sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
fe3840bfaeef3af6dea963228190efe9515d2c70bd0b6e2b5bc9ef7891f39307 | MATLAB | 7,687 | 184 | %==========================================================================
% This script identifies the trial halves that lead to the largest
% difference in memory performance between the early and the late data
% half.
%
% Lukas Kunz, 2022
%==========================================================================
... |
8a66ba2d84b9936411278ef99fc97be840253cd17ed2c467a98b74be19c5dc00 | MATLAB | 7,703 | 165 | % clear all
% working_folder = 'Z:\test' ;
% prefix = 'AJ_AJ';
% cd(working_folder)
% raiz = pwd;
% list = dir;
% isdir = [list.isdir].';
% list_dir = list(isdir,:); list_dir(1:2)=[];
% Converting labels to number (easier to handle in Diff maps)
T_classProb_orig = T_classProb;
T_classProb(strcmp(T_classProb.DL_out,'noi... |
bfea2a6c92365ace905ed11268573c91ce6a316b48bb5d7252b63360614e5490 | MATLAB | 7,708 | 252 | clear;clc;
close all
%% Figure 5a
colors={[51 103 161],[150 68 71]};legend_name={'Low-Depth','High-Depth'};
frequency=[8 24 40];
condition=2;
count1=1;
RefreshRate=240;
displayTime=1;
while(count1 <= RefreshRate*displayTime)
for fre=1:length(frequency)
freq=frequency(fre)
alti(1,fre,coun... |
7b42e466d47120c9450bf4fa544365a19be94b4d1d0e43a7034ed5aa240cb37b | MATLAB | 7,710 | 138 | % Help for file Mat2NlxTT
% Version 4.1.1
%
% Purpsose
% The purpose of this program is to take extracted Neuralynx data from the matlab environment and create the appropriate Neuralynx file.
%
% Composition
% This program is a matlab mex file compilation of matlab and C++ source code.
% C++ source code is use... |
8dfbce5e9fd779d9748101f980e1eb15686d43c2bfb6a1f19c162ed87c2fe96e | MATLAB | 7,715 | 149 | load('dualstate_freqPowerPart.mat')
n_theta = 5:6;
Fs=2000;
ripple_tmp_rate_ecd = squeeze(group_level_stat_input.tmp_re_ecd(1,:,:)) ;
ripple_tmp_rate_ecd=ripple_tmp_rate_ecd(1:2*Fs,:);
avg_theta_power = squeeze(mean(TFR_theta(n_theta,:,1:7),[1],'omitnan') );
avg_theta_power = avg_theta_power(Fs+1:(3*Fs),:) ;
... |
ee301373188996fc1375647105feae5a4bbf6b058726b04aee59e06595791219 | MATLAB | 7,734 | 198 | function out = LK_3DPermutationTest_TwoConnectedSamples_20220901(dat)
%
% LK_3DPermutationTest_TwoConnectedSamples_20220901 performs cluster-based
% permutation testing between two connected 3D datasets (e.g., time x
% frequency x channels).
%
% Note that the statistics are calculated across the third dimension of the
... |
3902745a98210b59a72f183c69bc5b91cbb1f06939ff2d40d0ea523681f8d00f | MATLAB | 7,737 | 148 | loadParameters;
filename_centroids = fullfile(params.punctaSubvolumeDir,sprintf('%s_centroids+pixels.mat',params.FILE_BASENAME));
load(filename_centroids,'puncta_centroids','puncta_voxels')
%% Collect the subvolumes we started this with, but now only with the pixels from the puncta!
num_insitu_transcripts = size(punc... |
86ff79f5ec952f76c52e14a826b7428cbe0db3f1ff9179c2c86ee8a9222cb9e9 | MATLAB | 7,737 | 255 | % io_CSIload_GErosette.m
% Jamie Near, Sunnybrook 2023.
% Louis Lauzon, University of Calgary 2023.
%
% USAGE:
% out = io_CSIload_GErosette('filename');
%
% DESCRIPTION:
% Reads in a GE Rosette MRSI dataset using the GELoad.m function.
%
% As input, this script accepts both .h5 files (for with GE systems with
% Ver... |
59c4a7bc66e325f86abf09d7a680a87890dc0f4ccc8da0affa8b4df36ccf31a9 | MATLAB | 7,741 | 166 | % clear all
% working_folder = 'Z:\test' ;
% prefix = 'AJ_AJ';
% cd(working_folder)
% raiz = pwd;
% list = dir;
% isdir = [list.isdir].';
% list_dir = list(isdir,:); list_dir(1:2)=[];
% Converting labels to number (easier to handle in Diff maps)
T_classProb_orig = T_classProb;
T_classProb(strcmp(T_classProb.DL_out,'noi... |
3c479b50e0d9d020be902b05aff5918680cef5d6e978646ee8c7d8fb419f21e6 | MATLAB | 7,744 | 187 | %Converts electrophisiology data to excel file.
%Params:
% baseDir - a directory which contains sub directories named: ESP data,
% SP data, SxP data. each of them contains mat files with names:
% CoherencePerBoutForFileNum??.mat where ?? stands for the session
% number(must be two digits). each... |
6f25bb77907ef2f00099391700788da8bb3ab6a6148e20e10d47b3897c23809c | MATLAB | 7,775 | 300 | load("ChR2_6P7G-5CM2MS-PS.mat");
poor=[1 4 6 7 10 11 14 16];%28, 34, 37, 38, 35, 33, 45, 44
poorChR2=CHR2(poor);
C=CHR2(poor);
C1=cell2mat(C);% all mice together
M=nanmean(C1,1);
S=nansem(C1,1);
figure,
subplot(2,6,1) %per sample CS
bar([1:1:3],M(1:3),'FaceColor','w');
hold on
errorbar([1:1:3],M(1:3),S(1:3... |
e5eeda618611eb130b9572aadf3649d069c36b56f44b0d71c4d910430c8d30d3 | MATLAB | 7,786 | 194 | function varargout = plot(self, varargin)
%plot - Plot a figure
%
% plot(OBJ) plots the default figure for each element of OBJ.
%
% plot(OBJ, H_FIG, FIG_NAME) plots the figure on the specified figure
% handle(s) H_FIG, and the particular figure specified by FIG_NAME.
% FIG_NAME must be one of the following:
%
%... |
859bddae561d4784ec9d649a712894e3d7b25de0f49941ad8d10f3b0c97dbd0f | MATLAB | 7,794 | 261 | function varargout = plot_ICAtraces(self, objPI, hAx, varargin)
% CellsortICAplot(mode, ica_filters, ica_sig, f0, tlims, dt, ratebin,
% plottype, ICuse, spt, spc)
%
% Display the results of ICA analysis in the form of paired spatial filters
% and signal time courses. This function implements only fract... |
2d170e7b61289a1683292e57747f8e8aa015e9e1b29b758b9bcb2b546b1f8028 | MATLAB | 7,797 | 191 | %==========================================================================
% This script illustrates the procedure for identifying ripples in the
% macro LFP data.
%
% Lukas Kunz, 2022
%==========================================================================
% start
clear; close all; clc;
addpath(genpath('E:\OpenFi... |
6e89cbc89f23b5925b76a1c44762399589bc5163eee5bcef56f92923e1b86507 | MATLAB | 7,802 | 125 | %% Use GLM to assess contribution of different variables
locoDeform_pred = cell(1,Nexpt); locoDeform_resp = cell(1,Nexpt); locoDeform_opts = cell(1,Nexpt); locoDeform_result = cell(1,Nexpt); locoDeform_summary = cell(1,Nexpt);
figDir = 'D:\MATLAB\LevyLab\Figures\3D\GLM\'; mkdir( figDir )
%rLocoPreFit = cell(1,Nexpt)... |
625d16365d4f11006db13b87cbcc33d9f70e73a932f7b1fc059ad105cbd33069 | MATLAB | 7,814 | 209 | % EEGfMRIPav_OutcomeLocked_9_TF_grouplevel_plot
% This is an interactive script---execute it step-by-step.
% Set the appropriate job settings for loading TF data aggregated across
% subjects, then create plots.
% - two-line plot contrasting two conditions of cotnrast
% - multi-line plot contrasting all conditions with... |
83be8cc88f8bec565fe76ad14d8f86d517c90f4cf051a86099225cb3bcab9d36 | MATLAB | 7,822 | 190 | %%
% Analyzes the experimental data to produce cellTable, which has the core
% statistics we are interested in (e.g., dF/F, OSI)
%
% This code accompanies the paper:
% IA Oldenburg, WD Hendricks, G Handy, K Shamardani, HA Bounds, B Doiron,
% H Adesnik. The logic of recurrent circuits in the primary visual
% cor... |
13d5c6b81fe61665991407e08d41a9ca579666776b514c1a44be90d1453f2b6d | MATLAB | 7,823 | 217 | % EEGfMRIPav_sliceDisplay_run.m
% Directories:
dirs = [];
dirs.root = '/project/3017042.02'; % root directory--needs to be adapted to users' folder structure
addpath(fullfile(dirs.root, 'Analyses/fMRI_Scripts/Display_Results'));
% ----------------------------------------------------------------------- %
%... |
a44452b0324cbfa154de638c48234138f0a6f94ff1cdc423e6e0c454c51e84bb | MATLAB | 7,838 | 192 | % FigureS12.m
% Create source data files for Supplementary Figure S12.
% Plots were created as screenshots from FSLeyes.
%
% EEG/fMRI STUDY, DONDERS INSTITUTE, NIJMEGEN.
% J. Algermissen, 2018-2023.
% Should work in Matlab 2018b.
% we are here:
% cd /project/3017042.02/Analyses/FiguresOutcomeLocked
% clear all; clos... |
bc061ab1edf1ca6f3e10c69fc48d8807014bc018737bcbd840fcb5a88bb71471 | MATLAB | 7,842 | 158 | function hardwareContinuousVoltageNoRegen
% Example showing hardware-timed continuous analog output without regeneration using the Vidrio dabs.ni.daqmx wrapper
%
% function vidrio.AO.hardwareContinuousVoltageNoRegen
%
% Purpose
% Demonstrates how to do hardware-timed continuous analog output usi... |
1bf942777ded0f5d539e6ac1f2678fde2d4e5528a595654dd0b2a3304d2df94b | MATLAB | 7,854 | 228 | %% Pipeline for processing fMRI phase and magnitude data for QSM using the QSM toolbox
%
% fMRI presents the possibility of saving phase data, which can be used for
% QSM or as input to other phase-sensitive MR imaging pipelines
% 29 Nov 2022
% Editors (alphabetical order):
% Alexander Jaffray: ajaffray@physics.ubc.ca... |
72efdc0515871fb7cf11450322a3451a34aa2e467a399e43bf10ba3265847fbf | MATLAB | 7,857 | 162 | function segmentation_data = MakeMask3D(sbxPath, sbxInfo, mask, trace_hp, trace_raw, segParams, zProj, varargin)
IP = inputParser;
addRequired( IP, 'sbxPath', @ischar ) % path to the .sbx+ file to be projected
addRequired( IP, 'sbxInfo', @isstruct ) % @isstruct
addRequired( IP, 'mask', @iscell )
addRequired( IP, '... |
22a9beae200b17f303f5d73636c4d42e2abfaf02f04050e6a70703a76f85ae17 | MATLAB | 7,864 | 229 | function h=subaxis(varargin)
%SUBAXIS Create axes in tiled positions. (just like subplot)
% Usage:
% h=subaxis(rows,cols,cellno[,settings])
% h=subaxis(rows,cols,cellx,celly[,settings])
% h=subaxis(rows,cols,cellx,celly,spanx,spany[,settings])
%
% SETTINGS: Spacing,SpacingHoriz,SpacingVert
% ... |
66582a5b6ce1f07a0cc11d1054ab6436f3831128c7e2b65eac790cec28927256 | MATLAB | 7,890 | 321 | clear all; close all;
%% Figure 1
%% 1A (bottom)
fig1A = figure;
fig1A.Position = [100 100 650 600];
hold on;
x = linspace(-2,2,100);
tcMus = linspace(-1.65,1.65,5);
sig = 0.4;
% Plot 5 example Gaussian tuning functions
for ii = 1:5
tcTint = [1 1 1]*0.75*(ii-1)/5;
tc = normpdf(x,tcMus(ii),sig);
... |
f3e3cf25418d1de5599b545e0d5e1688ef092569fe6a20dd353f0041404ece40 | MATLAB | 7,890 | 202 | classdef DataFindROIsFLIKA_2p5D < DataFindROIsFLIKA
%DataFindROIsFLIKA - Data from FLIKA-based ROI identification
%
% The DataFindROIsFLIKA class contains the data generated by
% CalcFindROIsFLIKA.
%
% DataFindROIsFLIKA_2p5D public properties inherited from Data:
% mask - A mask combining all of the ot... |
811eec8d8ff891701e7de355b3934ac0f0a57fff35d03173bc831742bc7431a5 | MATLAB | 7,892 | 187 | %==========================================================================
% This script aligns macrodata triggers and microwire triggers to get the
% spike times in macrotime.
%
% Lukas Kunz, 2021
%==========================================================================
% start
clear; clc; close all;
% paths
path... |
af1ab0abf4e671e933e37d9478e7715ecdda6e53f37bed4d47ea52375e1017b9 | MATLAB | 7,946 | 250 | function AOandDO_Synchronized
% Demonstration of simultaneous analog output and digital output with DAQmx .NET
%
% function vidrio.mixed.AOandDO_Synchronized
%
% Description:
% This example demonstrates how to continuously run analog signal generation (AO)
% and hardware-timed digital signal generation (DO) at th... |
73848f1f1582e9b85d2dc9b0ddd0030833c087c2a2e2b5c85695a553d1a6b08e | MATLAB | 7,962 | 247 | function [estMI_obj] = estimate_MI(input,output,options,max_time)
%ESTIMATE_RR Estimates the mutual information between the input and output ensembles.
if nargin<3 || isempty(options)
options='-par';
end
if contains(options,'-par') % Establish number of estimates to use in each step
p=gcp();
num_... |
cb62f160261b8ca116d51f964688383dd33b0bee2d6ff33691ca47af32c80c3c | MATLAB | 7,970 | 181 | function params = AlignPlanes(sbxInputPath, sbxInfo, params, varargin)
% Use TurboReg to affine register each plane of a volume scan movie
IP = inputParser;
addRequired( IP, 'sbxPath', @ischar )
addRequired( IP, 'sbxInfo', @isstruct )
addRequired( IP, 'params', @isstruct )
addOptional( IP, 'refVol', [], @isnumeri... |
fc2a3cc9e606499c8cb158b2f3719534f67d6246c88c9f6d9a3666cfc1a71338 | MATLAB | 7,980 | 204 | classdef CalcFindROIsFLIKA_2D < CalcFindROIsFLIKA
%CalcFindROIsFLIKA_2D - Class for FLIKA-based ROI identification (2D)
%
% The CalcFindROIsFLIKA_2D class is a Calc class that implements the 2D
% FLIKA algorithm for ROI identification. In the 2D case, the original 3D
% mask generated by FLIKA is collapsed to 2D u... |
99f15aaf3e302c1285e7bdc05c7196e8ca8f7701a3037ec902d74ee8cbbe5189 | MATLAB | 8,004 | 120 | %% Fit a master HMM using all available data
trainMouse = 'DL89';
xMouse = strcmpi(expt.mouse, trainMouse)
[transEst, emitEst, speedDiscreteExpt] = TrainLocoHMM(loco, 'dir',sprintf('%s%s', mainDir, );
%% Find locomotive and CSD bouts
sigThresh = 0.01;
boutSumm = repmat( struct('totBout',NaN), 1, Nexpt ); onStru... |
91a5056725bf24190540721f74aa6f69b9a5d15c181df8e658d94878828398fb | MATLAB | 8,025 | 224 | function add(self, varargin)
%add - Add children to the object
%
% add(OBJ) prompts for all required information to load/create RawImg
% objects, create Processable objects, and add them to the ImgGroup
% object OBJ.
%
% add(OBJ, RAWIMG, CONFIG, PROCTYPE) creates Processable objects of the
% type specified by... |
7ec8b24a547686bb4101c85150d16c420e0c0c5744962f5efadf0c05ec4c93f1 | MATLAB | 8,053 | 197 | % EEGfMRIPav_cbm_prepareData.m
%
% Execute this script to prepare the behavioral data for an appropriate format for the CBM toolbox.
% Mind adjusting the root directory.
%
% INPUTS:
% none.
%
% OUTPUTS:
% Saves all data as EEGfMRIPav_cbm_inputData.mat to indicated directory.
%
% EEG/fMRI STUDY, DONDERS INSTITUTE, NIJM... |
1545463459304de1aaa7ad5f37083a345ee08a4f4c5128cbefd6ea81d62f764e | MATLAB | 8,055 | 183 | function [projData, binLims, projPaths] = WriteSbxZproj(sbxPath, sbxInfo, varargin) % projPath, firstScan, Nscan, pmt,
checkInfo = @(x)(isstruct(x) || isempty(x));
IP = inputParser;
addRequired( IP, 'sbxPath', @ischar ) % path to the .sbx+ file to be projected
addRequired( IP, 'sbxInfo', checkInfo ) % @isstruct
... |
361d6d44f5ace77d30489db6f0df5de5e8eaf52c29f9bebae67fe2a3127be738 | MATLAB | 8,104 | 209 | classdef DateTime
Copyright (c) 2011
This program is a result of a joined cooperation of Energocentrum
PLUS, s.r.o. and Czech Technical University (CTU) in Prague.
The program is maintained by Energocentrum PLUS, s.r.o. and
licensed under the terms of MIT license. Full text of t... |
681e820936c7aa3c32a62cc9f47b69f65c34530fa12a851b3fde664225125238 | MATLAB | 8,111 | 207 | %==========================================================================
% This script:
% - computes an average MRI scan from all subject-specific MRIs.
% - creates a probability map of channels from a specific region.
% - creates Pylocator marker files to display the elctrode positions of
% select electrodes in P... |
523730b50dcd24ab05d7d6bf023e073582d118d950426bf45070f4c06f86cac4 | MATLAB | 8,115 | 252 | % op_addrcvrs.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [out,fids_presum,specs_presum,coilcombos]=op_addrcvrs(in,point,mode,coilcombos);
%
% DESCRIPTION:
% Perform weighted coil recombination for MRS data acquired with a reciever
% coil array.
%
% INPUTS:
% in = input spectrum in matlab structu... |
b2bdcb20c65360073fff6aaa45c4d8e0e6087d0d82e647849733f39b85b39e90 | MATLAB | 8,119 | 242 | function varargout = unmix_chs(self, useParallel, varargin)
%unmix_chs - Unmix image channels
%
% unmix_chs(OBJ) interactively unmixes image channels in OBJ using the
% utility function with the default method.
%
% unmix_chs(OBJ, USEPARALLEL) explicitly specifies whether to unmix the
% RawImg object in parallel... |
b442863a5d1e0b886c472b1695a156d544848479b3a2b45409465ffa81491c6c | MATLAB | 8,119 | 308 | load("ChR2_6P7G-5cm2ms-PS.mat");
good=[2 3 5 8 9 12 13 15];%29, 33, 35, 39, 34, 46, 47, 45
goodChR2=CHR2(good);
C=CHR2(good);
C1=cell2mat(C);% all mice together
M=nanmean(C1,1);
S=nansem(C1,1);
figure,
subplot(2,6,1) %per sample CS
bar([1:1:3],M(1:3),'FaceColor','w');
hold on
errorbar([1:1:3],M(1:3),S(1:3)... |
101c941b5cdeef6a3484702ee348eeff8b34241c218ac266e1cc34d51238ea55 | MATLAB | 8,136 | 195 | function [data, timestamps, info] = load_open_ephys_data_faster(filename, varargin)
%
% [data, timestamps, info] = load_open_ephys_data(filename, [outputFormat])
%
% Loads continuous, event, or spike data files into MATLAB.
%
% Inputs:
%
% filename: path to file
% outputFormat: (optional) If omitted, contin... |
04b22e6cfda4f40ababb785752ca1866780eff0958e852d88ef638757a8754eb | MATLAB | 8,147 | 210 | function EEGfMRIPav_plot_pstay(datatype)
% EEGfMRIPav_plot_pstay()
%
% Reads data by calling EEGfMRIPav_aggr_data(), then creates bar plot of
% p(Stay) as function of condition specified under datatype input.
%
% Mind setting root directory and target directory for saving.
%
% INPUT:
% datatype = string, ei... |
e0e4527fed062978edcde3531c6dc4ec74900c3512cd75b7911194da4e32b603 | MATLAB | 8,155 | 182 | function val_sequential
% Does sequential stopping reach the same answer as running every permutation?
%
% Instead of always running n_perm permutations, the loop stops once the observed
% GLOBAL maximum has been exceeded n_exceed_stop times by the permutation maxima
% (Besag & Clifford, 1991; the negative binomial met... |
22b5ddbd6d577174028dc512ab53015f14f9c12cab1331ddc3f423f85db2360f | MATLAB | 8,159 | 232 | function self = find_ROIs(self, objPI)
%find_ROIs - Identify regions of interest
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% 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 Softwa... |
e180001ef887a80314f3af29db357d8114df40b27be1492429dcc3afca3ef6a9 | MATLAB | 8,160 | 156 | function f = LK_PlotRipplesMacroAnalysisIllustration_20231030(dt)
%
% LK_PlotRipplesMacroAnalysisIllustration_20231030 plots an illustration of
% the ripple detection in macro LFP (iEEG) data.
%
% Input is a structure with multiple fields.
%
% Output is a figure handle.
%
% Lukas Kunz, 2023
% spike colors
spikeColors ... |
be93556128c32001e6663e81cf9f6db79b0b6bc009fb5cabcd54f0aaec1cbc41 | MATLAB | 8,171 | 195 | function [skelInt1 skelIntTubulin] = extractSkelInt(data,imgMarker1,imgMarkerTubulin)
label = data(:,1)';
type = data(:,2)';
data_xyz = data(:,3:5);
radius = data(:,6)';
connct = data(:,7)';
dim = length(label);
D= ones(dim,1);
normVecList = zeros(dim,3,3); % normalized direction vector list. Dimension1: label;... |
bf650c2b036881ca88ab1cb4deaf205a972db060da5570cd057bfcfed534b44e | MATLAB | 8,176 | 204 | function twoLinePlot(job, data, errorbar, within)
% twoLinePlot(job, data, errorbar, within)
%
% Creates lineplot for two conditions specified as contrast in job.
% Works for both ERP and TFR data.
%
% INPUTS:
% job = cell with relevant fields for plotting settings,
% required fields:
% .validSubs... |
b0e1c184dd769ff19d8cc3849758956e117b18746c6955b9ab1798cf7053fd0d | MATLAB | 8,187 | 228 | % SKEL_STACK Skeletonize a 3D image matrix.
% (trees package)
%
% [i1 i2 i3] = skel_stack (iM, thr, options)
% ------------------------------------------
%
% Inspired by algorithms described by Palagyi and Kuba. Nice piece of
% code, hopefully correctly interpreted from their papers. It involves
% numerous permutatio... |
8a51a3d7d067a573d96d12650808cd49c4ab48162382f3430385df7848aeb1b4 | MATLAB | 8,203 | 202 | classdef CalcVelocityLSPIV < CalcVelocityStreaks
%CalcVelocityLSPIV - Class for calculating velocity using LSPIV
%
% The CalcVelocityLSPIV class is Calc class that implements all basic
% functionality related to calculating the velocity of images using the
% line scanning particle imaging velocimetry (LSPIV) algo... |
b58f6639b6fe0b2f4683613ae62fe00e32951a609b37696f9cf2084218010ad7 | MATLAB | 8,266 | 252 | % SHOLL_TREE Real sholl analysis.
% (trees package)
%
% [s, dd, sd, XP, YP, ZP, iD] = sholl_tree (intree, dd, options)
% --------------------------------------------------------------
%
% Calculates a sholl analysis counting the number of intersections of the
% tree with concentric circles of increasing diameters. Di... |
22b35b6bab09016263212b1157a0b6ba45d7123f68556a275507e93d72bbcf03 | MATLAB | 8,281 | 218 | function ElectodesClassificationMatlabFunc(unifyContextClasses ,averageAllBoutsFromSession ,...
NumTrees,TakeJustTheta,TakeJustGamma,matlabImpute,imputeIters, substractMouseMean, usedMouseId)
rng(0)
paramsStr = ['Ntree',num2str(NumTrees),'_Unify',num2str(unifyContextClasses),'_JustT',num2str(TakeJustTheta),'_J... |
42cab5c87d56913269663c7abe07c4747c3620a05bb0aa5aa6dc0de023dad7ba | MATLAB | 8,284 | 254 | % read in captured PSFs at a single depth
% Calibration should be done in 'S' shape
% the point position moves opposite as PSF pattern
% the gap between each PSF capture is 1 mm
clear;
%% Read in psfs at each row
n = 1;
downsample = 1;
for folder_num = 1
foldername = ['Z',num2str(folder_num)];
p... |
238355973b98275284406f3fe1f636b09779908794f81bba8de412845ecf6f55 | MATLAB | 8,315 | 216 | %==========================================================================
% Double-check which units to use for the analyses.
%
% Lukas Kunz, 2021
%==========================================================================
% start
clear; clc; close all;
% paths
paths = [];
paths.data = 'C:\OpenField\... |
e45edcbd845ba1aa24441564d5936e8fa6574e239eada0b43d35b9d6454b7634 | MATLAB | 8,358 | 262 | function [freq_mat1, freq_mat2, maxfreq_store1, maxfreq_store2] = find_peak_freq_tf (sig_struct1, ...
sig_struct2, Fs, win_length, overlap, ylim, filt_freq, plt, waitbar, width,...
dataname, struct1_name, struct2_name)
% This function calculates the peak frequency of two signals over the course
% of several tim... |
fb84178e40a7c7204a8545e626a083b71e18c8e6b8e884d3b347423ecc60ebe8 | MATLAB | 8,365 | 272 | function varargout = peakClassMeasure(self, traceNorm, frameRate, fBand, ...
roiName, doPlot, flagVersion)
%peakClassMeasure - Measure and classify peaks
%
% [PEAKS] = peakClassMeasure(OBJ, TRACE, FRAMERATE) requires
% passing of a CalcMeasureROIsClsfy object (OBJ), the raw ROI signal
% trace (TRACE) and the ... |
c6c5275dd477e81521cad31712ba7c8b4aad18d113ce986831e0ace6ff7d63ba | MATLAB | 8,371 | 235 | classdef Test_XSectScan < matlab.unittest.TestCase
%TEST_XSECTSCAN Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
methods (Test)
function testConstructor(self)
% Var... |
793819f52e4360ceaa7bcd17a308691f21bcfc38121a704a9739b0e97de2dd03 | MATLAB | 8,379 | 191 | function [Rin, tau, cap, Vrest] = t2n_passTests(neuron,tree,targetfolder_results,ostruct)
% This function applies protocols to extract passive properties (input
% resistance, membrane time constant, capacitance and resting membrane
% potential) from each cell.
%
% INPUTS
% neuron t2n neuron structure (se... |
c470585de87ec8e4c0242dcd4b9a87cb92eae59dded0b0a11db0ec83f0dab5c4 | MATLAB | 8,395 | 274 | classdef camera < handle
% zapit.hardware.camera
%
% Purpose
% This class acts as an interface between the zapit.pointer class and the MATLAB
% image acquisition toolbox. This is necessary to provide consistent behavior across
% different camera drivers.
%
% Rob Campbell - 2018 SWC
%... |
451117d3f1633556bfb865916757e504ce1a9cc88c05ea8f600a6531d88239e5 | MATLAB | 8,417 | 222 | classdef (Abstract) DataMeasureROIs < Data
%DataMeasureROIs - Superclass for DataMeasureROIs classes
%
% The DataMeasureROIs class is an abstract superclass that implements (or
% requires implementation in its subclasses via abstract methods or
% properties) all basic functionality related to storing data from RO... |
1faac06fb71a2273f33bdea2c0f6dff8b5dde07e28b850c3b94f501e5ba2fd61 | MATLAB | 8,422 | 212 | classdef DataVelocityLSPIV < DataVelocityStreaks
%DataVelocityLSPIV - Data from LSPIV-based velocity calculation
%
% The DataVelocityLSPIV class is a data class that is designed to
% contain all the basic data output from CalcVelocityLSPIV.
%
% DataVelocityLSPIV public properties inherited from Data:
% mask ... |
723f48065ae25eee5480db3853a670f9c5c731f502a101fbed4ce2825e0111cb | MATLAB | 8,452 | 354 | %% dfof_byLoc
% Plots rolling average of dfof by track location for a batch of mice
clear all; close all; clc
%% Calculate spatial dfof rolling average for all FOV
base = 'D:\4m_imaging_analysis';
cd(base)
N=1; %rolling average
type = 'dfofaveragesmooth';
% suff = '';
suff = '_sig';
svName ... |
569dc8734055dc37cbba4967b7239e3e50f7b84f424c87bdb0c11768ed5caf91 | MATLAB | 8,455 | 261 | %% FrameScan
% Analyse frame scan images of vessels
%% Usage
% OBJ = FrameScan(NAME, RAWIMG, CONFIG, ISDS, COLS_V, ROWS_V, COLS_D)
%% Arguments
% * |NAME| is the name for this |FrameScan| object.
% * |RAWIMG| is the |RawImg| object that will be used to create the
% |FrameScan| object.
% * |CONFIG| contains the conf... |
ed1b522ec0c37db12f5d7c1528a2db248a2b801dbd6e00684628bc85d646a3b3 | MATLAB | 8,470 | 201 | % Voxel.m
% Brenden Kadota, SunnyBrook Hosptial 2021.
%
% USAGE:
% Voxel(position, voxelSize, rotationMatrix, fid_aIndex)
%
% DESCRIPTION:
% Class to hold voxel spatial information to plot onto mri. Could use
% refractoring to make seperate classes for edges, vertecies, and data.
%
% INPUT:
% position = po... |
b7303103fa7873bf8e373f3b17784eae22f560befe294ea1987f702724615371 | MATLAB | 8,510 | 215 | function val_tfce_exactness
% Is the max-tree TFCE the exact value of the TFCE integral?
%
% The mex-file is compared against an INDEPENDENT reference implementation
% written in plain MATLAB, which approximates
%
% TFCE(v) = int_0^{t_v} e_v(h)^E h^H dh
%
% by stepping through n thresholds and labelling connected com... |
0f3ffe76ec59a7204aefb9eb59a618a6f56cf1c1cfaeb64e1d58456ae7bccbc7 | MATLAB | 8,519 | 189 | classdef stimConfig_tests < matlab.unittest.TestCase
% Tests for load-time checks performed by zapit.stimConfig
%
% Currently focuses on checkLaserPower, which populates the observable property
% conditionsExceedingLaserPower when a config is loaded.
%
% The fixtures assume the test settings fil... |
f779c4bbf69e4d4491e1efb082b9199fe808c850bd8427d911e6151bd6865af6 | MATLAB | 8,530 | 217 | %% Snippet Plot Example
%
% <html>
% Import snippet data into Matlab using TDTbin2mat <br>
% Sort snippets based on channel number and sort code for any number of channels and sort codes <br>
% Plot the average waveform shape and standard deviation for 16 channels and three sort codes <br>
% Good for spike sortin... |
a4f188e5f128e79feead40b4da73c8c03d0f805dd381d43d6321888d73a57be7 | MATLAB | 8,531 | 312 | function [U,S,V] = pca(A,k,its,l)
%PCA Low-rank approximation in SVD form.
%
%
% [U,S,V] = PCA(A) constructs a nearly optimal rank-6 approximation
% USV' to A, using 2 full iterations of a block Lanczos method
% of block size 6+2=8, started with an n x 8 random matrix,
% w... |
033a9f265599e22967c8b647193866ce0b6a15070a5b0abe728ba2cfc98d8ffc | MATLAB | 8,549 | 229 | classdef Test_LineScanDiam < matlab.unittest.TestCase
%TEST_LINESCAN Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
methods (Test)
function testConstructor(self)
% V... |
16ab10bfaeb56fe0efb692957aa0c9de34ee8f3684cdf0f8269bb5e2aec3de65 | MATLAB | 8,575 | 262 | function [pacmat, freqvec_ph, freqvec_amp] = find_pac_shf_tf (sig_pac, Fs, measure, ...
win_length, overlap, ph_freq, sig_mod, ph_freq_bw, amp_freq_vec, plt, waitbar, width, nfft, num_shf, alpha,...
dataname, sig_pac_name, sig_mod_name)
% This function calculates a matrix of PAC values using either the ESC, MI ... |
f3e65a08c9c0e03aea2e7dda69e4ef03d2388411441b57d14ea166b2708b8517 | MATLAB | 8,586 | 267 | function varargout = plot_graphs(self, varargin)
%plot_graphs - Plot multiple graphs from the data object
%
% plot_graphs(OBJ, X) plots graphs of X vs the default variables for the
% appropriate Data subclass Y onto the current figure. X must be either
% a numeric array, or a character array corresponding to a v... |
daf0e33176bff23c95ad2193e877cb36de849248eb4f190a4d05a6908a5c3257 | MATLAB | 8,633 | 342 | clear
close all force
load('a0_0_bhv2trialStrct.mat');
%%
%individual
NIImage_Individual = [7
9
11
22
25
27
28
38
39
40
41
42
43
44
47
49
52
53
55
56
57
59
60
]';
%group
%
NIImage_Group = [
36
37
45
51
5... |
0a7a9c7bc45e0e6405e38d9c27adab152a684d29d6171fa182b1a4216466c9e8 | MATLAB | 8,652 | 251 | function varargout = opt_config(self, objPI, calcName, varargin)
%opt_config - Optimise parameters using a GUI
%
% opt_config(OBJ, OBJ_PI, 'calc') opens a GUI that allows interactive
% adjustment of the parameters in a Config object, using the ProcessedImg
% object OBJ_PI and the property name of the relevant Cal... |
5147c02621a9fd8f000bf9991a06425e31c5b72d68176be0b936caadd4e3ba94 | MATLAB | 8,653 | 391 | %mice are in this order:
%(different from here: Z:\SNM\labMembers\LC\Lian
%Cui\behavioralParamsByYG_NT\summary.mat')
%same as here: Z:\SNM\labMembers\LC\Lian Cui\IHC\IHC Matlab\data statistic graph
%rearranged the order in "summary" so that the order can be identical to
%the histology data
% %mouse order
%... |
2ca1d3ce27199d4fd676c5cb0cbed148019704eeabdbbe7cd59a72252b774534 | MATLAB | 8,674 | 245 | % SPREAD_TREE Extracts coordinates to display trees separately.
% (trees package)
%
% [DD, outtrees] = spread_tree (intrees, dX, dY, options)
% -------------------------------------------------------
%
% Creates a cell array DD same organization as intrees which gives X, Y and
% Z coordinates to display trees spread ... |
5d258a4b04017bb8c3aa7f17769497df611c4edce91bf1bcb01e4245ba16822f | MATLAB | 8,680 | 251 | clear all
close all
rng(0)
unifyContextClasses = false;
averageAllBoutsFromSession = true;
NumTrees = 80;
TakeJustTheta = false;
TakeJustGamma = false;
matlabImpute = true;
imputeIters = 80;
paramsStr = ['Ntree',num2str(NumTrees),'_Unify',num2str(unifyContextClasses),'_JustT',num2str(TakeJustTheta),'_Ju... |
c0884df68c6869e2318d2047d8028c273b2dcf79e195ce30157150d47146d642 | MATLAB | 8,686 | 233 | classdef CalcFindROIsDummy < CalcFindROIs
%CalcFindROIsDummy - Class for dummy ROI identification
%
% The CalcFindROIsDummy class is a Calc class that performs dummy ROI
% finding. That is, it simply 'finds' previously identified ROIs, or
% uses the whole frame as a ROI.
%
% CalcFindROIsDummy is a subclass of ... |
cd4057852568964da860eca2fc195ec6e23ff938336ec3af5db4861ec7d93a6f | MATLAB | 8,692 | 210 | function betas = taft_preprocess_combine_EEG_fMRI(job, X, Y)
% betas = taft_preprocess_combine_EEG_fMRI(job, X, Y)
%
% Take a design matrix X of trial-by-trial BOLD HRF estimates and a
% matrix Y including trial-by-trial EEG data,
% add behavioral (nuisance) regressors to X, compute the pseudo-inverse,
% perform a m... |
3193dc41b0998dcdae1b241bbb1435f581708a4d8b90e0a207611dda49725aeb | MATLAB | 8,707 | 334 | %io_loadspec_bruk_old.m
%Chathura Kumaragamage, McGill University 2016.
%Jamie Near, McGill University 2016.
%
% USAGE:
% [out,ref]=io_loadspec_bruk_old(filename);
%
% DESCRIPTION:
% Reads in Bruker MRS data (fid.raw, fid.ref).
%
% op_loadspec_bruk outputs the data in structure format, with fields corresponding to tim... |
fff6e39f86412c957ad7aaa14e4196437a5ccdb0104180faa848bbd78c5d72f0 | MATLAB | 8,723 | 188 | function AOandAI
% Demonstration of simultaneous analog input and output with the dabs.ni.daqmx wrapper
%
% function vidrio.mixed.AOandAI
%
% Description:
% This example demonstrates how to continuously run data acquisition (AI)
% and signal generation (AO) at the same time and have t... |
7dafc52eb1167e6cb2bf5fa6083f338f0d2af4dd82bfd0754cfa8259bcfac8cd | MATLAB | 8,769 | 241 | %% Clear previous data
clc; close; clear
%% Select targetlocation Manually from one file
[file, ~] = uigetfile('*.mat');
file=file';
load(file)
imshow(BackgroundCropped)
hold on
targetlocation = drawpoint('Color','g');
mask=false(size(ClearOutsideMaskCropped));
targetlocation = (targetlocation.Position(1,:))
... |
28cb65c8d54fb4a9ce1b11f1d0df83c6a10ec65b0aba6a59d1dc52f7fb958d97 | MATLAB | 8,784 | 186 | function EEGfMRIPav_OutcomeLocked_4_rejICs(rootDir, subVec)
% EEGfMRIPav_OutcomeLocked_4_rejICs(rootDir, subVec)
%
% Reject identified components (after ICA and visual inspection of plots),
% save data.
%
% INPUTS:
% rootDir = string, root directory of project
% subVec = vector of integers, numb... |
4121272ac0c2d3165d82232341494f5be2a4456f1236d804c656e7f6cb753b46 | MATLAB | 8,849 | 390 | %io_loadspec_dicom_siemens.m
%Jamie Near, Sunnybrook Research Institute, 2026.
%
% USAGE:
% [out,info]=io_loadspec_dicom_siemens(dicomFolder);
%
% DESCRIPTION:
% Reads in an MRS dataset in Siemens dicom format. The input is a folder
% of Siemens dicom files, and the output is a single FID-A structure. The
% resultin... |
50dec1209e49d7233a632481085e51ac4175a2af32770974e9729400dae029da | MATLAB | 8,861 | 224 | classdef CalcDetectSigsClsfy < CalcDetectSigs
%CalcDetectSigsClsfy - Class for detecting and classifying signals
%
% The CalcDetectSigsClsfy class is a Calc class that detects and
% classifies signals in previously identified ROIs. The signals are
% classified into up to three main categories: single peaks, plat... |
31c855e4c1711d47936dcca6b350998c5724fb55ad709c8c3282a36c42cd59b5 | MATLAB | 8,869 | 168 | function [DLCBodyPartsSpeed,DLCBodyPartsDistanceFromChambers,DLCBodyPartsCoordinatesFinal,DLCBodyPartsNames,DLCModelName]=Analyze_DLC_Video_Results_09052022(filenameBehavioralDLCData,filenameBehavioralVideoData,FramesTimesInSec,app)
%TRACKMICEPOPULATIONSUMMARY Summary of this function goes here
% The aim of this func... |
7b82c26424b35fa411cf33ab427ea3a6e77ab212b5fd44af5fc57477455d12e9 | MATLAB | 8,894 | 223 | function ExtractTrace3D(path,varargin)
p = inputParser;
addOptional(p,'hp_cutoff',51); %rolling hp filter cutoff
addOptional(p,'prctile_cutoff',10); %rolling hp filter prctile cutoff
addOptional(p,'t_max',20); %# timeframes to make mask-images
addOptional(p,'z_max',5); %# zplanes to make mask-i... |
73bf73aac3fa5b33484513908a7f0c28930e1883f0ba10b3aadf5ec84d508c33 | MATLAB | 8,895 | 253 | %% Fig 5
% Jiaxin Gao
% Zhejiang University
% email: jiaxin_gao@zju.edu.cn
%% exp3
clear
clc
fs = 100;
load('.\Fig5_data.mat')
pp_sum0(:,1,:) = Fig5_Data.A.pp_sum0_con1;
pp_sum1(:,1,:) = Fig5_Data.A.pp_sum1_con1;
pp_sum2(:,1,:) = Fig5_Data.A.pp_sum2_con1;
hh_sum0(:,1,:,1,:) = Fig5_Data.A.hh_sum0_con1... |
4b867c563f6d504f15578380c65aaf94e1cd03f5454612ae6a00162cbe12f7c3 | MATLAB | 8,910 | 192 | % EEGfMRIPav_OutcomeLocked_9_time_grouplevel_test
% This is an interactive script---execute it step-by-step.
% Set the appropriate job settings for loading TF data aggregated across
% subjects, then perform tests.
% - cluster-based permutation test with Fieldtrip.
% - evaluate stat output object.
% - perform t-test pe... |
ae3222b3f19faffd4f001ef6b2d7c43852d77fe89facf03dedb47cc7fb02d436 | MATLAB | 8,914 | 242 | classdef (Abstract) CalcFindROIs < Calc & IMeasureROIs
%CalcFindROIs - Superclass for CalcFindROIs classes
%
% CalcFindROIs is an abstract superclass that implements (or requires
% implementation in its subclasses via abstract methods or properties)
% most functionality related to CalcFindROIs objects. Typically... |
12dbd1497872295c863eab76931c4f4c1e6169acba315b3d5ad10be5d99aeb2d | MATLAB | 8,927 | 196 | % TIME_TF.m
%
% Setup and time-frequency decomposition. Run this once, then Analysis.m.
%
% The two are separate because this script needs a parallel pool and reads
% every subject's raw data, while Analysis.m works entirely from what this
% one writes. Re-run this only when something upstream changes: the
% frequencie... |
eff491ac51f4b17b900a1a4f4dc4e88cdd91bce6046098e120c040d575a5446b | MATLAB | 8,932 | 230 | function out = LK_ArtifactDetection_20220319(mycfg, myeeg)
%
% LK_ArtifactDetection_20220319 detects timepoint-specific artifacts based
% on several criteria.
%
% Use as: out = LK_ArtifactDetection_20220319(mycfg, myeeg);
%
% Input #1 is a structure with optional analysis settings:
% time2exclude --> time to exclu... |
d9a236536232561e44c6424061a8edfbb4c85763a5d1a2c0d94495587bfdd280 | MATLAB | 8,935 | 278 | % This script generates KSDs from the V1, V2, and MT neuronal datasets,
% samples from the true and bootstrapped BORIS image sets,
clear all; close all;
% load neuronal data for plotting RF location KSDs
load('./analysisFiles/physio/fittingResults_processed.mat');
% sampling rate
numSamps = 100; % number of times to... |
82f0e632eeabe09f0e8294aa39f55c86ddf68b324ae23bdd46aea024b97489ed | MATLAB | 8,948 | 195 | function [projData, binLims, projPaths, rgbData] = WriteSbxZproj(sbxPath, sbxInfo, varargin) % projPath, firstScan, Nscan, pmt,
checkInfo = @(x)(isstruct(x) || isempty(x));
checkz = @(z)(isnumeric(z) || iscell(z));
IP = inputParser;
addRequired( IP, 'sbxPath', @ischar ) % path to the .sbx+ file to be projected
a... |
019075f75453ab405e0ba9240c47f0d0c069952e1a75c11ba94f6d688bc05567 | MATLAB | 8,962 | 306 | function Message = gaFFT(fnTS,TS,DAVersion)
%% function Message = gaFFT(fnTS,TS,DAVersion)
%
% FFT BLK data over time for each trial
%
% STEPS:
% - Normalize BLK data
% - FFT data over time for each trial
% - Take data at peak frequency
%
% Input:
% - fnTS is the TS.mat filename, including pathname and extenti... |
56e30ec927e8412860d8431d4caab724387d5033f77bb73380bd6a88d2e9150a | MATLAB | 8,969 | 230 | %function ElectodesClassificationMatlabFunc(
% clear all
% unifyContextClasses =true
% averageAllBoutsFromSession=true
% NumTrees = 80
% TakeJustTheta = false
% TakeJustGamma = false
% matlabImpute=true
% imputeIters=80
function BalancedElectrodesClassification(unifyContextClasses,averageAllBoutsFromSession,..... |
76ad6a242c9dd64af2b04cda3fd4a927afd41eb362330705709dda3604996ca5 | MATLAB | 8,970 | 232 | classdef Test_FrameScan < matlab.unittest.TestCase
%TEST_FRAMESCAN Summary of this class goes here
% Detailed explanation goes here
% ================================================================== %
methods (Test)
function testConstructor(self)
% Var... |
c090fa07dbf39b1a2292b9a7a26a2b4c51d96cde9becccf46add59a8bfe9e0ab | MATLAB | 8,971 | 215 | function [perf, result, testlabel] = mv_classify_across_time(cfg, X, clabel)
% Classification across time. A classifier is trained and validate for
% different time points in the dataset X. Cross-validation should be used
% to get a realistic estimate of classification performance.
%
% Usage:
% [perf, res] = mv_classif... |
3259f75816eba1071547f63bbbc6027090cdb69b49d369f4f3cfc39de14e0931 | MATLAB | 8,974 | 256 | % UNDERSTANDING TRAIN AND TEST FUNCTIONS
%
% The backbone of MVPA Light's high-level functions such as mv_classify and
% mv_regress are the train and test functions of the models. They are found
% in the model subfolder. Many standard MVPA problems can be solved using
% the high-level functions, but for some advanced a... |
1be44976a7c312254e27619b3f10065a708deeeacde38554c0705c3c58d4885a | MATLAB | 8,975 | 259 | classdef (Abstract) Calc < matlab.mixin.Copyable
%Calc - Superclass for Calc classes
%
% Calc is an abstract superclass that implements (or requires
% implementation in its subclasses via abstract methods or properties)
% most functionality related to Calc objects. Typically there is one
% concrete subclass of... |
11919959fcb8e26991d1720ffbc820abf1f1bf07a9d11de9cbdd8266093be07f | MATLAB | 8,985 | 246 | function h = mv_plot_2D(varargin)
%Plots 2D results, e.g. a time x time generalisation. Plots the results as
%a color matrix. If a 3D matrix is given several subplots are created.
%
%%Usage: Two possible usages, either giving additional parameters in a cfg
% struct (with cfg.key1 = value1) or directly giving the ... |
bea741fd1c5a84b493f99fca177e78c4f471e76fc28e857c1c4f8a876ee058fd | MATLAB | 8,991 | 253 | cd 'C:/Work/MatlabCode/projects/BrainMetabolismModeling/BrainMetabolismModeling'
ihuman = load('C:/Work/MatlabCode/components/human-GEM/Human-GEM/model/Human-GEM.mat').ihuman;
modSimp = simplifyModel(ihuman,false,false,true,true); %remove dead-end reactions
%figure out which reactions that can carry flux
rxnsToKeepO... |
f3d4b3fbff2d60d791aae41da415a405a2cf0461f88b01fbca927394e39901c0 | MATLAB | 8,999 | 333 |
%clear
close all force
warning on
imSize = [733, 977];
pix2deg = 34.910;
figure(1)
set(gcf,'Position', [440 418 555 380])
load('a0_3_1_extractingTheMorphingDataFromAnalyze1', 'imgMorphAllSaved','imgAllSaved');
load('a0_0_bhv2trialStrct.mat');
load('a0_3_0_extractingTheMorphingDataFromAnalyze1.mat','fpMean')
... |
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