sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
5415a92e093ab58cec1cf189f8671fc08a391bb2894df46e9f22f5463066ce92 | MATLAB | 18,227 | 412 | function [out] = ro_freq_meeglet(dat,cfg)
% meeglet (ver 1.0)
% Denis Engemann & Jörg Hipp, Feb 2024
%
% Log-spaced frequency transform using Morlet wavelets for continous
% electrophysiological signals. Derive power, covariance and various
% conncetivity metrics
%
% % Input
% - dat ... [channels x samples], set inval... |
40314b567a3a37b6559450035204bfa43dea0d8af542319c2c12c593b9da0985 | MATLAB | 18,256 | 591 | function SNRvideo = AddROI(video,name,masks,video_SNR)
global CallBackInterrupted;
CallBackInterrupted = 0;
global IsPlaying
IsPlaying = false; % Play flag, playing when it is 'True'
global S;
S = 1;
global sno;
global Rmin; global Rmax;
global Img;
global title_text;
global alpha;
alpha = 0.5;
Tinterv = 100;
SFn... |
5189c3d571724fe4ff2ec13f2ef558a7a397667c5d1b07624d9c227dcbc428c7 | MATLAB | 18,258 | 453 | function [UniqueIDConversion, MatchTable, WaveformInfo, param] = UnitMatch(clusinfo,param)
%% Match units on neurophysiological evidence
% Input:
% - clusinfo (this is a struct that contains per unit the following information):
% * cluster_id (e.g. kilosort output clus_id)
% * Good_ID: ones for units that should be in... |
28e27f17ac5a00eb2b251e9bf85df9dd66cf1e8706722b80eb15a7b3eb385295 | MATLAB | 18,281 | 416 | function [] = C1_TFR_RFT(sub,av_type)
%RFT TFR analysis
%% Load clean MEG file
% proc_folder='/rds/projects/j/jenseno-avtemporal-attention/Load/MEG Data/proc_data/'; %Portal
% addpath /rds/projects/j/jenseno-avtemporal-attention/MATLAB/fieldtrip-20210328 %Portal
proc_folder='Z:\Load\MEG Data\proc_data\'; %Windows
add... |
902a11309f741ce3975697ac4d886a3997769fd91318ba0620827171b17a7076 | MATLAB | 18,354 | 405 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
% Run this code first.
% This code computes the mfr and pfr for different occupancy thresholds and
% then saves the results in folders needed by the other scripts.
close all
clear all
clc
% Paths
run('../load_figure_config.m')
INPU... |
7f8da3c311e8180c1ffdcfbf35213b6a10fb00b4e85c0551cf07d7c049a72a9d | MATLAB | 18,393 | 415 | classdef TimeSeries < types.core.NWBDataInterface & types.untyped.GroupClass
% TIMESERIES General purpose time series.
% READONLY PROPERTIES
properties(SetAccess = protected)
starting_time_unit; % (char) Unit of measurement for time, which is fixed to 'seconds'.
timestamps_interval; % (int32) Value is '1'
... |
fb068ed745df7c505be67bff286038e22d460325ff74111d17d02f4db42561ae | MATLAB | 18,417 | 304 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: OptoDoseResponse_PooledMatrices_2023
% Cohort: PFC dLight1.3b with opto
% May 2023 - Marie Labouesse, marie.labouesse@gmail.com
% 1- POOLED DATA
% loads FP data previously analyzed (with: OptoDoseResponse_DataExtraction) in matlab space "Individ... |
475f82e8d0fe4374d6864e89a5386b0310d67a800f8ea7ec36db9200c7b94476 | MATLAB | 18,506 | 418 | % saveLegStepParamCond_indpt.m
%
% Function that saves legStep parameters for all steps that meet the user
% specified conditions on bodytraj
% Treats all steps as independent, as long as bodytraj condition(s) are
% met, unlike saveLegStepParamCond_bouts.m
% Steps are included if at least for half their duration, th... |
34565a3dbbbe55dddf805399b2ada16bcdcec458fb72c1ad5195b8a58ec57c9c | MATLAB | 18,606 | 437 | % heatmapMoveCondData.m
%
% Function to generate heat map of movement conditioned data generated by
% moveCondPairData(). Similar to scatterMoveCondData() but as heat map,
% plots the value of the dependent variable z against two independent
% variables, x and y. Each value in heatmap is a mean of the values that
% ... |
60685b8f638b29293facb247f8e7b6e23742e73cb421a93b926ed9654fa2b6d5 | MATLAB | 18,632 | 604 | function [] = ExtDataFig09_TuningCurve_OptStim_SongProb
% Code for plotting the tuning curves in Extended Data Fig. 9e-g.
GT = 'pIP10_Chr';
% GT = 'dPR1_Chr';
% GT = 'TN1_Chr';
% GT = 'pMP2_Chr';
switch GT
case 'w_Chr'
Target = [1,2];
case 'pIP10_Chr'
Target = [3,4];
ylim1 = [-0.03,0.0... |
93204c9e0c24cf764b2c0a7ad64dd7cb43a1cff5346f12141b3c16c958789efa | MATLAB | 18,686 | 507 | clc
clear
%% Loading the Data for Model Development
% This code develops steady-state MCNN models for the cases when no noise
% or a constant bias with / without Gaussian noise is added to true data to
% generate training data
% This code requires the MATLAB Neural Network Toolbox to train the
% unconstrai... |
0426ddcc16e768e10274d689e60a61a763df1510ebd6ccebac7bf5b2f487b6eb | MATLAB | 18,688 | 437 | function fH = makeSupplFigure6_compareLMMs(ds,roisToPlot,saveFigs,saveFigDir)
% Function to reproduce supplementary figure 5:
% Compare goodness of fit for different linear mixed models
%
% Main LMM: fixed ampl & condition effects + random subject intercept and slope for each condition.
% LMM alternative 0: fixed ampl... |
59f0c64f6b1ca90e07d53907822d4025c0917f7cacb9e188fef69992d1fe5618 | MATLAB | 18,690 | 501 | function [HDR]=fltopen(arg1,arg3,arg4,arg5,arg6)
% FLTOPEN opens FLT file
% However, it is recommended to use SOPEN instead .
% For loading whole data files, use SLOAD.
%
% see also: SOPEN, SREAD, SSEEK, STELL, SCLOSE, SWRITE, SEOF
% HDR=fltopen(HDR);
% $Id: fltopen.m 8776 2013-11-14 09:04:48Z roboos $
% Copyright (... |
6d55e59412ae4b1632ae7bcb3e8499e16473761efd1873cc028c48969429b643 | MATLAB | 18,710 | 508 | clc
clear
%% Loading the Data for Model Development
% This code develops steady-state MCNN models for the case when a random
% bias with / without Gaussian noise is added to true data to generate
% training data
% This code requires the MATLAB Neural Network Toolbox to train the
% unconstrained neural net... |
a465825770d2de87c08a60134c75843c43dd325e263838b1841d22e39b56f23e | MATLAB | 18,782 | 474 | % clc
ManualMark_on=get(handles.cue_channel,'Value');
calmode=get(handles.calmode_pm,'Value');
switch calmode
case 1
modeindex='data405';
cal=passdata.data405;
case 2
modeindex='data470';
cal=passdata.data470;
case 3
modeindex='data580';
cal=passdata.data580;
... |
03922322d8044422452d8c5cbbb67687e79bace3e24f85cac987b7f51f268edb | MATLAB | 18,810 | 422 | function opt_out = simulate_1p_optical_propagation(vol_params,psf_params,vol_out)
% opt_out = simulate_optical_propagation(vol_params,psf_params,vol_out)
%
% Function to simulate optical propgation through the simulated volume.
% Generates the PSF and appropriate blurring representing aberrations
% within the tissue. ... |
c6c51eb44ce39f5af5e1a1cdb415d448a1d5de16fcc8357e711fd851e047d4c6 | MATLAB | 18,869 | 455 | %% Script to load, preprocess and save blood MNIST images to .amat format
close all
clear all
clc
disp('Hello!')
%% Cancer cells
myDir = 'K:\PhData\bloodmnist\train\0';
myFiles = dir(fullfile(myDir,'*.png')); %gets all png files in struct
total_length = 11959;
imglinearlength = 785;
final_file = zeros... |
ce33833897f84662f9835ee34c400f95ce45ad6e080f38b310e05d7ba23ca24f | MATLAB | 18,963 | 578 | function dimord = getdimord(data, field, varargin)
% GETDIMORD
%
% Use as
% dimord = getdimord(data, field)
%
% See also GETDIMSIZ
if ~isfield(data, field) && isfield(data, 'avg') && isfield(data.avg, field)
field = ['avg.' field];
elseif ~isfield(data, field) && isfield(data, 'trial') && isfield(data.trial, fiel... |
5050c2f12d910aad62a0c2fa0b26395133a2cf5ad11892749b1d5fe5689e333c | MATLAB | 18,979 | 533 | function [Out1, Out2, Out3] = fastica(mixedsig, varargin)
%FASTICA - Fast Independent Component Analysis
%
% NOTICE!
% THIS IS NOT THE ORIGINAL VERSION BUT A MODIFIED VERSION:
% this one does not compute the icasig if this is not necessary (otherwise
% there is no change, thus there is (should be) no change in behav... |
7b7e4da2e540d867ebada41a5b9b3aa9ad25288e7171f7aae45470455c372f44 | MATLAB | 18,996 | 439 | function all_Tcurves_correct_incorrect
k3d=2;%1= k3d, 0=k_hor, 2=newk
counter=0;
av_unit=0;
%fig2=figure;
folder=[{'Glu32_19092017H'};{'Glu32_21092017H'};{'Glu43_22122017H'};{'Glu35_10112017H'};{'Glu35_13112017H_1'};{'Glu35_13112017H_2'}];
%folder2=[{'Glu32_190917a_20170919_'},{'Glu32_210917a_20170921_'},{'Glu43_221217... |
168b4d65e1a6af5c42905e26161725b1e03912c733896d9911e0e2cbe4dc01cb | MATLAB | 19,033 | 491 | clc
clear
%% Loading the Data for Model Development followed by Partitioning
% This code develops dynamic (hybrid parallel) MCNN models for the case
% when a time-invariant bias with / without Gaussian noise is added to
% true data to generate training data
% This code requires the MATLAB Neural Network T... |
d0f039ea59554a5366faf6736b53e97174899817aa8a5d4904d81ff48b8d2331 | MATLAB | 19,041 | 456 | function result = stageFiles(img,recipePath,logPath,stageDir,varargin)
% Assemble the files for one web-preview upload in stageDir
%
% function result = webupload.stageFiles(img,recipePath,logPath,stageDir,'Param1',val1,...)
%
% Purpose
% Files written, under the names the server keeps (webuploa... |
11e9b9634d13275db29f51cbc24f887962d2ba8165cb6091164e1ea5f97a1b13 | MATLAB | 19,150 | 371 | function in = intriangulation(vertices,faces,testp,heavytest)
% intriangulation: Test points in 3d wether inside or outside a (closed) triangulation
% usage: in = intriangulation(vertices,faces,testp,heavytest)
%
% arguments: (input)
% vertices - points in 3d as matrix with three columns
%
% faces - descriptio... |
9305e0ea15e8396c8f9579e660a071e1c9ea5d8489417f9dc5bcd44b79f1944b | MATLAB | 19,164 | 375 | %% Clean-up
clear;
close all;
% warning('off', 'MATLAB:print:FigureTooLargeForPage')
% Specify parameters
Options.directory = 'D:\JG\Project Gi-DREADD\Auswertung\P11_Emx1_NaCl\';
Options.lengthFOVid = 12; % number of characters specifying animal & FOV
Options.timestamp = datestr(now, 'yymmdd_HHMMSS');
Options.... |
a510004d6d5290f92f69cc6466bf092abae746c13e453aee0bf0c13ea808fcf5 | MATLAB | 19,169 | 401 | clear
close all
%
% DirData = 'Y:\niels\Jianfeng\EEGDataScored\Matlab\';
% DirSave = 'Y:\niels\Jianfeng\Results\DetectedEvents\';
DirData = '/gpfs01/born/animal/niels/Jianfeng/EEGDataScored/Matlab/';
DirSave = '/gpfs01/born/animal/niels/Jianfeng/Results/DetectedEventsSpiNew/';
% DirData = 'Y:\niels\LunAMPASca... |
ff49fdda4681d37ec9a76b3dbe6dafa9c52d67e63482ebe67d734be6a5c36281 | MATLAB | 19,187 | 416 | function varargout = TDMS_handleGetDataOption(mode,optionsIn,metaStruct)
%TDMS_handleGetDataOption Processes input options
%
% Shouldn't be called directly by user
%
% This function does some initial verfication on the types of inputs
% that have been passed in. The second call generates instructions
% on ho... |
62f53236cfaf72d1a8258310cd566a6259340c67a4de16c81510fd68a5213687 | MATLAB | 19,197 | 462 | classdef MLContinuousPlacemap < handle
properties (SetAccess = private)
% Copies of the inputs
x = [];
y = [];
ts_ms = [];
trace_ts_ms = [];
trace_value = [];
x_input = [];
y_input = [];
ts_ms_input = [];
trace_ts_ms_input = [... |
4a41e1ff64e5755d96de6137d07293276e3e1cc4602f72dbd0e9462245820a51 | MATLAB | 19,223 | 667 | function fasticag(mixedsig, InitialGuess)
%FASTICAG - Fast Independent Component Analysis, the Graphical User Interface
%
% FASTICAG gives a graphical user interface for performing independent
% component analysis by the FastICA package. No arguments are
% necessary in the function call.
%
% Optional arguments can be g... |
ce1a4ee0d6e40269c03e2e93e0f19b15fad43e161c285dd188b750ab901415de | MATLAB | 19,267 | 541 | function spm_check_installation(action)
% Check SPM installation
% FORMAT spm_check_installation('basic')
% Perform a superficial check of SPM installation [default].
%
% FORMAT spm_check_installation('full')
% Perform an in-depth diagnostic of SPM installation.
%
% FORMAT spm_check_installation('build')
% Build signat... |
e2d21a4009a0524568e07a4d78031380c3904bfd60e1d071593a55dc3d859948 | MATLAB | 19,274 | 390 | function fH = plotDataModelFitSTRet_singleVoxel_StimulusConditionBlocks(projectDir,subjnrs,varargin)
% Function to plot single voxel time series for each SEQ-SIM stimulus
% condition. This function is used in Figures 2, 3, 6, Suppl figure 7,8,9
% in the paper:
%
% Title: Rethinking simultaneous suppression in visual ... |
5fbd53bb8c2f043cf0067f77925274ba7eabfe38881b6d93612fde2e5fd84196 | MATLAB | 19,293 | 615 | function [TR, TT, ER, t, info] = icp(q,p,varargin)
% Perform the Iterative Closest Point algorithm on three dimensional point
% clouds.
%
% [TR, TT] = icp(q,p) returns the rotation matrix TR and translation
% vector TT that minimizes the distances from (TR * p + TT) to q.
% p is a 3xm matrix and q is a 3xn matrix.
%
... |
8ea62ef9f1fd1cdf863d3ee969c704e68ae269224c07bf9a3fb135510c7b4d1e | MATLAB | 19,363 | 442 | classdef ImagingPlane < types.core.NWBContainer & types.untyped.GroupClass
% IMAGINGPLANE An imaging plane and its metadata.
% REQUIRED PROPERTIES
properties
excitation_lambda; % REQUIRED (single) Excitation wavelength, in nm.
indicator; % REQUIRED (char) Calcium indicator.
location; % REQUIRED (char) Loc... |
1c5219626e3b7f82d85ba74ab6ce8a9bcc7bef2fef48b50a1df43502a45a9948 | MATLAB | 19,364 | 502 | %% VOR_SineFit.m
% Input:
% data - dat structure with channels
% 'htvel'
% 'hhvel'
% 'hepos'
% 'vepos'
% 'stim pul'
% params.segStarts - time window start times
% params.segEnds - time wndow stop times
% sinefreq - frequency of stimulus for each segment
% labels - label for each segment
% time... |
19373ad6074ec89285511db8a26c994f7031aaae1b9f581c5af372f114800d3f | MATLAB | 19,404 | 425 |
function [Spikes,LFP,theta,nose,Fs, allo]=getSpikes(File, passNo);
%function [Spikes,nose,Fs]=getSpikesOF(File, passNo);
%getSpikesOF, modified from getSpikes to read OpenField data. ehud, Oct
%2016
%
%1. parse the data according to gaps in Timestamps (> 1s)
%Session_str, e.g.,'20150906Thalamus36\20150906Thal... |
1a7ca282c21f24e775974127325b11f927501d005d898ba20a8824cda1ae016f | MATLAB | 19,413 | 581 | function gui_cb(action)
%
% This file is used by FASTICAG
% This file holds the callbacks to the main window
% @(#)$Id: gui_cb.m 8776 2013-11-14 09:04:48Z roboos $
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Global variables
% Handle to the main figure
global hf_FastICA_MAIN;
... |
8c174dad1ce6fb61ddfebb03a81f2d26fbf55c02b2f87db4ab4be922863799fe | MATLAB | 19,413 | 481 | % gaborWavelet - Function for computing gabor features of a gray-scale image
%
% This function calculates gabor features. Mean-squared energy & meanAmplitude
% for each scale % and orientation is returned.
%
% There are potentially many arguments, here is the full usage:
%
% [gaborSquareEnergy, gaborMeanAmplitude] =... |
0ab04681f53553b0ea93612a42f9f9f629057b24f8cbb41963b73018acbc7d02 | MATLAB | 19,501 | 490 | classdef packsph < handle
% Packing spheres
%
% Usage:
% pc = packsph();
% pc.packing(maxdensity,hardwallBC,rinit,root,target,compileFlag,n,gap)
%
% Input:
% maxdensity: maximal sphere volume fraction
% hardwallBC: boundary condition, 0 for periodic, 1 for hard wall
% rinit: cyl... |
b561015806e7fe069b2665a8b19f247303eb7c10a59b463a3c34accf7b10fc9d | MATLAB | 19,582 | 490 | % extractOptomotorBoutsLegStepParams_fly.m
%
% Function that extracts turning bouts in response to optomotor stimulus
% and saves leg step parameters during these bouts, relative to yaw
% velocity peak.
% Adaptation of saveBallLegStepParamCond_bouts(), which extracts turning
% bouts in flies walking on the ball, wit... |
d0da4e7a85d5cba1b833e5d1d235a9fb2154d36d762e7f2afd202b181362bdde | MATLAB | 19,602 | 416 | function varargout = TDMS_handleGetDataOption(mode,optionsIn,metaStruct)
%TDMS_handleGetDataOption Processes input options
%
% Shouldn't be called directly by user
%
% This function does some initial verfication on the types of inputs
% that have been passed in. The second call generates instructions
% ... |
56be5e75f4e29af777df49a45fdbb4f12f2dd3986bee5f68ffa429cfaf4a434f | MATLAB | 19,622 | 463 | %% Clean up
clear
close all
clc
imgshow = 0;
addpath(genpath('J:\Data\Matlab'));
%% Load file
filepath = uigetdir;
cd(filepath);
allDat = dir('*.dat');
allData = {};
for aa = 1:size(allDat,1)
inputFile = HEKA_Importer(allDat(aa).name);
dataPart... |
f68178df197754cb256cc052430a207c2d830c18523472203f6fb27432a75fc6 | MATLAB | 19,718 | 545 | function [input] = ft_apply_montage(input, montage, varargin)
% FT_APPLY_MONTAGE changes the montage of an electrode or gradiometer array. A
% montage can be used for EEG rereferencing, MEG synthetic gradients, MEG
% planar gradients or unmixing using ICA. This function applies the montage
% to the inputor array. The ... |
4e0960b6faf1335d6bfd925756c910712ed2d11e5bf90f497c7fc5bc86679c54 | MATLAB | 19,768 | 503 | function [center, Cn, PNR] = initComponents_parallel(obj, K, frame_range, save_avi, use_parallel, use_prev)
%% initializing spatial/temporal components for calcium imaging data
%% input:
% K: scalar, maximum number of neurons
% frame_range: 1 X 2 vector indicating the starting and ending frames
% save_avi: save ... |
11923b2b0fe0f12ee1da5088d5015d8716290330cd5823db88892d280fcd221e | MATLAB | 19,818 | 666 | %%%%%%%%%%%%%%%%%%%%%%Beheaviour
cd C:\Users\xic58kn\Desktop\singleton2\dataprocessed2
load behaviourProcessed
acc_all2(:,1:24)=acc_all(:,1:24);
acc_all2(:,25)=nan;
acc_all2(:,26:30)=acc_all(:,25:29);
rt_all2(:,1:24)=rt_all(:,1:24);
rt_all2(:,25)=nan;
rt_all2(:,26:30)=rt_all(:,25:29);
stimInfo_all2... |
9d00d7f5f429df0e67c8b7348056141b32db288694cb7a0be6e9b8dcf21027f4 | MATLAB | 19,822 | 386 | %Averaging the data from the Unpredicted Reward experiment
%Author:Maria Wilhelm
%Clean the previous matlab sesion
close all
clearvars
clc
%give folder with matlab functions
folder_with_matlab_scripts = 'Y:\Chernysheva Maria\MATLAB\Matlab_scripts_AlloLight';
addpath (genpath(folder_with_matlab_scripts))
... |
5630bdf98d1acd7c251037eb33ec87319c01ef8e4011fc9fdcc0dd8135e10957 | MATLAB | 19,826 | 522 | %% SETUP
clear;clc;%close all
try
[dataTable] = readtable('G:\My Drive\Expmt Data\Max\Climbing Fiber Project\ExperimentMetadata_C.xlsx');
expmtDataFolder = 'G:\My Drive\Expmt Data\Max\Climbing Fiber Project\Jennifer Data\Jennifer Data Reorganized';
catch
[dataTable] = readtable('D:\My Drive\Expmt Data\Max\... |
6845905d33e7be876d4b543653c21cf15fbc3d2fb17bfa1e0cae6696b93af2ce | MATLAB | 19,839 | 509 | %% VOR_SineFit.m
% Input:
% data - dat structure with channels
% 'htvel'
% 'hhvel'
% 'hepos'
% 'vepos'
% 'stim pul'
% params.segStarts - time window start times
% params.segEnds - time wndow stop times
% sinefreq - frequency of stimulus for each segment
% labels - label for each segment
% time... |
b9095372109389eb321c2b0f50e60b2b539313110468ef7106ffa583161f75ec | MATLAB | 19,882 | 397 | % opto tagged neurons modulated the stimulus-induced neurons
BaseDir='OptoinducedFiles';
filelist=dir(BaseDir);
Eventtype={'VonfreyInON','VonfreyUnON','InjuredON','UninjuredON','VonfreyInOFF','VonfreyUnOFF','InjuredOFF','UninjuredOFF','OptoTag','airpuffON','airpuffOFF'};
for i=3:length(filelist)
tmpmat=matfile(fu... |
2b0b9858b40e70a272cb5ac03cbf248e65ae0f8e30c673fdb3c58d5e7c5e63e8 | MATLAB | 19,952 | 441 |
function [Spikes,nose,Fs]=getSpikesEM4Tagging(File, passNo);
% modified (ehud 2020) from getSpikesEM - for tagging PSTHs, in
% scanTagging.m
%function [Spikes,nose,Fs]=getSpikesOF(File, passNo);
%getSpikesOF, modified from getSpikes to read OpenField data. ehud, Oct
%2016
%
%1. parse the data according to gaps... |
8fec7b5d790c2808f48c5a45ef1de7e999b408971d6e78159480ce0f3d3e9218 | MATLAB | 19,953 | 441 |
function [Spikes,nose,Fs]=getSpikesEM4Tagging(File, passNo);
% modified (ehud 2020) from getSpikesEM - for tagging PSTHs, in
% scanTagging.m
%function [Spikes,nose,Fs]=getSpikesOF(File, passNo);
%getSpikesOF, modified from getSpikes to read OpenField data. ehud, Oct
%2016
%
%1. parse the data according to gaps... |
6908dca0bc1123dc7f9d14aeb5913290a45cd3a7731094eed92fe3248648165b | MATLAB | 20,001 | 583 | % Function file: lsqfit
%
% [x] = lsqfit (fun, x0, xdata, ydata)
% [x] = lsqfit (fun, x0, xdata, ydata, lb)
% [x] = lsqfit (fun, x0, xdata, ydata, lb, ub)
% [x] = lsqfit (fun, x0, xdata, ydata, lb, ub, options)
% [x, resnorm] = lsqfit (...)
% [x, resnorm, residual] = lsqfit (...)
% [x, resnorm, residual, exitfl... |
7714deaae24fc9b913defdcb063d40b4ed5e0b13a834d5495f1618bcf212f585 | MATLAB | 20,123 | 578 | % Author: Zachary Chiang, Buenrostro Lab, Harvard University
% Processes a single cell of in situ genome sequencing data
function[] = expt002_cell(exp,condition,fov,cell,run,umi_file,primers,ligations)
%% Manually set parameters
%exp = "expt002";
%condition = "well2";
%fov = 30;
%cell = 2;
%run = "b1";
%umi_file = "... |
ea1c040d4ca6220f9160c4970975f4c76593ed7385896d8753e061d0f2533da4 | MATLAB | 20,245 | 552 | function VO = spm_write_sn(V,prm,flags,extras)
% Write Out Warped Images.
% FORMAT VO = spm_write_sn(V,matname,flags,msk)
% V - Images to transform (filenames or volume structure).
% matname - Transformation information (filename or structure).
% flags - flags structure, with fields...
% interp ... |
2ff41755f6ea2cadc64d66896c379271e8be2c7e0942fc27041b3a3cc67d3bba | MATLAB | 20,271 | 670 | %% Passive Imaging Opto Script
% Enny van Beest, January 2019. Script made for passive Imaging + Opto.
%% Manual settings
arduino = 1; %Arduino connected?
MetaData = 1; %Metafile (Jason) saving?
debug = 0;%Debug mode (i.e. Destkop computer is cogent screen)
MovingGratings = 1; %if 1; stimuli move. If 0; stimuli don't ... |
89637116de4370acf0d1629a2636839516fa323bbc8dc4a37cbb9bf73e304fd9 | MATLAB | 20,277 | 451 | % extractFicTracOpto_fly.m
%
% Function to extract FicTrac values with optogenetic
% stimulation.
% Like extractContStepParamsOpto_fly(), allows filtering valid opto trials
% by the fly's behavior (has to be walking before, during, and
% after the stimulation) beyond move/not move and selects no stim periods
% as ... |
8f1ed393909481b7856703c6e5b6bb46ec13b0b28e97744d1a2fd8e98f6914d0 | MATLAB | 20,296 | 548 | function [M,scal] = spm_affreg(VG,VF,flags,M,scal)
% Affine registration using least squares.
% FORMAT [M,scal] = spm_affreg(VG,VF,flags,M0,scal0)
%
% VG - Vector of template volumes.
% VF - Source volume.
% flags - a structure containing various options. The fields are:
% WG - Weig... |
608a8f0552a7c27fdf76322e4a0883b287e2af7285fc6b4269c762f076a21ce8 | MATLAB | 20,344 | 403 | function [varargout] = read_plexon_plx(filename, varargin)
% READ_PLEXON_PLX reads header or data from a Plexon *.plx file, which
% is a file containing action-potential (spike) timestamps and waveforms
% (spike channels), event timestamps (event channels), and continuous
% variable data (continuous A/D channels).
%
%... |
6a73ff8c43ece3ca97a906401bfd08054d860d6a0b7f3a9896320c8c364c8f44 | MATLAB | 20,370 | 443 | %% Author: Jiri van Bergen and Xu Li
% Affiliation: Radiology @ JHU - Kirby Center
% Contact via xuli@mri.jhu.edu
% Updated by Xu Li, 2019-07-09
% Updated by Xu Li, 2019-12-19
% Updated 2021-06-28 X.L., cluster version
% Updated 2021-07-08 X.L.
% Updated 2021-08-05 X.L., added unreliable phase mask2
% Updated... |
4bacb360e080da18e09a0e3b1dcf6da5da9d46e7e12b6270b1d8ee601a9ca3cb | MATLAB | 20,428 | 517 | % visstimLegFictracOptoVInj.m
%
% Experimental Function
% For simultaneous acquisition of leg video and FicTrac behavior data while
% providing optogenetic stimulation by controlling the shutter in front of
% the mercury lamp for the scope (light through objective) and visual
% stimuli on the G3 panels that when in ... |
4c8fcb926e1415ac914bdbc4583624af2ac1edd63d2ee269d275879733bb0e01 | MATLAB | 20,542 | 169 | function [methodinfo,structs,enuminfo,ThunkLibName]=ceds32Prot
%CEDS32PROT Create structures to define interfaces found in 'ceds64int'.
%This function was generated by loadlibrary.m parser version 1.1.6.38 on Mon Nov 24 17:34:24 2014
%perl options:'ceds64int.i -outfile=ceds32Prot.m'
ival={cell(1,0)}; % change 0 to the... |
9affe355094f756cb9fe83a7d7fb06a77642368ca0c0eabf7354af27ca75aeb0 | MATLAB | 20,568 | 568 | function results = spm_preproc(varargin)
% Combined Segmentation and Spatial Normalisation
%
% FORMAT results = spm_preproc(V,opts)
% V - image to work with
% opts - options
% opts.tpm - n tissue probability images for each class
% opts.ngaus - number of Gaussians per class (n+1 classes)
% opts.warpreg ... |
4253ae25c1b2e9f0f6920fb4f95fd436a13c48d34ad9574e6a226858c9eeb9d4 | MATLAB | 20,596 | 464 | %In vivo analysis code used to generate data in Figure 1 of Ryan et al.,
%2024.
%Created by Michael B. Ryan 01/11/24
%% Compile neural data
%Open the folder with corresponding plexon data
cd(fullfile('Users','michaelryan','Documents','TRAP','Analysis','InVivo'))
animals = dir;
for i = 1:length(animals)
... |
95638343c190dfdfa669a9b08559ddd9c959821c133bfbd3c77e3888c9bac91b | MATLAB | 20,597 | 504 | %%%%% Fix for unsorted units!! %%%%%
close all
clear all
mouse='Thalamus25';
date='20150904';
CSCs=[1:7 10:16]; %Thalamus31 Thalamus25
% CSCs=[2:15]; %Thalamus36 Thalamus28
win=0.002;
win_sum=0.05;
baseline=0.05;
n_cyc=12;
z_Scr=2; %z-score
figCount=0;
for gg=1:length(CSCs)
%% Laser %%
... |
e314bcf1469e655ca3c3bea90576c8c8d1a9fb82dfe2a8ff3a5ad399fa296ea6 | MATLAB | 20,637 | 519 | % visstimLegFictracEphysOptoVInj.m
%
% Experimental Function
% For simultaneous acquisition of leg video, FicTrac behavior, and
% electrophysiology data while providing optogenetic stimulation by
% controlling the shutter in front of the mercury lamp for the scope
% (light through objective) and visual stimuli on... |
a8c20b1ecaa5b5987312f320753ab4404c81257e028a9249f092d863d7b9acf1 | MATLAB | 20,664 | 422 | function fH = plotDataModelFit_singleVoxel_StimulusConditionBlocks(projectDir,subjnrs,varargin)
% Function to visualize single voxel fMRI BOLD time series and model
% predictions per stimulus condition.
%
% Show in the paper:
% Title: Rethinking simultaneous suppression in visual cortex via
% compressive sp... |
7f2f9f04620d8c614e9b76b6fa48706920d2021758bb3d7ec652dcd4b0194d08 | MATLAB | 20,676 | 460 | classdef MLSpikePlacemap < handle
properties (SetAccess = private)
% Copies of the inputs
x = [];
y = [];
ts_ms = [];
spike_ts_ms = [];
% Either input or defaults
boundsx = [];%
boundsy = [];
nbinsx = [];
nbinsy = [];
... |
feac505263611097578449465854e939c3edb2c2a22c58178a8f9a96076ec9ee | MATLAB | 20,711 | 475 | % extractKernels.m
%
% Function that takes in metaDat struct of selected trials and returns
% linear filters, 1 per fly. Also returns mean and
% standard error of the mean.
%
% INPUT:
% selMetaDat - metaDat struct with only trials that will be incorporated
% in this analysis
% pdPath - full path to pData d... |
a1fe9d30389b52329eacddc8c262fa7a52d81d3f1b2fcd528d1473c882203041 | MATLAB | 20,743 | 498 | function varargout = cbires(varargin)
% CBIRES MATLAB code for cbires.fig
% CBIRES, by itself, creates a new CBIRES or raises the existing
% singleton*.
%
% H = CBIRES returns the handle to a new CBIRES or the handle to
% the existing singleton*.
%
% CBIRES('CALLBACK',hObject,eventData,handles,... |
10955bfd88ee685bd8ecd75a0c04b408f346fb96903df3e47a483bda8be14666 | MATLAB | 20,793 | 455 | function [sens] = ft_datatype_sens(sens, varargin)
% FT_DATATYPE_SENS describes the FieldTrip structure that represents
% an EEG, ECoG, or MEG sensor array. This structure is commonly called
% "elec" for EEG and "grad" for MEG, or more general "sens" for either
% one.
%
% The structure for MEG gradiometers and/or magn... |
50afc2492d02d232863e795bba77dd0712f72b5f96ff3091d51224d0dc35effe | MATLAB | 20,802 | 651 |
%% load data
% run compute_coherency_table and then summarize_coherency_table before you
% run the rest of this script.
%
% filepath = fileparts(mfilename('fullpath'));
% cd(filepath);
% compute_coherency_table;
% summarize_coherency_table;
%
%% Figure 5C
data = readtable('output/coherency_table.csv');
summary = re... |
43cb78a7eed719076f7556e1f0c6e6a2293ef7a36a73b0864f8b0adffa2182af | MATLAB | 20,831 | 443 | function [BKR,s]=bkropen(arg1,arg3,arg4,arg5,arg6)
% BKROPEN opens BKR file
% However, it is recommended to use SOPEN instead .
% For loading whole data files, use SLOAD.
%
% see also: SOPEN, SREAD, SSEEK, STELL, SCLOSE, SWRITE, SEOF
% $Id: bkropen.m 8776 2013-11-14 09:04:48Z roboos $
% Copyright (c) 1997-2008 by Alo... |
ca9732a24eb3072f16f1011f0e43ec0506098d0854964ff99c8124dcb0738a6a | MATLAB | 20,978 | 446 | % extractContStepParamsOpto_fly.m
%
% Function to extract continuous leg step parameters with optogenetic
% stimulation.
% This uses the continuous estimate of the step parameters using the
% envelope method (legStepsCont struct)
% Like extractLegStepParamsOpto_fly(), allows filtering valid opto trials
% by the fly... |
de66943f6d0c18b9dba659a33c30f24f8c47244d3946c0ee7da370b4fad40e37 | MATLAB | 21,070 | 603 | function syncAndCrunch(serverDir,chanToPlot,varargin)
% Pull data off acquisition system, pre-process, and send sample images to the WWW
%
% function syncAndCrunch(serverDir,chanToPlot, ... )
%
%
% Purpose
% Perform tile index generation, pre-processing of images, and send preview stitched
% images to the web.
%
% Set ... |
ceb4537be2e27dcc5004769ed10efc717e578a6b2b7659318848b01d6d30e749 | MATLAB | 21,085 | 552 | function save(this,filename,encoding)
% Save GIfTI object in a GIfTI format file
% FORMAT save(this,filename)
% this - GIfTI object
% filename - name of GIfTI file to be created [Default: 'untitled.gii']
% encoding - optional argument to specify encoding format, among
% ASCII, Base64Binary, GZipBase6... |
c197c47bb8b576bb677955f412d62db44222387c32f04fe06500d3091db6b9f0 | MATLAB | 21,091 | 466 | function result = updateSectionImage(img,varargin)
% Stage and upload the web preview for one section or run. Never throws
%
% function result = webupload.updateSectionImage(img,'Param1',val1,...)
%
% Purpose
% Sends the last completed section image to the web site, or marks the start or end
... |
eb1590598acf1498b61e0b50e87a68111c583d8c3bce50d5d290983917473ff4 | MATLAB | 21,117 | 490 | function [unitPresence, unitProbaMatch, days, EPosAndNeg, DataSetInfo] = summaryMatchingPlots(UMFiles,UIDtoUse,groupVector,computeFuncScores)
%% Settings
PlotIndividualMice = 0;
% Drifts2Exclude = 50; % more than 50 micron, expected to lose neurons. This has nothing to do with software but with quality of recordings
M... |
5d825da09f655f372029287fda9d4b9e87f364452b4689f01fecbc0e321746af | MATLAB | 21,179 | 575 | %-------------------------------------------------------------------------------------
% plot_voltages_noamp.m
% Generates a figure with
% 1) Voltage of CX L2 neurons over time
% 2) Average voltage of all CX L2 voltages over time (with no x or y axes)
% 3) Voltage of two individual neurons in CX L2
% 3) Histogram of vo... |
a9e60584b81ba774a6bcc4276cd9c6cac671b4fa6ab30e50b5659a58df65692b | MATLAB | 21,221 | 933 | clear all
close all
clc
%% Rejection analysis
values = 1002:4000;
UG_Reject = [];
for ii = 1:length(values);
try
name = ['Subject_' num2str(values(ii)) '_rejected.csv'];
T = readtable(name);
UG_Reject = vertcat(UG_Reject,T);
end
end
%% rejection rate
rejection... |
ca56aca583e6162e68c01f376a53ab7fe560ec948092f51891ed4c65e9cb8a7d | MATLAB | 21,302 | 474 | % Uses bootstrap to evaluate the likely number of real peaks (i.e. modes)
% in the distribution of a single set of data.
%
% -- Function File: H = bootmode (X, M)
% -- Function File: H = bootmode (X, M, NBOOT)
% -- Function File: H = bootmode (X, M, NBOOT, KERNEL)
% -- Function File: H = bootmode (X, M, NBOOT, KERNEL, ... |
a20fc76dc2b7f370e34faa2b4e07094180a6656a4cc19b23fc1e8938582223ee | MATLAB | 21,353 | 529 | function [tf, lthresh, uthresh, center] = isthisanoutlier(a,varargin)
% ISOUTLIER Find outliers in data
% TF = ISOUTLIER(A) returns a logical array whose elements are true when
% an outlier is detected in the corresponding element. An outlier is an
% element that is greater than 3 scaled median absolute deviati... |
cdc831de491f6fc618374656489e20e51473b6e38d9c8483fa7992528da78313 | MATLAB | 21,364 | 537 | %% VOR_SineFit.m
% Input:
% data - dat structure with channels
% 'htvel'
% 'hhvel'
% 'hepos'
% 'vepos'
% 'stim pul'
% params.segStarts - time window start times
% params.segEnds - time wndow stop times
% sinefreq - frequency of stimulus for each segment
% labels - label for each segment
% time... |
cde60d8e7250e739b1fb89d995b86cfe5d37ed2c0fa0f5b4b66768f03b4e1656 | MATLAB | 21,372 | 539 | function varargout = spm_jobman(varargin)
% Main interface for SPM Batch System
% This function provides a compatibility layer between SPM and matlabbatch.
% It translates spm_jobman callbacks into matlabbatch callbacks and allows
% to edit and run SPM5 style batch jobs.
%
% FORMAT job_id = spm_jobman
% job_id =... |
8f182da3449b1588211ccf06a666b18322283c0eb2320485cbf63363ffdd1852 | MATLAB | 21,388 | 690 | function fh=st_plot_data_quality(cfg)
% Copyright (C) 2022-, Roy Cox, Frederik D. Weber
%
% This file is part of SleepTrip, see http://www.sleeptrip.org
% for the documentation and details.
%
% SleepTrip is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Publi... |
d88ccfd1633038e64aaf9d39d3a8e24497bb5be9290929634d9ea8746dcc65c9 | MATLAB | 21,441 | 542 | function singleRun_simSeqPRF_varySize_x_Duration_mainExp(subject,runNum,versionNr,loadTrials,offset,atScanner, coil, useEyelink)
% Wrapper function to run a single experimental run of the
% simultaneous-sequential spatiotemporal pRF experiment
%
% FOR USAGE BUTTON BOX at the scanner:
% set trigger box to these options ... |
d82b7c8290ff5f1d4ccaabe4e99e66e5490a6296c9454acbc2c1ad5a280f4358 | MATLAB | 21,540 | 577 | classdef LinePlotReducer < handle
% LinePlotReducer
%
% Manages the information in a standard MATLAB plot so that only the
% necessary number of data points are shown. For instance, if the width of
% the axis in the plot is only 500 pixels, there's no reason to have more
% than 1000 data points along the width. Th... |
8f7c04e555c6e2681d27f2e985db5c517a907e2785e415002ee3cbbaf6904a11 | MATLAB | 21,542 | 579 | function script09_fods_dispersion(samplei,regioni,timei)
% Compute FOD and some of its properties for all axons in the EM sample
%
% samplei = the index of the EM sample to analyze
% regioni = 1 == cc only , 2 == cg only , 3 == cc+cg (combined) , 4 == cc and cg (separated at same run)
% timei = diffusion time (ms)... |
f20f6a460646e253491407a6de38ad260d1860397cc846791c6b73be9eaf140f | MATLAB | 21,544 | 779 | % ------------------------------------------------------------------------
% Method : ImportAgilent
% Description : Import data stored in Agilent (.D, .MS, .CH) files
% ------------------------------------------------------------------------
%
% ---------------------------------------------------------------------... |
0b36183ceb8849b0392d0d2b45c61511dc6d9ddbd2581702b8c65da401a3c109 | MATLAB | 21,584 | 490 | % extractOptomotorFicTracOptoCond_fly.m
%
% Function to extract FicTrac values in response to optomotor visual
% stimulus with optogenetic stimulation.
% Adaptation of extractFicTracOptoCond_fly with addition of visual stimulus
% Select all pData files for 1 fly through GUI
% Saves output file with name defined by fi... |
0a4d7d839be431aeba516349f33fbc878387dc9fa55a40caa071bf93cd414cbc | MATLAB | 21,652 | 536 |
% Link tracklets (sequences) to form continuous trajectories (no more than
% the expected number of flies indicated in calib)
%
% To link tracklets, use:
%
% trks = track_segment(trks, calib)
%
% where:
%
% trks - tracklets obtained from track_segment
% calib - calibration obtained fr... |
c45c32ef90b312c35549dc11a473203fa3f9d00a8f7cfdfd4b4b15a0b1155ad2 | MATLAB | 21,714 | 737 |
function bemcp_example
% Simple function to test/demonstrate how the Boundary element functions are
% used in combination with Fildtrip/Forwinv routines.
%
% 1. A model is created as 3 concentric meshed spheres (using FT's
% icosahedron routines),
% 2. then random electrodes are placed on the upper part of the outer... |
bff4e2ee574429bf6bfa66036cf95e5ce7421dc2eb7333afe8102a99533ee744 | MATLAB | 21,804 | 495 | % conditionedLegStepsFictracEphysIinj.m
%
% Function that takes reps extracted from
% computeLegStepsFictracEphysIinj_1Fly() and returns only those that
% meet the specified criteria: greater than or less than a threshold value
% on the variable to condition on, during a time window prioer to
% stimulation
% Retur... |
f4275d5b16cfad74f11131dd6124cae4dee1f840403a1d8d66e378a3fdfb76d3 | MATLAB | 21,948 | 524 | function [AllWVBParameters,param] = ExtractParameters(Path4UnitNPY,clusinfo,param)
% Prepare fitting
Interpolate = 0;
opts = optimset('Display','off');
%% Extract relevant information
nclus = length(Path4UnitNPY);
spikeWidth = param.spikeWidth;
Allchannelpos = param.AllChannelPos;
RecSes = clusinfo.RecSesID;
if isfiel... |
48c9aa89bdef6f88a5dcfa133fc3f058a729e7a1f04907ec12bff0efc6fde554 | MATLAB | 21,960 | 589 | classdef LinePlotReducer < handle
% LinePlotReducer
%
% Manages the information in a standard MATLAB plot so that only the
% necessary number of data points are shown. For instance, if the width of
% the axis in the plot is only 500 pixels, there's no reason to have more
% than 1000 data points along the width. Th... |
5a9430840f0642984c088ba729d0153ad42f65152ede2fd640407e64008e46d6 | MATLAB | 21,982 | 605 |
%# -*- texinfo -*-
%# @deftypefn {Function File} {@var{yi} =} interp1 (@var{x}, @var{y}, @var{xi})
%# @deftypefnx {Function File} {@var{yi} =} interp1 (@dots{}, @var{method})
%# @deftypefnx {Function File} {@var{yi} =} interp1 (@dots{}, @var{extrap})
%# @deftypefnx {Function File} {@var{pp} =} interp1 (@dots{}, 'pp')... |
9be1f548a563a9e0b1939f6a6e9480e68b1feabdd073b24d43665f0c6eff38ca | MATLAB | 21,982 | 492 | % extractFicTracIInj_fly.m
%
% Function to extract FicTrac values with current injection.
% Like extractContStepParamsIInj_fly(), allows filtering valid IInj trials
% by the fly's behavior (has to be walking before, during, and
% after the stimulation) beyond move/not move and selects no stim periods
% as deliberate... |
b29b5a30080757aa20370b8b166bbf03fbb93e0b64c5602a257cc08b95847834 | MATLAB | 22,286 | 567 | % getStimvolFromVarname.m
%
% usage: [stimvol stimNames] = getStimvolFromVarname(varnameIn,myscreen,task,[taskNum],[phaseNum],[segmentNum],[verbose])
% by: justin gardner
% date: 03/15/07
% purpose: returns the volume numbers for the stimulus variable in stimvol and also
% a string whi... |
14a920e45ee116da3a06b32a015c34782752ac72c5144715bcffaa5e8c3d939b | MATLAB | 22,308 | 572 | function generateSimSeqStim_VaryConditionsMulti60Hz()
% Function to generate variations of the sequential and simultaneous
% presentation of square stimuli in the upper right visual field, as in
% Kastner et al '98 (Science) and exp 1 in '01 (J Neurophys). Varations in-
% clude: longer durations, more transients in seq... |
99bd0c7f6f3286c7e807f867d5ad40d415ad56ed4b16509c0c14109a812b51b8 | MATLAB | 22,358 | 483 | %Function to conduct an Fmax permutation test for one-way and factorial
%within-subjects ANOVA
%
%EXAMPLE USAGE
% >> GND = FmaxGND(GND, 'bins', 1:6, 'factor_names', {'probability', 'emotion'}, ...
% 'factor_levels', [3, 2], 'time_wind', [500, 800], ...
% 'include_chans', {'Fz', 'Cz', '... |
99c82605b94ed22263bcb2034154c91e07aee0b84134262c13842288e2d2971a | MATLAB | 22,394 | 607 | function read_Intan_RHS2000_file(path, file)
% read_Intan_RHS2000_file
%
% Version 1.0, 30 January 2017
%
% Reads Intan Technologies RHS2000 data file generated by Intan
% Stimulation / Recording Controller. Data are parsed and placed into
% variables that appear in the base MATLAB workspace. Therefore, it is
% rec... |
943187c940c69bb96399e2e51ba01387176384b502bb58e98c25dc024929da0c | MATLAB | 22,435 | 479 | %Function to conduct an ANOVA with FDR correction across electrodes and
%time points for one-way and factorial within-subjects ANOVA
%
%EXAMPLE USAGE
% >> GND = FfdrGND(GND, 'bins', 1:6, 'factor_names', {'probability', 'emotion'}, ...
% 'factor_levels', [3, 2], 'time_wind', [300, 900], ...
% ... |
a7a344a499d700dfad2ca9dc2b1c8791904b04af556621cd9e442436cc044f19 | MATLAB | 22,448 | 535 | % This function plots figure 3 of Mackay et al. 2024
% (DOI:10.1038/s41467-024-52295-5)
%
% function figure3(alpha_resp, plot_visibility, ...
% narrow_ylims, seed, no_overlaps, which_half, binned_test,...
% read_from_excel, data_dir)
%
% INPUTS:
% alpha_resp (numeric): Threshold for detecting neurons (defa... |
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