sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
66f807a067cb864729a56baa28b8c2fbdc8ae86b42642c01db972a2f4ca583ec | MATLAB | 4,496 | 135 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [hFig] = plot_bestaligned_registered(BestAligned, MapsData, registeredCellName, doNormalization)
hFig = figure('position', get(0, 'screensize'));
maxTrials = 6+2;
cdata = BestAligned(ismember(BestAligned.regis... |
eeadf089c83df314154e3cf7c21dc70e14ec0ac9f63c988cd1bdba05191fd77b | MATLAB | 4,497 | 215 | function[]= check_redcells(redcell_vect,cell_stat,img,thresholds,shift)
xshift=shift(1);
yshift=shift(2);
cellstat_ids=1:length(cell_stat);
%%
figure
subplot(1,2,1)
%redcells on short image
imshow(img.short)
caxis([0 max(max(img.short))/thresholds(1)])
hold on
red_stat=cell_stat(redcell_vect);
red_ids=cel... |
1ff74f303742c872f27667a5ec472a961a239f846afec672414ea55eeb4b811a | MATLAB | 4,499 | 139 |
%# usage: y = filtfilt(b, a, x)
%#
%# Forward and reverse filter the signal. This corrects for phase
%# distortion introduced by a one-pass filter, though it does square the
%# magnitude response in the process. That's the theory at least. In
%# practice the phase correction is not perfect, and magnitude response
%#... |
a7ef9c5a6510f34d848013ba2c799f776fa974e9d72af7b7a8cb45b62a97d37a | MATLAB | 4,499 | 120 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
% This loads celias tetrode data into a form that can be used by the
% population vector code
function [T] = load_celia_data_structure_as_table_v3(data)
%data = load(dataFilename);
%data = data.ratemaps;
animalNames = ex... |
2ae4fcd32afa622c347d69566aa53ac13349797f7490d4e84a9011fb2d223d16 | MATLAB | 4,501 | 99 | % RIDGEORIENT - Estimates the local orientation of ridges in a fingerprint
%
% Usage: [orientim, reliability, coherence] = ridgeorientation(im, gradientsigma,...
% blocksigma, ...
% orientsmoothsigma)
%
% Arguments: im ... |
5705970372a7b900b55a347449a50fa9eb921148252718c3abfa6672593f67f5 | MATLAB | 4,501 | 169 | function [vol] = dipoli(vol, isolated)
% DIPOLI computes a BEM system matrix
%
% Use as
% [vol] = dipoli(vol, isolated)
% Copyright (C) 2005-2008, Robert Oostenveld
%
% $Log: dipoli.m,v $
% Revision 1.3 2008/12/24 10:25:41 roboos
% cleaned up the dipoli wrapper, replaced the binary by a better one and added a cop... |
5e3c524a3683143a9f98e6bdf70d3c07e7bea54c4972c2a5d7cf849e225322ff | MATLAB | 4,502 | 139 | %%%%%%%% edit these values %%%%%%%%
frequencies = [ 10 ...
20 ...
40 ...
80 ...
100 ...
160 ...
200 ];
delays = [ 0];
intertrialinterval = 5; % in seconds
numtrials = 5;
stimamplit... |
8790ed76c663e411fb8de3d311d80fdb2357fe5953f480ebc413aa9ff362a0cf | MATLAB | 4,502 | 123 | % getVarFromParameters.m
%
% $Id:
% usage: getVarFromParameters(varname,e,<allPossibleVals=0>)
% by: justin gardner
% date: 03/16/07
% purpose: get a variable name from task parameters, could be
% will return the full qualified name of the variable
% e is returned f... |
f317b17a27854f5f213ee8785f8ecccb95324e323b9939fd159fdabdaa15f4ac | MATLAB | 4,502 | 138 | function [TR,W]=TriQuad(TR,W)
% Subdivide a triangular surface mesh using generalized triangular
% quadrisection. Triangular quadrisection is a linear subdivision procedure
% which inserts new vertices into the input mesh at the edge midpoints
% thereby producing four new faces for every face of the original mesh.
%... |
5b6d5b45beee1bc89450be2cc5e191685291c4d4dce19af65c020510e6ec2d9f | MATLAB | 4,504 | 147 | % plotDFFCond_bouts.m
%
% Function to plot output of saveDFFCond_bouts(), pooled across
% multiple flies and conditions.
% User specifies number of conditions, and then selects files (1 per fly)
% for each condition through GUI. Plots mean for each fly and mean across
% flies for each condition (different colors ... |
ccd893ac94939497f70a8df3255b34b79ce602bd7f220b37065d1062178e7aec | MATLAB | 4,504 | 131 | function flag=SONImport(fid,varargin)
% SONIMPORT copies all channels into a MAT-file
%
% Note: Use ImportSMR in the sigTOOL package in preference to SONImport
% unless you want data stored in the same way as with previous versions of
% the SON library.
%
% SONIMPORT(FID, {OPTIONS});
% where:
% FID is the matla... |
e270bcb08a5e8920ceba3def834db2ec714674968e820919ac82bc7cbdda981f | MATLAB | 4,504 | 133 | %get statistics from Amo data
%First time learining data from Amo - assumes data in same directory as .m
%file. Otherwise need to set path for the .mat file
%Only first 40 trials, or less if there are less type 1 trials are used
%This is because ther seems to be a habituation of US response for a larger
%number of tria... |
edfceec0477266dae84daaaba762306003f4ef7eba9b1fa16dcffb885311dcc3 | MATLAB | 4,506 | 137 | %
% Please cite this paper if you use any component of this software:
% S. Soltanian-Zadeh, K. Sahingur, S. Blau, Y. Gong, and S. Farsiu, "Fast
% and robust active neuron segmentation in two-photon calcium imaging using
% spatio-temporal deep learning," Proceedings of the National Academy of Sciences (PNAS), 2019.
%
... |
4da7f5ac9473642440e0b718ec4271c5e84bafe44662b82e07429421e9b24345 | MATLAB | 4,507 | 120 | % initUserDAQ.m
%
% Function to initialize user DAQ (i.e. DAQ that coordinates experiment and
% collects appropriate voltage signals)
% Sets up channels and DAQ and channel settings. Does not set up any
% experiment-specific output streams.
%
% INPUT:
% settings - struct from ephysSettings() containing all DAQ sett... |
8089ac2ee52335f2e68a13131c8807cf762af1a718aa1921b057057d5e4c2c37 | MATLAB | 4,507 | 155 | function [] = ExtDataFig05_pIP10_OptStim_TuningCurve_Song
% Code for plotting the tuning curves of pulse and sine songs induced by optogenetics in Extended Data Fig. 5i.
GT = 'TN1dsx';
TargetPeriod = [0,10];
%% parameters
nTrials = 3;
nStim = 6;
T = 1370; % T
DAQrate = 10000;
x1 = [0:1/DAQrate:190-1/DAQrate];
PreD... |
19e9b848bc8919d98d0f8fcc15c611b9faf369c966c835d8e3fe05a51446a192 | MATLAB | 4,512 | 132 | % taskTemplate.m
%
% $Id: taskTemplate.m 217 2007-04-04 16:54:42Z justin $
% usage: taskTemplate
% by: eric dewitt
% date: 03/19/2010
% copyright: (c) 2006 Justin Gardner (GPL see mgl/COPYING)
% purpose: example program that demonstrates a gaze contingent experiment
% (displays... |
e5f0707a229704ef55900393a1bba55fe6da8dda1aefcc18db171c5740ffa904 | MATLAB | 4,513 | 113 | %% CREATE VARIABLES/ SET PARAMETERS
if ismac
base = '/Volumes/Runyan/Potter et al datasets/';
else
base= 'Z:\Potter et al datasets\';
end
datasets = {'EC1-1R/2021-11-05/', 'EC1-1R/2022-01-13/','FL5-3L/2022-03-09/','FL5-3L/2022-04-18/','FU1-00/2022-03-17/','FU1-00/2022-05-10/','GE3-00/2022-10-27/',...
'G... |
f18cffd2076e211db0a4dae52a5e4e9b0e9f73ddece5fe2ce418b47771d87043 | MATLAB | 4,514 | 148 | function script02_proofread_vols(samplei)
% merge axons, myelin & cells into one volume and remove small spurious
% objects from the segmented volumes for better visualization
% samplei = the index of the sample to analyze
%
% This script needs the original DeepAcson segmentations in folder
% White_Matter_EM/*/
% The... |
4adcd7e2614d28f83cb0cd51128dcfc4cf59a0459433d7fba43ed01395c51e76 | MATLAB | 4,515 | 83 | %put too much effort into these, I'm saving them in case they were needed.
%But basically left RFt on left sensors (and vice verca) doesn't make sense
%as the other hemifield is being flickered with another frequency and isn't
%a good control.
%% calculate MI-RFT left (MI_63_right + MI_70_right) on left sensors
%%%... |
d68da557cc13206008e862db414c55674205c975d4e3d6168e03e1ecefa7b82f | MATLAB | 4,517 | 116 | % BAYESIAN BOOTSTRAP CREDIBLE INTERVAL SIMULATION SCRIPT
clear
% bootbayes settings
nboot = 10000;
prob = 0.95;
prior = 1; % Simulation for prior set to either 1 or 'auto'
switch (prior)
% Set weight for estimates of the moments from the samples in the simulation
case 1
w = 1; % For standard deviation using d... |
1a167074cc0cff539e2728de8603be149e242c4df0965ceb4055d6e917192f6f | MATLAB | 4,519 | 98 | function fhand2 = smrCopy(smrFile, ending)
maxPointsToRead = 200000000;
%% Open file & gather info
activateCEDS64;
fhand1 = CEDS64Open(smrFile);
if (fhand1 <= 0); fprintf(fhand1); CEDS64ErrorMessage(fhand1); unloadlibrary ceds64int; return; end
[~, OldFileId] = CEDS64AppID( fhand1 );
timebase = CEDS64TimeBase( fh... |
14a76768146f11a8fa29f9c1ada6aca25da40319931dbe085c2dd5a7c7a4c478 | MATLAB | 4,523 | 153 | % mglMetalBltTexture.m
%
% usage: results = mglMetalBltTexture(tex, position, hAlignment, vAlignment, rotation, phase, width, height, socketInfo)
% by: justin gardner
% date: 09/28/2021
% copyright: (c) 2021 Justin Gardner (GPL see mgl/COPYING)
% purpose: Private mglMetal function to blt text... |
2f170c82726305851108a1f37d244e21654a013100f3719105e1146812daf795 | MATLAB | 4,534 | 153 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function [hFig] = plot_normal_bfo90_table_withinacross(NormalBFO90, DaysToSessions)
% Makes a figure with 4 subplots each with a BFO 90
SessionsEarly = DaysToSessions(ismember(DaysToSessions.dayNum, [1,2]),:);
MatchE... |
77b688a44756db896ea4a7177e223d0a1840226a05fce870483df4d4495ec7ab | MATLAB | 4,535 | 103 | %MGL library functions
%
%Main screen functions
% mglOpen : Opens the screen
% mglFlush : Flips front and back buffer
% mglClose : Closes the screen
% mglResolution : Sets the resolution of a display
%
%Other screen functions
% mglSwitchDisplay ... |
1c1e3e772552226d2a15c07cf83e9dc4c4e9f897863fb9fa370f9588e7d75c53 | MATLAB | 4,536 | 155 | %% structure parameters
num_columns = 3;
npp = 100;
ppc = 2*npp;
num_VTA = 100;
N = ppc*num_columns + num_VTA;
pop = num_columns*2;
n = N;
unit_num = 1:2:(2*num_columns);
% num_trials = 600;
num_trials = 160;
%% time parameters
dt = 1; %time step
T = 100/dt; %time stimulated
T_R = 150/dt; %time of reward
delta = 600/d... |
e7cd45d7883abc59f7eb33fd438938bdb8b541a28f3dd5725b5f7840f737009d | MATLAB | 4,542 | 166 | function hdr = load_nifti(niftifile,hdronly)
% hdr = load_nifti(niftifile,hdronly)
%
% Loads nifti header and volume. The volume is stored
% in hdr.vol. Columns and rows are not swapped.
%
% Handles compressed nifti (nii.gz) by issuing a unix command to
% uncompress the file to a temporary file, which is then deleted.
... |
1f54ecfb4015fbe8b61322d6b3455dede580900624df079282446485083cb711 | MATLAB | 4,543 | 104 | function varargout = spm_select(varargin)
% File selector
% FORMAT [t,sts] = spm_select(n,typ,mesg,sel,wd,filt,frames)
% n - Number of files
% A single value or a range. e.g.
% 1 - Select one file
% Inf - Select any number of files
% [1 Inf] - Select 1 to In... |
4c83db53f9a36ffe071a062c290bc0a4b65caaa0255fc1dde5df368a10fbecba | MATLAB | 4,544 | 156 | function dim = crossvalidate_fa(X, varargin)
%
% dim = crossvalidate_fa(X, ...)
%
% Cross-validation to determine optimal latent dimensionality for
% factor analysis
%
% xDim: data dimensionality
% N: number of data points
%
% INPUTS:
%
% X - data matrix (xDim x N)
%
% OUTPUTS:
%
% dim - structure whose ith e... |
73cbd6a25b7427bfbe985a9117e75878188a24ea9354e31b57a142e6c1656130 | MATLAB | 4,546 | 146 | function BNV_surface_and_nodes(data, NIFTI, node_coords, surface_node_idx, Config, surf, savename)
%BNV_surface_and_nodes Create a BNV image that colors both a brain surface
%and nodes (likely subcortex nodes) simultaneously.
% Usage:
% BNV_surface_and_nodes(data, NIFTI, node_coords, surface_node_idx, Config, s... |
42986bbccde8aeb1910ce18c94e405cb5762f6e7d89e81b0381fbcfd43d7729a | MATLAB | 4,547 | 120 | % fwhm.m
%
% Function to compute full width at half max (FWHM) given x and y. X is
% what width will be computed on; y defines peak.
%
% INPUTS:
% x - vector that defines width of peak
% y - vector that defines height of peak
% valInd - indices into x/y in which to find peak
% minOrMax - 'max' or 'min' for whe... |
678013261611506593e3e16ee6d527fdb05baf934a54791ad438ae199c5a1861 | MATLAB | 4,548 | 116 | function [newW,varargout] = minimiseMaximumRealEigenvalue(W,ICells,Options)
% minimiseMaximumRealEigenvalue optimises weight matrix to be stable
% newW = minimiseMaximumRealEigenvalue(W,IndexI,Options) iteratively alters
% the original NxN weight matrix W to minimise its maximum real eigenvalue
% and so enforce stabil... |
70bbbdc1a30719037e82d7401fbba422ae5eaea64075faf8ffc8b746f705a8be | MATLAB | 4,549 | 120 | function timelock = ft_datatype_timelock(timelock, varargin)
% FT_DATATYPE_TIMELOCK describes the FieldTrip MATLAB structure for timelock data
%
% The timelock data structure represents averaged or non-averaged
% event-releted potentials (ERPs, in case of EEG) or ERFs (in case
% of MEG). This data structure is usually... |
9d51e2e4fd418c0577a1ce3a2471f6aeec9fc9a0afc4974020f4011d9c817564 | MATLAB | 4,550 | 160 | function [chi_M, chik_tkd] =SFCR_m_SB_k(deltaB, D_k, maskErode, maskSS, wG, lambdaSet, itermax, thred)
% [chi_M, chik_tkd] =SFCR_m_SB_k(deltaB, D_k, maskErode, maskSS, wG, lambdaSet, itermax, thred)
% SFCR M-step using Split-Bregmen L1 solver, usin k-space based version
%
% Input: deltaB, D_k, maskErode, maskSS, wG... |
102bbc0329911d97b30f04a1b44bb3fbf1ce4f110ff4c6d7ff611a538f1e9967 | MATLAB | 4,551 | 163 | function [Blocal, chi_source] = dipolefit_v2(data, mask, weight, Params, tol, itermax, centerswitch)
% [Blocal, chi_source] = dipolefit_v2(data, mask, weight, Params, tol, itermax, centerswitch)
%% Author: Xu Li
% Affiliation: Radiology @ JHU
% Email address: xuli@mri.jhu.edu
%
% Purpose:
% dipole field fitting for rem... |
828375914cedeb5ce6ceda331ef7e81c5f4ee586e479ba37a3c3e4730e069b18 | MATLAB | 4,556 | 193 |
function batch_data=batch_do_data_crop(train_opts, imdb, work_info_epoch, batch_data, work_info_batch, work_info)
data_crop_config=train_opts.data_crop_config;
if work_info.ref.run_eva || ~data_crop_config.do_crop
batch_data.crop_info=[];
return;
end
img_data=batch_data.img_data;
mask_data=batch_data.la... |
5521be762d8fa6f3c660ae7a49f87cdefc931ca56f9553622e47caba5d3f0ff0 | MATLAB | 4,557 | 106 | function [] = plot_worm_frame_post_analysis_showing_path_mochi_data(I, center_lines, centerline_color, centerline_stimulus, debugimage,in_track_index,current_ellipse_ratio,smoothed_path_x,smoothed_path_y,stimulus_delivered,path_history,demo_mode)
% % % % % % [] = plot_worm_frame(I, center_lines, centerline_color, Unce... |
d242a0aa13c7c59ae26bafede0e17869f2ae52484b3c732ce7b87d67848a029f | MATLAB | 4,557 | 80 | % run amapOFshow
clear all; runMode = 'batch';
globals; initglobals;
PLOT_TYPE = {'tuning'}; % {'map'}, {'trajectory'}, {'tuning'}, {'map';'trajectory'} ;
VarMargin1=0; VarMargin2=0.01;
Nshuffling = 100;
runShuffling = 0;
%runRmap = 0; % make this option...
IncludeFileCell = {'opF'}; %{'opF';'nW'}
Exc... |
d3b64865198374d07a99b250fd6fa4d25ea41043de1b45e2231fc52b91015498 | MATLAB | 4,557 | 142 | %% Path & Parameters
HEM = {'LH','RH'};
SUB = 1:15;
ROIN = {'left HG','left TPJ','right HG','right mSTS'};
nROI = 4;
nROI_hem = 2;
% datapath: change to local path
dp = '../SOURCE_DATA';
load(fullfile(dp,'results_PATSIM.mat'));
addpath('./etc');
% make it easier to code
s2s_cor = single2scene_cor;
%% Figu... |
eb6d8eb6f83d63a6e3c0e3cddeb462c43ff868c00d8ce4d72e036d99f644592b | MATLAB | 4,558 | 82 | function [Tracks, number_of_behaviors] = find_stereotyped_behaviors_from_velocity(Tracks)
% not used in paper
number_of_behaviors = 5;
fps = 14;
duration_cutoff = 0.5 * fps;
if isempty(Tracks)
return
else
Tracks(1).BehavioralTransition = []; %preallocate memory
end
... |
7b42d9fe2338a72740310d38b50155f733035608f02fe84ac5179dcbae64cf77 | MATLAB | 4,559 | 147 | % BOOTSTRAP CONFIDENCE INTERVAL SIMULATION SCRIPT
% EVALUATION OF INTERVAL COVERAGE, TAIL PROBABILITIES, LENGTH AND SHAPE
clear
% Save warning states and turn off all warnings
state = warning ('query', 'all');
warning ('off', 'all');
% Set significance level
alpha = .05; % 95% confidence interval
%alpha = [.... |
63b263157ffb7807aa9c8ed4c17c0a0258484a7ee369b82aadd96b01aedd36ff | MATLAB | 4,560 | 146 | % mglBltTexture.m
%
% $Id$
% usage: results = mglBltTexture(tex, position, hAlignment, vAlignment, rotation, phase, width, height)
% by: justin gardner
% date: 05/10/06
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: Draw a texture to the screen in desi... |
1280edfa678f9fe6a27313dde6d9d74ea33bb5351bb3828c547d3f8c31750188 | MATLAB | 4,561 | 130 | classdef rpgdegibbs < handle
properties (GetAccess = public, SetAccess = private)
end
methods (Access = public)
function this = rpgdegibbs()
end
function imgdg = degibbs(this,img, dim, pf, params)
if nargin <= 4
... |
60b418ad32f454a46a22fd86fccf9fdf48212ed635948252d9ecd9064c41fbc2 | MATLAB | 4,561 | 123 | function mltp_compute_bfo_90_wc(obj, session)
% Allow the function to run so that other functions do not break,
% but give a warning.
if session.getNumTrialsToUse() < 2
warning('This function requires the session to have more than 1 trial.');
end
% We have to use the shrunk data if the ... |
a5c55fdd7360abd03905eaf46c546882703c06838d63b12c5bac17f718d48781 | MATLAB | 4,561 | 169 | function [vol] = openmeeg(vol, isolated)
% OPENMEEG computes a symmetric BEM system matrix
%
% Use as
% [vol] = openmeeg(vol, isolated)
%
% Attention: the normals of the mesh describing the volume conductor are by
% FieldTrip convention pointing outwards (with respect to the mesh center),
% whereas OpenMEEG binari... |
045b51ee5bed2abcb92e7d29184e3de9b1593960b1df5f00f1f925083f957016 | MATLAB | 4,562 | 137 | function [hdr, dat] = read_neurosim_evolution(filename, varargin)
% READ_NEUROSIM_EVOLUTION reads the "evolution" file that is written
% by Jan van der Eerden's NeuroSim software. When a directory is used
% as input, the default filename 'evolution' is read.
%
% Use as
% [hdr, dat] = read_neurosim_evolution(filename... |
44281dc3fd1c868d8e2a4a8a76a5cf3487ef7dec9c0c4bff342365529f117fc1 | MATLAB | 4,562 | 151 | function [change_explained_by_adap,FR_touch]=all_Tcurves_per_whisker(fig4)
do_extra_plot=0;
counter=0;
counter2=1;
av_unit=0;
percentile_1=0.95;
percentile_2=0.95;
NpointsTcurve=4;
ff=dir('*.mat*');
nunits=33;
FR_touch=nan(nunits,4);
h_atte=nan(nunits,1);
coeff1=nan(nunits,2);
coeff2=nan(nunits,2);
for f=1:size(ff,1)... |
9d3a977b7d7eb0ca2aea8a9077bd1487696a74b72993d18ebbf344ccc80cddbf | MATLAB | 4,562 | 145 | %--------------------------------------------------------------------------
% sampleparcels.m
% Identify 10 parcels, each belonging to one of 10 functional networks, and
% choose a column that is central to each parcel.
%--------------------------------------------------------------------------
%close all
% Note: I ca... |
69d4899f413125a71878aaa85fa56fd5e5d75426c2a7882155e732e978634884 | MATLAB | 4,570 | 150 | function [S,gammas]=eventSamples(A,n,varargin)
% eventSamples Compute multiresolution ensemble using event sampling.
%
% Syntax
%__________________________________________________________________________
%
% [S,gammas]=eventSamples(A,n)
%
% [S,gammas]=eventSamples(__,Name,Value)
%
%
% Description
%_________________... |
73d976194c916c9894f6c06b52436fb32719607f37b40578e3e62116c6ad65d5 | MATLAB | 4,573 | 159 | %
% Please cite this paper if you use any component of this software:
% S. Soltanian-Zadeh, K. Sahingur, S. Blau, Y. Gong, and S. Farsiu, "Fast
% and robust active neuron segmentation in two-photon calcium imaging using
% spatio-temporal deep learning," Submitted to PNAS.
%
% Released under a GPL v2 license.
%%
funct... |
361a7ebbc4968a98cb1e10342dfc74157fb2b859bec4e3ea1beb6d3e33c8dab5 | MATLAB | 4,574 | 144 | % plotIInjFicTracChangePos_allFlies.m
%
% Function that plots effect of current injection on FicTrac position
% parameters. Specifically, for each fly, plots the average across trials
% of the difference in cumulative position/angle between a start time
% point and an end time point relative to the current injectio... |
e9af141b488f4ee18d7dbdfd30b1eec48f8278c3b52aa54821cd99ec0b6b95d2 | MATLAB | 4,574 | 99 | % convert UGR raw behavioral to BIDS events
% set relative directories
filePath = matlab.desktop.editor.getActiveFilename;
[codedir,name,ext] = fileparts(filePath);
[basedir,~,~] = fileparts(codedir);
maindir = fullfile(basedir,'bids','sourcedata','Scan-Lets_Make_A_Deal');
% load subject list and loop through subs
su... |
28bdf144208528ead401c9c9b0f34ffc32c74e047fb769de876530b8cfc90b6d | MATLAB | 4,575 | 156 | function [] = ExtDataFig04_OptStim_TuningCurve_Song
% Code for plotting the tuning curves of calcium signals of each neuron induced by optogenetics in Extended Data Fig. 4f,i.
GT = 'dPR1'; % Extended Data Fig. 4f
% GT = 'TN1SG'; % Extended Data Fig. 4i
TargetPeriod = [0,10];
%% parameters
nTrials = 3;
nStim = 6;
T =... |
88d91cd30ed397bdbc65f9a11de63ad9afbab80012e0e45d71bfeadff5d1060c | MATLAB | 4,575 | 173 | function [lambda1,lambda2]=Tcurve_touches_dk_cross_val(touches,touches_whisker,psth,k_c1,k_c2,do_plot,N_first)
%this code assumes that the input is dk1 and dk2
counter=1;
k_hor(:,:,1)=k_c1;
k_hor(:,:,2)=k_c2;
window=100;
window_ad=600;
%N_first=5;
N_latter=N_first;
percentile_1=1;
percentile_2=0.95;
if do_plot
figu... |
06fa3f3eab7d81ac5db2e83fd9eea8144700a87a87d5f035960993bd4ae62cd8 | MATLAB | 4,577 | 144 | function [resmat,mdls,rpInfo] = getLastSpkResiduals(data,resopt)
%getLastSpkResiduals.m
concatWins = optCheck(resopt,'concatWins',false,[true false]);
oneModel = optCheck(resopt,'oneModel',true,[true false]);
model_order = optCheck(resopt,'order','auto',[]);
if isnumeric(model_order)
rpInfo.RPend = model_order;
e... |
639ab553b522a6207624b6d4ad5080af70cb69740cfa0418f2ef8d8afb47d704 | MATLAB | 4,578 | 135 | % ********** Setup the directory on your computer **********
clear
restoredefaultpath
filePath = matlab.desktop.editor.getActiveFilename;
root0 = fileparts(filePath);
addpath(genpath(fullfile(root0,'lib')));
root = fullfile(root0,'data');
projname = 'cylinder_1';
%% Read simulation result
files = dir(fullfile(root,pr... |
ad4a0bbb02ff22fe2fd65af4c5ae050616d65e2cb34477ab54d2f63d2db28702 | MATLAB | 4,580 | 127 | classdef MLVideoRecord < handle
%MLVideoRecord A video record
% This class loads and saves the timestamps and associated
% information for a sequence of videos representing one
% video record.
properties (SetAccess = private)
thisFilename = '';
datasetName = '';
su... |
e3dfc764ca3d8d79e7ab748065252cc9560a0bf1e5c883b25e5e90f67c5b6080 | MATLAB | 4,581 | 127 | function fH = makeSupplFigure4_DistributionCSTExponents(ds,roisToPlot,cmapROIs,saveFigs, saveFigDir)
% Function to reproduce supplementary figure 4:
% Plotting the distribution of fitted CST pRF exponents
%
% From the paper:
% Title: Rethinking simultaneous suppression in visual cortex via
% compressive sp... |
1a90d966ca0e717c3d21d3616908df4987e8a44dbaaf8df6d16b50d0c45d6065 | MATLAB | 4,582 | 96 | function [UL_results_A, HF_results_A, UL_results_C, HF_results_C] = ET_average_group(results, name)
all_participants = fieldnames(results);
UL_results_A_mean = zeros(2,6);
HF_results_A_mean = zeros(2,2);
UL_results_C_mean = zeros(2,6);
HF_results_C_mean = zeros(2,2);
HF_results_A = [];
... |
89f803f4f4aff236396a0330dd7878d2fb8ebeeda9d602459b7a3e58d4bc1931 | MATLAB | 4,582 | 128 | % zipFfmpgLegVid.m
%
% Function given trial with leg video, generates .mp4 file from individual
% tiffs and zip file of same tiffs for that trial.
% Called by preprocessLegVidFiles(). Does not stand alone.
%
% INPUTS:
% inputParams - metadata about trial, loaded from saved data
% scriptsPath - full path to where ... |
fb9cb5d5cd5efe2f840ab320891319f6d30795577fffe2066d929b575394078a | MATLAB | 4,583 | 207 | function DATA = aedes_readfdf(filename,varargin)
% AEDES_READFDF - Read Varian Flexible Data Format (FDF) Files
%
%
% Synopsis:
%
% Description:
%
% Examples:
%
% See also:
%
% This function is a part of Aedes - A graphical tool for analyzing
% medical images
%
% Copyright (C) 2006 Juha-Pekka Niskanen <Juha-Pekka... |
d0def538ad6295a0fde2f402cae5de2b1e87bfb0b10a575c650746e2e0038076 | MATLAB | 4,584 | 88 | % Function File: yf = hpfilter (y, t, Fc)
%
% Fast algorithm to high-pass filter y-values at the specified -3 dB
% filter cut-off (Fc) using binomial filters.
%
% This algorithm executes cycles of anti-alias filtering and data
% reduction for improved speed. The net result following sequential... |
ed61cdaedd0435148e362ebb1ae7f1a597886cf8e94587b731eb2ea0e0b74c5d | MATLAB | 4,584 | 129 | % findFlyNotMovingFt.m
%
% Function that takes in fly's smoothed, normalized total speed, a
% threshold on that speed, and a minimum bout length to extract when the
% fly is moving or not moving.
% Merges bouts that are too short and assigns
%
% Helper function for interactGetNotMovingIndWFt()
%
% INPUTS:
% totSpd... |
49101dcf41331f1c9095bb22bb7fd9a65d65bd5f62c346fd342bb9d0fa917e13 | MATLAB | 4,585 | 137 | function [corrs] = get_ms_partial_correlations(ds_events,activity_length,bin_size,type,ex_thresh)
start=0;
corrs=cell(3,length(ds_events));
%%
for d = 1:12
ds_som_corrs=[];
ds_pv_corrs=[];
ds_ex_corrs=[];
load(['Z:\Potter et al datasets\' ds_events(d).tag 'activity.mat'])
velocity= combined_... |
bd0e41b3b15e9fa5704d24ee162e151193d17a4ed06de0178053c613c61a3b07 | MATLAB | 4,586 | 159 | function header = ufmf_read_header(filename)
% header = ufmf_read_header(filename)
% This version is designed to shadow the version in JAABA/filehandling.
% Only difference is that it uses a file_object instead of a raw fid
% when opening the file. The file_object should work just like the fid
% except that it fclose(... |
753874070a307542cbe2224df2933f9277cbf4f587d7b352ba0265b1c2b82529 | MATLAB | 4,588 | 122 | % multiStepIInj.m
%
% Current Injection Function. Injects square current steps of user
% specified amplitudes of user specified durations. Durations can be
% different among steps. Has option to randomize amplitudes or not. User
% specified step duration and time between steps. User specified space
% amplitude.... |
ccd768ca0ad9a22c6b12a907acfe437adf4c6ff6f5278dc754c1e22c12a84b83 | MATLAB | 4,588 | 196 | function dataformat = aedes_getdataformat(filename)
% AEDES_GETDATAFORMAT - Try to determine the data format of a file
%
%
% Synopsis:
% dataformat=aedes_getdataformat(filename);
%
% Description:
% Returns an identifier string corresponding to the data format of
% the file FILENAME. If the data format... |
b516cccd612fbd5b705e692f147381730cd0619cc1ba3686a1252f5045dec6cf | MATLAB | 4,593 | 122 | <<<<<<< HEAD
function [gms, gmsTime, gmsTime_n] = createGMS(result_f, key_f, general)
% Calculate GMS
gmsTime = 0;
gmsTime_n = 0;
oldID = -1;
w_r = 0;
% Only for matching_function == 'library'.
% I load the library for better performance
if strcmp(general.MATCHING_function, 'library') == 1
loadlibrary(general.MATC... |
1a71275104f06a0bad496c18418a37ea9260dbef14ede063a2d7a295eec4c987 | MATLAB | 4,594 | 178 | function varargout=shadedErrorBar(x,y,errBar,varargin)
% generate continuous error bar area around a line plot
%
% function H=shadedErrorBar(x,y,errBar, ...)
%
% Purpose
% Makes a 2-d line plot with a pretty shaded error bar made
% using patch. Error bar color is chosen automatically.
%
%
% Inputs (required)
% x - vec... |
717c70397150f26524a49d45764f053a9cf593d803531982a04c136e87542428 | MATLAB | 4,597 | 143 | % run after SimulationFig4E.m & spkcounts.m
% spike counts data provided for nws=1 (set Nnws=1)
%% PARAMETERS
conditions = {'SOM', 'PV'};
Np=2; %%number of conditions?
Nsample=length(ds); % 10 samples per weight matrix realization
rs = 5; %%random resamples of the neurons
M=40; % latent dimensionality to fit data
N... |
aa2d2f4ddc41489ae5a2a555a1da16932ebb6971175026af30a7de425a807df5 | MATLAB | 4,597 | 154 | function PrepareFlyTracker4JAABA(expdirs,varargin)
if ~iscell(expdirs),
expdirs = {expdirs};
end
[rootoutdir,rootdatadir,dataloc_params,analysis_protocol,settingsdir,forcecompute] = ...
myparse(varargin,'rootoutdir','',...
'rootdatadir','',...
'dataloc_params',[],...
'analysis_protocol','current',...
'set... |
e38199bfee80872a2fd138c948cf1a4616b5c35e43fd30965f0a37b948353dc3 | MATLAB | 4,597 | 142 | % plotSpikerateCond_bouts.m
%
% Function to plot output of saveSpikerateCond_bouts(), pooled across
% multiple flies and conditions.
% User specifies number of conditions, and then selects files (1 per fly)
% for each condition through GUI. Plots mean for each fly and mean across
% flies for each condition (diffe... |
74ef8e01ec834f3d00eeafea350c7efd42c4258642f1086befffb7731d79e2bc | MATLAB | 4,599 | 153 | function obj = subsasgn(obj,subs,dat)
% Overloaded subsasgn function for file_array objects.
% _______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
%
% $Id: subsasgn.m 8776 2013-11-14 09:04:48Z roboos $
if isempty(subs)
return;
end;
i... |
ff56886badf207cec55c98182a64887ce4cefe01a56dcba799527262b8322a4e | MATLAB | 4,602 | 127 | function [ds_unit_angles,ds_within_angles,unit_angles,within_angles] = get_vector_angles(outcomes,ds_events)
sunit_angles=[];
swithin_angles=[];
punit_angles=[];
pwithin_angles=[];
eunit_angles=[];
ewithin_angles=[];
peunit_angles=[];
pewithin_angles=[];
seunit_angles=[];
sewithin_angles=[];
ds_unit_angles=nan(5,1... |
f970f4a2e98c2d2476f7bb23e0f32f0df439b8e0c0633c37e9e9e37b22ae7250 | MATLAB | 4,603 | 109 | % mglTestMultipleSockets.m
%
% $Id: mglTestMultipleSockets.m
% usage: mglTestMultipleSockets(socketCount=3, socketDir='/tmp')
% by: Benjamin Heasly
% date: 08/24/2022
% copyright: (c) 2006 Justin Gardner, Jonas Larsson (GPL see mgl/COPYING)
% purpose: Test socket connectivity, read, write,... |
9fd37e7ceb0ec4d1b78981e34f9d70df6e42cb45766c8a65f2f589e77c75d636 | MATLAB | 4,606 | 108 | function [colors1, colors2] = getROISummaryColors(type)
switch type
case 0
colors1 = [...
38,60,142; ... % V1: Dark blue
73,115,184; ... % V2: Medium dark blue
142, 189, 228; ... % V3: Light blue
15,104,53; ... % hV4: Dark green
132,197, 81; ... %... |
fbaeae0efd1e2172641992f8da0949874703d60035fe94394d1f8fbe9a3e6d8b | MATLAB | 4,606 | 113 | %% msBatchRun2018
% Version 1.0 GE
% Updated version of the msBatchRun script originally proposed by Daniel B
% Aharoni to analyse miniscope 1p calcium imaging data on large batches of
% data.
% This version is build on top of the original package to maximize compatibility.
% It includes NormCorre for image registratio... |
5f5681d052b7b541e01acef621d8643c756252919ada72946a820c4ef5dd9430 | MATLAB | 4,607 | 87 | function [VarList, SetxBins, SetyBins,VarMargin1, VarMargin2] = getVarList(DATA_TYPE)
globals;
switch DATA_TYPE,
case 'OF',
%Set = 'all';
Set = 'free';
Set = 'o0';
Set = 'do21';
switch Set
% Var1 -> x-axis and Var2 -> y-axis
case 'all',
... |
85657eb9769296abfa1bf2b505009d8fc3a95525093dc4ad529e986f7a5832ae | MATLAB | 4,607 | 113 | clc;
%Recreate needed property constants defined in nilibddc_m.h
DDC_FILE_DATETIME = 'datetime';
%Check if the paths to 'nilibddc.dll' and 'nilibddc_m.h' have been
%selected. If not, prompt the user to browse to each of the files.
if exist('NI_TDM_DLL_Path','var')==0
[dllfile,dllfolder]=uigetfile('*dll','... |
c515c12144bfb3c02c3893a33d9407bf0bcbc15c5e4c5ed5388be0be741cebe7 | MATLAB | 4,609 | 156 | function [] = ExtDataFig05_pIP10_AveTimeCourse_OptStim_Song
% Code for plotting the time course of and the proportions of pulse and sine song in Extended Data Fig. 5g.
GT = 'TN1dsx';
%% parameters
nTrials = 3;
nStim = 6;
T = 1370; % T
DAQrate = 10000;
x1 = [0:1/DAQrate:190-1/DAQrate];
PreDurImg = 10*DAQrate; % 10 s... |
49d3baa1d96bea9a25c50265d0665747a4b5eb4c0f8c6b2d057bea32c7dc8fdb | MATLAB | 4,610 | 112 | %% Constant Parameters for QSM_Toolbox_v3.0
% Authors: Jiri van Bergen and Xu Li
% Updated by Xu Li, 2019-06-20
% Updated by Xu Li, 2021-06-23 for cluster version
% Updated by Xu Li, 2023-06-01 added wsl support for pc
% Updated by Xu Li, 2023-10-11 added default values for TemplateEcho and AvgBeforeBR
handles.... |
e62285a8c5cc9354a663a5b09247557132c69e755f2ec7bb61fa5cf8c07aaf00 | MATLAB | 4,610 | 129 | function [data4violins, mdl] = data_transform_DMM(filename)
%plots superplots of data and compares using mixed model
%ask for directory name for outputs
prompt= 'Enter output directory name ';
name = input(prompt,'s');
mkdir(name);
%get names of sheets in input xls
sheets = sheetnames(filename);
%iterate through l... |
9bdb9a7b57aca3549ba508bc18d98ae95d70f5682e81cab38d4c4dc2444f837d | MATLAB | 4,611 | 107 | function isPloted = plotTC(r,pop, Iattn, Delta_e,Delta_i, time, rawORenv, envWdo)
%UNTITLED plot time course of the dynamics
% parameters include r,v,g
% save or not save, raw data or envelope
% which population
% rawOrEnv: 0 for raw data, 1 for envelope, 2 for both
popName = {'1L23e','1L23i','1L4e','1L... |
d3290876d525a3c657779e79f58be3babc36e76a9d4476c63198bb09c5268c3f | MATLAB | 4,611 | 113 | function PLOT_linearityComparison(mag_all, mag_chunks, vid_aligned, mag_aligned, keep, c, sacStarts, sacStops)
figure();
www = tight_subplot(2,2,[.055 .025],[.04 .025],[.03 .03]);
%%
axes(www(1))
scatter(vid_aligned(keep), mag_aligned(keep), 4, c(keep), '.'); hold on
colormap hsv
plot(mag_all.yfit', mag_all.range', '... |
6d4ccceb93a537af214d17a26726990c30a7288650b817eb63ae078f4e2db370 | MATLAB | 4,615 | 127 | % data_ind = 4;
addpath(genpath('.'))
gcp;
%%
% name of the videos
list_data_names={'blood_vessel_10Hz','PFC4_15Hz','bma22_epm','CaMKII_120_TMT Exposure_5fps'};
list_ID_part = {'_part11', '_part12', '_part21', '_part22'};
data_name = list_data_names{data_ind};
list_Exp_ID = cellfun(@(x) [data_name,x], list_ID_part,'Un... |
fe04c90e9298163a5ced76f97c4ec3ac0025a8559111946fe71eab591d22a35f | MATLAB | 4,617 | 122 | % function figure2_from_xlsx(results, item_or_loc, id)
%
% Produces a figure from summary data in an Excel sheet
% This function generates a figure based on the summary data provided in
% the input struct 'results', which is loaded from an Excel file. The
% figure produced corresponds to figure 2 in a publication, show... |
df7718ce0dab3d5f97665e490ee586e0eafcc7e2e9cb1940764aab804f57e41f | MATLAB | 4,619 | 137 | function[data,h]=SONGetRealMarkerChannel(fid, chan, varargin)
% SONGETREALMARKERCHANNEL reads an RealMark channel from a SON file.
%
% [DATA {, HEADER}]=SONGETREALMARKERCHANNEL(FID, CHAN{, START{, STOP{, OPTIONS}}})
% FID is the matlab file handle, CHAN is the channel number (1=max)
%
% [DATA, HEADER]=SONGETREAL... |
c1f952e8da40bf114aa5c081742b8ebfa66b8ca0b264e52fbf2fbc74df07b64f | MATLAB | 4,620 | 113 | %
% Draw a color-coded line by using the edge of a patch with no facecolor
%
% SYNTAX
% ======
% h = cline(x, y [, z, cdata])
%
% INPUT
% =====
% x vector with x-values
% y vector with y-values
% z (opt.) vector with z-values
% cdata (opt.) vecto... |
3bcf3bb65549955da09f9528efe02cec43cac856066644ebbfdfc5ee7e21f106 | MATLAB | 4,621 | 149 | function mosaic = sift_mosaic(im1, im2)
% SIFT_MOSAIC Demonstrates matching two images using SIFT and RANSAC
%
% SIFT_MOSAIC demonstrates matching two images based on SIFT
% features and RANSAC and computing their mosaic.
%
% SIFT_MOSAIC by itself runs the algorithm on two standard test
% images. Use SIFT_MOSAI... |
f39fc92c6959bf1ca8ed487d45ed77e9180cd69d53e45b594f156fac3946f8b8 | MATLAB | 4,621 | 134 | % TREX provides X-Y data in cm, using a default value of 30 cm as the image
% width. Use this value to recalibrate the data to the correct size
% To ignore this conversion (if for example TREX is correct) assign 0 to TREX_meta_real_width
% After measuring the number of pixels on the ruler and calculating from that the... |
534ee2c3fd1022de4691ebfbf36ec7e704c11c8b4ec5f89530a8b202a53bc13d | MATLAB | 4,622 | 82 | function tuningA(var,uspikes,Fs)
% I prepared a script (example.m) that calls all the functions needed to generate a directional tuning and compute the von Mises fits, so that you won't have to call each function separately. All the functions needed are in the zip file attached.
%
% If you run the example.m script... |
42100428e2e99d3a49c8fd829f5c559301deba88bd4b6417911586df2a8607bd | MATLAB | 4,628 | 72 | % Get header of mri
% [ Yokogawa MEG Reader toolbox for MATLAB ]
%
% brief:
% This function retrieves header information of specified mri file (*.mri).
%
% usage:
% mri_header = getYkgwMriHdr(filepath)
%
% arguments:
% filepath : file path of *.mri file
%
% return values:
% mri_header ... |
bc90d14c7f50d2cab6cbca91d3063716a4c0f406b28d95e484828584e4b5527c | MATLAB | 4,628 | 148 | function toon_prfRun(baseDir, subjID, session, paramPath, imgPath, prfModel)
% toon_prfRun(baseDir, expt, session);
%
% Step 4 of the workflow for analyzing toonotopy
% Runs the prf model (CSS)
%
% Example input values
% baseDir '/oak/stanford/groups/kalanit/biac2/kgs/projects/'
% expt 'subj01'
% sessio... |
deb097b7bff1d2bbe151c69a6992e727e40e7b687741b2e3f1c96ea565c29ab6 | MATLAB | 4,629 | 148 | function toon_init(baseDir, expt, session, canonXflag,clip, runBase)
%
% toon_init(baseDir, expt, session, canonXflag,clip, runBase)
%
% Step 1 of the workflow for analyzing toonotopy
% Initializes the data for mrVista
%
% Default Input values
% baseDir '/biac2/kgs/projects/'
% expt 'spatiotemporal/experiments/si... |
4449b290a8a6bf8f068962d307e6b6b2b431da335b2a4ed99aaab2873484155f | MATLAB | 4,634 | 157 | % Marc Normandin, Muzzio Lab, Psychological & Brain Sciences, University of Iowa, 2024
function make_stabilitybfo90_percell_formatted_for_sigmastats_v2(analysisSettings, analysisResults, outputFolder)
BestAligned = analysisResults.BestAligned;
F = 'NormalPerCell90';
T = analysisResults.(F);
[SessionsToGroups] = load... |
187e924cd0b76ddecb8a311f07473376208f7b4ae6f2b68ed735c828e5739485 | MATLAB | 4,635 | 131 | function flag=SONImport(fid,varargin)
% SONIMPORT copies all channels into a MAT-file
%
% Note: Use ImportSMR in the sigTOOL package in preference to SONImport
% unless you want data stored in the same way as with previous versions of
% the SON library.
%
% SONIMPORT(FID, {OPTIONS});
% where:
% FID is ... |
52454b9cab06173d1212d928c1a52753de733127c6ca0e59a073e1722951b7a4 | MATLAB | 4,636 | 121 | function [Net_para, Node_para] = gretna_batch_networkanalysis_bin(Mat_path, File_filter, Thr1, Thr2, Delta, N_rand, Stype, Ttype)
%==========================================================================
% This function is used to calculate several global and nodal network
% metrics for both binary and weighted netw... |
9e74539e9e494977832368245caa379eb64707b116d48a975ccc4fad80d96683 | MATLAB | 4,640 | 117 | % analyzes a group of experiments and saves the properties
% they will be saved inside the first folder; not used in paper
%function LNPStats = CreateBehavioralMappingExperimentGroup()
%clear all;
%set up parameters
recalculateSpectra = true;
parameters.numProcessors = 15;
parameters.numProjection... |
f1a6788fc384fd617d5b7c0137cce4e46f516776bb1c0da1802f770e26bed654 | MATLAB | 4,641 | 127 | % calculate all the things
filePath = fileparts(matlab.desktop.editor.getActiveFilename);
temp = load('all_epochs.mat', 'balancedgrouped');
balancedepochs = temp.balancedgrouped;
num_of_raters = 7;
num_initial_cols = 8;
rater_comps = NaN(num_of_raters);
for n=1:num_of_raters
col = n+num_initial_cols;
for m=1:n... |
7baa0344773709bba62ef03c4c8a1f1323f47b779a60a36ca46d88fd248197e3 | MATLAB | 4,643 | 132 | function [f, params] = get3DSpatiotemporalpRFs(params)
% Description: Function that creates spatiotemporal pRF models
% to use as linear filters.
%
% INPUT:
% params : (struct) Params struct should have the following fields:
% tktktk
%
% OUTPUT:
% prfs : (double) matrix with [x-pixels by y-pixels (in ... |
479f484482f29c9098537c5970625b561e71c5d7a2636ae07333376a6b4796d6 | MATLAB | 4,645 | 165 | %% Calculate Blood Vessel Width Based on Full-Width at Half-Maximum method
%Input: Single 8-bit tif image
%TO USE: Draw straight line perpendicular to blood vessel
%User drawn lines saved to image
%Calculates vessel width based off user defined pixel_size
%Output: Saves vessel width to excel file
%Made by Chris... |
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