Contextual gating of whisker-evoked responses by frontal cortex supports flexible decision making.

A correction to this paper has been published: the notice, 42486857, from Europe PMC.

Code ↔ Paper

4 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 4 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted

[1] § Methods › Histology and localization of electrode tracks ↔ UniversalProbeFinder.m, the whole file · a weak match · score 0.85 · Universal Probe Finder, Mouse Brain Atlas, Pre processing, Allen CCF, v3, alignment
[2] § Methods › Histology and localization of electrode tracks ↔ ProbeFinder.m, lines 1–42 · score 0.76 · Universal Probe Finder, Mouse Brain Atlas, Allen CCF, v3, alignment, MATLAB
[3] § Methods › Electrophysiology data analysis ↔ common/DP_DetectSpikes.m, the whole file · a weak match · score 0.62 · Spike detection, kilosort2, thresholds, median, channels
[4] § Results › Spatiotemporal dynamics of neocortical activity ↔ SHARP-Track/Convert_CCF_Coords_to_FP_Regions.m, lines 11–47 · score 0.52 · mouse brain atlas, Allen CCF, located, Neuropixels, tracks, probes

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

The paper is loaded when this pane is shown.

The paper is loaded by your browser, with JavaScript: read it at doi.org or on Europe PMC.

The authors' code

MATLAB · 128 lines · 5.4 KB · GPL-3.0 · 1 match

function UniversalProbeFinder
%The Universal Probe Finder consists of three independent programs:
% - SlicePrepper: pre-process your images & annotate traces
% - SliceFinder: align each slice to a brain atlas
% - ProbeFinder: use ephys data to fine-tune your probe's location & export the brain at each
% contact point or cluster
%
%To use any program, simply type the name of the program in the matlab prompt, e.g.:
%ProbeFinder
%
%Please read the manual for more detailed instructions.
%
%The Universal Probe Finder can use multiple atlases and ephys data formats, and calculates the
%stimulus responsiveness of your clusters with the zetatest using only an array of event-onset
%times. Using these neurophysiological markers will allow a more reliable alignment of your probe's
%contact points to specific brain areas.
%
%At this time, can use the following atlases:
%a. Sprague Dawley rat brain atlas, downloadable at: https://www.nitrc.org/projects/whs-sd-atlas
%b. Allen CCF mouse brain atlas, downloadable at: http://data.cortexlab.net/allenCCF/
%c. CHARM/SARM macaque brain atlas: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/nonhuman/macaque_tempatl/atlas_charm.html
%It is also possible to add your own Atlas by editing the configAtlas.ini file that is created
%when you first run the ProbeFinder (see manual).
%
%Please reach out to us (for example here: https://github.com/JorritMontijn/UniversalProbeFinder)
%if you wish to have a different atlas added with out-of-the-box support. Adding an atlas is
%very easy, and we're happy to extend the usefulness of our program for all its users.
%
%Acknowledgements
%This work is based on earlier work by people from the cortex lab, most notably Philip Shamash
%and Andy Peters. See for example this paper: https://www.biorxiv.org/content/10.1101/447995v1
%
%This repository includes various functions that come from other repositories, credit for these
%functions go to their creators:
%https://github.com/petersaj/AP_histology
%https://github.com/JorritMontijn/Acquipix
%https://github.com/JorritMontijn/GeneralAnalysis
%https://github.com/kwikteam/npy-matlab
%https://github.com/cortex-lab/spikes
%https://github.com/JorritMontijn/zetatest
%
%License
%This repository is licensed under the GNU General Public License v3.0, meaning you are free to
%use, edit, and redistribute any part of this code, as long as you refer to the source (this
%repository) and apply the same non-restrictive license to any derivative work (GNU GPL v3).
%
%The logo for the Universal Probe Finder uses this image as background (CC licensed):
%https://upload.wikimedia.org/wikipedia/commons/7/75/Massive_galaxies_discovered_in_the_early_Universe.jpg
%
%Created by Jorrit Montijn at the Cortical Structure and Function laboratory (KNAW-NIN)
%
%Rev:20240221 - v1.1.0
%ask which program to run
%set disable/enable global
global sUPF_ChooseGui
if isfield(sUPF_ChooseGui,'hMain') && ishandle(sUPF_ChooseGui.hMain),return;end
%create GUI
hChooseGui = figure('WindowStyle','Normal','Name','Universal Probe Finder',...
'Menubar','none','NumberTitle','off','Position',[500 500 400 200],'CloseRequestFcn',@UPF_DeleteFcn);
hChooseGui.Units = 'normalized';
%add paths
if ~isdeployed
strFullpath = mfilename('fullpath');
strPath = fileparts(strFullpath);
sDir=dir([strPath filesep '**' filesep]);
%remove git folders
sDir(contains({sDir.folder},[filesep '.git'])) = [];
cellFolders = unique({sDir.folder});
for intFolder=1:numel(cellFolders)
addpath(cellFolders{intFolder});
end
end
%change icon
try
warning('off','MATLAB:ui:javaframe:PropertyToBeRemoved');
warning('off','MATLAB:HandleGraphics:ObsoletedProperty:JavaFrame');
jframe=get(hChooseGui,'javaframe');
jIcon=javax.swing.ImageIcon(fullpath(SH_getIniPath(),'icon.png'));
jframe.setFigureIcon(jIcon);
catch
end
%create gui
ptrTextPrepper = uicontrol(hChooseGui,'Style','text','String','Select the program you wish to run:',...
'Units','normalized','FontSize',12,'Position',[0.1 0.8 0.8 0.15],'backgroundcolor',[1 1 1]);
ptrButtonPrepper = uicontrol(hChooseGui,'Style','pushbutton','String','Slice Prepper',...
'Units','normalized','FontSize',12,'Position',[0.2 0.63 0.6 0.15],...
'Callback',@SlicePrepper);
ptrButtonFinder = uicontrol(hChooseGui,'Style','pushbutton','String','Slice Finder',...
'Units','normalized','FontSize',12,'Position',[0.2 0.43 0.6 0.15],...
'Callback',@SliceFinder);
ptrButtonProber = uicontrol(hChooseGui,'Style','pushbutton','String','Probe Finder',...
'Units','normalized','FontSize',12,'Position',[0.2 0.23 0.6 0.15],...
'Callback',@ProbeFinder);
%check for ini file
strIni = strcat(SH_getIniPath(),filesep,'configPF.ini');
%load ini
ptrButtonSetter = uicontrol(hChooseGui,'Style','pushbutton','String','Settings',...
'Units','normalized','FontSize',12,'Position',[0.3 0.05 0.4 0.12],...
'Callback',@SetVariablesUPF);
if exist(strIni,'file')
ptrButtonSetter.Visible = 'on';
else
ptrButtonSetter.Visible = 'off';
end
%add handles to global
sUPF_ChooseGui = struct;
sUPF_ChooseGui.hMain = hChooseGui;
sUPF_ChooseGui.handles.ptrTextPrepper = ptrTextPrepper;
sUPF_ChooseGui.handles.ptrButtonPrepper = ptrButtonPrepper;
sUPF_ChooseGui.handles.ptrButtonFinder = ptrButtonFinder;
sUPF_ChooseGui.handles.ptrButtonProber = ptrButtonProber;
sUPF_ChooseGui.handles.ptrButtonSetter = ptrButtonSetter;
%move
movegui(hChooseGui,'center');
end

UniversalProbeFinder.m at commit d281538, under GPL-3.0 · at the source

Overview

Authors: Parviz Ghaderi¹, Sylvain Crochet¹, Carl C H Petersen¹

ORCID iDs: Parviz Ghaderi, Sylvain Crochet, Carl C H Petersen

Laboratory of Sensory Processing, Brain Mind Institute, School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland

Institutions: École Polytechnique Fédérale de Lausanne (Switzerland)

Journal: Nature communications, volume 17, issue 1, article 5982

Dates: received 8 July 2025; accepted 13 May 2026; published online 26 May 2026

Type: Research article · Language: English

License: CC BY

Identifiers: DOI 10.1038/s41467-026-73622-y · PMID 42191718 · PMCID PMC13346651 · OpenAlex W7162464462

Open access: gold, a free copy (OpenAlex)

Status: code verified

Categories: mouse (organism), cognitive (subfield)

Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning, Preprocessing, Connectivity, Single-unit activity, calcium imaging, fMRI & imaging

Keywords: Decision, Barrel cortex, Sensory processing, Cortex, Premotor cortex

MeSH: Decision Making*, Frontal Lobe*, Motor Cortex*, Vibrissae*, Animals, Cues, Male, Mice, Mice, Inbred C57BL, Optogenetics (* major topic)

Topic: Neural dynamics and brain function (Cognitive Neuroscience, Neuroscience), according to OpenAlex

Funding: Swiss National Science Foundation (182010, 310030_219343, 31003A_182010, TMAG-3_209271)

Citations: cited by 1 paper (Europe PMC); 59 references in the paper

Notices: A correction to this paper has been published (42486857, from Europe PMC)

Abstract

Context-dependent sensory processing underlies important aspects of flexible behavior. Here, we investigate how mice can use a briefly-presented auditory contextual Go or Nogo cue after a delay period to gate the transformation of a whisker deflection into licking for reward. Spatiotemporally-specific optogenetic inactivation demonstrated an important contribution of various cortical regions during distinct trial epochs, with only whisker secondary motor cortex (wM2) contributing strongly to all task epochs including auditory cue, delay and whisker stimulus. Electrophysiological recordings revealed prominent context representation in both wM2 and anterolateral motor cortex (ALM) in the form of persistent activity with stable population dynamics. Notably, we found that context and whisker sensory processing appeared to be integrated first in wM2, whose activity predicted future lick initiation in both correct hit trials and false alarm error trials already within 30 ms after whisker deflection. We thus identify wM2 as a key node for the contextual gating of the transformation of whisker sensation into motor commands for goal-directed licking.

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

Repositories

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

cortex-lab/allenCCF

License: none: the authors keep all their rights

State: the link answers, verified on 27 September 2026

Evidence: files inventoried

Commit: e5a57fe7e1c9fb333fec51c29a8471131c233a76, 15 July 2025

Languages: MATLAB (61)

Size: 75 files, 61 scripts

Software Heritage: not archived

Found in: the text, “Histology and localization of electrode tracks”

Holds: README

Not found: license file, CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Image Processing Toolbox (7 files), Statistics and Machine Learning Toolbox (1 file)

Availability: 1 check, the latest on 27 September 2026: the link answers

27 September 2026: the link answers

62 files

Browsing Functions/AtlasTransformBrowser.m, MATLAB, 1,196 lines
Browsing Functions/CCF_to_FP.m, MATLAB, 66 lines
Browsing Functions/addAllenCtxOutlines.m, MATLAB, 51 lines
Browsing Functions/aggregateAcr.m, MATLAB, 146 lines
Browsing Functions/allenAtlasBrowser.m, MATLAB, 658 lines
Browsing Functions/allenAtlasBrowser_original.m, MATLAB, 262 lines
Browsing Functions/allenCCFbregma.m, MATLAB, 8 lines
Browsing Functions/allenTilt.m, MATLAB, 172 lines
Browsing Functions/allen_ccf_2pi.m, MATLAB, 780 lines
Browsing Functions/allen_ccf_colormap.m, MATLAB, 10 lines
Browsing Functions/allen_ccf_npx.m, MATLAB, 1,087 lines
Browsing Functions/allen_ccf_npx_4shank.m, MATLAB, 931 lines
Browsing Functions/allen_ccf_npx_4shank_spherical.m, MATLAB, 987 lines
Browsing Functions/best_fit_line.m, MATLAB, 28 lines
Browsing Functions/customVectorSlice.m, MATLAB, 38 lines
Browsing Functions/distinguishable_colors.m, MATLAB, 152 lines
Browsing Functions/get_offset_map.m, MATLAB, 41 lines
Browsing Functions/gridIn3D.m, MATLAB, 80 lines
Browsing Functions/hierarchicalSelect.m, MATLAB, 130 lines
Browsing Functions/idRegionByAcr.m, MATLAB, 27 lines
Browsing Functions/isAreaOrContains.m, MATLAB, 31 lines
Browsing Functions/loadCCFtoFP.m, MATLAB, 17 lines
Browsing Functions/loadFPtable.m, MATLAB, 16 lines
Browsing Functions/loadStructureTree.m, MATLAB, 48 lines
Browsing Functions/makeSTtree.m, MATLAB, 45 lines
Browsing Functions/makeSmoothCoords.m, MATLAB, 23 lines
Browsing Functions/natsort.m, MATLAB, 330 lines
Browsing Functions/natsortfiles.m, MATLAB, 169 lines
Browsing Functions/plotAVoverlay.m, MATLAB, 28 lines
Browsing Functions/plotAVslice.m, MATLAB, 13 lines
Browsing Functions/plotAsProbe.m, MATLAB, 37 lines
Browsing Functions/plotBrainGrid.m, MATLAB, 35 lines
Browsing Functions/plotBrainOutlinesByAxis.m, MATLAB, 23 lines
Browsing Functions/plotDistToNearest.m, MATLAB, 123 lines
Browsing Functions/plotDistToNearestToTip.m, MATLAB, 252 lines
Browsing Functions/plotLabelsAsProbe.m, MATLAB, 110 lines
Browsing Functions/plotNeuronOnSliceFromCoord.m, MATLAB, 20 lines
Browsing Functions/plotTVslice.m, MATLAB, 12 lines
Browsing Functions/plotTopDownOutlines.m, MATLAB, 100 lines
Browsing Functions/sagittalSlices.m, MATLAB, 50 lines
Browsing Functions/sanitizeStructureTree.m, MATLAB, 31 lines
Browsing Functions/script_sliceMovie.m, MATLAB, 66 lines
Browsing Functions/selectStructure.m, MATLAB, 264 lines
Browsing Functions/sliceBrowser.m, MATLAB, 142 lines
Browsing Functions/sliceByVector.m, MATLAB, 55 lines
Browsing Functions/sliceOutlineWithRegion.m, MATLAB, 38 lines
Browsing Functions/sliceOutlineWithRegionVec.m, MATLAB, 74 lines
Browsing Functions/transformed_sliceBrowser.m, MATLAB, 171 lines
Histology Functions/HistologyBrowser.m, MATLAB, 161 lines
Histology Functions/HistologyCropper.m, MATLAB, 105 lines
Histology Functions/SliceFlipper.m, MATLAB, 177 lines
Histology Functions/natsort.m, MATLAB, 330 lines
Histology Functions/natsortfiles.m, MATLAB, 169 lines
SHARP-Track/Analyze_Clicked_Points.m, MATLAB, 131 lines
SHARP-Track/Analyze_ROIs.m, MATLAB, 158 lines
SHARP-Track/Convert_CCF_Coords_to_FP_Regions.m, MATLAB, 117 lines, 1 match
SHARP-Track/Convert_Clicked_Points_to_FP_coords.m, MATLAB, 145 lines
SHARP-Track/Display_Probe_Track.m, MATLAB, 229 lines
SHARP-Track/Navigate_Atlas_and_Register_Slices.m, MATLAB, 66 lines
SHARP-Track/Process_Histology.m, MATLAB, 133 lines
setup_utils.m, MATLAB, 47 lines
README.md, Text, 72 lines

At the source: github.com/cortex-lab/allenCCF

JorritMontijn/UniversalProbeFinder

License: GPL-3.0

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Commit: d2815385b6a980ffe2efba6560ab6d29a454f039, 20 March 2024

Languages: MATLAB (161)

Size: 172 files, 161 scripts

Software Heritage: not archived

Found in: the text, “Histology and localization of electrode tracks”

Holds: README, license file

Not found: CITATION.cff, environment file, tests, continuous integration, documentation

Tools: Image Processing Toolbox (9 files), Parallel Computing Toolbox (3 files), Statistics and Machine Learning Toolbox (3 files), Signal Processing Toolbox (2 files), CircStat (1 file)

Availability: 1 check, the latest on 28 September 2026: the link answers

28 September 2026: the link answers

163 files

ProbeFinder.m, MATLAB, 193 lines, 1 match
SetVariablesUPF.m, MATLAB, 25 lines
SliceFinder.m, MATLAB, 69 lines
SlicePrepper.m, MATLAB, 44 lines
UniversalProbeFinder.m, MATLAB, 128 lines, 1 match
atlasloaders/AL_PrepABA.m, MATLAB, 98 lines
atlasloaders/AL_PrepMCS.m, MATLAB, 174 lines
atlasloaders/AL_PrepSDA.m, MATLAB, 131 lines
common/DP_ChannelCountsIM.m, MATLAB, 10 lines
common/DP_ChannelCountsNI.m, MATLAB, 11 lines
common/DP_DetectSpikes.m, MATLAB, 136 lines, 1 match
common/DP_DetectSpikesInBinaryFile.m, MATLAB, 189 lines
common/DP_FindMins.m, MATLAB, 67 lines
common/DP_GetChanMap.m, MATLAB, 107 lines
common/DP_ReadBin.m, MATLAB, 116 lines
common/DP_ReadMeta.m, MATLAB, 36 lines
common/DP_SampRate.m, MATLAB, 10 lines
common/DP_gpufilter.m, MATLAB, 47 lines
common/assertBioFormats.m, MATLAB, 57 lines
common/catstruct.m, MATLAB, 165 lines
common/cellfill.m, MATLAB, 21 lines
common/circ_dist.m, MATLAB, 31 lines
common/clusterAverage.m, MATLAB, 27 lines
common/countUnique.m, MATLAB, 9 lines
common/czifinfo.m, MATLAB, 172 lines
common/cziinfo.m, MATLAB, 107 lines
common/cziread.m, MATLAB, 46 lines
common/flat.m, MATLAB, 6 lines
common/fullpath.m, MATLAB, 18 lines
common/getDate.m, MATLAB, 8 lines
common/getFlankedBy.m, MATLAB, 41 lines
common/getOr.m, MATLAB, 26 lines
common/getTrace3D.m, MATLAB, 72 lines
common/ini2struct.m, MATLAB, 29 lines
common/isaxes.m, MATLAB, 3 lines
common/loadClusterTsvs.m, MATLAB, 127 lines
common/loadKSdir.m, MATLAB, 96 lines
common/loadParamsPy.m, MATLAB, 48 lines
common/loadcsv.m, MATLAB, 89 lines
common/maxfig.m, MATLAB, 43 lines
common/median.m, MATLAB, 229 lines
common/modx.m, MATLAB, 7 lines
common/offsetaxes.m, MATLAB, 19 lines
common/parsecsv.m, MATLAB, 57 lines
common/readClusterGroupsCSV.m, MATLAB, 27 lines
common/readNPY.m, MATLAB, 37 lines
common/readNPYheader.m, MATLAB, 72 lines
common/redblack.m, MATLAB, 22 lines
common/redbluepurple.m, MATLAB, 12 lines
common/roundi.m, MATLAB, 25 lines
common/selectcolor.m, MATLAB, 518 lines
common/struct2ini.m, MATLAB, 34 lines
common/templatePositionsAmplitudes.m, MATLAB, 82 lines
common/tsvread.m, MATLAB, 122 lines
common/uitext.m, MATLAB, 71 lines
common/val2idx.m, MATLAB, 42 lines
common/xml2struct2.m, MATLAB, 172 lines
common/xsize.m, MATLAB, 34 lines
ephysloaders/EL_PrepEphys_AS.m, MATLAB, 101 lines
ephysloaders/EL_PrepEphys_KS.m, MATLAB, 141 lines
ephysloaders/EL_PrepEphys_NC.m, MATLAB, 60 lines
ephysloaders/EL_PrepEphys_SG.m, MATLAB, 123 lines
subfunctions/PF_AssertVersion.m, MATLAB, 12 lines
subfunctions/PF_GetAreaPerCluster.m, MATLAB, 21 lines
subfunctions/PF_getAtlasIni.m, MATLAB, 46 lines
subfunctions/PF_getEphysIni.m, MATLAB, 55 lines
subfunctions/PF_getIniVar.m, MATLAB, 103 lines
subfunctions/PH_BregmaVec2SphVec.m, MATLAB, 55 lines
subfunctions/PH_CartVec2SphVec.m, MATLAB, 31 lines
subfunctions/PH_DeleteFcn.m, MATLAB, 44 lines
subfunctions/PH_DeleteHelpFcn.m, MATLAB, 18 lines
subfunctions/PH_DisableButtons.m, MATLAB, 20 lines
subfunctions/PH_DiscardOtherCategs.m, MATLAB, 74 lines
subfunctions/PH_DisplayControls.m, MATLAB, 78 lines
subfunctions/PH_EnableButtons.m, MATLAB, 20 lines
subfunctions/PH_ExportClusters.m, MATLAB, 43 lines
subfunctions/PH_ExtractProbeCoords.m, MATLAB, 86 lines
subfunctions/PH_GenGUI.m, MATLAB, 425 lines
subfunctions/PH_GetBrainIntersection.m, MATLAB, 42 lines
subfunctions/PH_GetBregma.m, MATLAB, 3 lines
subfunctions/PH_GetClusterCategories.m, MATLAB, 29 lines
subfunctions/PH_GetClusterField.m, MATLAB, 17 lines
subfunctions/PH_GetClusterPropertyList.m, MATLAB, 20 lines
subfunctions/PH_GetProbeAreas.m, MATLAB, 30 lines
subfunctions/PH_GetProbeVector.m, MATLAB, 11 lines
subfunctions/PH_GetRefVector.m, MATLAB, 24 lines
subfunctions/PH_HelloWorld.m, MATLAB, 44 lines
subfunctions/PH_KeyPress.m, MATLAB, 212 lines
subfunctions/PH_LoadEphysFcn.m, MATLAB, 20 lines
subfunctions/PH_LoadProbeFcn.m, MATLAB, 12 lines
subfunctions/PH_LoadProbeFile.m, MATLAB, 43 lines
subfunctions/PH_LoadProbeLocation.m, MATLAB, 29 lines
subfunctions/PH_LoadTsvFcn.m, MATLAB, 41 lines
subfunctions/PH_LoadZetaFcn.m, MATLAB, 33 lines
subfunctions/PH_MergeClusterData.m, MATLAB, 90 lines
subfunctions/PH_OpenCoordsFile.m, MATLAB, 58 lines
subfunctions/PH_OpenEphys.m, MATLAB, 87 lines
subfunctions/PH_OpenZeta.m, MATLAB, 147 lines
subfunctions/PH_PlotProbeEphys.m, MATLAB, 358 lines
subfunctions/PH_Points2vec.m, MATLAB, 49 lines
subfunctions/PH_RemPrefixes.m, MATLAB, 14 lines
subfunctions/PH_ResetFcn.m, MATLAB, 19 lines
subfunctions/PH_SaveProbeFile.m, MATLAB, 43 lines
subfunctions/PH_SaveZeta.m, MATLAB, 15 lines
subfunctions/PH_SelectCategProp.m, MATLAB, 17 lines
subfunctions/PH_SelectPlotProp.m, MATLAB, 13 lines
subfunctions/PH_SelectProbeNr.m, MATLAB, 39 lines
subfunctions/PH_SetProbePosition.m, MATLAB, 35 lines
subfunctions/PH_ShowStructure.m, MATLAB, 62 lines
subfunctions/PH_SphVec2BregmaVec.m, MATLAB, 38 lines
subfunctions/PH_SphVec2CartVec.m, MATLAB, 18 lines
subfunctions/PH_ToggleControl.m, MATLAB, 23 lines
subfunctions/PH_ToggleFreeze.m, MATLAB, 18 lines
subfunctions/PH_UndoDiscardCategs.m, MATLAB, 28 lines
subfunctions/PH_UpdateProbeCoordinates.m, MATLAB, 185 lines
subfunctions/PH_UpdateSlice.m, MATLAB, 95 lines
subfunctions/PH_loadStructureTree.m, MATLAB, 48 lines
subfunctions/SF_DeleteFcn.m, MATLAB, 49 lines
subfunctions/SF_DisplaySliceFinderControls.m, MATLAB, 83 lines
subfunctions/SF_ExportSliceFinderFile.m, MATLAB, 40 lines
subfunctions/SF_GenSliceFinderGUI.m, MATLAB, 195 lines
subfunctions/SF_KeyPress.m, MATLAB, 414 lines
subfunctions/SF_LoadSliceData.m, MATLAB, 52 lines
subfunctions/SF_PlotIms.m, MATLAB, 78 lines
subfunctions/SF_PlotSliceInAtlas.m, MATLAB, 160 lines
subfunctions/SF_SaveSliceFinderFile.m, MATLAB, 29 lines
subfunctions/SF_SliceFile2TracksFile.m, MATLAB, 31 lines
subfunctions/SF_SlicePts2AtlasPts.m, MATLAB, 83 lines
subfunctions/SH_AddTrajectory.m, MATLAB, 30 lines
subfunctions/SH_AssertSliceValidity.m, MATLAB, 26 lines
subfunctions/SH_ButtonDownFilterFcn.m, MATLAB, 18 lines
subfunctions/SH_ClearClick.m, MATLAB, 24 lines
subfunctions/SH_DeleteFcn.m, MATLAB, 49 lines
subfunctions/SH_DeleteTrackVector.m, MATLAB, 18 lines
subfunctions/SH_DisplaySlicePrepperControls.m, MATLAB, 72 lines
subfunctions/SH_EditAssignment.m, MATLAB, 144 lines
subfunctions/SH_EditTrack.m, MATLAB, 38 lines
subfunctions/SH_FlipHorz.m, MATLAB, 32 lines
subfunctions/SH_GenSliceHeader.m, MATLAB, 35 lines
subfunctions/SH_GenSlicePrepperGUI.m, MATLAB, 149 lines
subfunctions/SH_HeaderClick.m, MATLAB, 17 lines
subfunctions/SH_KeyPress.m, MATLAB, 129 lines
subfunctions/SH_LoadSliceData.m, MATLAB, 49 lines
subfunctions/SH_LoadSlicePath.m, MATLAB, 590 lines
subfunctions/SH_MagicAssignment.m, MATLAB, 132 lines
subfunctions/SH_NewTrack.m, MATLAB, 40 lines
subfunctions/SH_PlotPrepIms.m, MATLAB, 83 lines
subfunctions/SH_ReadImages.m, MATLAB, 108 lines
subfunctions/SH_RemTrack.m, MATLAB, 71 lines
subfunctions/SH_SaveSlicePrepperFile.m, MATLAB, 26 lines
subfunctions/SH_SelectChannel.m, MATLAB, 13 lines
subfunctions/SH_SelectTrack.m, MATLAB, 29 lines
subfunctions/SH_SliceClick.m, MATLAB, 174 lines
subfunctions/SH_TrackUI.m, MATLAB, 70 lines
subfunctions/SH_UnpackCZI.m, MATLAB, 70 lines
subfunctions/SH_UpdateMousePointerLine.m, MATLAB, 27 lines
subfunctions/SH_getIniPath.m, MATLAB, 31 lines
subfunctions/SH_getRegexpIni.m, MATLAB, 53 lines
subfunctions/UPF_DeleteFcn.m, MATLAB, 10 lines
subfunctions/UPF_DisableButtons.m, MATLAB, 7 lines
subfunctions/UPF_EnableButtons.m, MATLAB, 7 lines
LICENSE, License, 674 lines
README.md, Text, 72 lines

At the source: github.com/JorritMontijn/UniversalProbeFinder

Zenodo 17973874

License: CC-BY-4.0

State: the link answers, verified on 28 September 2026

Evidence: files inventoried

Size: 2 files

Software Heritage: not checked

Found in: “Code availability”

Not found: README, license file, CITATION.cff, environment file, tests, continuous integration, documentation

Availability: 1 check, the latest on 28 September 2026: the link answers (HTTP 200)

28 September 2026: the link answers (HTTP 200)

At the source:

Code availability

MATLAB and Python code used for analyses are available via Zenodo at (10.5281/zenodo.17973874).

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

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:

3 repositories of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
222 scripts, each with its path and the digest of its content;
4 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

Datasets cited

zenodo:17973873, at Zenodo; found in DataCite

Data availability

The data described in this study are available via Zenodo at (10.5281/zenodo.17973874). Source data are provided with this paper.

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

Versions

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Version 1, 28 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 3 authors, 5 keywords, 10 MeSH terms, 1 funder, 57 references, 1 integrity notice.

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Ghaderi, P., Crochet, S., & Petersen, C. C. H. (2026). Contextual gating of whisker-evoked responses by frontal cortex supports flexible decision making. Nature communications, 17(1), 5982. https://doi.org/10.1038/s41467-026-73622-y

BibTeX

@article{ghaderi2026contextual, author = {Ghaderi, Parviz and Crochet, Sylvain and Petersen, Carl C H}, title = {{Contextual gating of whisker-evoked responses by frontal cortex supports flexible decision making}}, journal = {Nature communications}, year = {2026}, month = may, volume = {17}, number = {1}, pages = {5982}, publisher = {Nature Publishing Group}, issn = {2041-1723}, doi = {10.1038/s41467-026-73622-y}, url = {https://doi.org/10.1038/s41467-026-73622-y}, pmid = {42191718}, pmcid = {PMC13346651} }

RIS

TY - JOUR AU - Ghaderi, Parviz AU - Crochet, Sylvain AU - Petersen, Carl C H TI - Contextual gating of whisker-evoked responses by frontal cortex supports flexible decision making T2 - Nature communications J2 - Nat Commun PY - 2026 DA - 2026/05/26 VL - 17 IS - 1 SP - 5982 SN - 2041-1723 PB - Nature Publishing Group DO - 10.1038/s41467-026-73622-y UR - https://doi.org/10.1038/s41467-026-73622-y LA - en ER -

CSL-JSON

{ "id": "10.1038/s41467-026-73622-y", "type": "article-journal", "title": "Contextual gating of whisker-evoked responses by frontal cortex supports flexible decision making", "container-title": "Nature communications", "author": [ { "family": "Ghaderi", "given": "Parviz" }, { "family": "Crochet", "given": "Sylvain" }, { "family": "Petersen", "given": "Carl C H" } ], "container-title-short": "Nat Commun", "volume": "17", "issue": "1", "page": "5982", "DOI": "10.1038/s41467-026-73622-y", "PMID": "42191718", "PMCID": "PMC13346651", "ISSN": "2041-1723", "publisher": "Nature Publishing Group", "URL": "https://doi.org/10.1038/s41467-026-73622-y", "language": "en", "issued": { "date-parts": [ [ 2026, 5, 26 ] ] } }

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Contextual gating of whisker-evoked responses by frontal cortex supports flexible decision making.

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