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Software
MPScope 2.1
J. Driscoll and Q.-T. Nguyen. Pascal-based control and acquisition program for two-photon laser scanning microscopy.
ZIP
(XX Mb)
VIDA Suite 1.1
P. S. Tsai and J. P. Kaufhold. Matlab-based routines for the analysis of 3-D anatomical data sets.
ZIP (XX Mb)
Spike Sort 1.2.1
D. N Hill and S. B. Mehta. Matlab-based routines for the detction and clustering of putative single units from a multi-unit time series.
ZIP (1.1 Mb)
Solutions/Surgery
Surgical Guide for Rat Microdrive
Urethane Useage Guide
Artificial Cerebral Spinal Fluid
Preparation of 4 % Paraformadehyde
Nissl Staining
In vivo Laser Imaging
Headframe
Hamamatsu PMT
PMT Amplifier
PMT Holder (Linos Microbench Adapter)
Intermediate Analog Amplifier
Digital Integrator
Slow Current to Voltage Converter
Cambridge Scanners
Cambridge Drivers
National Instruments ADC Board
National Instruments DAC Board
Extracellular Recording
Headstage Buffer
Differential Preamplifier
200 Hz 5 Pole Highpass Filter Bank
0.1 to 100 Hz 1 Pole Highpass Filter / Amplifier Bank
Filter Bank for Frequency Devices Modules
Fullwave Rectification for EMG
National Instruments DAQ Board
Air Puff Controller
Documents on two-photon laser scanning microscopy (TPLSM)
Principles, design and construction of a two photon scanning
microscope for in vitro and in vivo studies. P. S. Tsai,
N. Nishimura, E. J. Yoder, A. White, E. Dolnick and D. Kleinfeld.
In Methods for In Vivo Optical Imaging (R. Frostig, editor), 2002,
CRC Press, pp. 113-171.
PDF (2,453kB)
MPScope 2.0: A computer system for two-photon laser scanning microscopy with
concurrent plasma-mediated ablation and electrophysiology.
Q.-T. Nguyen, J. Driscoll, E. M. Dolnick and D. Kleinfeld. In Methods for In Vivo Optical
Imaging, Second Edition, R. Frostig, editor, 2009, CRC Press,
4:117-142.
PDF (1.6 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
Documents on TPLSM applied to blood flow and stroke models
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)
Optical-based models of single vessel occlusion in rodent neocortex.
A. Y. Shih, N. Nishimura, J. Nguyen, B. Friedman, P. D. Lyden, C. B. Schaffer and D. Kleinfeld.
In Imaging in Neuroscience and Development, R. Yuste, series editor.
Book 2: Optical Imaging in Neuroscience, F. Helmchen and A. Konnerth, editors, 2009,
Cold Spring Harbor Laboratory Press, NY, Chapter 15, in press.
PDF (0.9 Mb)
Quantitative two-photon imaging of blood flow in cortex.
J. D. Driscoll, A. Y. Shih, P. J. Drew and D. Kleinfeld.
In Imaging in Neuroscience and Development, R. Yuste, series editor.
Book 2: Optical Imaging in Neuroscience, F. Helmchen and A. Konnerth, editors, 2009,
Cold Spring Harbor Laboratory Press, NY, Chapter 86, in press.
PDF (1.0 Mb)
Targeted occlusion to surface and deep vessels in
neocortex via linear and nonlinear optical absorption.
D. Kleinfeld, B. Friedman, P. D. Lyden and A. Y. Shih. In Animal
Models of Acute Neurological Injuries, J. Chen, Z. Xu, X.-M. Xu
and J. Zhang, editors, 2008, Contemporary Neuroscience Series,
The Humana Press, 14:169-185. PDF
(2.1 Mb)
Documents on all optical histology
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)
In vivo two-photon laser scanning microscopy with concurrent
plasma-mediated ablation: Principles and hardware realization.
P. S. Tsai and D. Kleinfeld. In Methods for In Vivo Optical Imaging,
Second Edition, R. Frostig, editor, 2009, CRC Press, 3:59-115.
PDF (6.2 Mb)
All-optical, in situ histology of brain tissue with femtosecond laser pulses.
P. S. Tsai, P. Blinder, J. D. Squire and D. Kleinfeld.
In Imaging in Neuroscience and Development, R. Yuste, series editor.
Book 2: Optical Imaging in Neuroscience, F. Helmchen and A. Konnerth, editors, 2009,
Cold Spring Harbor Laboratory Press, NY, Chapter 99, in press.
PDF (0.6 Mb)
Documents on spectral analysis
Spectral analysis for dynamical imaging data.
B. Pesarian, A. Sornborger, N. Nishimura, D. Kleinfeld and P.P.
Mitra. In Imaging in Neuroscience and Development: A Laboratory
Manual, R. Yuste and A. Konnerth, editors, 2005, Cold Spring
Harbor Laboratory Press, NY, 57:439-444. PDF
(1,175kB)
Applications of spectral methods in functional brain imaging.
D. Kleinfeld and P. P. Mitra.
In Imaging in Neuroscience and Development, R. Yuste, series editor.
Book 1: Optical Imaging Techniques, R. Yuste, editor, 2009,
Cold Spring Harbor Laboratory Press, NY, Chapter 7, in press.
PDF (3.2 Mb);
Movie of raw calcium dynamics in figure 4A AVI (11.5 Mb);
Movie of denoised calcium dynamics in figure 4B AVI (11.5 Mb)
Documents on extracellular recording and spike sorting
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)
Spike Sorting. D. N. Hill, D. Kleinfeld and
S. B. Mehta. In Observed Brain Dynamics by P. P. Mitra and H.
Bokil, 2007, Oxford Press, 9:257-270. PDF
(1.8 Mb)
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 (1997) 71:233. PDF
(0.2 Mb)
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