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Laminar architecture of visual and auditory responses in the supplementary eye field of macaques.

Code ↔ Paper

3 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 3 matches · 1 of them tie a paragraph to a whole file, not to given lines: a weak match, whose lines are not tinted
  1. [1] § Methods › Data analysis: current-source density ↔ my_splineCSD.m, lines 206–261 · score 0.65 · Gaussian filtering, iCSD, electrode contacts, spline, diameter, MATLAB
  2. [2] § Methods › Data analysis: current-source density ↔ my_stepCSD.m, lines 206–277 · score 0.64 · Gaussian filtering, iCSD, electrode contacts, diameter, spline, MATLAB
  3. [3] § Methods › Data analysis: cortical depth assignment ↔ methods/gaussian_filtering.m, the whole file · a weak match · score 0.52 · standard deviation, CSD matrices, zero

Paper

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The authors' code

MATLAB · 327 lines · 13 KB · GPL-3.0 · 1 match

  1. function varargout = my_splineCSD(varargin)
  2. % MY_SPLINECSD M-file for my_splineCSD.fig
  3. % MY_SPLINECSD, by itself, creates a new MY_SPLINECSD or raises the existing
  4. % singleton*.
  5. %
  6. % H = MY_SPLINECSD returns the handle to a new MY_SPLINECSD or the
  7. % handle to
  8. % the existing singleton*.
  9. %
  10. % MY_SPLINECSD('CALLBACK',hObject,eventData,handles,...) calls the local
  11. % function named CALLBACK in MY_SPLINECSD.M with the given input arguments.
  12. %
  13. % MY_SPLINECSD('Property','Value',...) creates a new MY_SPLINECSD or raises the
  14. % existing singleton*. Starting from the left, property value pairs
  15. % are
  16. % applied to the GUI before my_splineCSD_OpeningFunction gets called. An
  17. % unrecognized property name or invalid value makes property application
  18. % stop. All inputs are passed to my_splineCSD_OpeningFcn via varargin.
  19. %
  20. % *See GUI Options on GUIDE's Tools menu. Choose "GUI allows only one
  21. % instance to run (singleton)".
  22. %
  23. % See also: GUIDE, GUIDATA, GUIHANDLES
  25. % Edit the above text to modify the response to help my_splineCSD
  27. % Last Modified by GUIDE v2.5 13-Dec-2005 12:42:30
  29. % Begin initialization code - DO NOT EDIT
  30. gui_Singleton = 1;
  31. gui_State = struct('gui_Name', mfilename, ...
  32. 'gui_Singleton', gui_Singleton, ...
  33. 'gui_OpeningFcn', @my_splineCSD_OpeningFcn, ...
  34. 'gui_OutputFcn', @my_splineCSD_OutputFcn, ...
  35. 'gui_LayoutFcn', [] , ...
  36. 'gui_Callback', []);
  37. if nargin && ischar(varargin{1})
  38. gui_State.gui_Callback = str2func(varargin{1});
  39. end
  41. if nargout
  42. [varargout{1:nargout}] = gui_mainfcn(gui_State, varargin{:});
  43. else
  44. gui_mainfcn(gui_State, varargin{:});
  45. end
  46. % End initialization code - DO NOT EDIT
  49. % --- Executes just before my_splineCSD is made visible.
  50. function my_splineCSD_OpeningFcn(hObject, eventdata, handles, varargin)
  51. % This function has no output args, see OutputFcn.
  52. % hObject handle to figure
  53. % eventdata reserved - to be defined in a future version of MATLAB
  54. % handles structure with handles and user data (see GUIDATA)
  55. % varargin command line arguments to my_splineCSD (see VARARGIN)
  56. handles.pot = varargin{2};
  57. handles.dt = varargin{4};
  59. %image(imread('CSDplotter_logo.1.jpg'))
  60. axis off;
  62. % Choose default command line output for my_splineCSD
  63. handles.output = hObject;
  65. % Update handles structure
  66. guidata(hObject, handles);
  68. % UIWAIT makes my_splineCSD wait for user response (see UIRESUME)
  69. % uiwait(handles.delta_CSD);
  72. % --- Outputs from this function are returned to the command line.
  73. function varargout = my_splineCSD_OutputFcn(hObject, eventdata, handles)
  74. % varargout cell array for returning output args (see VARARGOUT);
  75. % hObject handle to figure
  76. % eventdata reserved - to be defined in a future version of MATLAB
  77. % handles structure with handles and user data (see GUIDATA)
  79. % Get default command line output from handles structure
  80. varargout{1} = handles.output;
  84. function gsigma_Callback(hObject, eventdata, handles)
  85. % hObject handle to gsigma (see GCBO)
  86. % eventdata reserved - to be defined in a future version of MATLAB
  87. % handles structure with handles and user data (see GUIDATA)
  89. % Hints: get(hObject,'String') returns contents of gsigma as text
  90. % str2double(get(hObject,'String')) returns contents of gsigma as a double
  93. % --- Executes during object creation, after setting all properties.
  94. function gsigma_CreateFcn(hObject, eventdata, handles)
  95. % hObject handle to gsigma (see GCBO)
  96. % eventdata reserved - to be defined in a future version of MATLAB
  97. % handles empty - handles not created until after all CreateFcns called
  99. % Hint: edit controls usually have a white background on Windows.
  100. % See ISPC and COMPUTER.
  101. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
  102. set(hObject,'BackgroundColor','white');
  103. end
  107. function filter_b1_Callback(hObject, eventdata, handles)
  108. % hObject handle to filter_b1 (see GCBO)
  109. % eventdata reserved - to be defined in a future version of MATLAB
  110. % handles structure with handles and user data (see GUIDATA)
  112. % Hints: get(hObject,'String') returns contents of filter_b1 as text
  113. % str2double(get(hObject,'String')) returns contents of filter_b1 as a double
  116. % --- Executes during object creation, after setting all properties.
  117. function filter_b1_CreateFcn(hObject, eventdata, handles)
  118. % hObject handle to filter_b1 (see GCBO)
  119. % eventdata reserved - to be defined in a future version of MATLAB
  120. % handles empty - handles not created until after all CreateFcns called
  122. % Hint: edit controls usually have a white background on Windows.
  123. % See ISPC and COMPUTER.
  124. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
  125. set(hObject,'BackgroundColor','white');
  126. end
  130. function ex_cond_Callback(hObject, eventdata, handles)
  131. % hObject handle to ex_cond (see GCBO)
  132. % eventdata reserved - to be defined in a future version of MATLAB
  133. % handles structure with handles and user data (see GUIDATA)
  135. % Hints: get(hObject,'String') returns contents of ex_cond as text
  136. % str2double(get(hObject,'String')) returns contents of ex_cond as a double
  139. % --- Executes during object creation, after setting all properties.
  140. function ex_cond_CreateFcn(hObject, eventdata, handles)
  141. % hObject handle to ex_cond (see GCBO)
  142. % eventdata reserved - to be defined in a future version of MATLAB
  143. % handles empty - handles not created until after all CreateFcns called
  145. % Hint: edit controls usually have a white background on Windows.
  146. % See ISPC and COMPUTER.
  147. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
  148. set(hObject,'BackgroundColor','white');
  149. end
  153. function top_cond_Callback(hObject, eventdata, handles)
  154. % hObject handle to top_cond (see GCBO)
  155. % eventdata reserved - to be defined in a future version of MATLAB
  156. % handles structure with handles and user data (see GUIDATA)
  158. % Hints: get(hObject,'String') returns contents of top_cond as text
  159. % str2double(get(hObject,'String')) returns contents of top_cond as a double
  162. % --- Executes during object creation, after setting all properties.
  163. function top_cond_CreateFcn(hObject, eventdata, handles)
  164. % hObject handle to top_cond (see GCBO)
  165. % eventdata reserved - to be defined in a future version of MATLAB
  166. % handles empty - handles not created until after all CreateFcns called
  168. % Hint: edit controls usually have a white background on Windows.
  169. % See ISPC and COMPUTER.
  170. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
  171. set(hObject,'BackgroundColor','white');
  172. end
  176. function diam_Callback(hObject, eventdata, handles)
  177. % hObject handle to diam (see GCBO)
  178. % eventdata reserved - to be defined in a future version of MATLAB
  179. % handles structure with handles and user data (see GUIDATA)
  181. % Hints: get(hObject,'String') returns contents of diam as text
  182. % str2double(get(hObject,'String')) returns contents of diam as a double
  185. % --- Executes during object creation, after setting all properties.
  186. function diam_CreateFcn(hObject, eventdata, handles)
  187. % hObject handle to diam (see GCBO)
  188. % eventdata reserved - to be defined in a future version of MATLAB
  189. % handles empty - handles not created until after all CreateFcns called
  191. % Hint: edit controls usually have a white background on Windows.
  192. % See ISPC and COMPUTER.
  193. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
  194. set(hObject,'BackgroundColor','white');
  195. end
  198. % --- Executes on button press in run_all.
  199. function run_all_Callback(hObject, eventdata, handles)
  200. % hObject handle to run_all (see GCBO)
  201. % eventdata reserved - to be defined in a future version of MATLAB
  202. % handles structure with handles and user data (see GUIDATA)
  205. % --- Executes on button press in run_this.
  206. function run_this_Callback(hObject, eventdata, handles)
  207. % hObject handle to run_this (see GCBO)
  208. % eventdata reserved - to be defined in a future version of MATLAB
  209. % handles structure with handles and user data (see GUIDATA)
  211. % filter parameters:
  212. gauss_sigma = str2num(get(handles.gsigma,'String'))*1e-3; % mm -> m
  213. filter_range = 5*gauss_sigma; % numeric filter must be finite in extent
  214. if gauss_sigma<0
  215. errordlg('The gaussian filter width cannot be negative.')
  216. return
  217. end;
  219. % electrical parameters:
  220. cond = str2num(get(handles.ex_cond,'String'));
  221. if cond<=0
  222. errordlg('Ex. cond. has to be a positive number');
  223. return
  224. end;
  225. cond_top = str2num(get(handles.top_cond,'String'));
  227. % size, potential (m1 has to equal number of electrode contacts)
  228. [m1,m2] = size(handles.pot);
  230. % geometrical parameters:
  231. diam = str2num(get(handles.diam,'String'))*1e-3; %diameter in [m]
  232. if diam<=0
  233. errordlg('Diameter has to be a positive number.');
  234. return
  235. end;
  237. el_pos = str2num(get(handles.electrode_pos,'String'))*1e-3;
  238. if cond_top~=cond & (el_pos~=abs(el_pos) | length(el_pos)~=length(nonzeros(el_pos)))
  239. errordlg('Electrode contact positions must be positive when top cond. is different from ex. cond.')
  240. return;
  241. end;
  242. if m1~=length(el_pos)
  243. errordlg(['Number of electrode contacts has to equal number of rows in potential matrix. Currently there are ',...
  244. num2str(length(el_pos)),' electrodes contacts, while the potential matrix has ',num2str(m1),' rows.'])
  245. return
  246. end;
  248. % compute spline iCSD:
  249. Fcs = F_cubic_spline(el_pos,diam,cond,cond_top);
  250. [zs,CSD_cs] = make_cubic_splines(el_pos,handles.pot,Fcs);
  251. %[pos1,my_CSD_spline]=new_CSD_range(zs,CSD_cs,0,2.4e-3);
  252. if gauss_sigma~=0 %filter iCSD
  253. [zs,CSD_cs]=gaussian_filtering(zs,CSD_cs,gauss_sigma,filter_range);
  254. % [new_positions,gfiltered_spline_CSD]=gaussian_filtering(zs,CSD_cs,gauss_sigma,filter_range);
  255. end;
  257. % % plot_CSD_with_axes(new_positions,delta_t,gfiltered_spline_CSD,1)
  258. % [gpot_pos,gfiltered_spline_CSD_short]=new_CSD_range(new_positions,gfiltered_spline_CSD,zstart_plot,zstop_plot);
  260. % plot CSD
  261. plot_CSD(CSD_cs,zs,handles.dt,1,0) %length(el_pos) must equal rows of CSD!
  263. function electrode_pos_Callback(hObject, eventdata, handles)
  264. % hObject handle to electrode_pos (see GCBO)
  265. % eventdata reserved - to be defined in a future version of MATLAB
  266. % handles structure with handles and user data (see GUIDATA)
  268. % Hints: get(hObject,'String') returns contents of electrode_pos as text
  269. % str2double(get(hObject,'String')) returns contents of electrode_pos as a double
  272. % --- Executes during object creation, after setting all properties.
  273. function electrode_pos_CreateFcn(hObject, eventdata, handles)
  274. % hObject handle to electrode_pos (see GCBO)
  275. % eventdata reserved - to be defined in a future version of MATLAB
  276. % handles empty - handles not created until after all CreateFcns called
  278. % Hint: edit controls usually have a white background on Windows.
  279. % See ISPC and COMPUTER.
  280. if ispc && isequal(get(hObject,'BackgroundColor'), get(0,'defaultUicontrolBackgroundColor'))
  281. set(hObject,'BackgroundColor','white');
  282. end
  285. % --------------------------------------------------------------------
  286. function new_figure_Callback(hObject, eventdata, handles)
  287. % hObject handle to new_figure (see GCBO)
  288. % eventdata reserved - to be defined in a future version of MATLAB
  289. % handles structure with handles and user data (see GUIDATA)
  292. % filter parameters:
  293. gauss_sigma = str2num(get(handles.gsigma,'String'))*1e-3; % mm -> m
  294. filter_range = 5*gauss_sigma; % numeric filter must be finite in extent
  296. % electrical parameters:
  297. cond = str2num(get(handles.ex_cond,'String'));
  298. cond_top = str2num(get(handles.top_cond,'String'));
  299. % geometrical parameters:
  300. diam = str2num(get(handles.diam,'String'))*1e-3; %diameter in [m]
  301. el_pos = str2num(get(handles.electrode_pos,'String'))*1e-3;
  303. % compute step iCSD:
  305. Fcs = F_cubic_spline(el_pos,diam,cond,cond_top);
  306. [zs,CSD_cs] = make_cubic_splines(el_pos,handles.pot,Fcs);
  307. %[pos1,my_CSD_spline]=new_CSD_range(zs,CSD_cs,0,2.4e-3);
  308. if gauss_sigma~=0 %filter iCSD
  309. [zs,CSD_cs]=gaussian_filtering(zs,CSD_cs,gauss_sigma,filter_range);
  310. % [new_positions,gfiltered_spline_CSD]=gaussian_filtering(zs,CSD_cs,gauss_sigma,filter_range);
  311. end;
  313. % % plot_CSD_with_axes(new_positions,delta_t,gfiltered_spline_CSD,1)
  314. % [gpot_pos,gfiltered_spline_CSD_short]=new_CSD_range(new_positions,gfiltered_spline_CSD,zstart_plot,zstop_plot);
  316. % plot CSD
  317. figure()
  318. plot_CSD(CSD_cs,zs,handles.dt,1,0) %length(el_pos) must equal rows of CSD!
  321. % --------------------------------------------------------------------
  322. function file_menu_Callback(hObject, eventdata, handles)
  323. % hObject handle to file_menu (see GCBO)
  324. % eventdata reserved - to be defined in a future version of MATLAB
  325. % handles structure with handles and user data (see GUIDATA)

my_splineCSD.m at commit ea083be, under GPL-3.0 · at the source

Overview

Authors: Pranavan Thirunavukkarasu1, Steven P Errington2, Amirsaman Sajad3, Benjamin W Corrigan1, Jeffrey D Schall1
ORCID iDs: Steven P Errington, Jeffrey D Schall
  1. Centre for Integrative and Applied Neuroscience, Centre for Vision Research, Department of Biology, York University, 4700 Keele Street, Toronto, ON M3J 1P3, Canada
  2. Biosciences Institute, Faculty of Medical Sciences, Newcastle University, Tyne and Wear, Newcastle upon Tyne NE1 7RU, United Kingdom
  3. International Center for Primate Brain Research, Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, No. 500 Qiang Ye Road, Songjiang District, Shanghai 201602, P.R. China
Institutions: York University (Canada); Newcastle University (United Kingdom); Chinese Academy of Sciences (China); Center for Excellence in Brain Science and Intelligence Technology (China)
Journal: Cerebral cortex (New York, N.Y. : 1991), volume 36, issue 6, article bhag064
Dates: received 10 March 2026; accepted 22 April 2026; published online 19 June 2026; in print June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1093/cercor/bhag064 · PMID 42319229 · PMCID PMC13280951 · OpenAlex W7165365704
Open access: hybrid, a free copy (OpenAlex)
Status: code verified
Categories: behavior only (modality), non-human primate (organism)
Methods: Spectral & time-frequency, Preprocessing, Connectivity, Statistics, Smoothing, state filtering, decompositions, Machine learning, Single-unit activity, calcium imaging, Physiology & signal measures
Keywords: auditory response, current-source density, laminar architecture, supplementary eye field, visual response
MeSH: Auditory Perception*, Visual Fields*, Visual Perception*, Acoustic Stimulation, Animals, Interneurons, Macaca mulatta, Male, Photic Stimulation, Pyramidal Cells, Reaction Time (* major topic)
Topic: Neural dynamics and brain function (Cognitive Neuroscience, Neuroscience), according to OpenAlex
Funding: Canadian Research Chairs Program; NIH (R01-MH MH55806, P30-EY08126); Natural Sciences and Engineering Research Council of Canada (RGPIN-2022-04592); CIHR Post-Doctoral Fellowship; QEII-GSST Scholarship; Vision to Application program at York University
Citations: not cited yet (Europe PMC); 97 references in the paper

Abstract

We describe properties and laminar organization of visual and auditory responses sampled with linear electrode arrays in and around the supplementary eye field of four macaque monkeys performing a visually guided task with a tone secondary reinforcer. Of pyramidal neurons in all layers and interneurons in L3 and L5/6, one-quarter were visually responsive, one-quarter, auditory, with 30% bimodal. Visual neurons were less common rostral, lateral, and medial to the supplementary eye field. Facilitated visual and auditory responses were much more common than suppressed. Pyramidal and interneurons responded to the stimulus in either hemifield with a weak bias for contralateral targets. Visual response latencies were comparable to values previously reported and later than auditory responses. Facilitated visual responses of interneurons preceded those of pyramidal neurons. Transient visual responses preceded sustained. Current-source density revealed visually evoked current sinks after auditory sinks that were transient for bright flashes and prolonged for the discrete task target. The earliest sink appeared at the L3 to L5 border and spread superficially and deeper with idiosyncratic variability across monkeys. These findings reveal new details about sensory processing in medial frontal cortex and complement our previous descriptions of the functional properties and laminar organization of neurons supporting cognitive control.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 3 matches between paragraphs and lines of code.

espenhgn/CSDplotter

License: GPL-3.0
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: ea083be8ffe4581950f0da672d59512748f8982b, 11 April 2018
Languages: MATLAB (23)
Size: 44 files, 23 scripts
Software Heritage: not archived
Found in: the text, “Data analysis: current-source density”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
25 files
At the source: github.com/espenhgn/CSDplotter

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.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 23 scripts, each with its path and the digest of its content;
  • 3 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

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.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 5 authors, 5 keywords, 11 MeSH terms, 6 funders, 95 references.

Cite

This paper

Thirunavukkarasu, P., Errington, S. P., Sajad, A., Corrigan, B. W., & Schall, J. D. (2026). Laminar architecture of visual and auditory responses in the supplementary eye field of macaques. Cerebral cortex (New York, N.Y. : 1991), 36(6), bhag064. https://doi.org/10.1093/cercor/bhag064

BibTeX

@article{thirunavukkarasu2026laminar,
author = {Thirunavukkarasu, Pranavan and Errington, Steven P and Sajad, Amirsaman and Corrigan, Benjamin W and Schall, Jeffrey D},
title = {{Laminar architecture of visual and auditory responses in the supplementary eye field of macaques}},
journal = {Cerebral cortex (New York, N.Y. : 1991)},
year = {2026},
month = jun,
volume = {36},
number = {6},
pages = {bhag064},
publisher = {Oxford University Press},
issn = {1047-3211},
doi = {10.1093/cercor/bhag064},
url = {https://doi.org/10.1093/cercor/bhag064},
pmid = {42319229},
pmcid = {PMC13280951}
}

RIS

TY - JOUR
AU - Thirunavukkarasu, Pranavan
AU - Errington, Steven P
AU - Sajad, Amirsaman
AU - Corrigan, Benjamin W
AU - Schall, Jeffrey D
TI - Laminar architecture of visual and auditory responses in the supplementary eye field of macaques
T2 - Cerebral cortex (New York, N.Y. : 1991)
J2 - Cereb Cortex
PY - 2026
DA - 2026/06/01
VL - 36
IS - 6
SP - bhag064
SN - 1047-3211
PB - Oxford University Press
DO - 10.1093/cercor/bhag064
UR - https://doi.org/10.1093/cercor/bhag064
LA - en
ER -

CSL-JSON

{
"id": "10.1093/cercor/bhag064",
"type": "article-journal",
"title": "Laminar architecture of visual and auditory responses in the supplementary eye field of macaques",
"container-title": "Cerebral cortex (New York, N.Y. : 1991)",
"author": [
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"family": "Thirunavukkarasu",
"given": "Pranavan"
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"given": "Steven P"
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{
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{
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{
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"given": "Jeffrey D"
}
],
"container-title-short": "Cereb Cortex",
"volume": "36",
"issue": "6",
"page": "bhag064",
"DOI": "10.1093/cercor/bhag064",
"PMID": "42319229",
"PMCID": "PMC13280951",
"ISSN": "1047-3211",
"publisher": "Oxford University Press",
"URL": "https://doi.org/10.1093/cercor/bhag064",
"language": "en",
"issued": {
"date-parts": [
[
2026,
6,
1
]
]
}
}

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In common: non-human primate, 2 references
[10] doi:10.7554/elife.109498 [code]
Neural computations in the foveal and peripheral visual fields during active search.
Journal: eLife
In common: behavior only, non-human primate, 1 reference

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