sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
ddd5b878f2dbab47e68264f7bc60671473f925a72d1ba39e70deafdd193e9f4c | MATLAB | 20,022 | 491 | % ============ Opening function ==========================
function varargout = tracks_GUI(varargin)
% TRACKS_GUI MATLAB code for tracks_GUI.fig
% TRACKS_GUI, by itself, creates a new TRACKS_GUI or raises the existing
% singleton*.
%
% H = TRACKS_GUI returns the handle to a new TRACKS_GUI or the ... |
9a77f73a638d4b8bf5153dcb1e47a0f810e69b7dd96f2b4702bbe0fe04177c77 | MATLAB | 20,080 | 660 | function TEXT = writeFCS(fname, DATA, TEXT, OTHER)
%writeFCS Save numeric data into FCS format used in flow cytometry.
% writeFCS(FNAME, DATA) creates a ver 3.1 FCS file with file name FNAME
% from the numerical matrix data. The program assings the parameters
% by analyzing the properties of the numerical... |
9630a6a1857dcee51ce5960e9f515297de77779b4ca9eba8304f5f72e8e3e2ad | MATLAB | 20,119 | 639 | function [ subject, data ] = nmri_artifactrejection(subject, data, params)
%[ subject, data ] = nmri_artifactrejection(subject, data, params)
%
% This function will do visual artifact on one subject
% it requieres user interaction / presenece
%
% subject = subject structure, see nmri_read_subject
% ... |
3cb620d262664d98d114b3fb7666fe67938c55ab326c45f1612e8fa7a8d10e98 | MATLAB | 20,263 | 204 | function SUBJECT = ASLSaveResultsCBFAATCVR(SUBJECT, ORprefix)
% ClinicalASL toolbox 2023, JCWSiero
%% CBF using 2ndtolast PLD, compute CVR
% register postACZ to preACZ, save BASIl results: NIFTI and PNG - loops over smoothed BASIl data
% Registration postACZ to preACZ space using T1fromM0 AFNI 3dAllineate, 6 do... |
b5dee63e7bed3d1157150d4bb186216db01b1013b96c915858e5433982ccd770 | MATLAB | 20,685 | 690 | %IMDISP Display one or more images nicely
%
% Examples:
% imdisp
% imdisp(I)
% imdisp(I, map)
% imdisp(I, lims)
% imdisp(I, map, lims)
% imdisp(..., param1, value1, param2, value2, ...)
% h = imdisp(...)
%
% This function displays one or more images nicely. Images can be defined
% by arrays, ... |
25e482ec87a78c30a171e77c505d675a08e90f624964b74784238b945acebde2 | MATLAB | 21,089 | 492 | %% How to Run This Code
% Run sections #1, #2, and #3 sequentially
% (Optional) For displaying other correction maps, change ROI_index in section #2 and then rerun sections #2 and #3.
%%
clc
clear
close all
%% #1 Generating Zernike Modes
tic
for llll=1
% Generating full-NA size Zernike modes
fo... |
0f1a4993e4c8a9ffcbe9be055e19222d06a595f7562a320624a56a285fc24500 | MATLAB | 21,203 | 575 | function varargout = aggregate_removal_gui(varargin)
% AGGREGATE_REMOVAL_GUI MATLAB code for aggregate_removal_gui.fig
% AGGREGATE_REMOVAL_GUI, by itself, creates a new AGGREGATE_REMOVAL_GUI or raises the existing
% singleton*.
%
% H = AGGREGATE_REMOVAL_GUI returns the handle to a new AGGREGATE_REMOVAL_G... |
d892e05c25f25c1c664f91b3810f934e54b5e0f15bce53b1f06f021442352fd3 | MATLAB | 21,796 | 447 | %% Continuous Random Dots Motion task
% Code written by Simon P. Kelly and data collected Hannah Craddock in 2016
% for her Master's thesis, 2016:
% 'Electrophysiological and behavioural indices of decision criterion
% adjustments across context of weak and strong evidence.'
% Current code is additionally anno... |
e932c90cb8364be9774f629078b1939dfa695a94042a4cc890e94090f320976a | MATLAB | 22,227 | 737 | %IMDISP Display one or more images nicely
%
% Examples:
% imdisp
% imdisp(I)
% imdisp(I, map)
% imdisp(I, lims)
% imdisp(I, map, lims)
% imdisp(..., param1, value1, param2, value2, ...)
% h = imdisp(...)
%
% This function displays one or more images nicely. Images can be defined
% by arrays, ... |
c6d25db8e4c4f2316c87c62bd8ca89be9ebf571f945ed24011fd1e2411b175d4 | MATLAB | 22,356 | 520 | function [xPoints, yPoints,lineFormat] = plotSpikeRaster_FigS1(spikes,varargin)
% PLOTSPIKERASTER Create raster plot from binary spike data or spike times
% Efficiently creates raster plots with formatting support. Faster than
% common implementations. Multiple plot types and parameters available!
% Look at Param... |
873488953f4af01639bb3ae7b620dc1829a6a53fa6fcf3d1a3ad403320d6928e | MATLAB | 22,360 | 438 | classdef CocoEval < handle
% Interface for evaluating detection on the Microsoft COCO dataset.
%
% The usage for CocoEval is as follows:
% cocoGt=..., cocoDt=... % load dataset and results
% E = CocoEval(cocoGt,cocoDt); % initialize CocoEval object
% E.params.recThrs = ...; % set parameters as... |
fe5f022fcfab162435dabfe51df8ad1f60b4df5fce981eed69b6cf08d9a7546a | MATLAB | 22,372 | 621 | %% organize sourcedir
% define and create dirs
basedir='C:\Users\lukas\Dropbox (Dartmouth College)\fMRI_emotion_Giao';
bidsdir=fullfile(basedir,'BIDS');
cd(bidsdir);
mkdir('sourcedata');
sourcedir=fullfile(bidsdir,'sourcedata');
% create list of subjects in basedir
cd(basedir);
dirs=string(ls);
idx=startsWith(dirs,["H... |
07eee7b7315a75b493fe81dcdff2578ce6908bb11a52fa23702b0fdd7ecdfb08 | MATLAB | 22,926 | 640 | function [ subject, data ] = cs_nmri_make_hdm_suma(subject, data, params)
%[ subject, data ] = nmri_make_hdm_suma(subject, data, params)
%
% This function will deal with reading the MRI info
% per default will read from SUMA, other options we be integrated later
% will assume that the subject.id = basename
% otherw... |
4ccb6ad85e6b6c179f933aa6fff26dc8fc51cc1b931b0fb6d72c66831094c613 | MATLAB | 23,413 | 364 | function SUBJECT = ASLSaveResultsCBFAATCVR_vTRASL(SUBJECT)
% ClinicalASL toolbox 2023, JCWSiero
% copy NIFTIs to ASL_vTR folder
% M0
preACZ_M0_path = fullfile(SUBJECT.ASLdir, 'preACZ_M0.nii.gz');
postACZ_M0_path = fullfile(SUBJECT.ASLdir, 'postACZ_M0.nii.gz');
if isunix
system(['cp ' SUBJECT.preACZM0filena... |
38be53a1515ec4d2d4b889c5ffa34358c28caae8af4e3e64285c7ec3bcfaf086 | MATLAB | 23,944 | 675 | function [ subject, data ] = cs_nmri_make_hdm_suma_compile(subject, data, params)
%[ subject, data ] = nmri_make_hdm_suma(subject, data, params)
%
% This function will deal with reading the MRI info
% per default will read from SUMA, other options we be integrated later
% will assume that the subject.id = basename
... |
a795603820f034e396f7a2085ac4cf76ef71c352adacc084db413e1de1c3e391 | MATLAB | 24,003 | 578 | function varargout = titration_gui(varargin)
% TITRATION_GUI MATLAB code for titration_gui.fig
% TITRATION_GUI, by itself, creates a new TITRATION_GUI or raises the existing
% singleton*.
%
% H = TITRATION_GUI returns the handle to a new TITRATION_GUI or the handle to
% the e... |
8bc2bb8b65126ffdfe1121754aaafacc85129b85d763830f9fb6e7ae6e204e83 | MATLAB | 25,856 | 707 | function varargout = fft_removal_gui(varargin)
% FFT_REMOVAL_GUI MATLAB code for fft_removal_gui.fig
% FFT_REMOVAL_GUI, by itself, creates a new FFT_REMOVAL_GUI or raises the existing
% singleton*.
%
% H = FFT_REMOVAL_GUI returns the handle to a new FFT_REMOVAL_GUI or the handle to
% the existing si... |
4792b6eddb8d90339a65baf1c2385492027a6ec280a78dd0a8e1b38be2ec9010 | MATLAB | 26,534 | 647 | % Thing I'd like to add: ability to lock all the figures from a point, so
% that when you zoom in or scan one fig, you zoom in and scan all the figs
% for that point. Probably have to keep track of each figure, and also add
% listeners to all them or something.
function varargout = background_removal_gui(varargin)
% B... |
b46e5f5f07312080c082a93ae8934a90d364d549a54df4e0277a1d75f030f666 | MATLAB | 26,853 | 529 | %% Main code for Figures.
% This code creates some of the Figures entirely (e.g. Figures 4 to 12) or part of them,
% which will require further "edition" (e.g. Figures 3B-C). Even though
% some figures are obtained directly from Matlab, it required further
% manual arrangement (e.g. moving legends or figure position ar... |
162518a7138bdeaaf1b3a48009a7dce3f4824ac44562381b4b2e5e4d964f668a | MATLAB | 26,875 | 632 | function count = cprintf(style,format,varargin) %#ok<*JAPIMATHWORKS>
% CPRINTF displays styled formatted text in the Command Window
%
% Syntax:
% count = cprintf(style,format,...)
%
% Description:
% CPRINTF processes the specified text using the exact same FORMAT
% arguments accepted by the built-in SPRINTF an... |
f69e03c8f604a8a42766689ff67e2a197586c93788eed451bc7ebb7e25474e81 | MATLAB | 26,941 | 422 | % Author: Jan Hirtz - 2022
clearvars;
threshold_factor = 2; % how many standart deviations above mean for correlation per cluster
root_path ='fill_in';
all_cluster_files = dir([root_path, '\**\name_of_original_file.mat']);
for ii = 1:size(all_cluster_files)
cur_cluster_file = fullfile(all... |
4af7038f02e45084094b03494c637198fe3c79bd2dedce8749a27fa1c2012cc0 | MATLAB | 28,057 | 685 | % Thing I'd like to add: ability to lock all the figures from a point, so
% that when you zoom in or scan one fig, you zoom in and scan all the figs
% for that point. Probably have to keep track of each figure, and also add
% listeners to all them or something.
function varargout = background_removal_gui_2(varargin)
%... |
1f74c8d5d69e7ff35b0d8cc49d3c928c2e179b26010502a4ea6c2685993a0eaf | MATLAB | 28,395 | 580 | % Excluding Irrelevant Components and Determination of TOI and ROI
% This code is to apply 2-way ANOVA on the decomposed subjects' signatures after
% applying tensor-decomposition.
% The significant bases will be saved to ANOVA/significant_entity,
% significant_action, significant_interaction
% in this version, A... |
1f7a27597c9fb87ea4830a656dcc1920a6258531b02606c5ef4c649973ed4882 | MATLAB | 28,716 | 662 | function camera_db = camera_parser_module_tif_to_mat(p_name, ...
f_name, snr_times, out_dir, experimenter, do_images) %[image_arr, LED_arr, loc_arr, bg_image]
% Function integrator_script creates linear set of rects out of the raw .tif images as produced by
% the RatTracker, RIFF.
% Modified by Ana 240119 to work ... |
dad17e1ddfa131a0322391cd5e68801435d09488593ff7c895831025a5ae0cf8 | MATLAB | 29,942 | 1,042 | clear
close all
load('AllFigureData.mat');
savePlots = 1;
%% DEPENDENCIES
% ecogutils.plotAdj
% ecogutils.scatterText
%% Figure 2
f2bName = 'Fig2b Example normalized adjacency matrix';
f2b = figure('Name',f2bName);
ecogutils.plotAdj(fig2.Psymm,1:size(fig2.Psymm,1),fig2.colorMap,false);
f2cName = 'Fig2c E... |
1a17ca96bcc5c03f3f49e3d1b662c75785e5514573c6c93cfd9c47f2cbb497c7 | MATLAB | 30,285 | 736 | % Thing I'd like to add: ability to lock all the figures from a point, so
% that when you zoom in or scan one fig, you zoom in and scan all the figs
% for that point. Probably have to keep track of each figure, and also add
% listeners to all them or something.
function varargout = background_removal_gui_3(varargin)
%... |
bd09f9a6a9dfb41ddfdaeb977933b368982b187e3776ac53684da3143f151709 | MATLAB | 31,451 | 772 | function varargout = denoising_gui(varargin)
% DENOISING_GUI MATLAB code for denoising_gui.fig
% DENOISING_GUI, by itself, creates a new DENOISING_GUI or raises the existing
% singleton*.
%
% H = DENOISING_GUI returns the handle to a new DENOISING_GUI or the handle to
% the e... |
c8c4afb99e75709b324bb2f20f9e1390b1dcee6521356981cc7483c1f513d25f | MATLAB | 32,016 | 1,091 | function varargout = FEEDBACk_3(varargin)
% Begin initialization code - DO NOT EDIT
gui_Singleton = 1;
gui_State = struct('gui_Name', mfilename, ...
'gui_Singleton', gui_Singleton, ...
'gui_OpeningFcn', @FEEDBACk_3_OpeningFcn, ...
'gui_OutputFcn', @FEED... |
42a9bc341e4b83461c6750b7f6b8dd8eb6ef60e3140a9cace39912734fcf03cb | MATLAB | 32,667 | 898 | %SC Display/output truecolor images with a range of colormaps
%
% Examples:
% sc(image)
% sc(image, limits)
% sc(image, map)
% sc(image, limits, map)
% sc(image, map, limits)
% sc(..., col1, mask1, col2, mask2,...)
% out = sc(...)
% [out, clim map] = sc(...)
% sc
%
% Generates a truecolo... |
16b877522d4abc3cf74251ed71ef5a62dffa740cb1fb286d0c94a7ab622a0ab9 | MATLAB | 33,682 | 859 | function varargout = mem_plot(varargin)
%MEM_PLOT M-file for mem_plot.fig
% MEM_PLOT, by itself, creates a new MEM_PLOT or raises the existing
% singleton*.
%
% H = MEM_PLOT returns the handle to a new MEM_PLOT or the handle to
% the existing singleton*.
%
% MEM_PLOT('Property','Value',...) cre... |
b94bf4f04157c80aea23bfdded0c27afe7a68e9ad808c368f7c52621df115e7d | MATLAB | 34,175 | 736 | %Authors: Tatjana Schmitt & Simon Wadle, 2019-2022
%
%% v2 adds: -deletion of sequences where the mouse moved
% -the option to not overwrite existing complete_data_Fall.mat files
% -to do batch processing of all animals (if you want to process
% only one animal just change th... |
744391f999eb7216df36e2ee2e5c5374243171e0d5e2df995173b9e9058a4dd0 | MATLAB | 34,536 | 843 |
function varargout = RatTracker_single(varargin)
% RatTracker_single MATLAB code for RatTracker_single.fig
% RatTracker_single, by itself, creates a new RatTracker_single or raises the existing
% singleton*.
%
% H = RatTracker_single returns the handle to a new RatTracker_single or t... |
d47314ac13d0b867986dfce26459d22f01b447147c0e11c5113fcd76b6a88c68 | MATLAB | 34,995 | 1,025 | function [zgrid,xgrid,ygrid] = gridfit(x,y,z,xnodes,ynodes,varargin)
% gridfit: estimates a surface on a 2d grid, based on scattered data
% Replicates are allowed. All methods extrapolate to the grid
% boundaries. Gridfit uses a modified ridge estimator to
% generate the surface, where the bi... |
76c09e00f38196630cae6aaf766e04f42b8ab641736e28648a7a8b7385ccb6af | MATLAB | 36,102 | 813 | %% DEFINE PATHS AND LOAD VARIABLES
% -------------------------------------------------------------------------
% SET PATHS AND DEFINE DIRS
addpath(genpath('C:\Users\lukas\Documents\GitHub\proj-emosymp')); % add proj-emosymp Github repo to your path
addpath(genpath('C:\Users\lukas\Documents\GitHub\RainCloudPlots')); %... |
2381dab7571814fb3a17ceab98aa609fd4b5b0569975de1d31731604f4db5502 | MATLAB | 37,368 | 918 | classdef PointManager < handle
%UNTITLED3 Summary of this class goes here
% Detailed explanation goes here
properties
offset;
namesToPaths % map from names to paths
pathsToNames % map from paths to names
pathsToPoints % map from paths to Points
% for background... |
2e50c6439d5b9c4728df0d57ce73815154ca6f3ed21ff40f5fd04569607501dd | MATLAB | 38,760 | 767 | %% How to Run This Code
% Run sections #1, #2, #3, and #4 sequentially
% (Optional) For measuring width in other ROIs, chane ROI by rerunning sections #2 and #3, and then rerun section #4.
%%
clc
clear
close all
%% #1 Reading Images
folder_path='C:\Users\Sanghyeon Park\Dropbox (IBS)\CLASS-SMLM Paper\N... |
40b2a11bc6e4a42c9f7309d839f045b1760bfced07a9001b5df711c5d42e7889 | MATLAB | 39,986 | 943 | function final_db = create_db_Kilosorted_files(mdata)
% Function create_db_Kilosorted_files is the automated wrapper for the clustering results of
% the KiloSort2 pipeline.
%
% Created by AlexKaz 02.2020
% === Load file from .npy files ====
if nargin == 0
mdata.do_plot = false;
... |
fdb6e3c6ebb088c5461dfd93c313f068f6f594e3964cfbfa1769ee9f0c3985c5 | MATLAB | 40,415 | 970 |
function varargout = RatTracker_three(varargin)
% RatTracker_three MATLAB code for RatTracker_three.fig
% RatTracker_three, by itself, creates a new RatTracker_three or raises the existing
% singleton*.
%
% H = RatTracker_three returns the handle to a new RatTracker_three or the hand... |
fc8e335e0e8b3a2d1674b6adfdb9f5b2ad1a82c3ab4faf4139fa850b35591b49 | MATLAB | 42,379 | 1,049 |
function varargout = RatTracker(varargin)
% RatTracker MATLAB code for RatTracker.fig
% RatTracker, by itself, creates a new RatTracker or raises the existing
% singleton*.
%
% H = RatTracker returns the handle to a new RatTracker or the handle to
% the existing singleton*.
... |
0f41268c047167035caa6482636e1be99882d6d00102f098cb372778824041e9 | MATLAB | 42,774 | 852 | %% Behaviorual and neurally-informed modelling
% Data collected Hannah Craddock for her Master's thesis, 2016:
% 'Electrophysiological and behavioural indices of decision criterion
% adjustments across context of weak and strong evidence.'
%
% Current code is written by A.C. Geuzebroek and part of:
% Geuzeb... |
b933014d35d8200359b9dad77869d946046e20c57bf3dacb6092cbf97ae7b570 | MATLAB | 43,340 | 921 | %% Data preprocessing and EEG waveform analysis.
% Data collected Hannah Craddock for her Master's thesis, 2016:
% 'Electrophysiological and behavioural indices of decision criterion
% adjustments across context of weak and strong evidence.'
%
% Current code is written by A.C. Geuzebroek and part of:
% Geuz... |
f0a1d671cc13a9379dcbc1fe44d4fe697845b036d806317c96d4fe6892fe3acf | MATLAB | 44,079 | 1,070 |
function varargout = RatTracker_fast(varargin)
% RatTracker_fast MATLAB code for RatTracker_fast.fig
% RatTracker_fast, by itself, creates a new RatTracker_fast or raises the existing
% singleton*.
%
% H = RatTracker_fast returns the handle to a new RatTracker_fast or the handle to
... |
1ac3f4619c62fa9a56728f3a683fd5bb5c6c22891f63cda3aca57220996b8063 | MATLAB | 45,010 | 1,185 | %SC Display/output truecolor images with a range of colormaps
%
% Examples:
% sc(image)
% sc(image, limits)
% sc(image, map)
% sc(image, limits, map)
% sc(image, map, limits)
% sc(..., col1, mask1, col2, mask2,...)
% out = sc(...)
% [out, clim map] = sc(...)
% sc
%
% Generates a truecolo... |
caad4d656fdeb3d7f9221cf4345f072011c3187ad7d32425f85b40861822e2b9 | MATLAB | 46,169 | 1,143 | function [nuer1mask,nuer2mask,nuer3mask,nuer4mask,dendInterp,n1,n2,n3,n4,dendWidth] = trackDendrites(dendCrop,imFeatures,sFactor)
% Function to track dendrites from image. Takes in cropped dendrite image
% and tracks the four individual dendrites for future analysis
% Updated: 08/30/2022
%% Initialization for speed
... |
3c4fa5236dbcf1f9cb52a0ea82c50fcbadfd8af053a94cc79f4a8d1597ab81f4 | MATLAB | 47,320 | 1,179 |
function varargout = calibrate_RIFF(varargin)
% calibrate_RIFF MATLAB code for calibrate_RIFF.fig
% calibrate_RIFF, by itself, creates a new calibrate_RIFF or raises the existing
% singleton*.
%
% H = calibrate_RIFF returns the handle to a new calibrate_RIFF or the handle to
% ... |
a39f487accf20b9a703b7d5420dbf46789883c8b58ddf69844ca5b27d1f679e2 | MATLAB | 49,527 | 1,183 | combineddatafile='ElectroData.mat';
load(combineddatafile);
%% Determining sound responsiveness on track
speedthresh=4;
respwin1=551:1000;
prewin1=101:550;
tracksoundresponsivenessNEWIMMOB=[];
for xx=1:length(combinedSBTrackData)
if any(strcmp(fieldnames(combinedSBTrackData{xx}),'TRACKmat'))
... |
886090d091b4cdf7e33230a3655db2ffcc8b3f44204c48c245d5128bbd5711a4 | MATLAB | 53,139 | 1,125 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% sections of this code were contributed by Allen A. Champagne, a.champagne@queensu.ca
% <lagCVR: calculates hemodynamic parameter maps with associated statistical maps >
%
% This program is free software: you can redistri... |
21c368dbd32ed6d554e5c4c3b25f0b7d01e41c3ad14d041dc613026b11ffa39a | MATLAB | 53,217 | 1,071 | %% GUI file for ez_segmenter_nextGen
% Author: Bryan Cannon 2019 - Stanford University
function varargout = ez_segment_gui(varargin)
% EZ_SEGMENT_GUI MATLAB code for ez_segment_gui.fig
% EZ_SEGMENT_GUI, by itself, creates a new EZ_SEGMENT_GUI or raises the existing
% singleton*.
%... |
cba16ab81b4364ee9bc9a75506b9d6fe6c684783c5892452d3b441eff8f31ef2 | MATLAB | 57,400 | 1,557 | function [d,si,h]=abfload2(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-fixed le... |
255cc56a275c2b00cf93b25fe60ab005ebacf573a3c1343ab4af5585d6a7b60b | MATLAB | 62,870 | 1,173 | % This code is to apply 2-way ANOVA on the decomposed subjects' signatures after
% applying tensor-decomposition.
% The significant bases will be saved to ANOVA/significant_entity,
% significant_action, significant_interaction
% in this version, ANOVA function was used for unbalanced conditions.
% This verion ha... |
d51778f9930d176534771053333fab1175141ee16de424ba73156a7559786957 | MATLAB | 69,285 | 1,212 | function p = pathdef
%PATHDEF Search path defaults.
% PATHDEF returns a string that can be used as input to MATLABPATH
% in order to set the path.
% Copyright 1984-2016 The MathWorks, Inc.
% DO NOT MODIFY THIS FILE. IT IS AN AUTOGENERATED FILE.
% EDITING MAY CAUSE THE FILE TO BECOME UNREADABLE TO
% THE ... |
e425c62ee1b917e454fe84c55d9726c715fce0548747acb309724cb8e8eff0bc | MATLAB | 72,185 | 1,354 | classdef dataModelling < handle
properties
% set up parameters
inputFolder
outputFolder
logFolder
figFolder
ppNames
conditions
condNames
numBlocks
numTrials
order
stim
mode... |
422cabefd298850a432300a94f3d93d9bd29530556199a275c0778fafb37424f | MATLAB | 75,371 | 1,805 | % The toolkit RIFF_player.m simulates a single experiments of the RIFF.
%
% Creating date: 21/02/2019 by AlexKaz
% ============ Opening function ==========================
function varargout = RIFF_player(varargin)
% RIFF_PLAYER MATLAB code for RIFF_player.fig
% RIFF_PLAYER, by itself, creates a new R... |
3ed3737ca9d7098511a749c8696e50b1beebd360d949ceeb6f850cabadf2ae04 | MATLAB | 76,215 | 1,503 | % Author: Jan Hirtz - 2022
% based on concepts published in Beathellier et al. (2012): Discrete Neocortical Dynamics Predict Behavioral Categorization of Sounds. Neuron 76: 435–449
% allows for multiple sound cartegories to be stacked for analysis
% excluded reps with animal running and cells that are not acti... |
276584ee9d62ba7d4c84f592f68d32c082602f294156133a383aada79364faf1 | MATLAB | 79,093 | 1,535 | % Author: Jan Hirtz - 2023
% based on concepts published in Beathellier et al. (2012): Discrete Neocortical Dynamics Predict Behavioral Categorization of Sounds. Neuron 76: 435–449
% allows for multiple sound cartegories to be stacked for analysis
% excluded reps with animal running and cells that are not acti... |
93fcd0304cc1811b0c6885cf914ad6c1ffeee3aef856008e8cd2660c71a3821c | MATLAB | 83,109 | 1,746 | %% Housekeeping
clear; close all;
addpath('D:\Documents\Software\spm12\FILversion');
spm('defaults', 'eeg');
addpath('D:\Documents\Scripts\opmeg_fieldmapping_code\HelperFunctions\icp')
addpath('D:\Documents\Software\FIL-OPMEG\optitrack');
addpath('D:\Documents\Software\FIL-OPMEG\OPM');
addpath('D:\Documents\Software\... |
6104db6c2afd10557b2a2f4c2a1eb4c95900ea8d5c705c794822dee30eab11f2 | MATLAB | 91,686 | 2,105 |
resultsFile='ImagingData.mat';
load(resultsFile)
rng(77)
animalstatetorun='AWK';
plotcellsresponsiveness=0;
minCellsSigCorrsPerSession=4;
toPrintIndividualExps=0;
toCorrectSignificance=1;
allResponsiveSigCorrs=[];
allResponsiveSigCorrsPerSession=[];
allResponsiveNoiseCorrs=[];
allMeanResponses=[]... |
d75356087d61daf4cf9626aef88a957917d00007d3811784e4b3d969f9cdf4c4 | MATLAB | 165,144 | 3,127 | function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1,*DATST,*TNOW1>
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig ... -<format>
% export_fig ... -nocrop
% export_fig... |
d5cf6377a1bd43d7e49f5dfc06b8e2cc3377b40c0f5b8bde53745a656ea3aae5 | MATLAB | 200,000 | 3,293 | classdef dataAnalysis < handle
properties
% set up parameters
dataFolders
inputFolder
outputFolder
logFolder
figFolder
dataFiles
ppNames
conditions
condNames
numBlocks
numTrials
... |
deb9bd0b7775d6a2ed57aa6f8854a891470325414f3006218672da08905ea810 | MATLAB | 200,000 | 4,669 |
% Code for https://www.biorxiv.org/content/10.1101/2020.11.11.377895v4
% Questions valk@cbs.mpg.de
for load_data_and_dependencies = 1
%BrainSpace: brainspace.readthedocs.io
%Colorbrewer colormaps: https://de.mathworks.com/matlabcentral/fileexchange/58350-cbrewer2
%Surfstat / brainstat: brainstat.read... |
211ed34a560656e2d0c1db931c5e84c763e27f07bf96d62d9c2e64277bbf8fb9 | Mathematica | 200,000 | 3,705 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 11.0' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
3ff574d75b48c3e02bc76c7800cdb9c38679fcf2d02d4d12f3846a22ae334f29 | Mathematica | 200,000 | 3,544 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 12.1' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
eb18a9345364aa219a76d29ca80344007ad7a432465b888205b0dd12b2b10685 | Mathematica | 200,000 | 3,735 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 12.1' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
0b18130b03df2e51a4880c51d6ea186cf52f462a69eb1cf168c4a56b038a7a4d | NEURON | 48 | 2 | load_file("nrngui.hoc")
xopen("fig4A-model.hoc") |
2daf7891941ff96758886c713352a473085d4020c2f2b444e7648fd39babdcfa | NEURON | 949 | 48 | : $Id: xtra.mod,v 1.4 2014/08/18 23:15:25 ted Exp ted $
: 2018/05/20 Modified by Aman Aberra
: how to use https://senselab.med.yale.edu/ModelDB/showmodel?model=241165&file=/AberraEtAl2018/interpCoordinates.hoc#tabs-2
NEURON {
SUFFIX xtra
RANGE es, os : (es = max amplitude of the potential, os = max intensity of the ... |
a0674dfadeccaa06b3cafe1b33146d5b532ba2b19e33c42cc9617b5fb8b97d61 | NEURON | 1,029 | 76 | : $Id: optopulse.mod, v1.0 2021/04/12 11:30AM Ruben Schoeters$
COMMENT
pointprocess optic pulse
ENDCOMMENT
NEURON{
POINT_PROCESS OPTO_pulse
RANGE osstart, osprp, osdc, osdur, Amp, Io
}
UNITS {
(W) = (watt)
}
PARAMETER{
osstart = 0 (ms)
osprp = 0 (ms)
osdc = 1
osdur = -1 (ms)
Amp... |
20fbb81a960bd6a2402bd48873267f8b4adeea719b4e082007da9284bb60f164 | NEURON | 1,042 | 92 | TITLE CA1 KM channel from Mala Shah
: M. Migliore June 2006
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
}
PARAMETER {
v (mV)
ek
celsius (degC)
gbar=.0001 (mho/cm2)
vhalfl=-40 (mV)
kl=-10
vhalft=-42 (mV)
a0t=0.003 (/ms)
zetat=7 (1)
gmt=.4 (1)
q10... |
f7a096b8b31184ed348e2c61ae193f35b804f2f73be9e4776293bac1829a2415 | NEURON | 1,099 | 57 | COMMENT
calcium accumulation into a volume of area*depth next to the
membrane with a decay (time constant tau) to resting level
given by the global calcium variable cai0_ca_ion
Modified to include a resting current (irest) and peak value
(cmax)
i is a dummy current needed to force a BREAKPOINT
ENDCOMMENT
NEURON ... |
8ace915c19bcf1617691338862432b170dcdc6e36630dc9b4dc6cbdbe3049c34 | NEURON | 1,978 | 123 | : $Id: ChR2H134R.mod, v1.0 2021/04/12 11:30AM Ruben Schoeters$
COMMENT
ChR2H134R
ENDCOMMENT
NEURON{
SUFFIX chr2h134r
NONSPECIFIC_CURRENT i
RANGE gchr2bar, gchr2, o, r, echr2, o0, r0, i
RANGE tauoIV, taurIV, oinf, rinf, Iopto
}
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(mS) = (millisieme... |
812ede964a3228f95f3f1243c9629ee6648e6d1515f94df71f677efc2d8cbcb0 | NEURON | 2,278 | 121 | TITLE nax
: Na current for axon. No slow inact.
: M.Migliore Jul. 1997
: added sh to account for higher threshold M.Migliore, Apr.2002
: WVG @ BBP 2018: add ttx sensitivity
NEURON {
SUFFIX nax
USEION na READ ena WRITE ina
USEION ttx READ ttxo, ttxi VALENCE 1
RANGE gbar, sh
GLOBAL minf, hinf, mtau, htau,thinf,... |
83795c5c20a83e0d63762a4a17d203b84a58904ee1cf11cd5f3362f8a34326f9 | NEURON | 2,739 | 138 | load_file("nrngui.hoc")
cvode_active(1)
celsius=34
objref stim, g, testcell1, testcell2, testcell3, testcell4, testcell5, testcell6, testcell7, testcell8
objref testcell
tstop=1200
flag1=0
flag2=0
flag3=0
flag4=0
flag5=0
flag6=0
flag7=0
flag8=0
xpanel("",0)
xcheckbox(" int cNAC 0.4 nA ",&flag1, "foo()")
xcheckbox(... |
1c2ca600aa727e6a35401fb37bdb52de4acc78e1409792f26cbda4bf9a29ebb7 | NEURON | 3,125 | 156 | TITLE na3
: Na current
: modified from Jeff Magee. M.Migliore may97
: added sh to account for higher threshold M.Migliore, Apr.2002
: WVG @ BBP 2018: add ttx sensitivity
NEURON {
SUFFIX na3
USEION na READ ena WRITE ina
USEION ttx READ ttxo, ttxi VALENCE 1
RANGE gbar, ar, sh
GLOBAL minf, hinf, mtau, htau, sin... |
df5071167dc0e64a0607b5e850b8476cfedefef31b8fda4344fc0d61d5ae957e | NEURON | 9,327 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:32:09.686226
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
55d446c370eb815360a326eedcfc96315b6b3dba07d259b5ee91138ccefd4ade | NEURON | 9,329 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:34:43.312674
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
895ca6b8f9fc58e36754874113402e64aa17fc5113b854fce19534b7264c97ef | NEURON | 9,329 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:26:20.790469
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
9ee5c3ae7987ba80edce37aff22497bbf81f954da08f0ae9256f66f6c5aacabc | NEURON | 9,329 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:23:12.775254
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
04ea5bd4850adda68900eead9e9a6b11661c242ffe12629a4535bc08d7bf992a | NEURON | 9,333 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:36:36.194344
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
67d0ec05516edd871aaf06caf5b4733742601740f2d9516374dcc1759fa59dd7 | NEURON | 9,333 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:23:56.825243
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
2d17c2c0cc73e96918e1140331f850cbfc9b0a27f167f25543f89e116f2b2b49 | NEURON | 9,334 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:30:42.896190
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
3831303dbd2dd692380cf5cdf1d4bc0341c0e9a9fbb3da310a06733a769461b4 | NEURON | 9,338 | 398 | /*
Created by BluePyOpt(1.5.29) at 2019-03-13 14:27:37.248184
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
f8d615bc92a632bda3132e0183af3424fde037f5e6795f767e6b1738410df29a | NEURON | 9,342 | 399 | /*
Created by BluePyOpt(1.5.29) at 2018-02-02 10:34:25.862199
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
217a0e47e29455f23f52b0173ebbf04a66d7d5ecba27792ecd8bb4e3e4314ae2 | NEURON | 9,344 | 399 | /*
Created by BluePyOpt(1.5.29) at 2018-02-02 14:45:31.929725
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
46531b7d59c8fb75f0d61af19902c5874e315bea145eee7f8017daad44413f6b | NEURON | 9,350 | 399 | /*
Created by BluePyOpt(1.5.29) at 2018-02-02 11:47:32.967266
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
f1d1066a6c586ace169fa54c77ab90bf81280dde6cb1e96bdda4fd4c12f30c7c | NEURON | 9,354 | 399 | /*
Created by BluePyOpt(1.5.29) at 2018-02-02 14:23:51.660653
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
ca1e9178da2761a4cae1b7d5a7aab87aa2dff7c93d9f0c2801960cf30667658a | NEURON | 9,360 | 399 | /*
Created by BluePyOpt(1.5.29) at 2018-02-02 11:21:57.766008
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
3606031729f13f75d8142d4f2728d8f8b41523ed94baa5db9e14f3e05e007e83 | NEURON | 9,665 | 396 | /*
Created by BluePyOpt(1.5.29) at 2019-03-28 10:32:52.783644
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
1d5d4f943f76ffb7d89f9a26700df3054c8ca3c6ad3ee269082b3ba2f68e1cf3 | NEURON | 9,669 | 397 | /*
Created by BluePyOpt(1.5.29) at 2019-03-28 10:37:21.216634
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
3a36809104805e8e909185f05d74f328697636228f2da20fb7e34b6fea15607a | NEURON | 9,669 | 397 | /*
Created by BluePyOpt(1.5.29) at 2019-03-28 10:38:54.114144
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
b33e90568983d77cbad0cace8f194188e44b3668da4cc81bf1a8e8333ccc32b6 | NEURON | 9,669 | 396 | /*
Created by BluePyOpt(1.5.29) at 2019-03-28 10:31:02.909534
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
559b364e897a1d152a05b4286bf9773f675499b604ca70193ce8c5be4bb05361 | NEURON | 9,712 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-13 11:01:44.283613
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
631dc8ab0e2ab90ab6a821f057d2ca69af73f273e1edbbcc5acf21f48d2b481f | NEURON | 9,713 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-08 10:23:07.536432
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
2b8969c675ceda58ef288761ac7bde53044b71d8a5bd7f595f18042a8fc7bff9 | NEURON | 9,716 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-08 12:01:08.367015
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
bef0778bbdc10c2b1f42748e237ccb283ff507c1f70a57c2c2bd3227160ae055 | NEURON | 9,716 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-08 10:21:59.412574
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
04ed470640f6c2fb55430f9e47b8a60fb263d5cfc350a36a2dd3f4527a4f7d2a | NEURON | 9,717 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-13 11:31:30.819573
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
41f9de5a7ade1ef04789ba7d9e1c02f0b2c446277a693c899695ba02fafcab90 | NEURON | 9,717 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-13 11:14:58.774250
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
cae4387cedfdc03e40bf0ba23d0a9b9e467493c1eb4d29a4dc67c846018fecf1 | NEURON | 9,717 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-11 10:25:06.138007
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
0f3d42d72c493f58806fe8d3ea0f57079d23c617a0bdbe365fa85e7521c85013 | NEURON | 9,718 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-08 11:00:53.852384
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
179a67d188646f34c9fd2d5e11bfa65d705bcf50ac16a9b1d69ac978ff592d0f | NEURON | 9,718 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-08 12:14:40.475711
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
312d566daa2b1d2e94d844f90ecd9e5b3eb3741ad1d4e08e4e27093607c9cd73 | NEURON | 9,718 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-13 10:49:32.341869
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
6489ec24df04cb0b1956634c4a98e7e6ec6c339b01cbf7400b00d5b36fe04814 | NEURON | 9,718 | 414 | /*
Created by BluePyOpt(1.6.56) at 2019-03-08 12:16:18.876720
*/
{load_file("stdrun.hoc")}
{load_file("import3d.hoc")}
/*
* Check that global parameters are the same as with the optimization
*/
proc check_parameter(/* name, expected_value, value */){
strdef error
if($2 != $3){
sprint(error, "Parameter %s has ... |
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