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

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Please let us know if we have forgotten anyone!