sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ccb32f2ede48e2c1c3dd78f3d03c563f9fca4abb4202baec0dbfffe84b049f97 | MATLAB | 45,276 | 1,162 | function [rew,raw] = ltsregres(x,y,varargin)
%LTSREGRES carries out least trimmed squares (LTS) regression, introduced in
%
% Rousseeuw, P.J. (1984), "Least Median of Squares Regression,"
% Journal of the American Statistical Association, Vol. 79, pp. 871-881.
%
% The LTS regression method minimizes the sum of... |
3eee032daa8602d3a142c6443cc003c80d6255940f6cc48b1743d8484a218a1b | MATLAB | 45,643 | 1,394 | function aedes_export_gui(DATA,ROI,Clim_in,colmap_in,roiTransp,showRoiEdges,overlay,currentVol)
% AEDES_EXPORT_GUI - Graphical user interface for exporting mri images
%
%
% Synopsis:
%
% Description:
%
% Examples:
%
% See also:
% AEDES
% This function is a part of Aedes - A graphical tool for analyzing
% med... |
da186a1f48398c555f85ad96205e1f8669b978be0cb2f2a73c5cb66192fafaed | MATLAB | 45,725 | 1,410 | function [DATA,msg_out] = aedes_readvnmr(filename,varargin)
% AEDES_READVNMR - Read VNMR (Varian) FID-files
%
%
% Synopsis:
% [DATA,msg]=aedes_readvnmr(filename,'PropertyName1',value1,'PropertyName2',value2,...)
% [DATA,msg]=aedes_readvnmr(filename,'header')
% [DATA,msg]=aedes_readvnmr(filenam... |
056d63a13f24bb17faa8de76757f7454b3fd5d63e989c17cf1d133909ed72e75 | MATLAB | 47,314 | 850 | % presents response maps in units of spikes/paired-event. why > 1??
%amapOF - modified from amap to analyze OpenField data. Oct 2016, ehud.
%
%amap. ehud,Feb 2016. analyze response maps for pairs of variables. can
%plot or save to data base
%
% run:
% a loop over Sessions (SesList = {'ses1';'ses2';,...})
% a lo... |
99ac388a53802eaa0b11070f49e10c2ab25c52f6dc917b0e620f14451d147e25 | MATLAB | 47,895 | 1,514 | %% Code Outline
% The following code runs the main GLM analyses but using 1000 Schaefer cortical nodes.
%% Load in task data
% Baseline + Rotation
rootdir = 'D:\PhD\visuomotor_Gallivan\BIDS'; %set path of root directory
filelist = dir(fullfile(rootdir, '**\*ses-01_task-rotation_events.tsv*')); %get list of .... |
f785c15e3b313d33239fb183b4a62b60e979b79639c05cb64ded1e3783f7ec7c | MATLAB | 48,376 | 1,085 | function [HDR,data] = iopen(HDR,PERMISSION,CHAN,MODE,arg5,arg6)
% IOPEN opens image files for reading and writing and returns
% the header information. Many different IMAGE formats are supported.
%
% HDR = iopen(Filename, PERMISSION, [, CHAN [, MODE]]);
%
% PERMISSION is one of the following strings
% 'r' read ... |
4eef93f3887d9e804ce28b6b2811afce59700a3cca7384b6ef98bca8516c0018 | MATLAB | 48,611 | 1,146 | %
% NeuronFilter - Temporal Labeling GUI for calcium imaging videos of active neurons
% Last updated 8/29/2019 by Agnim Agarwal
%
function NeuronFilter(vid, Mask, markings, trace, DirSave) % markings variable = for external markings OR 0 for no file input
% vid is the input video
% Mask is the mask of neurons
% marki... |
835e6b01f7ce7862c83634b94ea01924223099b9a5a6a9d95e92095890b7bd75 | MATLAB | 49,579 | 1,745 | % makePatternsScript.m
%
% Script for making all the patterns, ordered in numerical order
%
% CREATED: 2/14/21 - HHY
%
% UPDATED:
% 2/14/21 - HHY
% 3/10/21 - HHY
% 1/7/24 - HHY
%% Some constants
gsVal = 3; % for pattern.gs_val, means 8 possible pixel vlaues
% luminance levels
meanLum = 3;
darkLum = 0;
lightLum =... |
258368af5afec22b6f8e8c2adc5c3025c31f30323302f5f669d76897a6ef1c25 | MATLAB | 49,722 | 1,248 | function varargout = nii_tool(cmd, varargin)
% Basic function to create, load and save NIfTI file.
%
% rst = nii_tool('cmd', para);
%
% To list all command, type
% nii_tool ?
%
% To get help information for each command, include '?' in cmd, for example:
% nii_tool init?
% nii_tool('init?')
%
% Here i... |
e0ac68157d896018e6f34268a8bca3decdd033067f085e24c919d27e07cacfa4 | MATLAB | 49,915 | 822 | %% Neurofeedback: comparisons between conditioned and control animals
animals = {'jaq','roquefort','despereaux','montague','remy','gus','bernard','fievel'};
epochfilter{1} = ['(isequal($cond_phase,''pre'') | isequal($cond_phase,''early'') ) & (isequal($environment,''goal'')| isequal($environment,''hybrid2'') | isequ... |
e1ec6830da6c9691f2ea721d4181992c8f61328fb57ca75ec1c12bdc6ccf1e0c | MATLAB | 49,920 | 1,217 |
% Match detections between consecutive frames.
%
% To match detections, use:
%
% trks = track_match(detections, calib, [chamber_str])
%
% where:
%
% detections - detections obtained from track_detect
% calib - calibration obtained from calibrator or tracker_job_calibrate
% chamber_str ... |
80227694c9abd10ed621678e5ccf70e430225de0a00fc502e539a827fbdbc8ea | MATLAB | 50,054 | 962 | % This script checks for operational errors in the functions of this package
lasterror ('reset');
try
% boot
boot (3, 20);
boot (3, 20, false, 1);
boot (3, 20, true, 1);
boot (3, 20, [], 1);
boot (3, 20, true, 1, [30,30,0]);
% bootknife
% bootknife:test:1
y = randn (20,1);
strata = [1;1;1;1;1;... |
d22fbd1420f20756a125e7da712a240053d68393482ae30d2566a613b3570e81 | MATLAB | 51,266 | 1,495 | % Function File: eventer
%
% peak = eventer(file,TC,s,SF)
% peak = eventer(file,TC,s,SF,...,'exclude',exclude)
% peak = eventer(file,TC,s,SF,...,'criterion',criterion)
% peak = eventer(file,TC,s,SF,...,'rmin',rmin)
% peak = eventer(file,TC,s,SF,...,'hpf',hpf)
% peak = eventer(file,TC,s,SF,...,'lpf',lpf)
% peak ... |
2cb80c46506eedf05a7918e68f3e491be68b9f22b734513aab440230840cf5b0 | MATLAB | 51,802 | 2,182 | function atlas = ft_read_atlas(filename, varargin)
% FT_READ_ATLAS reads an template/individual segmentation or parcellation
% from disk. The volumetric segmentation or the surface-based parcellation
% can either represent a template atlas (eg. AAL or the Talairach Daemon),
% it can represent an individualized atlas (... |
1070bda22cc256dc00bc425c68c9e71828736f1b51e13cbb577890fe150c4550 | MATLAB | 52,362 | 1,034 | %% Prompt User for Variables
clear;clc;close all
warning off
prompt = {'Path: ', 'R^2 Threshold: ', 'Bad Segment Count: ', 'Removed Data Percentage: ', 'Gain Type (1 = norm, 2 = raw}', 'Training Block Size (5 or 10 minute, 1 for OKR)'};
dlgTitle = "Input: ";
dims = [1 40];
definput = {'F:\1 Jaydev Bhateja\Cohort 4\Data... |
9c2cf34431fdeec95aef9f528c4eb4bfa9bce8bf5ff760b06a2fcfa817c2ef69 | MATLAB | 52,561 | 1,264 | function param = ExtractSimilarityMetrics(Scores2Include,AllWVBParameters,clusinfo,param,drawthis)
anglecorr = 0; % Cross tested, 0 seems best
UseFlipCombis = 0; % Cross tested, 0 seems best
%% Extract fields and parameters
ExtractFields({AllWVBParameters})
waveidx = param.waveidx;
Allchannelpos = param.AllChannelPos... |
ae80ab290a4123c177567bae54c4dcc8571cf03a2659c70b1ec95293da20dfea | MATLAB | 52,580 | 818 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: ChemoSLA_DataExtraction
% Cohort: NAc dLight1.3b with chemogenetic inhibition and temporal window
% Sep 2023 - Marie Labouesse, marie.labouesse@gmail.com
% extracts FP data (select folder from a particular day eg day 1, containing multiple animals... |
1323f0f7669c6983a17b994c32dd70237130cdd9a27ebd32d4333426074782e7 | MATLAB | 52,618 | 1,278 | %% Script that is a variation of the stats script that gets the information for individual hypoxic events
% Antonis Asiminas, PhD
% Center for Translational Neuromedicine
% University of Copenhagen, 28 Sep 2023
% Last updated 9 July 2024
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% (1) Load the file with ... |
8f62cabe1e0a82d996b8f3402012b739e1b12d7d89b1b67f24b9e2735a723b10 | MATLAB | 52,742 | 819 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: WeeklyDETQ_SLA_DataExtraction
% Cohort: NAc dLight1.3b with chemogenetic inhibition and temporal window<
% or effect of food restriction
% Sep 2023 - Marie Labouesse, marie.labouesse@gmail.com
% extracts FP data (select folder from a particular d... |
721dd6f189915cb39d6608f12d588b1f59f480d5493a077cc70434791c24a6de | MATLAB | 52,773 | 1,511 | function GUI_refine(video,folder,masks,update_result)
% global video;
% global masks;
% global Lx;
% global Ly;
% global T;
% global N;
global thred_IoU;
global thred_IoU_split;
global thred_jaccard_inclass;
global thred_jaccard;
global auto_on;
% global variables calculated outside the GUI
global list_weight;
% globa... |
98122ac8989546d8bbabdcdc2bc0b6e28a043f4bf1734a2983caf7a302f5e263 | MATLAB | 53,128 | 1,524 | %Training Script Enny van Beest for Mice: EasyLickTask. Start with
%water-restriction. Habituation
%to head-restriction before start training.
% Moving Stim is rewarded (80%) and still stim is not rewarded (20%)
% (eventually, but first trai n on 100% moving)
%% Manual User Settings
ProcMoving = 100; %Moving stimulus ... |
6bef13cc88ea2a2d376daec25ea5b8b498ea63ed71b7dfdb756067296b0875c6 | MATLAB | 53,891 | 1,562 | % Function File: eventer
%
% peak = eventer(file,TC,s,SF)
% peak = eventer(file,TC,s,SF,...,'method',method)
% peak = eventer(file,TC,s,SF,...,'exclude',exclude)
% peak = eventer(file,TC,s,SF,...,'criterion',criterion)
% peak = eventer(file,TC,s,SF,...,'rmin',rmin)
% peak = eventer(file,TC,s,SF,...,'hpf',hpf)
% ... |
fc208f9cd4090995bbf1458963ae60a56528554ed854315daf1dadd272a87d9f | MATLAB | 54,376 | 1,447 | function [d,si,h]=abfload(fn,varargin)
% ** function [d,si,h]=abfload(fn,varargin)
% loads and returns data in ABF (Axon Binary File) format.
% Data may have been acquired in the following modes:
% (1) event-driven variable-length (currently only abf versions < 2.0)
% (2) event-driven fixed-length or waveform-fi... |
bbf24370d6e687ad08ed1ed6fb16e16b153d9fbd83d6482ee5b7bdf907c89911 | MATLAB | 54,643 | 1,457 | function [d,si,h]=abfload(fn,varargin)
% ** function [d,si,h]=abfload(fn,varargin)
% loads and returns data in ABF (Axon Binary File) format.
% Data may have been acquired in the following modes:
% (1) event-driven variable-length (currently only abf versions < 2.0)
% (2) event-driven fixed-length or waveform-fixe... |
d1bbf6ac8bd6f90f98aa5052039687fe3da792b8337db2b61389fdd7ecbc09d8 | MATLAB | 55,149 | 1,289 | function [matData, meta, nseries, tree, stimTree]=ImportHEKA(thisfile, targetpath)
% ImportHEKA imports HEKA PatchMaster and ChartMaster .DAT files
%
% Example:
% OUTPUTFILE=ImportHEKA(FILENAME)
% OUTPUTFILE=ImportHEKA(FILENAME, TARGETPATH)
%
% FILENAME is the path and name of the HEKA DAT file to import.
%
% The kcl f... |
bc5e7662be001968a1e2988707b076689e6c31bc225c356ba44bba3527a58c20 | MATLAB | 55,502 | 1,092 | classdef NWBFile < types.core.NWBContainer & types.untyped.GroupClass
% NWBFILE An NWB file storing cellular-based neurophysiology data from a single experimental session.
% READONLY PROPERTIES
properties(SetAccess = protected)
nwb_version; % (char) File version string. Use semantic versioning, e.g. 1.2.1. This ... |
499a433f2c0d013f5218a442899c91613e03dc0ad539ac093daac8dec277362a | MATLAB | 55,686 | 1,061 | % CLEAN_DATA_WITH_ZAPLINE_PLUS - Removial of frequency artifacts using ZapLine to remove noise from EEG/MEG data. Adds
% automatic detection of the noise frequencies, chunks the data into segments to account for nonstationarities, detects
% the appropriate number of removed components per chunk, based on the individual... |
efee0d5da0c22a87a0dd7516623a4f9b69cb97f034fce8d7ba3a154b85448469 | MATLAB | 55,795 | 1,382 | function [dat] = ft_read_data(filename, varargin)
% FT_READ_DATA reads electrophysiological data from a variety of EEG, MEG and LFP
% files and represents it in a common data-independent format. The supported formats
% are listed in the accompanying FT_READ_HEADER function.
%
% Use as
% dat = ft_read_data(filename, ... |
85e6384565a2d9a8be037cde92ca5d3bab0bedd3d4a5f70092218ca3bfffd371 | MATLAB | 55,962 | 1,281 | % sdfopen() - Opens EDF/GDF/SDF files for reading and writing. The EDF format is specified
% in [1], GDF in [2]. SDF is the SIESTA convention (see [3], pp.8-9); SDF uses
% the EDF format.
% Usage:
% >> EDF = sdfopen(Filename,'r' [,CHAN]); % prepare to read CHAN channels
% >> E... |
f74ee8be3ce3bab535cadba60e8485d3f5ed908a23283cb1f11be9b912122f76 | MATLAB | 56,488 | 1,089 | % computes corr instead of tunings
% uses the structs and functions of tune and tuning, but saves them corr
% uses unitsTable while running, but saves the data in:
% - unitsTable (mat and xlsx) if UPDATE_unitsTable==1
% - corrTable (mat and xlsx) if UPDATE_corrTable==1
% generates and use shuffled data:
% ... |
2d187f8c4296b45b97b78554b4292f42d06126fefdaf689722236838963ed6ec | MATLAB | 57,437 | 1,121 | function [HDR]=scpopen(arg1,CHAN,arg4,arg5,arg6)
% SCPOPEN reads and writes SCP-ECG files
%
% SCPOPEN is an auxillary function to SOPEN for
% opening of SCP-ECG files for reading ECG waveform data
%
% Use SOPEN instead of SCPOPEN
%
% See also: fopen, SOPEN,
% $Id: scpopen.m 8776 2013-11-14 09:04:48Z roboos $
%... |
6e40a4cf6232b6f7517dd8abd74258b52253d7c35f416d8e079e6e4075cb5253 | MATLAB | 57,503 | 1,868 | % mglSetSID.m
%
% $Id:$
% usage: mglSetSID()
% by: justin gardner
% date: 04/20/14
% purpose: Sets the subject ID which is used by initScreen
% and mglTaskLog. Subject ID is then retrieved with
% mglGetSID
%
% To set a known SID:
% mglSetSID(... |
90c051b4ce32abc533381193061c6024df38fc0b10a202020693ab8864a7d01a | MATLAB | 58,340 | 1,358 | function [h,yy,zz] = arrow(varargin)
% ARROW Draw a line with an arrowhead.
%
% ARROW(Start,Stop) draws a line with an arrow from Start to Stop (points
% should be vectors of length 2 or 3, or matrices with 2 or 3
% columns), and returns the graphics handle of the arrow(s).
%
% ARROW uses the mouse (cl... |
fcfeca667f6619d5f47bb1fdf89b05a225f11337423378b273c99545d57f4102 | MATLAB | 58,889 | 1,523 |
function [d,si,h]=abfload(fn,varargin)
% ** function [d,si,h]=abfload(fn,varargin)
% loads and returns data in ABF (Axon Binary File) format.
% Data may have been acquired in the following modes:
% (1) event-driven variable-length (currently only abf versions < 2.0)
% (2) event-driven fixed-length or waveform-fi... |
00aa17742880da08341761b60f4aaf217ec1a2ce32ee1b91915f77334fd69535 | MATLAB | 59,576 | 1,566 | function [d,si,h]=abfload(fn,varargin)
% ** function [d,si,h]=abfload(fn,varargin)
% loads and returns data in ABF (Axon Binary File) format.
% Data may have been acquired in the following modes:
% (1) event-driven variable-length (currently only abf versions < 2.0)
% (2) event-driven fixed-length or waveform-fixe... |
b0bb1c3fe1cc16d617dbdd68268fbe06945a521e8b1fe724776be11ed9ce96ec | MATLAB | 60,799 | 1,865 | function [DATA,msg_out] = aedes_readfid(filename,varargin)
% AEDES_READFID - Read VNMR (Varian) FID-files
%
%
% Synopsis:
% [DATA,msg]=aedes_readfid(filename,'PropertyName1',value1,'PropertyName2',value2,...)
% [DATA,msg]=aedes_readfid(filename,'header')
% [DATA,msg]=aedes_readfid(filename,out... |
08b7af8e3c1ce4451f5c078b5f9989e58e80fcdf88740330210ecd97c9a45d43 | MATLAB | 61,516 | 966 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT:
% Name: Shock_DataExtraction
% First creation Sept 2020; Updates for Zurich May 2021, August 2021, March
% 2023, March 2024
% Marie Labouesse, marie.labouesse@gmail.com
% Cohort: dLight1.3b or GCAMP with shock
% extracts FP data (select folder from a pa... |
70679ea4ed1f62734a90caf3a8ddb55a5570ecf34a579515287ade79764d0dab | MATLAB | 61,538 | 964 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT:
% Name: Shock_DataExtraction
% First creation Sept 2020; Updates for Zurich May 2021, August 2021, March 2023
% Marie Labouesse, marie.labouesse@gmail.com
% Cohort: PFC dLight1.3b with shock
% extracts FP data (select folder from a particular day eg day ... |
63f5a7ccfbf27b2bd091933812c27672f6a21d7aa6a1f70493c604c3317fdbfe | MATLAB | 61,892 | 1,756 |
% Obtain tracking parameters via user input.
%
% To start the calibration, use:
%
% success = calibrator(f_vid, f_info)
%
% where:
% success - indicates wheter calibration was completed
% f_vid - path of input video
% f_calib - path to which calibration file will be saved
%
function suc... |
73acfe85af892a8bba63c1f0f5d1b34bc91af89dc83edd878e10211f07b7a505 | MATLAB | 62,399 | 1,059 | % computes corr instead of tunings
% uses the structs and functions of tune and tuning, but saves them corr
% uses unitsTable while running, but saves the data in:
% - unitsTable (mat and xlsx) if UPDATE_unitsTable==1
% - corrTable (mat and xlsx) if UPDATE_corrTable==1
% generates and use shuffled data:
% ... |
0f2295b975c57d2608d09d3df39fbe6919546d8863c7a4613f614f2e3636ae10 | MATLAB | 63,157 | 1,375 | function [type] = ft_filetype(filename, desired, varargin)
% FT_FILETYPE determines the filetype of many EEG/MEG/MRI data files by
% looking at the name, extension and optionally (part of) its contents.
% It tries to determine the global type of file (which usually
% corresponds to the manufacturer, the recording syst... |
6430f2f8439b451749839c8d37dff95dc8a6530b0749ffc0d025393842b1a577 | MATLAB | 64,715 | 1,553 | % runica() - Perform Independent Component Analysis (ICA) decomposition
% of input data using the logistic infomax ICA algorithm of
% Bell & Sejnowski (1995) with the natural gradient feature
% of Amari, Cichocki & Yang, or optionally the extended-ICA
% algorithm of Lee, G... |
4481ba03d4d8f95b04b8c0c598d87592374b7b06f27d8a8af6f74d81bdb3429e | MATLAB | 65,507 | 1,331 | function [HDR] = getfiletype(arg1)
% GETFILETYPE get file type
%
% HDR = getfiletype(Filename);
% HDR = getfiletype(HDR.FileName);
%
% HDR is the Header struct and contains stuff used by SOPEN.
% HDR.TYPE identifies the type of the file [1,2].
%
% see also: SOPEN
%
% Reference(s):
% [1] http://pub.ist.ac.at/~sch... |
53dd38f719a2cfdd8a582428616f9ab4d5674097e086a593428b85f496a355be | MATLAB | 66,390 | 1,619 | % mglRetinotopy.m
%
% $Id$
% usage: mglRetinotopy(varargin)
% by: justin gardner
% date: 04/06/07
% copyright: (c) 2007 Justin Gardner (GPL see mgl/COPYING)
% purpose: Displays a retinotopy stimulus, there are many
% parameters you can set, you can set as many
% or ... |
cd33addf02df98ad5145ae4f90f02ff02db9944166f42dbdab0595250ab763e2 | MATLAB | 66,462 | 992 | %% Neurofeedback: main analyses. Plateau phase only
animals = {'remy','gus','bernard','fievel'};
%epochfilter{1} = ['isequal($cond_phase,''pre'') & (isequal($environment,''goal'') | isequal($environment,''hybrid2'') | isequal($environment,''hybrid3'')) '];
%epochfilter{2} = ['isequal($cond_phase,''early'') & (isequ... |
553fe012b1899651add6298b43ce47d353c033e9ff1d0f0e1096162ab53d136a | MATLAB | 66,752 | 1,002 | %% Neurofeedback: full timecourse
animals = {'remy','gus','bernard','fievel'};
epochfilter{1} = ['isequal($cond_phase,''pre'') & (isequal($environment,''goal'') | isequal($environment,''hybrid2'') | isequal($environment,''hybrid3'')) '];
epochfilter{2} = ['isequal($cond_phase,''early'') & (isequal($environment,''goa... |
6f926bdd6536462afab3f78e58d01b1bf0cbaaa07a7fa824886e73c37d460b1e | MATLAB | 67,788 | 1,563 | function [S,HDR,time] = sread(HDR,NoS,StartPos)
% SREAD loads selected segments of signal file
%
% [S,HDR] = sread(HDR [,NoS [,StartPos]] )
% NoS Number of seconds, default = 1 (second)
% StartPos Starting position, if not provided the following data is read continously from the file.
% no re... |
268bb63bfbf8b3257edc50bd5caa894fea2581a4556e553177adce0287b150ed | MATLAB | 67,970 | 1,652 | % mglRetinotopy.m
%
% $Id$
% usage: mglRetinotopy(varargin)
% by: justin gardner
% date: 04/06/07
% copyright: (c) 2007 Justin Gardner (GPL see mgl/COPYING)
% purpose: Displays a retinotopy stimulus, there are many
% parameters you can set, you can set as many
% or ... |
443f2b9aebf3484dd0f98d4f687f761c8a9fde5a79d6b3439a928a99d935d4f7 | MATLAB | 68,255 | 1,352 | classdef MLCalciumImagingPipeline < handle
properties
experimentParentFolder = '';
analysisParentFolder = '';
experiment = {};
verbose = true;
includeOtherRoi = true;
availablePerTrialTasks = { ...
'per_trial... |
03594ae6f27855814fecb71efa3655d46310bd72e5d9f083a2fcb6c347230f8f | MATLAB | 69,864 | 1,181 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
db9b3a962262ba0a212dba48f8f885d91e3c4ef0a176f9fc1b02128cc11465f5 | MATLAB | 70,483 | 1,596 | function [ConvertedData,ConvertVer,ChanNames,GroupNames,ci]=convertTDMS(varargin)
%Function to load LabView TDMS data file(s) into variables in the MATLAB workspace.
%An *.MAT file can also be created. If called with one input, the user selects
%a data file.
%
% TDMS format is based on information provided by Nation... |
8ad25ac829762dae641518e94322f45eb3ffdbf9c1a90f859cb8b6d38a90575f | MATLAB | 71,529 | 1,263 | % computes corr instead of tunings
% uses the structs and functions of tune and tuning, but saves them corr
% uses unitsTable while running, but saves the data in:
% - unitsTable (mat and xlsx) if UPDATE_unitsTable==1
% - corrTable (mat and xlsx) if UPDATE_corrTable==1
% generates and use shuffled data:
% ... |
a27a8b2923740f54da54783bed0de8203f022ef991c4ef4972f6ee795137b30d | MATLAB | 72,414 | 1,701 | % Performs one or two levels of bootknife resampling and calculates bootstrap
% bias, standard errors and confidence intervals.
%
% -- Function File: bootknife (DATA)
% -- Function File: bootknife (DATA, NBOOT)
% -- Function File: bootknife (DATA, NBOOT, BOOTFUN)
% -- Function File: bootknife ({D1, D2, ...}, NBOOT, BOO... |
203321e99a3c7e24d8590ecf19fdc033f604bb31e4726aef74aab368aad21c3c | MATLAB | 72,877 | 1,676 | %% User-Input
Scriptsdir = '\Path\To\GitHub\Scripts';%
storepath = '\Path\To\Storage\' %Main storage --> Will contain all processed data & model of the brain
RawDataDirectory = '\Path\To\RawImagingData\' %Raw images.
DataDirectory = RawDataDirectory; %Might be different when downsampling data first
miceopt = {'Faraday'... |
0c2e08c1ed8c24f1e5d822acd7c40da27eade271d4bf05ae76dd438174363683 | MATLAB | 73,184 | 1,280 | % computes corr instead of tunings
% uses the structs and functions of tune and tuning, but saves them corr
% uses unitsTable while running, but saves the data in:
% - unitsTable (mat and xlsx) if UPDATE_unitsTable==1
% - corrTable (mat and xlsx) if UPDATE_corrTable==1
% generates and use shuffled data:
% ... |
d33c72da7e09723622dc6dfaa3dd85da0c02609ee2838bb2550ebc646c708150 | MATLAB | 73,322 | 2,330 | % mglSetSID.m
%
% $Id:$
% usage: mglSetSID()
% by: justin gardner
% date: 04/20/14
% purpose: Sets the subject ID which is used by initScreen
% and mglTaskLog. Subject ID is then retrieved with
% mglGetSID
%
% To set a known SID:
% mglSetSID(... |
17de5c03b5b7a47cc48ef2bd82407fe968a82b43365503adf35603a7f406f6ff | MATLAB | 73,789 | 1,484 | classdef MLCalciumImagingPipeline < handle
properties
experimentParentFolder = '';
analysisParentFolder = '';
experiment = {};
verbose = true;
includeOtherRoi = true;
availablePerTrialTasks = { ...
'per_trial... |
2a6696c18c5c9db88a63c63762f8c3bc95c4fcca806dff54ce76fc357ca86378 | MATLAB | 74,159 | 1,112 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: OptoSLA_DataExtraction
% Cohort: NAc dLight1.3b with opto-inhibition (eNPHR)
% May 2023 - Marie Labouesse, marie.labouesse@gmail.com
% extracts FP data (select folder from a particular day eg day 1, containing multiple animals inside)
% generates... |
5a7df795595fce785348f1d6d734647551e6441b662d5105ad13e216d47b8416 | MATLAB | 76,674 | 1,189 | %
%Main script for Time-Series Analyses
%Used in:
% Pisanski, A., Prostebby, M., Dickson, D., Pagliardini, S. (2024).
% "Mapping responses to focal injections of bicuculline in the
% lateral parafacial region identifies core regions for maximal generation
% of active expiration"
%Requires Functions:
% L... |
afb65cba29af968d417a5cb7dd9635b94b7ac75c53245ba184fcc85c4a37da5e | MATLAB | 77,147 | 2,112 | classdef EMCM < handle
% EMCM (Eigen Manifold Cross Mapping) Class for eigen time delaying
% time series as high dimensional manifolds and assessing how well
% they predict each other.
% This class is able to get two time-series, embed them in higher
% dimensional attractors, and apply cross-ma... |
56c6b7efc7cbd122266c2528c10d4596963444575f4faff118624dc9ef8a560a | MATLAB | 77,148 | 2,112 | classdef EMCM < handle
% EMCM (Eigen Manifold Cross Mapping) Class for eigen time delaying
% time-series as high dimensional manifolds and assessing how well
% they predict each other.
% This class is able to get two time-series, embed them in higher-
% dimensional attractors, and apply cross-m... |
544fbc69b84c845f8a04c9d893538472e8e72d480ebf1ae6accbd27bb9772a43 | MATLAB | 77,339 | 1,952 | function varargout = spm_orthviews(action,varargin)
% Display Orthogonal Views of a Normalized Image
% FORMAT H = spm_orthviews('Image',filename[,position])
% filename - name of image to display
% area - position of image
% - area(1) - position x
% - area(2) - position y
% - area... |
edc3b930b9762ee58c0f049e12752395f9a1448480b668ddfe139dd4dc627999 | MATLAB | 77,665 | 2,220 | function [data] = ft_checkdata(data, varargin)
% FT_CHECKDATA checks the input data of the main FieldTrip functions, e.g. whether
% the type of data strucure corresponds with the required data. If neccessary
% and possible, this function will adjust the data structure to the input
% requirements (e.g. change dimord, a... |
3b13eea4b0cde25e57f917034cd32296f92402ee6bfa7a24a252dfb39ba25ab7 | MATLAB | 77,823 | 1,436 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
%clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
ea870090ff262ab19deda7e1d887c6144559379f6f40ce95ce768b36e8e56ff4 | MATLAB | 77,915 | 1,900 | function [event] = ft_read_event(filename, varargin)
% FT_READ_EVENT reads all events from an EEG/MEG dataset and returns
% them in a well defined structure. It is a wrapper around different
% EEG/MEG file importers, directly supported formats are CTF, Neuromag,
% EEP, BrainVision, Neuroscan and Neuralynx.
%
% Use as
... |
294fdc74a2123d551d5a89bdaac36330a48959d66359fcb3ccf17cf7047eb423 | MATLAB | 82,338 | 1,271 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: CocaineNAc_DataExtraction
% Cohort: NAc AllodLight-ctrl with opto and drugs (DETQ, cocaine)
% Feb 2023 - Marie Labouesse, marie.labouesse@gmail.com
% extracts FP data (select folder from a particular day eg day 1 vs. day2, containing multiple anim... |
b3091db32c7e213592dba2fde3fc0a76edb37c698e884d390540c20baf15e901 | MATLAB | 82,854 | 2,182 | %% Working Memory Trainin g + Opto + Imaging Script
%Training Script Enny van Beest for Mice: Working memory. Start
%wa ter-restriction. Habituation
%to head -restriction before start training.
%Increase level of paradigm pvo (motor) l ickspout. At the end of an
%imaging session, passive licker mouse. This script has 5... |
cd36ac0a6e44f0917f1a6a481b69cea2b9ad23db288366ab4610a24081492fda | MATLAB | 83,477 | 1,382 | % OptoDoseResponse_PooledGraphs_2023
% DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: OptoDoseResponse_PooledGraphs_2023
% Cohort: PFC dLight1.3b with opto
% May 2023 - Marie Labouesse, marie.labouesse@gmail.com
% 1- POOLED GRAPHS
% loads FP data previously analyzed (with: OptoDoseResponse_... |
035d25dc29dea40616d8e638a1dec985f1a87af0a025c0be1185784b0ced2e02 | MATLAB | 83,864 | 1,412 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
%clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
8f581ec1531c802ed152d0631495bd4795114da1e6303b5ce42a15b91c54aeab | MATLAB | 84,567 | 1,427 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'singl... |
3788d89ffc4bb6249838901c026e1a03522fa15c69927d451e8933f7f8988595 | MATLAB | 85,433 | 2,489 | % legTracksAnalysisScript.m
%
% Quick and dirty script for starting to look at leg tracking data
%
% various cells are things tried
%
% 8/5/21 - HHY
%% analysis constants
% indicies for specific body parts
% fit line to head and 3 pts defining midpt b/w legs
refPts.lineFitInd = 7:10;
refPts.midPtInd = 9;
refPts.headP... |
58685d11354371b98e644c4a0b792b6bdfdbe55e0761b561ac0ddcd7f7deba77 | MATLAB | 85,641 | 1,448 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
% modified again by ehud, Jan 2019, to process the new structs (39-49)
% TODO
% 1. Nuu=262, unitsTable length=142
% 2. check tuning, with discontinuous movies
%%
... |
3a44b42729346e7d1f6afc2b7f649bc2813bc5dbd8c48df848987018937ec0b4 | MATLAB | 85,837 | 1,444 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'singl... |
5d987228ecc309c38f73b08cf4f5515101617251a3c9d92e5d6bed4c9466471a | MATLAB | 86,777 | 2,731 | % Function File: ephysIO
%
% USAGE: To save a column-major XY array of electrophysiology data:
% ephysIO (filename,array,xunit,yunit,names,notes,datatype)
%
% To load column-major XY array of electrophysiology data:
% data = ephysIO (filename)
% [array,xdiff,xunit,yunit,names,not... |
d61f2de0301d36c4188cb335e6a5d1f5bac5090cc62f63023c028dab1546bd5c | MATLAB | 87,499 | 2,217 | function [hdr] = ft_read_header(filename, varargin)
% FT_READ_HEADER reads header information from a variety of EEG, MEG and LFP
% files and represents the header information in a common data-independent
% format. The supported formats are listed below.
%
% Use as
% hdr = ft_read_header(filename, ...)
%
% Additional... |
b7f517342e4743d55ce63bb757b5ef875e55ab65cd32638bdbfd6ec49f0107f8 | MATLAB | 88,401 | 1,477 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
%clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
18728c951c43dce8d7390f9625c6d2f17550fb17c6257f4ea28ec78cf33ac0e1 | MATLAB | 89,304 | 2,372 | function varargout = spm_input(varargin)
% Comprehensive graphical and command line input function
% FORMATs (given in Programmers Help)
%_______________________________________________________________________
%
% spm_input handles most forms of interactive user input for SPM.
% (File selection is handled by spm_select... |
7f5be23c4fc3c863374b461f0c1496f52dfa4ce38273cc5f5dd75b7ae330d5df | MATLAB | 89,427 | 2,626 | % moncalib.m
%
% usage: To run a calibration:
% calib = moncalib;
%
% To display a previously run calibration
% moncalib(calib);
%
% Options that you can use:
% calib = moncalib('numRepeats=4','stepsize=1/256',...
% numRepeats = number of r... |
b583f49c6a8c50ea66bba01ab45a81eaa76e85430db8b80141deac0bfd7d5010 | MATLAB | 89,446 | 1,528 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
%clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
6504696e6b65c4063545a58a1465d975403eb48708d76f8d6f321ad03773c8a4 | MATLAB | 89,514 | 3,694 | function label = ft_senslabel(type, varargin)
% FT_SENSLABEL returns a list of predefined sensor labels given the
% EEG or MEG system type which can be used to detect the type of data.
%
% Use as
% label = ft_senslabel(type)
%
% The input sensor array type can be any of the following
% 'ant128'
% 'biosemi64'
% 'bi... |
49839c673f920ee67c758cd62d1aa5aab9ca54e8bc967a20eb7905634eedca8f | MATLAB | 89,647 | 2,175 | classdef Sources2D < handle
% This class is a wrapper of Constrained NMF for standard 2D data. It
% Both CNMF and CNMF-E model can be used.
% Author: Pengcheng Zhou, Columbia University, 2017
% zhoupc1988@gmail.com
%% properties
properties
% spatial
A; % s... |
7a3deae9d20733c2d8d2ccd629e7a4bf3a79cef3a0f029120d414a98fb4e76a6 | MATLAB | 90,267 | 1,429 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'singl... |
89e7aa86d4b85c450c842bb970892b8371dce7c81e92cc677961e178e43d8c13 | MATLAB | 90,337 | 2,852 | function varargout = labelerrorsgui(varargin)
% TRX = LABELERRORSGUI(SEQS,MOVIENAME,TRX,ANNNAME,PARAMS,[LOADNAME])
% SEQS: array of suspicious sequences
% MOVIENAME: name of movie
% TRX: positions of flies over time
% ANNNAME: name of annotation file
% PARAMS: parameters used to determine suspicious sequences
% LOADNAM... |
417d22ea684e0302d21844d5a7d2b7068408d337cd1a3be19fe7a9b13c63ad00 | MATLAB | 91,010 | 1,533 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
%clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
30db75052dbb2f158111b60ade0de8ac2136d8c16635e58979fbbe4d7d6b2c51 | MATLAB | 91,458 | 1,534 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
%clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
108f6ca72ce35b7af4738979a50508a5430d0ed430f1e222e9167b79a96f4759 | MATLAB | 91,631 | 2,666 | % moncalib.m
%
% usage: To run a calibration:
% calib = moncalib;
%
% To display a previously run calibration
% moncalib(calib);
%
% Options that you can use:
% calib = moncalib('numRepeats=4','stepsize=1/256',...
% numRepeats = number of r... |
c5ffb991b113fb7c07d1ede35f46084a16eb72733665f7bfb6959a806d7ef310 | MATLAB | 93,952 | 1,414 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT
% Name: OptoDoseResponse_DataExtraction
% Cohort: PFC dLight1.3b with opto-dose response and temporal window
% May 2023 - Marie Labouesse, marie.labouesse@gmail.com
% extracts FP data (select folder from a particular day eg day 1, containing multiple anim... |
9d37e57480ee82cb7705a8053ddd8c9e7177c831200037402caf7157c564a56d | MATLAB | 94,115 | 2,178 | function varargout=spm_conman(varargin)
% Contrast manager: GUI for defining valid contrasts
% FORMAT varargout=spm_conman(varargin)
% - An embedded callback, multi-function function
% - For detailed programmers comments,
% see format specifications in main body of program (below user help)
%_______... |
9360794e839cd44fe47adf5b3d2ba3b0b034e96b9154c77c2c9198fea57887d9 | MATLAB | 94,245 | 1,592 | % presents response maps in units of spikes/paired-event. arrange selected
% cells from all sessions together
%modified from amapOF Oct 2016, ehud.
%%
%clear all; runMode = 'single'; % leave when running this script. comment out when running a batch from runAmapOF
%%
globals;
switch runMode,
case 'sing... |
c4660ae33d67bebc4aeedeade0dd024727d1ac6de1db50bccd1f4f38752e6d93 | MATLAB | 95,289 | 2,832 | function varargout = fixerrorsgui(varargin)
% TRX = FIXERRORSGUI(SEQS,MOVIENAME,TRX,ANNNAME,PARAMS,[LOADNAME])
% SEQS: array of suspicious sequences
% MOVIENAME: name of movie
% TRX: positions of flies over time
% ANNNAME: name of annotation file
% PARAMS: parameters used to determine suspicious sequences
% LOADNAME: p... |
398e277ee8f28098bed819f1fa6e3dd2f0e71a5f3eedbc25ec2f1f882c34b01e | MATLAB | 97,407 | 1,491 | function [lambda, xFcn, yFcn, zFcn] = mglColorMatchingFunctions(formulary)
%
%
%
%colorMatchFcn Popular color matching functions.
%
% [LAMBDA, XFCN, YFCN, ZFCN] = colorMatchFcn(FORMULARY) returns the
% color matching functions XFCN, YFCN, and ZFCN at each wavelength in
% the vector LAMBDA. FORMULARY is a s... |
549a8203a35c69908e9a32df31d50f516443b8bef460d7bc93d6074fc63b6500 | MATLAB | 98,859 | 2,310 | datapath = '\Path\To\Data\';
AllMice2Use = {'Alaska','Becquerel','Berlin','Cherry','China','Darwin','Druif','Faraday','Galilei','Grape','Haydn','Holland','HongKong','Jemison','Jenkins','Joule','Karlsen','Kirchoff','Leeuwenhoek','Lully','Ising','Mahler'};
Gentype = {'Control','D2','D2','D1','D1','Control','Control','D2'... |
b1144897688946edc0ca2d24be2026b795fcf67ff779bd3a5e393e4138a69c70 | MATLAB | 107,942 | 2,374 | % Empirical Bayes penalized regression for univariate or multivariate outcomes,
% with shrinkage tuned to minimize prediction error computed by .632 bootstrap.
%
% -- Function File: bootridge (Y, X)
% -- Function File: bootridge (Y, X, CATEGOR)
% -- Function File: bootridge (Y, X, CATEGOR, NBOOT)
% -- Function File: b... |
0cac6cadd574e5c05acb0b27bbe90e181dfb348b396f898fc1b825fc452b6004 | MATLAB | 112,912 | 3,412 | % Function File: ephysIO
%
% USAGE: To save a column-major XY array of electrophysiology data:
% ephysIO (filename,array,xunit,yunit,names,notes,datatype)
%
% To load column-major XY array of electrophysiology data:
% data = ephysIO (filename)
% [array,xdiff,xunit,yunit,names,not... |
8f176d6afed70950c7d891ddb8538dbb6fb69c125cdd0fefffa0d2481f5bc8d8 | MATLAB | 113,530 | 3,423 | % Function File: ephysIO
%
% USAGE: To save a column-major XY array of electrophysiology data:
% ephysIO (filename,array,xunit,yunit,names,notes,datatype)
%
% To load column-major XY array of electrophysiology data:
% data = ephysIO (filename)
% [array,xdiff,xunit,yunit,names,not... |
b5f96380b5470a08ec7c812e93bf5272e1a0725f9b76e3088984000bed64c829 | MATLAB | 115,015 | 2,087 |
%% Neural differences between young and older adults in automatic and conscious auditory predictive coding (using musical sequences)
%% Maxfilter
%OBS! before running maxfilter you need to close matlab, open the terminal and write: 'use anaconda', then open matlab and run maxfilter script
maxfilter_path = '/neuro/bi... |
2eb789b35dc7f0c77e18922469295e52c6a32397c34d68d20c6aac0a7f39d48b | MATLAB | 120,384 | 2,792 | function varargout = OtherFunction(varargin)
% OTHERFUNCTION MATLAB code for OtherFunction.fig
% OTHERFUNCTION, by itself, creates a new OTHERFUNCTION or raises the existing
% singleton*.
%
% H = OTHERFUNCTION returns the handle to a new OTHERFUNCTION or the handle to
% the existing singleton*.
%
% ... |
3dbe9abdf9bc49c6e582a49441a086a624cccfae525eca60ca1834154b6d41bf | MATLAB | 122,632 | 2,942 | % p_HFOAnalysisTool.m
% [As a part of HFO Detection Project]
% Intrface for visualization and classification of putative HFO events
% Written by:
% Miguel G. Navarrete Mejia
% Electrical Engineering MS.
% UNIVERSIDAD DE LOS ANDES
% Colombia, 2012
% mnavarretem@gmail.com
%
% Copyright (C) 2015... |
7503a37d1a467eb8c8860dcf2c67d2118fc83682affc510e365f916a8bf5e575 | MATLAB | 123,149 | 2,461 | classdef MLCalciumImagingPipeline_v1 < handle
properties
experimentParentFolder = '';
analysisParentFolder = '';
experiment = {};
verbose = true;
includeOtherRoi = true;
trackerParams = {};
availableTasks = {'phase_1', '... |
7e35fdad12df673a686f0ea9c2d69f86a78826e720768d4a31f88ef73b1a8d92 | MATLAB | 123,871 | 3,305 |
% Visualize tracked videos, correct identities, and annotate behavior.
%
% To run interface, use:
%
% visualizer
%
function visualizer()
% files
files.video_dir = '.'; % default video directory
parentdir = fileparts(mfilename('fullpath'));
defpath = fullfile(parentdir,'actio... |
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