cottler, I. Ramadan, G. A. Rosenberg, E. L. Schiffrin, P. Searson, N. Stachenfeld, R. V. Stan, Y. Suarez, E. E. Ubogu, Z. S. Vexler, C. M. Weyand and B. V. Zlokovic.
What advances in microscopy are required for combined MRI and optical functional brain imaging?
D. Kleinfeld.SPIE Conference on Adaptive Optics and Wavefront Control for Biological Systems II, San Francisco, CA. Proceedings of SPIE, Volume 9717, Article Number UNSP 97170D (2016).
Neurovascular and immuno-imaging: From mechanisms to therapies.
K. Akassoglou, D. Agalliu, C. J. Chang, D. Davalos, J. Grutzendler, E. M. C. Hillman, B. S. Khakh, D. Kleinfeld, D. McGavern, S. J. Nelson and B. V. Zlokovic. Proceedings of the Inaugural Symposium, San Francisco, CA, March 2015 In Frontiers in Neuroscience, Neurodegeneration (2016).
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(2011 - 2015)

Spatio-temporally focused femtosecond laser pulses for anisotropic writing in optically transparent materials.
D. Vitek, E. Block, Y. Bellouard, D. E. Adams, S. Backus, D. Kleinfeld, C. Durfee and J. A. Squier. In Proceedings of CLEO (2011).
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(2006 - 2010)

Spatially chirped pulses for high aspect ratio micromachining by femtosecond laser ablation.
D. Vitek, D. Adams, A. Johnson, D. Kleinfeld, S. Backus, C. Durfee and J. A. Squier. In Proceedings of CLEO (2010).
Threshold relaxation is an effective means to connect gaps in 3D images of complex microvascular networks.
J. Kaufhold, P. S. Tsai, P. Blinder and D. Kleinfeld. In Proceedings of the 3rd Workshop on Microscopic Image Analysis with Applications in Biology (in conjunction with MICCAI 2008).
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Winner of the 2009 SAIC "Best Conference Paper" award.
Computational intelligence in electrophysiology: Trends and open problems.
C. G√ľnay, T. G. Smolinski, W. W. Lytton, T. M. Morse, P. Gleeson, S. Crook, V. Steuber, A. Silver, H. Voicu, P. Andrews, H. Bokil, H. Maniar, C. Loader, S. Mehta, D. Kleinfeld, D. Thomson, P. P. Mitra, G. Aaron and J.-M. Fellous In Applications of Computational Intelligence in Biology, volume 122, chapter 14, pp. 325-359 of the series Studies in Computational Intelligence, T. G. Smolinski, M. G. Milanova and A.-E. Hassanien, editors, Springer-Verlag (2008).
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Dynamics and resilience of blood flow in cortical microvessels.
D. Kleinfeld. In Proceedings of a Workshop on Statistics on Networks, National Research Council, The National Academies Press, Washington, DC (2007) pp 292-316.
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Dynamics and resilience of blood flow in cortical microvessels revealed with optical imaging and manipulations.
D. Kleinfeld. In Proceedings of the Fifth Inter-Institute Workshop on "Optical Diagnostic Imaging from Bench to Bedside", National Institutes of Health, Bethesda, MD (2006).
RAM Video
Transcript PDF (0.1 Mb)
In vivo manipulation of biological systems with femtosecond laser pulses.
N. Nishimura, C. B. Schaffer and D. Kleinfeld. In Proceedings of SPIE Vol. 6261 High-Power Laser Ablation VI, (2006) pp 62611J.
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Applying optical imaging to study neurovascular coupling in cerebral cortex: From populational scale to single-cell single-vessel measurements.
A. Devor, E. Hillman, N. Nishimura, I. U. S. Narayanan, I. Teng, A. Dunn, D. Boas, D. Kleinfeld and A. Dale. In Proceedings of the Optical Society of America, Biomedical Optics meeting (BIOMED 2006), Fort Lauderdale, FL (2006).
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Ultrafast third harmonic micro-spectroscopy reveals a two-photon resonance in human hemoglobin.
G. O. Clay, C. B. Schaffer, J. A. Squier, and D. Kleinfeld. In Proceedings of the SPIE/Photonics West (Commercial and Biomedical Applications of Ultrafast Lasers VI, J. Neev, S. Nolte, A. Heisterkamp and C. B. Schaffer, editors), San Jose, CA (2006) paper 6108-8.
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(2001 - 2005)

Ischemic islands in the infarct and penumbra after MCA occlusion.
B. Friedman, Q. Cheng, S. W. Yu, N. Nishimura, C. B. Schaffer, F. F. Ebner, D. Kleinfeld and P. D. Lyden. Annals of Neurology (2005) 58:S9.
 
Heterogeneous changes in blood flow in response to single vessel blockages and MCA occlusions in rat parietal cortex as revealed by in vivo two-photon laser imaging.
B. Friedman, N. Nishimura, C. B. Schaffer, D. Kleinfeld, and P. D. Lyden. Stroke (2004) 35:81.
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Targetted disruption of deep-lying neocortical microvessels in rat using ultrashort laser pulses.
N. Nishimura, C. B. Schaffer, B. Friedman, P. S. Tsai, P. D. Lyden and D. Kleinfeld. In Proceedings of the SPIE (Commercial and Biomedical Applications of Ultrafast Lasers IV, J. Neev, C. B. Schaffer and A. Osterdorf, editors), vol. 5340 (2004) pp 179-187.
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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)
Featured in "Micro-scalpel Offers Unprecedented Precision" by K. Schmidt, New Scientist (25 March 2005) 40-45. PDF (1.0 Mb)
All optical histology: Serial ablation and multiphoton imaging of neuronal tissue with femtosecond laser pulses.
P. S. Tsai, B. Friedman, V. Lev-Ram, C. B. Schaffer, Q. Xiong, R. Y. Tsien, D. Kleinfeld, A. I. Ifarraguerri, B. D. Thompson and J. A. Squier. In Proceedings of the Lasers and Electro-Optics Society of the IEEE, Tuscon, AZ (2003).
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Real-time two-photon fluorescent microscopy of blood flow dynamics following photothrombotic stroke in rat neocortex.
C. B. Schaffer, F. F. Ebner, N. Nishimura, B. Friedman, P. S. Tsai, L. F. Schroeder, P. D. Lyden and D. Kleinfeld. In Proceedings of the Lasers and Electro-Optics Society of the IEEE, Tuscon, AZ (2003).
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Two-photon fluorescence microscopy of collateral blood flow following photoyhtombotic stroke in rat neocortex.
C. B. Schaffer, F. F. Ebner, N. Nishimura, B. Friedman, P. S. Tsai, L. F. Schroeder, P. D. Lyden and D. Kleinfeld. In Proceedings of the Optical Society of America, Tuscon, AZ (2003).
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Customization of microfluidic devices using femtosecond laser micromaching.
T. N. Kim, A. Groisman, D. Kleinfeld and C. B. Schaffer. In Proceedings of the Optical Society of America, Tucson, AZ (2003).
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All optical histology of brain tissue: Serial ablation and multiphoton imaging with femtosecond laser pulses.
P. S. Tsai, B. Friedman, V. Lev-Ram, Q. Xiong, R. Y. Tsien, D. Kleinfeld, A. I. Ifarraguerri, B. D. Thompson and J. A. Squier. In Proceedings of CLEO, Baltimore, MD (2003).
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All optical thrombotic stroke model for near-surface blood vessels in rat: Focal illumination of exogenous photosensitizers combined with real-time two-photon imaging.
C. B. Schaffer, P. S. Tsai, N. Nishimura, L. F. Schroeder, B. Friedman, P. D. Lyden, F. F. Ebner and D. Kleinfeld. In Proceedings of the SPIE/Photonics West (Commercial and Biomedical Applications of Ultrafast Lasers III, J. Neev, A. Osterdof and C. B. Schaffer, editors), San Jose, CA (2003) pp 222-231.
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Traveling electrical waves in cortex: Measurements with optical imaging techniques and insights from phase dynamics.
D. Kleinfeld. In Proceedings of the SPIE, San Diego, CA (2001).
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(1996 - 2000)

Anatomical loops and their electrical dynamics in relation to whisking by rat.
D. Kleinfeld, R. W. Berg and S. M. O'Connor. In Proceedings of Barrels XI. Somatosensory and Motor Research (1999) 16:163-164.
 
In vivo imaging of electrical activity in vibrissa cortex.
D. Kleinfeld. In Proceedings of Barrels X. Somatosensory and Motor Research (1998) 15:00.
 
Natural stimuli induce waves of electrical activity in visual cortex in turtle.
D. Kleinfeld, and J. C. Prechtl. In Proceedings of Neural Information Processing Systems XII, Breckenridge, CO (1997) 12:00.
 
Motor modulation of sensory input: Exploratory whisking by rat as a model system.
D. Kleinfeld, P. P. Mitra and M. S. Fee. In Proceedings of Barrels IX. Somatosensory and Motor Research (1997) 14:63.