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WaveMAP analysis of extracellular waveforms from monkey premotor cortex during decision-making

Lee, Eric; Balasubramanian, Hymavathy; Tsolias, Alexandra; Anakwe, Stephanie; Medalla, Maria; Shenoy, Krishna; Chandrasekaran, Chandramouli

Cortical circuits are thought to contain a large number of cell types that coordinate to produce behavior. Current in vivo methods rely on clustering of specified features of extracellular waveforms to identify putative cell types, but these capture only a small amount of variation. Here, we develop a new method (WaveMAP) that combines non-linear dimensionality reduction with graph clustering to identify putative cell types. We apply WaveMAP to extracellular waveforms recorded from dorsal premotor cortex of macaque monkeys performing a decision-making task. Using WaveMAP, we robustly establish eight waveform clusters and show that these clusters recapitulate previously identified narrow- and broad-spiking types while revealing previously unknown diversity within these subtypes. The eight clusters exhibited distinct laminar distributions, characteristic firing rate patterns, and decision-related dynamics. Such insights were weaker when using feature-based approaches. WaveMAP therefore provides a more nuanced understanding of the dynamics of cell types in cortical circuits.

Instructions for how to use the data files used in the analysis and to generate manuscript figures (in Python) are contained in the Readme.md contained in the Zip file WaveMAP_Paper.zip. Manuscript figures are also included in the zipped folder Manuscript_figures.zip

Instructions for pre-processing raw averaged waveforms (in MATLAB) and associated data are contained in the README.md file in the zipped Preprocessing folder.

Raw confocal images with stereological cell count annotations are uploaded in the Zip file Image_data.zip.

Funding provided by: National Institute of Neurological Disorders and Stroke
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000065
Award Number: R00NS092972

Funding provided by: National Institute of Neurological Disorders and Stroke
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000065
Award Number: K99NS092972

Funding provided by: National Institute of Neurological Disorders and Stroke
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000065
Award Number: R00MH101234

Funding provided by: National Institute of Neurological Disorders and Stroke
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000065
Award Number: R01MH116008

Funding provided by: National Institute of Neurological Disorders and Stroke
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000065
Award Number: NS095548

Funding provided by: National Institute of Mental Health
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000025
Award Number: R01MH116008

Funding provided by: Whitehall Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100001391
Award Number: 2019-12-77

Funding provided by: Brain and Behavior Research Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000874
Award Number: 27923

Funding provided by: NIH Office of the Director
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000052
Award Number: DP1HD075623

Funding provided by: National Institute on Deafness and Other Communication Disorders
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000055
Award Number: DC014034

Funding provided by: National Institute on Deafness and Other Communication Disorders
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000055
Award Number: DC017844

Funding provided by: National Institute of Neurological Disorders and Stroke
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000065
Award Number: NS098968

Funding provided by: Defense Advanced Research Projects Agency
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000185
Award Number: N66001-10-C-2010

Funding provided by: Defense Advanced Research Projects Agency
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000185
Award Number: W911NF-14-2-0013

Funding provided by: Simons Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000893
Award Number: 325380

Funding provided by: Simons Foundation
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000893
Award Number: 543045

Funding provided by: National Institute of Neurological Disorders and Stroke
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000065
Award Number: 122969

Funding provided by: Office of Naval Research
Crossref Funder Registry ID: http://dx.doi.org/10.13039/100000006
Award Number: N000141812158

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Preprocessing.zip
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WaveMAP_Paper.zip
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