sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2f26befef34db2348d12d5aef7fb19ed12177adcdfcb8b3b82e7fbc7334e86d1 | MATLAB | 3,652 | 108 |
clc
clear
%% settings
type_of_method = 'LDA'; % options: discharge, action_preference, LDA
filename_p_values = 'p_kruskalwallis_per_bin_and_neuron';
c = lines(7);
marker_size = 4;
line_color = [0.5 0.5 0.5];
color_obs_only = [.7 .7 .7];
color_match = c(2,:);
color_nonmatch = 'k';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%... |
0c5520db48aef175caaf47721dea37863dbf0550cafe5055932dc293d9eca5ec | MATLAB | 3,658 | 104 | classdef ExperimentGUI < DetectionGUI
%EXPERIMENTGUI is a GUI to control a stimulus detection experiment.
% Author: Lasse Osterhagen
properties (Access = private)
% GUI components
txtCurrentTrial
txtNumRewards
% Number of received rewards
numRewards = 0;
end
methods
function t... |
e97846f1e0d87289372c9b8fa12130b3d67a1f5e9a14a5385a69d0ae7e1d995d | MATLAB | 3,680 | 127 | function [phi_star, I, beta_opt] = phi_star_Gauss(Cov_X,Cov_XY,Cov_Y,Z,beta_init)
%-----------------------------------------------------------------------
% FUNCTION: phi_star_Gauss.m
% PURPOSE: calculate integrated information "phi_star" based on mismatched decoding
% See Oizumi et al., 2016, PLoS Comp for the deta... |
f54c3ffdb80df1bb9dbe9ab6f41cb33342c6871e2ce519efc3a5a6c813919795 | MATLAB | 3,689 | 71 | function [behavior_table, event_timing_struct] = behavior_parser(filenames, timing_table)
% The code of this function was adapted from behavioral processing of the RIFF_player_nightRIFF.m
% * * AlexKaz, 29/07/19 * *
[total_struct] = create_table_from_all_csvs(filenames);
cleaned_beh_cellarr = cell(1, 3);
s... |
b91b058c67fb88aac3b40d7a9bfea756b2a0ec5dc41f07081518f56e0a39fced | MATLAB | 3,694 | 108 | classdef ToneStimulusSampleFactoryTest < matlab.unittest.TestCase
%TONESTIMULUSSAMPLEFACTORYTEST tests ToneStimulusSampleFactory
% It only tests one fixed factory object.
% Author: Lasse Osterhagen
properties(Constant)
sF = 192e3;
gateDuration = .0005;
dur_freq_set = [.5, 10000; .1, 15000; .1, 20000... |
486561da9b9440b3a46a25c963e839aa5201647f1ebcd4c88940aa7d0f02a7dd | MATLAB | 3,697 | 131 |
clear
close all
clc
%% settings
filename_o2o = 'xx_108_4_single_o2o_perf';
filename_e2o = 'xx_108_4_single_e2o_perf';
filename_e2o_sig = 'same_or_diff_LDA'; % 1: e2o sig, -1: e2o n.s. but neuron was tested
bins_to_consider = 9:20;
boundary_angle = 25.9; % in deg (read from Fig04E command win output)
c = lines(7);... |
14fac3d240f24adc8f4bc630138d55d08f247934444d58462e21b5620f9fb868 | MATLAB | 3,703 | 118 | % Main frame acquisition loop - timings
imaqreset
len_of_run = 10;
cam = videoinput('tisimaq_r2013',2,'Y800 (1280x960)');
src = getselectedsource(cam);
% frame = getsnapshot(cam);
bg = imread('bg.tiff');
h = imshow(bg(1:2:end, 1:2:end)); title('RIFF real time picture'); hold on;
h_rat = plot(1,1);
fileID = fopen('lo... |
aa43ca980c1b2291ef92de966952a9b1ad4a08d6887a3f806c1a5d4e20b61bd5 | MATLAB | 3,739 | 94 | function [data_mat, noise_locs] = flatten_noise_areas(data_mat, is_uV, neural_mode, bit_resolution)
% changes by AP, 061220, adding options for both deuteron and tbsi
if strcmp(neural_mode, 'deuteron')
SAMP_RATE = 32000;
elseif strcmp(neural_mode, 'tbsi')
SAMP_RATE = 22000;
end
NOI... |
ff9fcd57bf3c9f479cc8fc7ae684e320b8f1401fbddf214d79efbd2b555e254e | MATLAB | 3,745 | 78 | %Author: Tatjana Schmitt, 2019-2022
function [subfield_maps_filled, subfield_borders_rotated_switched, subfield_maps, tonotopy_axes] = ...
subfield_assignment(BF_borders_broad,subfield_borders_rotated, coordinates_BF_map_rot_norm,...
coordinates_BF_map, tonotopy_axes_rotated)
%% transform subfield borders b... |
53110425ed9ebb0997ab96a2bb9aa61e1c14bdcfa65354fbd650afa224673407 | MATLAB | 3,752 | 102 | function [saturatedFrames] = whichDataSaturated(data, varargin)
% function [saturatedFrames] = whichDataSaturated(data)
% Find where the OPMs have railed/saturated during a recording
% Will return all the frames where any OPM has saturated
%
% It's quite fiddly so you may have to change the options to appropriately
% t... |
a863daa9567d710ace0dc6ba9a3943e7c7d62b854077346578a2d98bdb22ca88 | MATLAB | 3,752 | 97 | %% LaBGAS_2_spm_fit_firstlvl_models
%
% This script runs first level analysis from
% a CANlab style first level DSGN structure array and
% CANlab/spm style onset/duration and noise regressor files
% using CANlab's canlab_glm_subject_levels function
%
% See canlab_glm_single_subject('dsgninfo'), or documentation in
%... |
e255ffd8cdcbe3566f92188576ddefc12b7f8c44beb68567be48415ac17956d7 | MATLAB | 3,768 | 107 | %--- Script generating figure 4 ---
%% Initializes everything
clear, close all
run StartupAnalysis
rng(1949)
%% Sets Figure parameters
% db1FigSize = [100 100 1600 900];
db1FigSize = [50 50 1200 600];
iFig = 0; hFIG = [];
chOutDir = 'C:\Users\perre\Cardin-Higley Lab Dropbox\Quentin Perrenoud\PerrenoudCardin_Fi... |
4fab30c9c7febc07da0acca9d470cc49a88a8615363d68ac90d8cfec92225750 | MATLAB | 3,770 | 159 |
function FS_AV_Parse(DIR,varargin)
% FS_AV_Parse
% Parse Data from FreedomScopes
% Created: 2015/08/02
% By: WALIII
% Updated: 2019/05/02 % added better wireless and large file handeling
% By: WALIII
% FS_AV_parse will do several things:
%
% 1. Seperate Audio and Video, and place them into .mat files in a... |
edde168f39019a73d8fca319dbac966fbac2896a3eac522da876a3dd5c45b674 | MATLAB | 3,773 | 101 | %%% Parameters of model %%%
c = .5; %contrast
sigma = .5; %semisaturation constant
sigma_opp = .9; %semisaturation constant for opponency cells
p.varNoise = 0.03; %noise intensity
p.varImpResp = 800; %temporal correlation of OU noise (ms)
p.s = [sigma,sigma,si... |
2f7547be9ecdf3037664e8e1e35ff358f7bb678ffb53787fb22627da2de782c9 | MATLAB | 3,792 | 101 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <convHRF: convolved an input signal with a double-gamma hemodynamic response function (HRF) >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public L... |
a0352e1525a8f27193a9950d33f28fa7e46c222cd69d791f925e53b6e3291312 | MATLAB | 3,824 | 83 | function preprocess_anatomical_maskcreation(fsldir, subjectdir, diratlas)
warning('off','all');
cd(subjectdir);
k = strfind(subjectdir,'subject');
sub = [subjectdir(k:end),' - '];
clear k
% fprintf('%=============== Generating Anatomical Masks ===============%\n\n')
% SPM: Anatomic... |
b2642bfb484a8edc50913509c9ed7cd09a3af8a7412573ca830094272b7b4be8 | MATLAB | 3,831 | 113 | clear all;close all;clc;
preproc_dir='E:\mouse_development';
template_dir = 'E:\mouse_development\md_brain_atlas';
FWHM=0.5;
interx = 0.25;
intery = 0.25;
interz = 0.75;
cd(preproc_dir)
age_list = dir('mouse*');
for i = 1:length(age_list)
age = char(regexp(age_list(i).name,'\P\d+','match'));
... |
f33c5396a37e635fb7899323643821c8c5c09694dba3926caa083fbae1a5f484 | MATLAB | 3,833 | 98 | clear
close all
clc
%% settings
alpha_level = 0.05;
correction_type = 'BH'; % options: 'uncorrected', 'Bonferroni', 'BH'
bins_to_test = 1:24; % bins in which the significance test should be done
save_figure = 'off';
%% load data
load data_Fig3A.mat
%% prepare data for figure
x = 1:24;
y = NaN(4,24); % rows: mean ... |
2943741549b3908c7a6c7defa499cfb66292fe3866564e888c16af34ab90f11e | MATLAB | 3,842 | 151 | %Tried to make everything TanH
function [output] = integrate_dynamics_revised_cla_vip(W, params, x0,It, input_c)
%It = linspace(0,params.tfinal, params.n_timepoints);
%input_c = input_C(x0,It);
[output.t, X] = ode45(@rate_dynamics_ode, ...
linspace(0, params.tfinal, params.n_timepo... |
85e684a586d791a07bb448bf5f8d31fcb33ca773cae1a836ca952b28aa1766a0 | MATLAB | 3,856 | 99 | function findOutlierInZscoreResp(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM;
%% Grab Monoc ... |
cbcc42b0b5a9fa22d66ed9c35768f85d793fc17d6cb3ce8ed3739174a585f8f0 | MATLAB | 3,860 | 152 | % Integrate Dynamics
% Nair et al., 2021, Aditya Nair
function [output] = integrate_dynamics_revised_cla(W, params, x0,It, input_c)
%It = linspace(0,params.tfinal, params.n_timepoints);
%input_c = input_C(x0,It);
[output.t, X] = ode45(@rate_dynamics_ode, ...
linspace(0, params.tfi... |
169507187d2b23671b3afa5f68d49aaa2411df20fb2d94b68f4cf5cd38c16575 | MATLAB | 3,869 | 177 |
%this is just an example of how to use the matlab functions
clc
clear all;
%cd C:\MATLAB6p1\work\ethernetStandAlone
%tesitning is concted function
'tesitning is AO_IsConnected function';
ret=AO_IsConnected;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Connect
%%%%%%%%%%%%%%%%%%%%%... |
33025d9d22395a16d1af57c15f4c98bc5271d449e6594a249fb93a888634e970 | MATLAB | 3,871 | 121 | function s_comp = set(s_comp,varargin)
% SET Set Sig_comp properties and return the updated object
% Property names are:
% Input_method, Static_value, Value_formula, Static_reps, Reps_formula,
% Seq_values, Seq_values_str, Coord_index, Index_formula, Wrap, Sweep.
global INPUT_METHODS;
INPUT_METHODS={'STATIC_VALUE','SW... |
320eecef4c3459a5b57b5f1e81dc12634e3e54a9e07174f145b9fb9857a21bc5 | MATLAB | 3,874 | 109 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <remLV: removes unwanted signals from large vessels or CSF >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Fre... |
6599b3796bc5080c3ca17a4711fef9f6f811cc8ce509490e3b991588d96a67eb | MATLAB | 3,877 | 99 | function gramm_dCOS_line_testMedian(IDX)
%% Goal
% use gramm and plot the simultaneous congruent, incongruent, and monoc
% preferred.
% line plots using "methods for visualizing repeated trajectories"
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
TM = IDX.allV1(1).TM;
%% Grab Mon... |
57c745bc0e63e1d56c6806d8be58e72369ce2b7a195a03b6ad2c1f1830f28d1f | MATLAB | 3,878 | 103 | function s_comp = Sig_comp(varargin)
% Sig_comp class constructor.
% s=Sig_comp(STATIC_VALUE) creates a Sig_comp object which represents a
% Signal component.
% Sig_comp is the base class of all numerical signal components (Level_comp, Freq_comp ...etc)
% and static value is the value of the Signal component ... |
8b825ea55bff9dbb47d210ada1cc7cfbf2533c4cf6aa62f856bb7be886896fd0 | MATLAB | 3,881 | 79 | function [Angles, TurnAngles, Length, AlignedLength,Branches] = Angle(name) %creates function called Angle that can be called on in other scripts with outputs: Angles, TurnAngles; Input: name
newname = [name '.txt']; %adds .txt to name to create complete file name
[DataX,DataY] ... |
de943f2ada03bc7e478a5508d6c3919645586ff79fdbd4db2fdd8b617fda43c9 | MATLAB | 3,881 | 100 | function [db2Power, in1CntrIdx] = NS_FourierPowerHann(db1Trace, inSampleRate, varargin)
%[DB2POWER, IN1CNTRIDX] = NS_FourierPower(DB1TRACE, INSAMPLERATE,
%[DBWINLENSEC, INNSTEP, BLDOPLOT]) computes the spectral power of DB1TRACE
%over time. DB1TRACE is divided into segments whose length is specified by
%DBWINLENSEC... |
2beb062a6775942ad36e675c2aa5bbc568c81c6fdf6ddbdfb710126b6eeb97e4 | MATLAB | 3,882 | 68 | % Changed by AlexKaz on 110520 to create the 32x1 linear channel map for the Deuteron system
function createChannelMapFile_16x2_Cambridge_NeuroTech_new_layout()
PIN_LAYOUT_TYPE = 'old'; % {'old', 'new'}
Nchannels = 32;
connected = true(Nchannels, 1);
layout_dir = 'C:\Users\Owner\Desktop\global_integ... |
f1a4c8dac1e30bfcf1af8c038c598b0084e1f8c8d1fa3030df06634fc5ccf8a2 | MATLAB | 3,885 | 112 | classdef AdjMatrix < handle
%AdjMatrix
% Class to handle adjacency matrices with labels
properties (SetAccess = private)
Adj double
MetaData struct
Emb Embedding
end
properties (Dependent,SetAccess = private)
Contacts double
ROI cell
end
... |
7338f2e5d2aa535f47537c5cbf518588cbf597d750625974882d60e8352d5ee4 | MATLAB | 3,894 | 102 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <resampleEndtidalBreathing: resampled breathing data to the time-step defined by TR >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as pu... |
2df4936a7f4fc20d9a25e1522606b0f7f5a509b9b8581dc1daa39791fb9d9bb7 | MATLAB | 3,904 | 116 | % MIBI smooth stitching script used by the all channel stitch loop
% Author: Dmitry Tebaykin
% Contact: dmitry.tebaykin@stanford.edu
% if exist(xmlFileName, 'file')
% textXML = fileread(xmlFileName);
% paramNames= {'XAttrib', 'YAttrib'};
% pointsLoc = zeros(0,2);
% for i=1:length(paramNames)
% patt... |
27be87a7f80d5795117acfa16135f60c52e7047578a298e5c2fb9b745c98953d | MATLAB | 3,924 | 44 | function SUBJECT = ASLPrepareASLDataDICOM(SUBJECT, filename, prefix , fast)
% ClinicalASL toolbox 2023, JCWSiero
% Prepare (multidelay) ASL data: interleave control and label files per PLD, M0 and perform Look Locker Correction
DATA = double(niftiread([SUBJECT.NIFTIdir filename]));
DIMS = size(DATA);
SUBJECT.(... |
0a2affd1b895cb204f646b00cc9a90ad07a8805c7e23b59e38ce97116e1a34eb | MATLAB | 3,927 | 42 | function SUBJECT = ASLPrepareASLDataPARREC(SUBJECT, filename, prefix)
% ClinicalASL toolbox 2023, JCWSiero
% Prepare (multidelay) ASL data: interleave control and label files per PLD, M0 and perform Look Locker Correction
DATA = double(niftiread([SUBJECT.NIFTIdir filename(1,:)])); % read in first PLD NIFTI for DIM... |
ccffc238db66c632990ce661c4ccfa775d535f01ae4bf7d282e9906e1d2a2e95 | MATLAB | 3,929 | 145 | function [dataPC,pc2un,varnrm] = tdrPca(data,pcapars,plotflag)
% tdrPca Principal components analysis of population responses
%
% Inputs:
% data: population response (simultaneous, see 'help tdr')
% pcapars.trial_pca: trials/conditions to compute PCs
% pcapars.trial_prj: trials/conditions to project onto PCs
% pcap... |
e0575488f34befc9150dd7a629f38ff6f4bdb0285910896340463bdec7516b43 | MATLAB | 3,932 | 110 | function [options, remaining_arguments] = getOptions(options, varargin)
%GETOPTIONS Get options from variable length arguments.
%
% options = getOptions(options, 'option1', value1, 'option2', value2, ...);
% [options, remaining_arguments] = getOptions(options, ...);
%
% GETOPTIONS parses variable length arguments... |
e807923a89309f158d01aa47fe6198de8504002c075d351c00b7e1161fd4d195 | MATLAB | 3,941 | 106 |
clear all; close all; clc
%% Parameter Settings
%%%% Setup main directory which hosts /Data, /resources/, and /partialbrain_preprocessing_pipeline2020_nx folders
cd ../
dirhead=pwd;
% %% install spm12 under the Matlab home folder following
% %% https://en.wikibooks.org/wiki/SPM/Installation_on_Windows#Preamble
addpat... |
c74363a65883aa5934c172d605658341ab55ecc5aec75ca8ed2a197df406a214 | MATLAB | 3,954 | 87 | function generatePanels_FigS4_rev(FigS4)
%% Constants
p10Maps(1,:)=FigS4.constants.colormap(3,:);
p10Maps(2,:)=FigS4.constants.colormap(2,:);
p10Maps(3,:)=FigS4.constants.colormap(1,:);
p10_ArousalStates=fieldnames(FigS4.P10.Histograms);
p15_ArousalStates=fieldnames(FigS4.P15.Histograms);
p15Maps(1,:)=FigS4.co... |
3719423b1324c09fb7a493f69e045586cad4abd02a7b12ef931b69b5f1c1db11 | MATLAB | 3,963 | 109 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <chopTimeseres: shortens timeseries data to within a specified epoch >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
... |
8d8042509d414d23b4c0e362e03db1217c114b5c4f046bb882cdda9c9494c3f7 | MATLAB | 3,969 | 102 | %% LaBGAS_extract_pmods_phenotype_trial_tsv.m
%
% This script will extract symptom ratings as parametric modulators
% from the phenotype_trial.tsv file for each condition of the emosymp study
%
% DEPENDENCIES
% BIDS data organization
%
% INPUTS
% phenotype_trial.tsv file
%
% OUTPUT
% noise_regs & onsets files that ... |
9c966347f96ed8c58a2227137c670997f75a9b6031664305858d6518417cd561 | MATLAB | 4,003 | 119 | %%
% This code runs multiple examples of the spatial network used in Handy
% and Borisyuk, 2023
%
% The examples show the default network (no astrocyte ensheathmenth) and
% one example of the network with astrocyte ensheathment. Similar to Fig 6
% in the main text
%
% Important notes:
% The examples are run in parall... |
bb16ff857e5d211419ad23e451ee84d5aabcf4ba841451378fb16cd8989f5281 | MATLAB | 4,015 | 144 | function [minPos,fmin] = polyinterp(points,doPlot,xminBound,xmaxBound)
% function [minPos] = polyinterp(points,doPlot,xminBound,xmaxBound)
%
% Minimum of interpolating polynomial based on function and derivative
% values
%
% It can also be used for extrapolation if {xmin,xmax} are outside
% the domain of the po... |
18692f70f454b4e5b1efb0c10a73ec4deec19690ca8f41b593372b9ffbe11675 | MATLAB | 4,021 | 147 | %% significance of distance
clear; clc;
%%%% distance in subspace %%%
%load data
load('permutation_A.mat');
perm_a = sdata;
load('permutation_B.mat');
perm_b = sdata;
% null
distance = struct('A',[],'B',[]);
distance.A = struct('high',[],'low',[]);
distance.B = struct('high',[],'low',[]);
for r = 1:1000 %samples
... |
d20e74643afda5d3c9321c5800bda3b17540bf332a378a756230391c20614f2e | MATLAB | 4,021 | 147 | %% MIRO Demo
% Demo file to demonstrate MIRO processing workflow. You can modify this
% code and use with your own data.
%% Load Data
% Paths
FilePath_calibration = '.\Calibration_files\';
FilePath_data = '.\Raw_data\';
SavePath = '.\Results\';
% Load calibration data
load([FilePath_calibration, 'sCMOS_calibration.... |
2e84c5abcf71581a320e3e6ac6073272690a3bef56d68c65f2e54120e447689a | MATLAB | 4,024 | 119 | % F-value time-frequency analysis
% 'F' is F-values of data.
% 'F' will be a 3D shape (channels * time * frequency)
% 'TF' is time-frequency spectra of data.
% 'TF' will be a 5D shape (channels * time * frequency * trials * events)
% 'data' should be a 4D shape (channels * time * trials * events)
% 'sf' is a sa... |
bc45966de3b6a131fc637f9b0804775863a05803c35876a144cdcde6a6faf096 | MATLAB | 4,025 | 77 | function [similarity,similarity_shuffle] = neuronal_similarity_session(calcium_data,calcium_time,calcium_fps,behav_data,behav_time,behav_fps,min_behav_duration,type_str)
% This function calculates the similarity in average neuronal activation
% for each behavior. Uses Eucliden distance or dot product between first
% ... |
1deae41714c80900aa785677f750de5a533d070d160c8141b24654c08e0edc03 | MATLAB | 4,029 | 120 | function errorflag=mAO_populate(lastflag)
global mAO
errorflag=0;
SWTRIG=zeros(length(mAO.TRIGChannels),1);
while mAO.TRIGind(1)<2
for ic=1:length(mAO.TRIGChannels)
[Result,SWTRIG(ic)]=MexFileEthernetStandAlone(24,mAO.TRIGChannels(ic),mAO.TRIGdata{ic});
end
for ic=1:length(mAO.TRIGChannels)
... |
90669853b384d93651166aa52f3225dbc2894ace8b36d4848b9261469fcf7550 | MATLAB | 4,033 | 83 | function [pairwise_table] = GeneratePairwiseSpreadsheet(T,sensor_feats,clin_vars,time_diff_range)
% 'T' is the table of demographic data and feature data
% 'sensor_feats' contains a cell array of feature names for modeling
% 'clin_vars' contains a cell array of pertinent contextual variables: diagnosis, se... |
9f1384427cc3874f34d4f7ae38c34624de3f06caf76f255bebef109a017693e7 | MATLAB | 4,034 | 66 | %DISCO High contrast colormap with strong gradient discontinuities
%
% Examples:
% map = disco;
% map = disco(len);
% B = disco(A);
% B = disco(A, lims);
%
% A colormap designed to highlight contours. It has strong gradient
% discontinuities, and maximizes the range of colors used in order to
% imp... |
84d0285cb2ef1eab4ba43beebaa23ddd57d2bfd6d9eaab216a57967dab18dd8c | MATLAB | 4,050 | 102 | function generatePanels_Fig03(Fig03)
%% Pre-Whitened Resting state HbT power spectrum
Age=fieldnames(Fig03.data);
reorder=[2,3,4,5,6,1];
figure(30);
subplot(2,3,5); hold on
for AgeNum=1:length(Age)
plot(Fig03.data.(Age{reorder(AgeNum)}).FrequencyLow(:,1),(10*log10(Fig03.data.(Age{reorder(AgeNum)}).AveragedDa... |
4a0f5ee0acfdb1c037e4dff539a106afd104e72b14bb22c9c1c2cba622daef78 | MATLAB | 4,052 | 79 | function [t_sim_times, cam_inds] = make_ind_ars_for_triggers(t_behavior, t_sound, t_camera, t_state)
% Function make_ind_ars_for_triggers sub-samples the 30FPS frame stream to 10FPS sequence, that is
% found to be empirically optimal for both replay and compactness of data representation and storage.
% The function f... |
50e65d764beb1413d6843f727d0515d36f9f2e95312b24257004bac5c7f07f94 | MATLAB | 4,052 | 146 | function q_probs = est_q(Z, N_st, probs)
%-------------------------------------------------------------------------------------------------
% PURPOSE: estimate mismatched probability distribution q from the original probability distribution p
%
% INPUTS:
% p_past: probability distribution of past state (X^t-tau)
% ... |
ec8953368d1f36019b60166bc2331a8386782f163e78034eb2bf7636041ca8eb | MATLAB | 4,065 | 104 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <import_EndTidal: imports GEN4 RespirAct data >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software F... |
2d7f122be52e16e5234cad4180736e6fe6cab09f596ba6765dcbfde02177dd08 | MATLAB | 4,080 | 133 | function expdata = prepare_session_folders(data_folder, rat_num)
% JN 2020-04-24
fname = fullfile(data_folder, 'rat_sessions.csv');
table_rat_sessions = readtable(fname);
idx = (table_rat_sessions.DoProcess == 1) & ...
(table_rat_sessions.Rat == rat_num);
rat_table = table_rat_sessions(idx, :);
if ~any(idx)
... |
7b4d1e1175d33065b0cc312d0b50002518a141f22022b060a2d7c48fcbf3a213 | MATLAB | 4,083 | 120 | %% Plot mean trace of all trials
% The script was used to generate Figure 1B in manuscript
% "Brain rhythms control microglial response and cytokine expression via NFκB signaling"
% Plots are generated in a new folder named 'plots' in the parent directory
%% Dependency:
% 1. 'Statistics and Machine Learning T... |
fa86f35f7245dfc8eb18ead8c73a3f5be81f240bf65ba928018b3aae2596ad19 | MATLAB | 4,085 | 66 | %DISPARITY High contrast colormap with subtle gradient discontinuities
%
% Examples:
% map = disparity;
% map = disparity(len);
% B = disparity(A);
% B = disparity(A, lims);
%
% A colormap designed for depth and disparity maps. It has subtle gradient
% discontinuities to bring out contours, and maximi... |
a9f444a5740b9ac77b294ee319b8c76d7ae5a3cbbf16963254f9e2ba8c1eda48 | MATLAB | 4,097 | 99 | function [similarity_map_neuron,similarity_map_behav,corr_coeff,corr_pval] = neuronal_behavioral_similarity_session(calcium_data,calcium_time,calcium_fps,...
behav_data,behav_time,behav_fps,...
behav_distrib_feat,min... |
d824abe21c2d192e056f8a552c385d4458dc27ec4d70e47fd4990547723997ee | MATLAB | 4,097 | 185 | function fb_plot_allpxs(MOV_DATA,MIC_DATA,FRAME_IDX,varargin)
%fb_plot_allpxs uses the center of mass (df/f here) (COM) across time to define
% a color, and the opacity is dictated by the max df/f
%
% fb_plot_allpxs(MOV_DATA,MIC_DATA,FRAME_IDX,varargin)
%
% MOV_DATA
%
% MIC_DATA
%
% FRAME_IDX
%
% the following may be p... |
d4eecaaa4728ebed4501b305ae5b8a8d5b5f9808a0b2fae07b29fc468603288b | MATLAB | 4,110 | 199 | function FS_BatchDff(DIR, varargin)
%run thorough directory and make Background Subtracted Movies in AVI format
% This Script is for 'unprocessed' videos
% WALIII
% For unprocessed videos
% 09.05.15
%% Default Paramaters:
filt_rad=10; % gauss filter radius
filt_alpha=10; % gauss filter alpha
lims=3; % contrast prct... |
99e1f30cf48066ce9c6c5f3dc38039aa3e79520fd8a85c335e3d48610569f101 | MATLAB | 4,129 | 131 | function sampled_points=generate_signal(handles,trial_index)
% GENERATE_SIGNAL generates the sample points of the Signal.
% SAMP_RATE=GENERATE_SIGNAL(SIG,SAMP_RATE,PARAMS) generates the sample
% points of the given Signal. The number of points is determined by the
% given samp_rate.
% params is a collumn vector that h... |
4de79f7277396a9be6dea0dc115444c875f7aa40d2b1f80f54b88535bae90f23 | MATLAB | 4,148 | 102 | %% stimuli sensitive units (5a-d)
load(fullfile('..','data','auditory_units.mat'));
unitnum = [16,2,5,2];
sounds = [10,1,5,1];
ylimsize = [2,10,8,10];
xlimsize = [1500,2500,1000,1000];
t = linspace(0,2500,192000*2.5);
figure('Position',[100,100,1500,800]);
loc = [3,4,2,1];
for day = 1:4
tsounds = data(loc(day)).sou... |
e96890a98ce85725e160af5b6963f7c6e9d36a0d9ec150e705149676a083906d | MATLAB | 4,154 | 115 | classdef BinCodeGenerator < handle
% BinCodeGenerator can create binary code from (7-bit ASCII) char arrays.
% The binary code can then be sent to a sound card for asynchronous
% communication.
% Each char is represented by its binary ASCII code. It is framed by a
% start bit (1) and a stopbit (0).
... |
e6e4c421455e4bee4fb9eb6fd92a89eb708273fc67fa50c443372659b88f4a9a | MATLAB | 4,157 | 117 | %%
% This code provides a demo for the spiking simulation and mean field
% theory for Kumar et al., 2023
%
% The spiking simulation uses mex code and a par-for loop
% The simulations run for 2 seconds (of simulation time), which is shorter
% than the default 5 second, but finishes faster (~30 seconds depending on
% c... |
dd1f9e21639e128097c441079db66ba6ece0cf8af94092d782fcd7eeb2853c35 | MATLAB | 4,159 | 131 | function generatePanels_FigS1(FigS1)
%% Constants
MUA_Time=((1:length(FigS1.SingleAnimal.P10.MUA))/20000)-1;
LineFormat.Color = [0 0 0];
LineFormat.LineWidth = 0.5;
LineFormat.LineStyle = '-';
lineColors=FigS1.Constants.colormaps([3,6,9,12],:);
%% Plot Single Animal P10 example
figure(501);subplot(3,1,1);
... |
09041669466575fb82d23b29128ed18541c207c2740f9f19257fce99162e3e3c | MATLAB | 4,162 | 118 | %Function for CEEMDAN
%WARNING: for this code works it is necessary to include in the same
%directoy the file emd.m developed by Rilling and Flandrin.
%This file is available at %http://perso.ens-lyon.fr/patrick.flandrin/emd.html
%We use the default stopping criterion.
%We use the last modification: 3.2007
% ... |
dbd48d53fd87de16ab4d8b8b101ff8e070f963790efd60ae095ce0ff7448e1a8 | MATLAB | 4,171 | 93 | function c = nanconvn(a, k, varargin)
%Full credit to Benjamin Kraus for making this code. This implementation in N dimensions simply
%extends the Matlab Exchange entry https://www.mathworks.com/matlabcentral/fileexchange/41961-nanconv
% NANCONVN Convolution in ND ignoring NaNs.
% C = NANCONVN(A, K) convolves... |
170e09bae448b45988532dfde43667989140d949a98b99f4b548c40018317ab0 | MATLAB | 4,179 | 101 | function [indexChans] = goodChannelIndices(dataTable,hemisphere,completeChannelSet,printDebug)
%goodChannelIndices Considers bad channels and hemisphere/cross-set options
% This function also creates correct channel ordering for patients with
% specified "contact" IDs rather than channels
% Options:
% - he... |
20c24f7506e4dad3fb3689ed9053f3eeb2ff9df812a841111f97e1f0b975f9a2 | MATLAB | 4,188 | 89 | % Always run this first before you run other scripts.
%
% NOTES:
% - standard folders and variable names are created by these scripts
%
% - in "prep_" scripts:
% image names, conditions, contrasts, colors, global gray/white/CSF
% values are saved automatically in a DAT structure
%
% - extracted fmri_data objects ... |
658cef7d7f324bcba033bdb9efc233ad3ff4babe9961c3269676c9fe4b3728af | MATLAB | 4,198 | 89 | % Always run this first before you run other scripts.
%
% NOTES:
% - standard folders and variable names are created by these scripts
%
% - in "prep_" scripts:
% image names, conditions, contrasts, colors, global gray/white/CSF
% values are saved automatically in a DAT structure
%
% - extracted fmri_data objects ... |
869f86ee3195d1b1e42393368de81e53b441d157046eaf6d79407019d92b1774 | MATLAB | 4,198 | 121 | function [ctxidx, hpidx] = poolcells_acrossep(animaldir, animalprefix, day, eps,exclude_list)
%%
tetinfo = loaddatastruct(animaldir, animalprefix, 'tetinfo');
cell = loaddatastruct(animaldir,animalprefix,'cellinfo');
spks = loaddatastruct(animaldir, animalprefix, 'spikes', day); % get spikes
%%
for ep = eps
% ge... |
f33e5f44d57ad33ef26fb0e2e1e731a78708b9be6d61e3b4d0d49622f7f4730b | MATLAB | 4,213 | 107 | function shearletIdxs = SLgetShearletIdxs2D(shearLevels,full,varargin)
%SLgetShearletIdxs2D Compute a index set describing a 2D shearlet system.
%
% Usage:
%
% shearletIdxs = SLgetShearletIdxs2D(shearLevels)
% shearletIdxs = SLgetShearletIdxs2D(shearLevels, full)
% shearletIdxs = SLgetShearletIdxs2D(shearLe... |
f4e031ebb7eea3ad493387e09cf6f78f4ef2886d5c62e13c862e84f54a58ffb8 | MATLAB | 4,213 | 40 | function SUBJECT = ASLSaveResultsCBFAAT(SUBJECT, prefix, ORprefix)
% ClinicalASL toolbox 2023, JCWSiero
% save BASIl results: NIFTI and PNG - loops over smoothed BASIl data
% load BASIL output data : %% CBF Arrival transit time (AAT), aCBV, arterial transit artefact (ATA) for spatial COV computation, allPLD for anot... |
10c480190a5506e5aca577700c2477d8f74ab5201dab4f48af463f22ba402bcb | MATLAB | 4,244 | 139 | function robot_calibration(soundOn)
global vars
delete(instrfind);
delete(timerfindall);
if(nargin < 1)
vars.soundOn = false;
else
vars.soundOn = soundOn;
end
if(soundOn)
vars.tcp = tcpip('132.64.61.88', 80, 'NetworkRole', 'client');
try
fopen(var... |
257b3de5098178eb01492926f69bb95a463c39a0c992b3bfd0ffe19b9dbf469c | MATLAB | 4,261 | 135 | %% First Step: FPN correction
disp('FPN correction...');
tic;
for i = 1:n_frames
[fpn(:,:,i),Bias(i),Scale(i)] = MIRO_FPN_correction(im(:,:,i),Parameters);
end
toc;
%% Second Step: microlocal image processing
% Frequency Re-Weighting & Shearlet Thresholding
tic;
[a, fpn, ka, SNRa, Parameters] = MIRO_Spectral_weig... |
2485ee095c3dc5ae143d9dc146a34abadd20cef197c25afa20da0b569725516c | MATLAB | 4,290 | 119 | %---------------------------------------------------------------%
% This is the script for calculating trajectory selectiviy %
% indices for all cells -- Wenbo Tang (Jan 06, 2023) %
%---------------------------------------------------------------%
clc
clear all
close all
%%
animalprefix_list = {'AM2','J... |
18d44dde92018c1fa0bb2ea5c22a5b5e32c6585c49f79fcb2d39b45e97708f36 | MATLAB | 4,350 | 192 | function IDX = laminarLabeling_LFP
%% For each session - format the LFP (ch x time x trls)
% This needs to be trial-wise bl corrected
% Do NOT trial avg.
% Keep all stimulus presentations (no condition selection at all)
% Make sure stimulus was on screen for 500ms.
%% load session data
global STIMDIR
cd(STIMDIR)
... |
17eb1190eb7e5af1ae8e336cf9245ec78aa63e6db5b4c78dd4807aa4c1262d9c | MATLAB | 4,357 | 138 | classdef LogbookEvaluator < handle
%LOGBOOKEVALUATOR extracts data from a LogBook of a behavioral experiment.
% Arguments:
% logbook - event log of a LogBook instance.
%
% Evaluation of data from a behavioral experiment starts in this class.
% It extracts trials, sham trials, and other AudioObjects from an even... |
74dc5454ee4f25cf243e4a48d509cea9a7653c43d91192a78575586b779025f1 | MATLAB | 4,361 | 169 | S = load(fullfile('..', 'data', 'zone_angles.mat'));
zones = S.zones;
clustering_data = load(fullfile('..', 'data', 'running_trajectories.mat'));
do_sub = ones(1, 6);
data = [[2019 10 22 4 4.5]; [2019 10 23 4 20]];
pinfo = array2table(data, 'VariableNames', ...
{'Year', 'Month', 'Day', 'Rat', 'StartMinute'});
... |
0ce62cb7226ae8068c1ec26376f7c0c49899aa1807b2794e8160a29d975ef2f8 | MATLAB | 4,366 | 107 | %Author: Tatjana Schmitt, 2019-2022
function [radial_vectors_fitted, borders] = fitting_BF_vectors(stats, idx_vectors, ...
radial_vectors_BF, radial_vectors_mean_BF_smoothed)
% fits BF course of vectors, calculates turning points, sets borders and
% calculates edges of auditory cortex
%% initialize variables... |
35b49455989098d1cb820ad5803e6fedcc24ed32eb761459800d37b1fb230829 | MATLAB | 4,375 | 119 | function [TTL, CD] = DT_parse_deutoron_autologs(folder)
% JN 2020-04-15
files = dir(fullfile(folder, 'AutoLOG_*.txt'));
% JN 2020-05-08
if isempty(files)
error("No deuteron AutoLOG files found in %s", folder)
end
n_files = length(files);
all_ttl_tables = cell(n_files, 1);
all_cd_tables = cell(n_files, 1);
for... |
623354bf0946c427e41eb55b45aae5884014d91ca11e6ba0929dcacdb2e3e7c9 | MATLAB | 4,386 | 116 | function runExperimentSession(kind, configurationFile)
%RUNEXPERIMENTSESSION opens a GUI to run a detection experiment session.
% Arguments:
% kind - a string identifying the kind of experiment:
% 'gap' - simple gap detection experiment [default]
% 'tone' - a simple tone detection experiment
% 'la... |
32612c4c3a79381caa278b9ca951b384525e34af06d53c51c44c82040c36d21f | MATLAB | 4,388 | 124 | function plotsingleEvent_Fig04(Fig04)
%% READ ME
%This function plots the data generated by the single trial loaded in
%'filname' and includes, behavior, EMG, HbT and LFP
%Subscripts: brewermap
%% Filter for EMG
[z,p,k]=butter(3,[300 5000]/(0.5*Fig04.constants.an_fs),'bandpass');
[sos_EMG,g_EMG]=zp2sos(z,p,k);
... |
8d237e0feb2bbce189c5d946d9da74fa2c29ac31a1b5bca524a19272cf35e003 | MATLAB | 4,397 | 115 | function [ directionalFilter,scalingFilter,waveletFilter,scalingFilter2,shearLevels ] = MIRO_SLcheckFilterSizes(rows,cols,shearLevels,directionalFilter,scalingFilter,waveletFilter,scalingFilter2)
%% Check filter sizes
%% configuration 1
filterSetup{1}.directionalFilter = directionalFilter;
filterSetup{1}.scalingFilter... |
2ee89c152860bab4ace3625f64ab238e67acac592991d3bfb7c7ccdfbe5b543b | MATLAB | 4,399 | 80 | function [clean_env_t, erased_env_t] = align_beh_snr_trigs(snr_t_orig, beh_t_orig)
% Function align_beh_snr_trigs aligns the triggers from SNR and behavioral system.
% The behavioral triggers are derived from a single .csv file, of one of the three environments.
%
% Assumptions:
% 1. Every SNR tri... |
7db3c2712eff9f0478109fa969433cb684ac6b12df438d25daacf1eeee78c195 | MATLAB | 4,404 | 218 | function [ROI STATS]=FS_image_ROI(IMAGE,varargin)
% FS_image_ROI.m
% FS_Image_ROI takes in image, and allows user ot selet ROIs, outputs a file to
% run through and extract ROIS frim data.
% Created: 2015/08/02
% By: WALIII
% Updated: 2015/11/18
% By: WALIII
% select file to load
nparams=length(varargin);
... |
d05988d49eec8aed6f9e2a5b949bd20badc8895ee77fff908cf3400accf39793 | MATLAB | 4,407 | 151 | function [coef_fix,coef_nrm,average_time] = tdrVectorTimeAverage(coef_time,vecpars,plotflag)
% tdrVectorTimeAverage Define fixed regression vectors by time averaging coefficients
%
% Inputs:
% coef_time: regression coefficients
% .name: regressor names [nvc 1]
% .response: coefficients [nun npt nvc]
% .ti... |
6e71293fc4805379ae372be0501bd154eb75c8a8e242ea80a9b01d779206d19d | MATLAB | 4,408 | 195 | %% Clocking the denoising
frame = imread('background_dark.tiff');
disp('uint8(filter2(fspecial("average", 3), frame))');
tic;
for i = 1:100 % One operation takes 12.7 mSec
a = uint8(filter2(fspecial('average', 3), frame));
end
toc
disp('wiener2(frame, [3 3]);');
tic;
for i = 1:100 % Oneoperation takes 61... |
ba1112585d80a26cbda7b3955a13ad94522b19c00c6bed1a786dd4960f3ceeac | MATLAB | 4,438 | 118 | %%
% Creates a spatial network of neurons, using the design by
% Rosenbaum et al., 2017
%%
function [Wex1, Wex2, Wix1, Wix2,target_neuron, firing_neuron,...
id_start_firing, synapse_num_default,synapse_type]=...
create_spatial_network(Ne1, Kee, betaee, Kie, betaie,...
... |
97afdf0dfb776892588a9f25cd91410bb935b7bb34553e406a53bbe2df2b8131 | MATLAB | 4,451 | 104 | function [accuracy_training,accuracy_test,accuracy_shuffle,p_value,Model] = decoding_CCGP_linearSVM_simple(dat_all,figopt)
%---------------------------------------------------------------%
% This is the function for cross-condition generalization
% performance using linear decoder (linear SVMs) %
% -- ... |
18514d99875f9f72c4bb9d6aad4c22bd65a8eb988962b70b7aa990f01d9bda82 | MATLAB | 4,463 | 117 | function [group_step1 group_step2 group_step3 thresh] = micca_clustering(data, data_corr, indx_sample, threshold)
%
% [group_step1 group_step2 group_step3 thresh] = micca_clustering(data, data_corr, indx_sample, threshold)
%
% clustering method
%
N = length(unique(indx_sample));
if nargin < 4
%% automatic threshol... |
2b63f541a7744e593b54909797bf2cd3923f33fd1d1d78ed4da0c6394102b6fb | MATLAB | 4,470 | 121 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% sections of this code were contributed by Jeroen Siero, j.c.w.siero@umcutrecht.nl
% <smthData: smoothes input images using a gaussian kernel >
%
% This program is free software: you can redistribute it and/or modify
% it... |
adbbd73e5e1bef0c0a903a7ba55eadb7f887fce3eb370220d670292b0a0d2673 | MATLAB | 4,484 | 160 | function STIM = findAllTrials(Date,e)
%% TuneList setup
%load everything in from TuneList
TuneList = importTuneList(2);
% % case {1,'all di tasks','dionly','ditasks'}
% % ditasks = {'cosinteroc','mcosinteroc','dmcosinteroc','brfs','dbrfs', 'rsvp'};
% %
% % case {2,'brfs','Brock'} % Brock
% % dita... |
902d4783d4df3970288b571b30fc6d0ca7d17b8049240201209d02b43b1388e2 | MATLAB | 4,500 | 133 | %%
% This code runs multiple examples of the non-spatial network used in Handy
% and Borisyuk, 2023 with two feedforward input
%
% The examples show the default network (no astrocyte ensheathmenth) and
% one examples of the network with astrocyte ensheathment. Similar to Fig 5
% in the main text
%
% Important notes:
% ... |
775135e62d1eaa0816739e1f617a95d5607c03c639f0e9de2a23f532ef41367d | MATLAB | 4,513 | 166 | function hdr = load_nifti(niftifile,hdronly)
% hdr = load_nifti(niftifile,hdronly)
%
% Loads nifti header and volume. The volume is stored
% in hdr.vol. Columns and rows are not swapped.
%
% Handles compressed nifti (nii.gz) by issuing a unix command to
% uncompress the file to a temporary file, which is then deleted.
... |
459237917f784912a762502f12f3cfe4690829fc04918c8f057e69e68af5ba63 | MATLAB | 4,535 | 129 | classdef GapStimulusSampleFactory < AudioObjectSampleFactory
%GAPSTIMULUSSAMPLEFACTORY creates gaps in continuous background sound.
% This class is an AudioObjectSampleFactory that inserts gaps in a
% continuous background sound (e. g. white noise).
% Attention: The gate duration may be at most as long as the sho... |
a99c77335ca81497d8d9c70cb9e51e4a629d3d9c684d6a46120214c1c6239c5e | MATLAB | 4,535 | 127 | %--- Script generating figure 3b ---
%% Initializes everything
clear, close all
run StartupAnalysis
rng(1949)
%% Sets Figure parameters
% db1FigSize = [100 100 1600 900];
db1FigSize = [50 50 1200 600];
iFig = 0; hFIG = [];
chOutDir = 'C:\Users\perre\Cardin-Higley Lab Dropbox\Quentin Perrenoud\PerrenoudCardin_F... |
844ba69938250bccd3a7aa2ded1aa28d73559ea187f3f7958602ce5d0de344ae | MATLAB | 4,537 | 108 | function perm_id = rotate_parcellation_lh(coord_l, nrot)
%
% Usage:
% perm_id = rotate_parcellation(coord_l, nrot)
%
% Description:
% Rotate parcellation (authors: @frantisekvasa, @saratheriver)
%
% Inputs:
% coord_l (double array) - Coordinates of left hemisphere regions on the sphere, size = [m x 3]
%... |
ff344590d33f6a148373f1ccb0db69da8384b804c83964729cd8626f6f76cb1b | MATLAB | 4,540 | 126 | %%
% Analyze and plot the official results of the DiRT simulations (reproduces
% Fig 1)
%
% Loading DiRT_Results adds three items to the workspace:
% 1) DiRT_results: # time points x 2 x # trials x # phi values
% The first column contains the time vectors, while the second
% contains the number of activa... |
65a04cac74db584fdee089cd9c06b99bbbdc1735f3581f3dc96356ef647ce77f | MATLAB | 4,554 | 130 | %--- Script generating figure S5 ---
%% Initializes everything
clear, close all
run StartupAnalysis
rng(1949)
%% Sets Figure parameters
% db1FigSize = [100 100 1600 900];
db1FigSize = [50 50 1200 600];
iFig = 0; hFIG = [];
chOutDir = 'C:\Users\perre\Cardin-Higley Lab Dropbox\Quentin Perrenoud\PerrenoudCardin_F... |
9f43371843b6dd3aa7e4b0fc6d006d6e876ab0678867387b11b9b20960bbde6d | MATLAB | 4,557 | 126 | classdef FileStatsAccumulator < handle
%FILESTATSACCUMULATOR accumulates session stats from saved experimental
%data.
% Author: Lasse Osterhagen
properties (SetAccess = private)
% Higher false alarm rates will let the session to be excluded
falseAlarmRejectionRate = 0.2;
% Session will be excluded if valu... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.