Reporting summary
Further information on research design is available in the Nature
Research Reporting Summary linked to this paper.
Data availability
The data generated in this study are available from the corresponding
author on reasonable request.
Code availability
Code for automatic annotation of behaviour and behavioural waypoint
estimation is available at https://github.com/kristinbranson/JAABA.
Code for hand tracking is available at https://github.com/kristinbran-
son/APT. Code for spike sorting is available at https://github.com/
JaneliaSciComp/JRCLUST, https://github.com/MouseLand/Kilosort2,
and https://github.com/kwikteam/phy. Other code is available from
the corresponding author on reasonable request.
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Acknowledgements We thank B. Yu and the Yu laboratory, S. Edgley, J. Dudman, A. K. Lee, M.
Ahrens, A. Finkelstein, J. Fitzgerald and K. Shan for discussions and comments on an earlier
version of the manuscript; A. Lee for tracking software; T. Harris, B. Barbarits, B. Karsh, S.
Sawtelle, P. Polidoro, D. Flickinger and the Neuropixels Project for instrumentation
development and support; W. Sun for probe sharpening and PEDOT application; A. Taylor for
development of WaveSurfer; J. Jun and M. Pachitariu for spike-sorting software; S. Chung for
assistance with video labelling; S. DiLiso for fibre implantation surgeries; K. Ritola and the
Janelia Virus Tools facility for providing viruses; J. Kuhl for the mouse drawings; and the Janelia
Vivarium, Histology and Scientific Computing facilities for support.Author contributions B.A.S., J.-Z.G., J.D.C. and A.W.H. designed the experiments. B.A.S. and
J.-Z.G. performed electrophysiological recordings in motor cortex. J.-Z.G. performed
recordings in cortex with thalamic inactivation. J.D.C. performed simultaneous recordings in
cortex and thalamus and recordings in cortex during stimulation of thalamic terminals. J.-Z.G.
performed behavioural experiments. B.A.S. analysed electrophysiology and behaviour data
and generated the figures. J.-Z.G. and W.G. analysed behaviour data. M.M. developed and
performed the neural decoding analyses. B.A.S., M.M. and A.W.H. interpreted the results. N.V.
and K.B. developed preliminary analyses for decoding of behavioural waypoints. M.K. and K.B.
developed computer vision algorithms and software. B.A.S., A.W.H., M.M., B.M. and K.B. wrote
the paper with input from all authors. A.W.H. supervised the project.Competing interests The authors declare no competing interests.Additional information
Supplementary information is available for this paper at https://doi.org/10.1038/s41586-019-
1869-9.
Correspondence and requests for materials should be addressed to A.W.H.
Peer review information Nature thanks Jesse Goldberg and the other, anonymous, reviewer(s)
for their contribution to the peer review of this work.
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