sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
1f5a6cd7c3ddc99a914b12777c7f759d1237f3da90f93a544a2aef83d87bf5d9 | MATLAB | 4,567 | 86 | function [similarity,similarity_shuffle,similarity_neighbor] = neuronal_similarity_longitudinal(calcium_data_1,calcium_time_1,...
calcium_data_2,calcium_time_2,long_reg,...
centroid_location_1, centroid_location_2,ca... |
fc0d2fcbb48f2d434c380942f2e0b7024a852f45e1ea043108970228bd44c684 | MATLAB | 4,577 | 115 | %--- Script generating figure 2 ---
%% Initializes everything
clear, close all
run StartupAnalysis
rng(1949)
%% Sets Figure parameters
% db1FigSize = [100 100 1600 900];
db1FigSize = [50 50 1200 600];
iFig = 0; hFIG = [];
chOutDir = 'C:\Users\perre\Cardin-Higley Lab Dropbox\Quentin Perrenoud\PerrenoudCardin_Fi... |
28c0d858f5af7f4605b13f4712145846e59c14f88f5ea7b4d664f2566438286d | MATLAB | 4,584 | 109 | %% This scripts runs the spin-test for the correlation between the age-effects on cortical thickness and MEG levels
% Based on the toolbox by Alexander-Bloch et al., 2018: https://doi.org/10.1016/j.neuroimage.2018.05.070
%
% Step 1:
% Load the statistical map for the age effects on cortical thickness (here t-stats for... |
8240f6efc63577b3e48e6f8e5a1445d6fc0528f96d922bb803bfb33abdfdcac5 | MATLAB | 4,606 | 137 | %This script can be used to analyze voltage clamp traces containing sEPSC.
% WRITTEN BY: Nina Doorn (11-07-2022)
%It will return a matrix with every row one of the cells/traces you
%analyzed, and the columns:
% -number of the run
% -average sEPSC amplitude
% -sEPSC frequency
% -The threshold used for event detection
%... |
f1462e60f7b266b80b64876901745efb8a601792aa5cd962f8339ffe91ec7cdd | MATLAB | 4,609 | 125 | %% Plot mean PSA of all trials
% The script was used to generate Figure 1C in manuscript
% "Brain rhythms control microglial response and cytokine expression via NFκB signaling"
% Plots are generated in a new folder named 'plots' in the parent directory
% Dependencies
% 1. 'Statistics and Machine Learning Too... |
4402ec24b16788df1ded5ae854124224928ac3e6f6690f556bf36a5d6a66376d | MATLAB | 4,627 | 180 | function [analysis params] = SDT_MLE_fit(nR_S1, nR_S2)
% [analysis params] = SDT_MLE_fit(nR_S1, nR_S2)
%
% Find a maximum-likelihood fit of the unequal variance signal detection
% theory model to the input data.
%
% INPUTS
%
% * nR_S1, nR_S2
% these are vectors containing the total number of responses in
... |
f3499bdcc18cc76efdbde0e9b61cf9c723063d7931531a4622c8b5b093709c2b | MATLAB | 4,637 | 114 | %% LaBGAS_create_single_trial_fmri_data_st_obj
%
% This script creates an fmri_data_st object from the single trial con
% images written in rootdir\secondlevel\model_x_yyy\data\sub-zz by
% LaBGAS_copy_single_trial_con_imgs_CANlab_folder_struct.m and adds a
% convenient metadata_table field containing
% 1. single trial ... |
99d68210fc6a9a2f5a43bd2ac3b350e37063d987c7558314aa3a7e5ec0145cdd | MATLAB | 4,638 | 116 | function FR_sim_Network(load_file, I0, w0, w_max, save_file, w1_range)
load(load_file, "P", "D", "M", "s", "Env_track", "final_weight", "phase", "N")
% load the weight matrix and necesarry inf
[tau, d_t, err, check_dynamic, plot_mean, activation_all, tracker, max_step] = FR_sim_setup();
... |
7d589293c01a5d83902a999e25f0b72b84093b44292718c3caa2670071865f5f | MATLAB | 4,649 | 104 | function [bestpmFits, EE] = applyNIModelling(obj, modelName, numRepeats, modelPar, initialGuess, jitter, freeParams)
%% applyNIModelling
% as if for now, this is a seperated code, but eventually this will be
% intergrated in applymodelling in the dataModelling object.
% Needs a urgency signal and reflectingbound i... |
3c53040d83187f21b880b25e7777f9229a5074f39abdf8f58524d5c0e43e84f8 | MATLAB | 4,661 | 151 | %% Study 1 EEG
%% Patient List
patientList = {'201','202','203','205','206','208','209','210','211','213','214','215','216','218','219','220','222','223','226','228','229','230','231','232','233','234','235','236','238','239','240','241','243','244','246','247'};
dataDir = 'C:\Users\\OWNER\\Dropbox\\Berkeley post... |
2396c2a4938a10181e45931abc70367e0d94144020202f4893c93c062f8fd584 | MATLAB | 4,670 | 138 | % Script modified from Reference:
% Christopher Fietkiewicz and Kenneth A. Loparo, �Analysis and Enhancements of a Prolific Macroscopic Model of Epilepsy,� Scientifica, vol. 2016, Article ID 3628247, 10 pages, 2016. doi:10.1155/2016/3628247
% Description: Original model used for Figure 2 in Fietkiewicz and Loparo 20... |
c607ebb80607fe0602e49c12ac100a3586dbf1bd2dfafa418a0046a6228da029 | MATLAB | 4,671 | 210 | function FS_DFF_STD_Image(DIR,varargin)
% FS_DFF_STD_Image.m
%run thorough directory and make STD and MAX images for every mat file in directory
% This Script is for 'unprocessed' videos
%
% Created: 2016/03/09
% By: WALIII
% Updated: 2016/03/10
% By: WALIII
%% Custom Paramaters
nparams=length(varargin);
... |
219672548b25863363de7427c2e4f153cc998fb31d8e8fc80d015e2fb99d21da | MATLAB | 4,672 | 126 | %Author: Tatjana Schmitt, 2019-2022
clearvars
path_to_matlab_file ='directory to whole tonotopy';
load(path_to_matlab_file)
%% set parameter
save_flag = true;
frequency_hub = 1; % select the frequency you want to extract/analyse (1,2,3,4,5 for 4,8,16,32,64 kHz respectively)
se = strel('disk', 1); ... |
ca28567f7870092e4d8187820a7660157905cd188ca43982d798a043251816e0 | MATLAB | 4,681 | 161 | %% MIRO main MATLAB script
% MIRO Multiscale Image Restoration by Optimally-sparse representation
%
% SYNOPSIS:
% [miro, Parameters, intr, fpn, im] = MIRO(im,PropertyName,PropertyValue)
%
% INPUTS:
% im
% Noisy image: variable name or file name (only .tif files). If left
% void, the program opens a di... |
bcda982df156a6728c25877385182e64832e2039496510198c4a48884f32c85f | MATLAB | 4,690 | 118 | %Author: Tatjana Schmitt, 2019-2022
function [subfield_borders_rotated, BF_borders_broad, coordinates_BF_map, coordinates_BF_map_rot_norm,...
subfield_idx, tonotopy_axes_rotated, axes_idx] = roi_creation(BF, complete_boundaries_map, stats, rotation_angle)
disp('Calculating rotated coordinates for visualisation .... |
5ed3960f36296f80cad2ed4b159405b609351681ef200b67b0a6e2e57bc6c4cd | MATLAB | 4,702 | 246 | function fig_num=fb_visualize_rois(ROI,varargin)
%
%
%
%
%
%
nparams=length(varargin);
roi_map=[1 0 1];
bg_map='gray';
label_fontsize=9;
label_color=[1 1 0];
clims=[0 1];
label=0;
fig_num=[];
filled=0;
weights=[];
weights_map='winter';
weights_range=[ -inf inf ];
ref_image=[];
ncolors=[];
weights_correction=0;
wei... |
478ab0f549b4b7d02b43703ac3e8930a6618d5beae79d0c90f20c08701eb213f | MATLAB | 4,705 | 174 | function [Y,ndx,dbg] = natsortrows(X,rgx,varargin)
% Natural-order / alphanumeric sort the rows of a cell array or string array.
%
% (c) 2014-2021 Stephen Cobeldick
%
% Sort text by character code and by number value.
% SORTROWS <col> input is supported, to select columns to sort by.
%
%%% Example:
% >> X = {'x2','10';... |
50636e1f3e2dfcdafab63dc7b88db0fd9a483d281593a2019c43dca33ed41139 | MATLAB | 4,732 | 196 | function fb_detrend_and_align(ROIS,varargin)
%detrends and aligns data aligned to silence
%
%
%
%
%
nparams=length(varargin);
fs=22;
per=12;
cut=25;
out_dir='extraction_silence';
save_dir='detrended_aligned';
disp_minfs=1;
disp_maxfs=9e3;
dat_dir='trace_data';
padding=[0];
fs=24.414e3;
colors='hot';
minlength=.2;
if... |
855a36b965c105b60ef0b1d8fbe6496a0ae3ab9c6b929b34bc4479c5b332eb05 | MATLAB | 4,753 | 129 | function [valid_flag,err,is_formula]=check_if_legal(comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given String_comp property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(COMP,PROP,VAL,DEF_ARR,
% VAR_ARR) checks that VAL is a legal value for the Sig_comp property-PROP.
% VAL will be le... |
279bec30eae8b81aa94fe0eb5be34752e3c22733141611e9ec3e190ffc91bc03 | MATLAB | 4,763 | 135 | function linfields = DFSwb_HPexpt_placefield2_savefields_crossvalid_fun(animalprefix,ep,exclude_trajtime, savedir)
%---------------------------------------------------------------%
% This is the function for calculating linearized place fields %
% for cross-validation %
% Pre... |
c1e93102a6fcfd9e9aea73e6544941f21ae74c8dd0c036cd9c940586b1955144 | MATLAB | 4,763 | 168 | function [phi_G, Cov_E_p, A_p] = phi_G_Gauss_LBFGS( Cov_X, Cov_E, A, Z )
%------------------------------------------------------------------------------------------
%PURPOSE: calculate integrated information "phi_G" based on information geometry
% with a combination of an interative method and a quasi-Newton (LBFGS) ... |
73d766d7386d06575c366bd2efec3bbf1ecf20099670d68df6d1fd1dc3ebf460 | MATLAB | 4,776 | 142 | %%
% Default parameter values for Kumar et al., 2023
%
% Takes in the firing rate of the background, whether pre- (0) or post- (1)
% damage, and the number of populations (3: PN, PV, and SOM; 4: same + VIP)
%%
function [params] = A1_params(r_bg,damaged,Npop)
if Npop ~= 3 && Npop ~=4
error('Code only tested for 3 an... |
4d07c8bdfd9b4edcbdae43642871742180e8b6010f81a178829df1957feb5ddd | MATLAB | 4,778 | 109 | %---------------------------------------------------------------%
% This is the main script for gathering behavioral performance %
% for all the animals -- Wenbo Tang (Jan 05, 2023) %
%---------------------------------------------------------------%
clc
clear all
close all
%%
% set directory
denovo_dir = ... |
76b59cc980f6407c5dc624c70f66283f1d16671e29e04adfc2e84476e017db83 | MATLAB | 4,780 | 129 | %--- Script generating figure 3 ---
%% Initializes everything
clear, close all
run StartupAnalysis
rng(1949)
%% Sets Figure parameters
% db1FigSize = [100 100 1600 900];
db1FigSize = [50 50 1200 600];
iFig = 0; hFIG = [];
chOutDir = 'C:\Users\perre\Cardin-Higley Lab Dropbox\Quentin Perrenoud\PerrenoudCardin_Fi... |
95a72c6653952110ccea1e597fcc062834becc222bc29cb443a22ab6eee6c11a | MATLAB | 4,785 | 136 | function FR_sim_Ring(load_file, I0, w0, w_max, save_file, include_noise, sigma, w1_range)
load(load_file, "P", "D", "M", "s", "phase", "N", "n")
% setup
[tau, d_t, err, check_dynamic, plot_mean, activation_all, tracker, max_step] = FR_sim_setup();
% set simulation range
if nargin < 7... |
c05511e50ba9a77d7c104a7b19a5b2b88ef48d63bb352b98a42faf1723233def | MATLAB | 4,797 | 172 | function varargout=shadedErrorBar(x,y,errBar,lineProps,transparent)
% function H=shadedErrorBar(x,y,errBar,lineProps,transparent)
%
% Purpose
% Makes a 2-d line plot with a pretty shaded error bar made
% using patch. Error bar color is chosen automatically.
%
% Inputs
% x - vector of x values [optional, can be... |
620e97c6db3b09e71f51fdbaa0165076aab57d6820784bb92c46d5d68367ecc4 | MATLAB | 4,811 | 248 | function [LOCS,VALS]=fb_compute_peak(CA_DATA,varargin)
% Computes the peaks for a calcium trace or series of calcium traces
%
%
%
% algorithm: schmitt trigger, double exponential fit (for now)
%
%
thresh_hi=1.2;
thresh_lo=-1;
thresh_t=.05;
thresh_int=8;
thresh_dist=.3;
fs=22;
method='p'; % f-min, simulated annealing... |
8026cb1c9b505668ba8c27b96bf99bf2fb9883274645c541b1e992c5a42f2dbe | MATLAB | 4,832 | 179 | function [rsq_simult,rsq_adapted] = visIDX_scatterRESPocc(IDX,flag_SaveFigs)
%% Goal
% 2 plots; dII index vs occ.
% plot 1 - simult
% plot 2 - adapted
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
uctLength = length(IDX.allV1);
% B. pull out all laminar matrices 3x(6,450,el#... |
15341ea9a30d6766cffcf7f71c5f44b525d10132e3bbcac0a841b97804488079 | MATLAB | 4,863 | 119 | classdef Coll_tiff_handler < handle
%collaged_tiff operates a multipaged .tif file where each directory is
%a collage of NxN images or rats.
properties
num_rects_horz % Number of rects in a horizontal line in collage
led_area %
rect_len % Length of a single rect
led_l... |
51d62e55de184a9987dd974e9de1300c789714950816294e09cf3fccd477609e | MATLAB | 4,886 | 118 | function [ directionalFilter,scalingFilter,waveletFilter,scalingFilter2 ] = SLcheckFilterSizes(rows,cols,shearLevels,directionalFilter,scalingFilter,waveletFilter,scalingFilter2)
%SLcheckFilterSizes
%% configuration 1
filterSetup{1}.directionalFilter = directionalFilter;
filterSetup{1}.scalingFilter = scalingFilter;
f... |
085415915ee228bf0c04ccbed8a93f2fd1042b02f6cd863e1e0987ed640d388e | MATLAB | 4,902 | 147 | function [SDF_fulltm,SUA_fulltm,condition,CondTrialNum] =...
continuousDatMonocCompare(STIM,ContinuousDat)
%% BMC -- 10-29-20
sdf = ContinuousDat.SDF; % timepoints x trials
sua = ContinuousDat.SUA;
warning('hardcoding DE and PS')
DE = 2;
NDE = 3;
PS = 90;
NS = 180;
% 1 - simult
% 1. Monoc 1
% 2. ... |
84d67d5d41088fc0cf1858f622b6f5172b6f8e688a3592ce3bf5e9f1a3d00f2b | MATLAB | 4,925 | 149 | %%
% Simulation results for the non-spatial two populations model for networks
% with and without astrocyte ensheathment of exc synapses
%%
%% Figure 5A and B: correlation across neurons for a specific example
% Load the data
prob_ensheathed_I = 0.0;
prob_ensheathed_E = 0.8;
ensh_strength = 0.5;
num_ffwd_inputs=2;
nu... |
d7318e8f833729128e5a36f226cde28780bf2e39f1493a3c785e1c6d742d1591 | MATLAB | 4,940 | 132 | function [valid_flag,err,is_formula]=check_if_legal(comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given Sig_comp property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(COMP,PROP,VAL,DEF_ARR,
% VAR_ARR) checks that VAL is a legal value for the Sig_comp property-PROP.
% VAL will be legal... |
73c22d77689cc2130cac2c25afa589f733ee11f9b0b7c8e3e95b878b768bcb82 | MATLAB | 4,949 | 133 | function AY = mm_fun(A,Y,chunk_size,run_paralel,FOV)
if ~exist('run_paralel', 'var') || isempty(run_paralel); run_paralel = true; end
if ~exist('chunk_size', 'var') || isempty(chunk_size); chunk_size = 2e4; end
if ~exist('FOV', 'var') || isempty(FOV); FOV = [512,512]; end
% multiply A*Y or A'*Y or Y*A or Y*C' depending... |
d0264431b21fc25d133381247e1076a5f37dde511c1eb7d423e6604baba7c654 | MATLAB | 4,955 | 177 | function value = load(str, varargin)
%LOAD Load matlab value from a JSON string.
%
% value = json.load(str)
% value = json.dump(..., optionName, optionValue, ...)
%
% The function parses a JSON string into a matlab value. By default,
% numeric literals are converted to double, string is converted to a char
% array,... |
4cdd0eb0dc2f645c308cca3d4f75fe673b8202858a309ffe21fab74389e3dd1c | MATLAB | 4,959 | 157 | %% Study 3 EEG
%% Patient List
patientList = {'102', '103', '104','105','106','109','110','111','112','113','114','115','116','117','119','120','121','122','124','125','126','127','128','129','130','131','132','133','134','135','136','138','139','140','141'};
dataDir = 'C:\Users\\OWNER\\Dropbox\\Berkeley postdo... |
8931797603b933d91132e2cf2f929dc69247ea1e79bccc881bd9654c9be7ecb3 | MATLAB | 4,979 | 116 | classdef MaskApi
% Interface for manipulating masks stored in RLE format.
%
% RLE is a simple yet efficient format for storing binary masks. RLE
% first divides a vector (or vectorized image) into a series of piecewise
% constant regions and then for each piece simply stores the length of
% that piece. For ... |
611d6b4e1f37f311779a1bf76217efbaa0ab8fca8fe526b06b901ee677c2fc7b | MATLAB | 4,997 | 113 | %create objects from masks and export to fcs for ez_segmenter
function create_objects(point_index, pipeline_data)
%% Pre-processing steps to mask data, convert into fcs / csv usable format, and create attributes to be saved later
% get point from provided index
point_names = pipeline_data.points.getNames(... |
2a92cb54e16955605f543f5068d3dd6f753f5e6af978cd31d311d7396bc64790 | MATLAB | 5,001 | 170 | % Experimental data for simulation
% Fig. 3
%
% go to 'SVM.m' or 'PVD_and_MLE.m' to simulate and decode data
%% Data of one monkey using Circular Gaussian fitting
clear; clc; close all;
load('neural.mat');
%% Reshape data of each monkey
for m = 1:2
Data = [];
if m == 1
monkey = 'A';
mRe... |
f856255c77ecfda059a0217354262823fb891782ac086c8ceafb03466c75b2f5 | MATLAB | 5,016 | 155 | %%
% Reproduces the modeling panels in Fig 3 for Kumar et al., 2023
%
% Uses compressed spiking datasets for the 3-population spiking simulations
% (panel b, c, and d)
% Reruns the code for the mean field theory for panel c (i.e., simulations
% vs theory firing rates)
% Uses the compressed datasets corresponding to t... |
e7cea457454890cf149f0d06538334168100e0409f98cbd52c19b674fd218907 | MATLAB | 5,025 | 146 | %Author: Tatjana Schmitt, 2019-2022
function [idx_vectors, radial_vectors, radial_vectors_BF, radial_vectors_mean_BF, ...
radial_vectors_mean_BF_smoothed] = vector_analysis(BF, stats, varargin)
% creates vectors with specific step size and plots BFs along these
% vectors, calculates mean BFs and smoothes data p... |
38c4fffd3bbfcdb2171e67013c5ad6987628734afbf43632e69abe6829e70dfa | MATLAB | 5,030 | 146 | function bmcSuperBarAdaptation(IDX)
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
uctLength = length(IDX.allV1);
% B. pull out all laminar matrices 3x(6,450,el#)
%preallocate
% RESPout = nan(size(IDX.allV1(1).RESPout,1),size(IDX.allV1(1).RESPout,2),uctLength);
% dII = nan(size... |
5660f03fe534814a8b677b5305c90ee0ec8e423cfdfbd4a2f866b2e10c072769 | MATLAB | 5,038 | 147 | function bmcSuperBarAdaptation_ICPSDE(IDX)
%% Initial variables
conditNameForCC = IDX.allV1(1).condition.Properties.RowNames;
uctLength = length(IDX.allV1);
% B. pull out all laminar matrices 3x(6,450,el#)
%preallocate
% RESPout = nan(size(IDX.allV1(1).RESPout,1),size(IDX.allV1(1).RESPout,2),uctLength);
% dII = n... |
1a5560fb5bb9757798b860bb07475bd5e085247db5d731e2c6ca2409441460dd | MATLAB | 5,043 | 154 |
function prep_for_fig05B(type_of_method,count_or_relative,...
isubplot,legend_flag)
marker_size = 2;
plot_linewith = 1;
% line_color = [0.5 0.5 0.5];
c = lines(7);
color_match = c(2,:);
color_nonmatch = 'k';
color_segment_exist = [0.5 0.5 0.5];
color_segment_nonexist = [.85 .85 .85];
%%%%%%%%%%%%%%%%%%%%%%%%%%... |
5c02ee4a20f26b88dced5824f866043ead34fdf71e669ca143c9c3bcca87ad6b | MATLAB | 5,049 | 117 | % Neuromag layout of magnetometer
% This function returns the positions of 102 MEG channels
% Copyright by Hong Gi Yeom
% You can use this code for academic purposes
function [position]=neuromag_layout_mag()
p=[
3 -67.416206 35.916687 10.000000 10.000000
6 -53.602242 40.989067 10.000000 10.000000
9 -62.018288 21.176... |
bb9e4988fb63147ec1626d4cbb2c3d7cbcc1ec6e5b6d21e0fbe808b3bb399d5b | MATLAB | 5,051 | 154 | %REAL2RGB Converts a real-valued matrix into a truecolor image
%
% Examples:
% B = real2rgb(A, cmap);
% B = real2rgb(A, cmap, lims);
% [B lims map] = real2rgb(...);
%
% This function converts a real-valued matrix into a truecolor image (i.e.
% double array with values between 0 and 1) using the colormap ... |
0bbe97076e8332fb320b285d2c117ba3ab44b189d12b30196a1e5dafe5e9efc7 | MATLAB | 5,053 | 154 | %REAL2RGB Converts a real-valued matrix into a truecolor image
%
% Examples:
% B = real2rgb(A, cmap);
% B = real2rgb(A, cmap, lims);
% [B lims map] = real2rgb(...);
%
% This function converts a real-valued matrix into a truecolor image (i.e.
% double array with values between 0 and 1) using the colormap ... |
3685913fdb90d0e994780493cbf322a88cfa01f2dccf56641705131f7258e5b3 | MATLAB | 5,060 | 151 | function [SDF_fulltm,SUA_fulltm,condition,CondTrialNum] = continuousDatConditionSelect(tune,STIM,ContinuousDat)
%% BMC -- 10-2-2020
DE = tune.DE;
NDE = tune.NDE;
PS = tune.PS;
NS = tune.NPS;
sdf = ContinuousDat.SDF; % timepoints x trials
sua = ContinuousDat.SUA;
% 1 - simult
% 1. Monocular DE PS
% 2. Cong Simu... |
dceb232f48010be011b56d5e09c8faefcb79c969122f6308e705344642065bfa | MATLAB | 5,071 | 118 | function [area_num, area_type, rat_angs, rat_rs] = rat_locs_to_Maciek_MDP_area(rat_locs, ar_ports)
% Function rat_locs_to_Maciek_MDP_area calculates the MDP spatial state of the rat out of its
% cartesian location.
%
% ASSUMPTION:
% # All input value are given in pixels as produced by the came... |
a8f01e8b287cc6b3e35cb30d98c97f599d6dcadcdca9226ac6c1b4dd0410e5ec | MATLAB | 5,081 | 141 | function plotScatterPlots_Fig01(Fig01)
%INPUTS:
%SUBSCRIPTS:
%% Constants
plotOrder=[3,4,5,6,2,1];
%% Avg whisker evoked response Population
frameRate=Fig01.constants.dal_fr;
leadTime=5;
plotTime=((1:size(Fig01.Whisk_Evoked.Population_dHbT,1))/frameRate)-leadTime;
figure(11);
subplot(2,3,1); hold on
for... |
1be5cac7848b9958d3328ba4aebdfaa3a136a1e099a62007c64390e2c91c1eda | MATLAB | 5,084 | 121 | %%% Script to compute the output measures of the Computational Model Drave article of the simulated.
% It takes all data files in a folder that are .mat format and containing electrode numbers (first column)
% and spiketimes (second column). It detects network bursts based on spike
% rate, exactly the same as for exp... |
09ddcc6f49fd41a06fea901610723fb832afff2731e4a1f27efbbc8c14416f7d | MATLAB | 5,089 | 170 | %%%%create graph within school
tbl = readtable('37070-0001-Data.csv');
var = tbl.Properties.VariableNames';
SCHID = table2array(tbl(:,1));
UsID = unique(SCHID);
UID = table2array(tbl(:,2));
ID = str2double(table2array(tbl(:,5)));
%spend time with: ST1-ST10
ST = table2array(tbl(:,66:75));
ST(ST==-99|ST==-97... |
3a512dc290bd1aed61be2cd456d42bf9dda3b92395d3ca07a73dbfc7d374e11f | MATLAB | 5,096 | 145 | % raster_CompareUnits
% adapted from twoUnit_TestSortConfigs.m
%BMC - 10/8/2020
%The purpose of this code is to plot a condition-specific 2xN subplot
%where N is the number of units in the SORTDIR,
% i.e. monoc PS compared across all sorted units as visualized by a stacked
% SDF and raster in each column. Each column... |
19839f9862ff0b907a68a97692d906e38bf46c26eaa60ccb3b8faf44f1459167 | MATLAB | 5,100 | 180 | function check_mdp_sound_timing(mdp_table, sounds_table, stats, ...
experimenter, fig)
% JN 2020-04-30
% refactor the code
% JN 2020-05-24
% The strig column is not really suited for the mdp sound
% timing checks because time passes between strig is taken and the
% actual playing of sounds. start_t versus start_t ... |
d4ed62f5cbc985fcf5a63790d222647c0164b300d479eb56953ab784de4382fe | MATLAB | 5,104 | 140 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <scrubData: GLM based nuisance signal regression >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as published by
% the Free Software... |
ff41eb0cf421bf160f0c66d106efae303979e9f9eb8b1bbd6966739d85751896 | MATLAB | 5,104 | 130 | function GLM_ndLevel()
%parametric modulator at first level
dbstop if error
%does t-test and full_factorial
do_ttest = 1;
removesub = 0;
%% define path
cd ~
home = pwd;
homedir = [home '/OBIWAN'];
task = 'hedonicreactivity';
mdldir = fullfile (homedir, '/DERIVATIVES/GLM/SPM', task);% mdl directory (timing and o... |
8662969fec8065e1b00f579b001fb3160f5e71c0fd20d813f270b01b2372c8e7 | MATLAB | 5,106 | 127 | function varargout = cameras_GUI(varargin)
% CAMERAS_GUI MATLAB code for cameras_GUI.fig
% CAMERAS_GUI, by itself, creates a new CAMERAS_GUI or raises the existing
% singleton*.
%
% H = CAMERAS_GUI returns the handle to a new CAMERAS_GUI or the handle to
% the existing singleton*.
%
% CAMERAS_G... |
422f372b87b01d57d63a0cb1b844c374bf2ab24ab04031c32a4dba8edb8fd0ad | MATLAB | 5,107 | 115 | function [valid_flag,err,is_formula]=check_if_legal(sig,comp,prop,val,def_arr,var_arr)
% CHECK_IF_LEGAL checks the legacy of the given Signal component property.
% [VALID_FLAG,ERR,IS_FORMULA]=CHECK_IF_LEGAL(SIG,COMP,PROP,VAL,DEF_ARR,VAR_ARR)
% checks that VAL is a legal value as the Signal component-object proper... |
6b135ed92723c1613f478ec883ddc49e359baee635836f99d5a0dd2882aa85b1 | MATLAB | 5,113 | 154 | % HEADER:
% This script preprocesses the real data. It removes line noise in human
% data, segments all data into 5sec (can be set differently below)
% segments, calculates chosen features and allows visual labeling via prompt
% input.
%
%
% YOU DO NOT NEED TO RUN THIS SCRIPT IN ODER TO TRY OUT THE CLASSIFICA... |
e96bcd363e93414e8832a7f34b2f9f64e28b4ea9bc37dad7fbc56dc07f5c9baf | MATLAB | 5,140 | 155 | clear
clc
close all
%% Constant decleration and loading
constants
options = odeset('RelTol',1e-4,'AbsTol',1e-4);
%% Choice of stimulation parameters
start_stim = 0; % [s] When to start the current stimulation
end_stim = 0; % [s] When to end it
f_stim = 1; % [Hz] At what frequency do you want th... |
0f2d6a1cc95f8722173bef4bf76532e8d73c6df0a5f5a8430cbb275e73c238a9 | MATLAB | 5,164 | 164 | %%
% Reproduces the modeling panels in Kumar et al., 2023
%
% Uses compressed spiking datasets for the 4-population spiking simulations
% (panel b and c)
% Reruns the code for the mean field theory for panel c (i.e., simulations
% vs theory firing rates)
% Uses the compressed datasets corresponding to the parameter s... |
261959afa3956730bc55d5e52a2ad4d1fdbd2ba1f372e91c3043214b8f3bafef | MATLAB | 5,166 | 158 | function oimg = loadtiff(path)
%% loadtiff('yourfile.tiff')
% Copyright (c) 2012, YoonOh Tak
% All rights reserved.
%
% Redistribution and use in source and binary forms, with or without
% modification, are permitted provided that the following conditions are
% met:
%
% * Redistributions of source code must re... |
d9ae6858f3ffb66faee3aa537aa1859848e7d1c580f231bb7d58c75be6c2b559 | MATLAB | 5,167 | 137 | %Author: Tatjana Schmitt, 2019-2022
function frequency_response_area(root_path, red_cell)
%% set parameters
save_flag = true;
%% get file
temp_filepath_SPLanalysis = [root_path, '\**\Tono_analysis_ANOVA*'];
SPL_file = dir(temp_filepath_SPLanalysis);
SPL_path = SPL_file.folder;
SPL_name = SPL_file.name;
load... |
7e31ca82f962fc685a44d7dbd1c834f397bf474340431e72e7e7aff65b9e3c6c | MATLAB | 5,187 | 139 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <convHRF: convolved an input signal with a double-gamma hemodynamic response function (HRF) >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public Licens... |
af1492349f7bab0568efd8937fef29b2b109c045f9798a1bf07b98a0b70f035e | MATLAB | 5,208 | 150 | function seg = local_AC_UM(Img,mask_init,rad,alpha,num_it,epsilon)
% This function aims to implement Shawn Lankton's local active contour. And
% the energy model is the UM model as defined in eq.(11)-(14).
% The local variables are calculated by filtering operation instead of
% iterating inspired by Chunming Li's I... |
350a2262d065bb63f8dc8e279885d3fb90d48a046607194674660bff525572d0 | MATLAB | 5,225 | 73 | function SUBJECT = ASLOutlierRemoval(SUBJECT, prefix, method)
% ClinicalASL toolbox 2023, JCWSiero
tic
outputmap = [SUBJECT.ASLdir prefix '_BASIL_perDYNAMIC/'];
if ~exist(outputmap,'dir')
mkdir(outputmap)
end
DIMS = size(SUBJECT.(prefix).ASL_label1label2_allPLD);
if ~exist([outputmap 'DYNAMIC_1'],'dir')... |
a9e5fbb36c96f181dc794dd081905480c13fe237aa57ba6ea55eb2f88a44ab27 | MATLAB | 5,245 | 160 | %%
% Simulation results for the non-spatial one population model for networks
% with and without astrocyte ensheathment
%
% Creates S1 Fig for realization 2 from Fig 3C
%%
% Load the data
load('./CompressedData/NonspatialOnePop/balancedCompressed.mat')
load('./CompressedData/NonspatialOnePop/brokenEx2Compressed.mat')
... |
61d335bb9b5a52f64653148ad8e6cdacd51ea97f5450a2424c34968518791a1e | MATLAB | 5,250 | 179 | function [lc,cmap,ic] = linecolors(nc,cmap)
% linecolors extract ordered line colors from colormap
%
% Inputs:
% nc: number of colors to be extraced
% cmap: colormap ([ncol 3] or string)
% custom maps: 'shortjet','blue','darkgray'
%
% [lc,cmap,ic] = linecolors(nc,cmap)
if nargin<2 || isempty(cmap)
... |
582381789870666401965dbc72f3767da8399a8524eb7cd12326ff7999ae4362 | MATLAB | 5,256 | 132 | function GLM_ndLevel()
%parametric modulator at first level
dbstop if error
%does t-test and full_factorial
do_ttest = 1;
removesub = 0;
%% define path
cd ~
home = pwd;
homedir = [home '/OBIWAN'];
task = 'hedonicreactivity';
mdldir = fullfile (homedir, '/DERIVATIVES/GLM/SPM', task);% mdl directory (timing and o... |
129e4eb94657b4eaf274d15d2e357af0330d5eb75eec5ab0b3e5efc669dc8ba5 | MATLAB | 5,280 | 201 | function [ subject ] = cs_nmri_qcplot_power_mag(subject, data, params, title_txt)
%[ subject ] = nmri_qcplot_power_sensor(subject, data, params, title_txt)
%
% Generates a QC plot for power at sensor space
%
%
% subject = subject structure, see nmri_read_subject
% could be a struct or .m file or .m... |
ac36984f88fa2f43ee35dd8164706632883b3dcfa05d1e54a0d3a6adb1e5fec3 | MATLAB | 5,291 | 133 | function [phase, Env_track, final_weight, weight_before, weight_mean, weight_var] = Sim_CA3RecNetowrk(n_ca3_per_track, n, M, s, P, D, plot_figure, seed, use_gpu)
%{
We use Sim_CA3RecNetwork to simulate the weight matrix of N = n_ca3_per_track * M CA3 cells
over n distinct environments, which mimic the animal explor... |
6eda1862f545be2ae62c8f25422333e0df1c009bf0ad0098da7e7f11bc0fe7be | MATLAB | 5,317 | 163 | % Main frame acquisition loop - timings
function acquisition_loop_new()
imaqreset
cam = videoinput('tisimaq_r2013',2,'Y800 (1280x960)');
src = getselectedsource(cam);
% frame = getsnapshot(cam);
fileID = fopen('locations.txt','w');
fprintf(fileID, '%s\t %s:%s\r\n', 'Frame_ID', 'X', 'Y');... |
686fcbb60bb2e814676a8afc652d0ff2343e0e382d12f6c841e3663f5125b2ed | MATLAB | 5,319 | 127 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <fALFF: calculates (fractional) amplitude of low frequency fluctuations ((f)ALFF) >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as ... |
0c1843de5f2090fe14b88265a3931f2b418bb403ec8d728a42dbfdcd7d2401b7 | MATLAB | 5,323 | 153 | function seg = local_AC_MS(Img,mask_init,rad,alpha,num_it,epsilon)
% This function aims to implement Shawn Lankton's local active contour. And
% the energy model is the MS model as defined in eq.(15)-(19).
% The local variables are calculated by filtering operation instead of
% iterating inspired by Chunming Li's I... |
edbccde6e08b0a917ff9f233e207c6f234f2a394cfec7b055d73e6bcc4de3d30 | MATLAB | 5,323 | 158 | function [ outMat,minMatIdx ] = hammDist(truncatedPep, fileName, hammdist)
% % Written by Leah V. Sibener 20141001
% % Edited by Timothy F. Miles 20190114
% This function will output a nx3 matrix of paired peptides and their reverse
% hamming distance. In this version of the program the hamming distance is
% co... |
2b0033b74567a62d074d37042f6e409902bd5cafe017cce3740487af5c291920 | MATLAB | 5,324 | 82 | % Set options used in various core scripts
% --------------------------------------------------------------------
%
% You can change these values on your local computer, but do not commit the
% changed version to the repository.
% prep_2_load_image_data_and_save options & prep_3_calc_univariate_contrast_maps_and_save
... |
98d5964092205b5c966e63026f8b0694b1a39847ad4054b06b249899c56a1f89 | MATLAB | 5,333 | 135 | % Function used to place features with their respective dendrites and
% create an over neurodegeneration feature table.
% Updated: 08-30-2022
function [blebs1data,blebs2data,blebs3data,blebs4data,blebsNoneData] = ...
blebAnalysis(n1,n2,n3,n4,imFeatures,sFactor,totBreakProp,dLength,imOrigBig,dendIntensity)
% Comb... |
6e5c97bd7d6b16797741aee68f7a30a9dbeacb133afdf2dd9bd2c287b7b6aa71 | MATLAB | 5,350 | 137 | function out = set(out,varargin)
% SET Set Output_manager properties and return the updated object
% Property names are:
% Plot_falgs, Plot_handles.
property_argin = varargin;
while length(property_argin) >= 2,
prop = property_argin{1};
if ~isa(prop,'char')
treat_error(['The property input is not a val... |
8287df0b42953aafc287f3ac83452cfabf8ebde9d89484ef478115f36a230349 | MATLAB | 5,359 | 135 | %---------------------------------------------------------------%
% This is the script for calculating path-equivalent %
% coefficients for all cells -- Wenbo Tang (Jan 07, 2023) %
%---------------------------------------------------------------%
clc
clear all;
close all;
%%
animalprefix_list = {'AM2',... |
df212dc18c9a8148a593af52c66346a54ff1ccbfcea13ba64ab9d251b79920aa | MATLAB | 5,366 | 137 | %%
% This code runs a demo for the DiRT simulations used in Handy and
% Borisyuk, 2023 (corresponding to Fig 1)
% This code interfaces with mex for speed
% Also makes use of parfor across trials (see inner loop)
% Runs over specified values of phi (i.e., fraction of the cleft blocked
% by protruding astro... |
13930fde752a01a8f7d092a7e2d6d02a86736a11a16fbaacac2ba8ea980e91a3 | MATLAB | 5,404 | 117 | function [dataTable,ROIsToProcess,ROIlogicals,mapToNewROI,mapToRSGroup] = loadGoodData(varargin)
o = ecogutils.postHocOptionsParser(varargin{:});
dataTable = loadECoG.loadMergedDataFiles(o);
ROI_table = ecogutils.loadROItable();
mapToNewROI = containers.Map(ROI_table.oldROI,ROI_table.newROI);
mapToRSGroup = ... |
46c3b724494186f9529baf7cba1ce0778fa4ba541420cb46dec54dcacd6fa46f | MATLAB | 5,404 | 263 | % Gridfit test script
% This script file is designed to be used in cell mode
% from the matlab editor, or best of all, use the publish
% to HTML feature from the matlab editor. Older versions
% of matlab can copy and paste entire blocks of code into
% the Matlab command window.
%% Topographic data
load bluff_data;
x=... |
dab4b8a5b8772d25c99a130acf580c5ab71bb87f49792a9450042bc1e42963a8 | MATLAB | 5,412 | 174 | function [FR_evn, FR_tracker, FR, n_step] = FR_simulation(n_ca3_per_track, M, s, map, phase, synaptic_weight, eta, eta_IC, I0, d_t, tau, err, ...
check_dynamic, plot_mean, FR_init, max_step, activation_all, tracker)
%{
Simulation for the firing rate network.
Parameters:
n_ca3_per_track: number of CA3 populat... |
17ef4152cda688b375bc90643a7b13c6677a4c48d107c388629bdecb8373a326 | MATLAB | 5,422 | 152 | clear all
clc
close all
%% Define parameters
dir = 'dir\';
Input_name={'group1' 'group2'};
Save_name={'subBG_'};
%Save_cell_area={'cell_area'};
frame_number=120;
pixel_number=400;
ext = '.txt';
ext_xls = '.xls';
ext_fig = '.fig';
ext_jpg = '.jpg';
%% Main code
for a=1:1:2
for j=1:1:6
%% input data... |
91de4fc7dbef9bf5891b478564964edb1d63ea36e719460fe1f69672cf25d8e6 | MATLAB | 5,449 | 113 | function file_format_data=get_file_format_vals(signal,signal_table,line_num,chan_num,line_trial_num,...
num_lines,line_trials,line_max_trials)
% GET_FILE_FORMAT_VALS returns a string that consist of a number of MATLAB
% commands. These are initializa... |
f3eb31b2efde1235246c977fdaf7451b2c7f791565cae23592c2c235282a67c5 | MATLAB | 5,471 | 128 | function [shearlets, RMS, dualFrameWeights] = SLgetShearlets2D(preparedFilters,shearletIdxs)
%SLgetShearlets2D Compute 2D shearlets in the frequency domain.
%
%Usage:
%
% [shearlets, RMS, dualFrameWeights] = SLgetShearlets2D(preparedFilters)
% [shearlets, RMS, dualFrameWeights] = SLgetShearlets2D(preparedFilters, shea... |
0ce1369c25002e132387f599e57098ddae256cac0d6d961e39514548a2b0948c | MATLAB | 5,476 | 202 | function [ subject ] = nmri_qcplot_power_grad(subject, data, params, title_txt)
%[ subject ] = nmri_qcplot_power_sensor(subject, data, params, title_txt)
%
% Generates a QC plot for power at sensor space
%
%
% subject = subject structure, see nmri_read_subject
% could be a struct or .m file or .mat... |
66a4888a4a3188e60d80e466171fb9be002096177940e64bab5132b4e7eeeec1 | MATLAB | 5,485 | 143 | function [delay] = CalculatePacketDelay(vid, fps)
% CalculatePacketDelay Calculates recommended packet delay for a GigE Vision camera.
%
% DELAY = CalculatePacketDelay(VID, FPS) calculates recommended packet
% delay DELAY for a GigE Vision camera, represented by an image
% acquisition videoinput or gigecam ob... |
7b004a2564de3759be354fa6923e1b2f3076dcf18f9f4f510c5473dc1ce6d18d | MATLAB | 5,501 | 142 | % MIBI smooth stitching script
% Author: Dmitry Tebaykin
% Contact: dmitry.tebaykin@stanford.edu
%% Necessary parameters
% Provide the XML file path from the run, stitching parameters will be
% extracted automatically. Example: xmlFileName = '180501_Hip_Panel3ug_Final-2b.xml';
xmlFileName = '';
% Output folder for st... |
e1e99d0427770bad932a3e7b50f6bf39a31c3ceb7de53039498f50376ae6b221 | MATLAB | 5,509 | 155 | %IMSEQ Open an image sequence as if it were a video stream.
%
% h = imseq(filename)
%
% This class creates an interface to a sequence of images similar to that
% of MATLAB's VideoReader class. However, the read method can only read an
% image at a time.
%
% The format of the filename is assumed to contain a... |
eea442cde1f12f2429ef4c8795ee56d78e4ac3f7c7f9ac8b9f5a6078c4459be0 | MATLAB | 5,538 | 116 | function Estimatetheta_Voxelwise(varargin)
% Varargin:
Porg = varargin{1}; % Original images
Prot = varargin{2}; % Coregister or aligned images
Vvector = varargin{3}; % V1 or main diffusion vector (depending on the model you are using)
Vvector_Vol = load_nii(Vvector);
VvectorImg = double(Vvector_Vol.img());
[pthname_t... |
16d0b268a7ad133a893aa19b4f5ba16e569f5f046d2cfeef14368517dd9606df | MATLAB | 5,540 | 167 | % Spontaneous neural activity during pursuit task
% Fig. 5a, fig. S7a, and fig. S9, a-e
%% PSTH of spontaneous activity
clear; clc; close all;
monkey = 'A'; % A for Monkey A, B for Monkey B
load(['mSpikes_' monkey '.mat']);
% Gaussian smoothing
for i = 1:size(wide,1)
wide(i,:) = gaussianFilter(wide(i,:),10);
e... |
04854e723088fbbe9cb11aaa405ea3583da9dc8e68fd9b941605afcd7eb2b4fd | MATLAB | 5,571 | 202 | clear all;
c1 = [121 180; 136 180; 151 180; 166 180]; % window before NP, 1s = 30units
c2 = [181 240; 181 225; 181 210; 181 195]; % window after NP
c = [c1 c2];
load('riNPrnr.mat'); load('rrNPrnr.mat')
crossN = 4; repeatN = 1; sampleN = 400;
%% rr reward or not
rrRw={};
for i=1:size(c,1)
t = c(... |
7ad917f06868953ff28ca9405a782fe5e4930f714cf7d09571e9aa2f7b44f5d0 | MATLAB | 5,574 | 188 | function err = save_nifti(hdr,niftifile)
% err = save_nifti(hdr,niftifile)
%
% Pixel data should be in hdr.vol
%
% Handles data structures with more than 32k cols by setting
% hdr.dim(2) = -1 and hdr.glmin = ncols. This is FreeSurfer specific,
% for handling surfaces. The exception to this is when the total
% number of... |
d57743d74d329951c5695e2506275d4dc3c4cb428388c4a3e79a468b1e1698c2 | MATLAB | 5,587 | 139 | %---------------------------------------------------------------%
% This is the main script for CCGP of trajectory phases %
% using linear SVMs; Libsvm MATLAB toolbox (V3.22) is needed %
% (https://www.csie.ntu.edu.tw/~cjlin/libsvm/). %
% -- Wenbo Tang (Jan 07, 2023) ... |
d85e25b52bfcd2505d85bf860d6ea9767869daae272aa37c50360365c20446c6 | MATLAB | 5,595 | 100 |
% ClinicalASL toolbox 2023, JCWSiero
%%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 25-05-2023 for the MOYAMOYA study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL analysis, CBF, map smo... |
32b54be6aa487f16d93ea8d6dd0b7d9851c2bc1671cf1aa3a176662fed253051 | MATLAB | 5,617 | 147 | % Copyright (C) Alex A. Bhogal, 2021, University Medical Center Utrecht,
% a.bhogal@umcutrecht.nl
% <filterData: performs a variety of smoothing operations depending on parameter inputs >
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License... |
5208ad54973ad2d1e0ccd9d747f096f57e12b699d5dd26c4dbe69e1fae0dddbe | MATLAB | 5,622 | 172 | clear
close all
clc
figure('Units','normalized','OuterPosition',[.1 .1 .08 .2])
isubplot = 0;
prep4fig5D('action_preference',isubplot)
isubplot = 1;
prep4fig5D('LDA',isubplot)
function prep4fig5D(type_of_method,isubplot)
%% settings
c = lines(7);
color_match = c(2,:);
marker_size = 2;
line_width = 1;
color_nonmatc... |
83508a13a31985f1b6b5a938a140acc80db7781de7850fb9e67215b34bc8c347 | MATLAB | 5,624 | 206 | function coef = tdrRegression(data,regpars,plotflag)
% tdrRegression linear regression on population responses
%
% Inputs:
% data: population response (sequential or simultaneous)
% regpars.regressor: cell array of regressors {nrg 1}
% Each entry is a string, corresponding to the name of one of the fields
% i... |
27d386bd55d77b2d5b0aa5977fe3fb2c11c31cff1df2774ee892745379b0f01c | MATLAB | 5,651 | 94 | % ClinicalASL toolbox 2025, JCWSiero
%%%%%%%%%%%%%%%%%%%%% ASL Analysis %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% written by Jeroen Siero 30-04-2025 for the APRICOT/MOYAMOYA/PXE/STROKE study
% includes automatic DICOM file loading, anatomy segmentation and registration, outlier removal, data construction, BASIL anal... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.