Acknowledge_Packages

Open-source Contributions

This work would not have been possible without the following open-source packages and functions (in no particular order):

FilterM Copyright (c) 2011, Jan Simon
- We took advantage of the fast digital filter to perform the pre-processing stage.
Scrollable GUI panels Copyright (c) 2018, Yair Altman
- We used this for the GUI. This code places the specified uicontrol or uipanel inside a panel with a scroll bar. Take a look at undocumented Matlab by Yair Altman (sometimes referenced as YMA in our comments) for other useful code.
InPolygon MEX Copyright (c) 2009, Guillaume JACQUENOT
- This MEX file implements a fast detection of points inside a polygonal region. It may be deprecated for more-recent Matlab versions, but we would like to acknowledge it here regardless since it was very helpful during development.
SPC from wave_clus by Quian Quiroga.
- Paper: A novel and fully automatic spike sorting implementation with variable number of features. F. J. Chaure, H. G. Rey and R. Quian Quiroga. Journal of Neurophysiology; 2018.
- We make use of this in the doAutoClustering method, if the 'SPC' option is set in +defaults/AutoClustering.m
Freedrawhand Copyright (c) 2009, Brett Shoelson
- This function draws smooth lines freehand on images or plots and returns the handle and xy data of the line object.
cprintf Copyright (c) 2015, Yair Altman
- This code displays sprintf-formatted strings in the Command Window using the specified color/underline style.
getopt by dgleich 2003.
- The function returns a modified properties structure, given an initial properties structure, and a list of paired arguments. It is useful for parsing variable-length method input arguments.
DataHigh by Benjo Cowley and Byron Yu
- Paper: Graphical user interface for visualizing and interacting with high-dimensional neural activity, by B. R. Cowley, M. T. Kaufman, Z. S. Butler, M. M. Churchland, S. I. Ryu, K. V. Shenoy, and B. M. Yu. J Neural Eng, vol. 10, 2013, 066012.
- Paper: Gaussian-process factor analysis for low-dimensional single-trial analysis of neural population activity, by B. M. Yu, J. P. Cunningham, G. Santhanam, S. I. Ryu, K. V. Shenoy*, and M. Sahani*. J Neurophysiol, vol. 102, 2009, pp. 614-635.
- We drew inspiration from this excellent toolkit in the HighDimsUI for visualizing high-dimensional spike waveform snippets for sorting spike clusters in a high-dimensional space using nigeLab.Sort
Widget Toolbox Copyright (c) 2019, The MathWorks, Inc. Modular components and controls to efficiently develop advanced user interfaces in MATLAB.
- Most user interfaces make use of components from this toolbox, which may be deprecated for versions of Matlab more recent than R2017a (which was primarily used during development).
Simple Clust Jakob Voigts (v0.5, 2013)
- I don't think anything from simple_clust.m was implemented directly in the current version of nigeLab, but this toolkit was a source of inspiration for the "progress load circle" and (more importantly) the "flattening" procedure that allows cluster cutting on millions of spikes at a time in a more efficient way.
Rollover effect on pushbuttons by Laurent Vaylet (2020). MATLAB Central File Exchange. Retrieved January 3, 2020.
- This was adapted and used in the nigelDash interface to allow "mouse-over" highlight on nigelButton class.
Get Git Info Copyright (c) 2011 Andrew Leifer
- This was used to associate versioning/release numbers with nigelObj objects.
LinePlotReducer Copyright (c) 2015 by Tucker McClure
- This was used to reduce the graphics burden of some of the user interfaces, such as nigeLab.libs.TimeScrollerAxes