Software

MPScope 2.0

Download: ZIP (6.0 Mb)
Documentation: For MPScope 1.1
Coded by Q.-T. Nguyen and refined by P. S. Tsai and J. D. Driscoll. Pascal-based control and acquisition program for two-photon laser scanning microscopy.
If you use this software, please reference Nguyen et al. (J Neurosci Meth 2006) - PDF (0.6 Mb) snd Nguyen et al. (In Methods for In Vivo Optical Imaging, 2nd ed., R. Frostig, Ed., 2009, CRC Press) - PDF (1.6 Mb)

VIDA_suite, version 4 of Mar 2015

Download: ZIP (3.4 Mb)
Coded by P. S. Tsai and J. P. Kaufhold. Matlab-based routines for the analysis of 3-D anatomical data sets. Upgraded to run on Matlab R2013b(8.2.0.701). Please contact Dr. Philbert Tsai for questions on the operation and maintenance of this software.
If you use this software in your research, please reference Tsai et al. (J Neurosci 2009) - PDF (6.4 Mb) & PDF (0.7 Mb)

UltraMegaSort2000, version of Feb 2012

Download: ZIP (1.1 Mb)
Manual: PDF (1.0 Mb)
Coded by D. N Hill and S. B. Mehta following an initial version coded by M. S. Fee. Matlab-based routines for the detection and clustering of putative single units from a multi-unit time series, along with quality metrics. Please contact Dr. Daniel N. Hill for questions on the operation and maintenance of this software after consulting the manual.
If you use this software in your research, please reference Hill et al. (J Neurosci 2012) - PDF (1.2 Mb) and Fee et al. (J Neurosci Meth 1997) - PDF(0.5 Mb) & PDF (0.2 Mb)

Intelligent_scanning 1.0

Download: ZIP (0.9 Mb)
Coded by I. Valmianski and J. D. Driscoll. Matlab-based routines for the automatic identification of fluorescently labeled brain cells in two-photon scanning microscopy image stacks and the subsequent calculation of an optimized scan path through these cells. This program makes concurrent use of JBoost. Please contact Mr. Ilya Valmiansky for questions on the operation of this software.
If you use this software in your research, please reference Valmianski et al. (J Neurophysiol 2010) - PDF (3.5 Mb)

Hilbert transform

Download: ZIP (0.1 Mb)
Coded by D. N. Hill, this makes use of Matlab-based routines for the extraction of amplitude, midpoint, and phase from a rhythmic signal using Black's technique. Please contact Dr. Daniel N. Hill for questions on the operation of this software.
If you use this software in your research, please reference Hill et al. (Neuron 2011) - PDF (2.1 Mb)

Radon transform

Download (Algorithm & Demo Code): m-code (0.1 Mb)
Download (Routines for use with MPScope 2): ZIP (0.7 Mb)
Coded by P. J. Drew, this makes use of Matlab-based routines for the extraction of blood flow velocity from scanning space-time data. Please contact Prof. Patrick Drew for questions on the operation of this code.
If you use this software in your research, please reference Drew et al. (J Comput Neurosci 2010) - PDF (0.6 Mb)

Analysis of neuronal spike trains, deconstructed

Download (Code & Datasets): ZIP (66.1 Mb)
Further: (1) commercial software from MathWorks (http://www.mathworks.com) is required, including MATLAB, the Image Processing Toolbox, the Optimization Toolbox, the Signal Processing Toolbox, the Statistics Toolbox, and the Symbolic Math Toolbox. (2) download Daniel Hill’s code (above) for the Hilbert transform (http://neurophysics.ucsd.edu/software.php); (3) download Partha Mitra’s Chronux Toolbox (http://www.chronux.org); (4) download Jonathan Pillow’s Generalized Linear Model (GLM) implementation for spike trains (http://pillowlab.princeton.edu/code_GLM.html); (5) download Mark Schmidt’s L1-norm function L1GeneralGroup_Auxiliary.m (https://www.cs.ubc.ca/schmidtm/Software/thesis.html); and (6) download multidimensional histogram function histcn.m download at http://www.mathworks.com/matlabcentral/fileexchange/23897-ndimensional-histogram/content/histcn.m.
If you use this software in your research, please reference Aljadeff et al. (Neuron 2016) - PDF (9.1 Mb)