Brain-wide arousal signals are segregated from movement planning in the superior colliculus of the macaque.
Paper
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The authors' code
MATLAB · 25 lines · 1.2 KB · no license
- % Wrapper for using the network to classify waveforms with sample data.
- filename = 'sampleData.mat'; %filename that contains the variable "waveforms",
- % waveforms is an Nx52 array, where N is the number
- % of waveforms, and 52 is the number of samples in
- % each waveform.
- gamma = 0.2; %minimum P(spike) value for a waveform to be considered a spike
- netName = 'Issar_et_al_2020'; %name of network
- %the 4 outputs of the trained NASNet must
- %exist. For this example they would be
- %Issar_et_al_2020_w_hidden
- %Issar_et_al_2020_b_hidden
- %Issar_et_al_2020_w_output
- %Issar_et_al_2020_b_output
- slabel = runNASNet(filename,gamma,netName); %classify waveforms
- %plot a selection of the labeled waveforms
- load(filename);
- spikes = waveforms(logical(slabel),:);
- noise = waveforms(~logical(slabel),:);
- figure;
- h1=plot(noise(randi(size(noise,1),50),:)','k'); hold on;
- h2=plot(spikes(randi(size(spikes,1),50),:)','g');
- ylim([-500,500]); xlim([1,52]);
- ylabel('uV'); legend([h1(1),h2(1)],'noise','spike');
Issar_et_al_2020_wrapper.m at commit b2109e0, no license · at the source
Overview
- Department of Biomedical Engineering, Carnegie Mellon University Pittsburgh United States
- Neuroscience Institute, Carnegie Mellon University Pittsburgh United States
- Center for the Neural Basis of Cognition, Carnegie Mellon University Pittsburgh United States
Abstract
The superior colliculus (SC) is traditionally considered a brain region that functions as an interface between processing visual inputs and generating eye movement outputs. Although its role as a primary reflex center is thought to be conserved across vertebrate species, evidence suggests that the SC has evolved to support higher-order cognitive functions, including spatial attention. When it comes to oculomotor areas, such as the SC, it is critical that high precision fixation and eye movements are maintained even in the presence of signals related to ongoing changes in cognition and brain state, both of which have the potential to interfere with eye position encoding and movement generation. In this study, we recorded spiking responses of neuronal populations in the SC while two rhesus macaque monkeys performed a memory-guided saccade task and found that the activity of some of the neurons fluctuated over tens of minutes. By leveraging the statistical power afforded by high-dimensional neuronal recordings, we were able to identify a low-dimensional pattern of activity that was correlated with pupil size and simultaneously recorded data in the prefrontal cortex (PFC), consistent with slow changes in the monkeys’ arousal levels while they were performing the task. Importantly, we found that the spiking responses of deep-layer SC neurons were less correlated with this brain-wide arousal signal, and that neural activity associated with changes in pupil size and saccade tuning did not overlap in population activity space with movement initiation signals. Taken together, these findings provide a framework for understanding how signals related to cognition and arousal can be embedded in the population activity of oculomotor structures without compromising the fidelity of the motor output.
Reproduced under the paper's license (CC BY), from the paper cited above.
Repository
Its files are read in the Code ↔ Paper reader above.
SmithLabNeuro/nasnet
b2109e0cbc7194b298aaabb4a2acfda45ba14aa2, 25 June 2026Availability: 1 check, the latest on 27 September 2026: the link answers
- 27 September 2026: the link answers
21 files
- Issar_et_al_2020_wrapper
.m , MATLAB, 25 lines - classifySpikes.m, MATLAB, 76 lines
- classifySpikes_keepWvfs.
m , MATLAB, 93 lines - getNumPackets.m, MATLAB, 102 lines
- nasnet.m, MATLAB, 111 lines
- net_in_matlab.m, MATLAB, 83 lines
- nev2sortedStruct.m, MATLAB, 30 lines
- online implementation example code/
simOnlineNASNet.m , MATLAB, 41 lines - online implementation example code/
timingTest_wrapper.m , MATLAB, 47 lines - read_nev_block.m, MATLAB, 162 lines
- sort2bcistruct.m, MATLAB, 34 lines
- training/
NASNet.py , Python, 101 lines - utils/
classify_waveforms.m , MATLAB, 67 lines - utils/
mypaths.m , MATLAB, 21 lines - utils/
nevtomat_forclassificati , MATLAB, 54 lineson.m - utils/
nevtomat_fortraining.m , MATLAB, 90 lines - utils/
plot_classified_waveform , MATLAB, 102 liness.m - utils/
runNASNet.m , MATLAB, 240 lines - utils/
runNASNetMiSO.m , MATLAB, 205 lines - utils/
writelabels_tonev.m , MATLAB, 67 lines - README.md, Text, 46 lines
The paper's code and data availability statement is in the Data section.
Tracing map
Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.
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- 20 scripts, each with its path and the digest of its content;
- no match between paragraphs and code yet;
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Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.
Data
No dataset and no data link were found in the paper.
Data availability
The data for this manuscript are available at https://
The following dataset was generated:
JohnstonR SmithMA 2026Data from "Brain-wide arousal signals are segregated from movement planning in the superior colliculus"Carnegie Mellon University10.1184/
Reproduced under the paper's license (CC BY), from the paper cited above.
Versions
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Version 1, 27 September 2026: the first record
Recorded: type, language, journal, volume, pages, dates, 2 authors, 5 keywords, 8 MeSH terms, 1 funder, 107 references.
Cite
This paper
Johnston, R., & Smith, M. A. (2026). Brain-wide arousal signals are segregated from movement planning in the superior colliculus of the macaque. eLife, 13, RP99278. https://
BibTeX
@article{johnston2026bra
author = {Johnston, Richard and Smith, Matthew A},
title = {{Brain-wide arousal signals are segregated from movement planning in the superior colliculus of the macaque}},
journal = {eLife},
year = {2026},
month = jun,
volume = {13},
pages = {RP99278},
publisher = {eLife Sciences Publications, Ltd},
issn = {2050-084X},
doi = {10.7554/
url = {https://
pmid = {42258377},
pmcid = {PMC13246003}
}
RIS
TY - JOUR
AU - Johnston, Richard
AU - Smith, Matthew A
TI - Brain-wide arousal signals are segregated from movement planning in the superior colliculus of the macaque
T2 - eLife
J2 - Elife
PY - 2026
DA - 2026/
VL - 13
SP - RP99278
SN - 2050-084X
PB - eLife Sciences Publications, Ltd
DO - 10.7554/
UR - https://
LA - en
ER -
CSL-JSON
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"publisher": "eLife Sciences Publications, Ltd",
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