Software

Neuropixels Trajectory Explorer adaptated for Sutter Manipulator, version of 15 December 2023

Access at: https://github.com/ActiveBrainAtlas2/neuropixels_trajectory_explorer
Description: Coded by D. P. Harel, added to the Neuropixels Trajectory Explorer (NTE) by Prof. A. Peters (Oxford), to include support for the MP285 Sutter micromanipulator with the MPC200 Controller and the ROE200 Interface. This feature enables real-time visualization of the Sutter manipulator movements. It provides an automated means for planning and performing electrode placement with the sutter manipulator. Please contact Mr. Dan P. Harel for questions on the operation of this software. The underlying NTE software is available at https://github.com/petersaj/neuropixels_trajectory_explorer.

Neocortical arteriole dynamics, version of 15 October 2023

Access at: https://github.com/JDuckworth1/NeurovascularDynamics
Coded by J. Duckworth and T. Broggini. Matlab-based routines for extracting spatiotemporal neurovascular dynamics from wide-field and two photon microscopy images. Scripts quantify propagating signals using the dominant vasomotor frequency and corresponding phase throughout the pial vasculature. The software also processes two photon data sets to quantify penetrating arteriole traveling dilations, vasomotor variations in red blood cell flux, and the relationship between smooth muscle calcium and vessel diameter. Please contact Mr. Jacob Duckworth for questions on the operation and maintenance of this software.
If you use this software in your research, please reference Broginni, Duckworth et al. (xxxx 2024) - PDF (X.X Mb)

Vascular connectome reconstruction and analysis, version of 22 February 2021

Download: ZIP (4.7 MB)
Coded by X. Ji. Matlab-based routines to reconstruct serial two-photon microscopy data of labeled vascualture and analyze the data Please contact Mr. Xiang Ji for questions on the operation and maintenance of this software. See also https://github.com/xiangjiph/VCRA.
If you use this software in your research, please reference Ji et al. (Neuron 2021) - PDF (7.0 MB)

Bassler_Camera_control, version of 22 November 2020

Download: ZIP (0.2 Mb)
Coded by C. Foo. Matlab-based routines to acquire video (1280x1024 frames) at high frame rates (>200Hz) for hardware-dependent periods; we currently achieve continuous acquisition of 720x720 frames at ~350 Hz. Please contact Dr. Conrad Foo for questions on the operation and maintenance of this software.
If you use this software in your research, please reference Foo et al. (Current Biology 2021) - PDF (2.2 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 (8.1 Mb)

VIDA_suite, version of 4 March 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 February 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)

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)

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)

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)