sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
7b42ff689d5c47ddccdc894c7d1ddee754a2c0513050b7d04141ac2ccd10bf05 | MATLAB | 23,247 | 671 | classdef RoiUtil < handle
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Copyright (c) 2022 The Board of Trustees of the Leland Stanford Junior University; Herzenberg Lab
% License: BSD 3 clause
pro... |
5f1c462ad311d1fe1000dc1fa58db9cea6572652a6925b67678ee326487bcc49 | MATLAB | 23,380 | 620 | clc;
addpath('Visuallization_matlab/Code');
addpath('cbrewer');
% set the root_dir to the directory where the Code and visualization data is located
root_dir = 'fig3';
% Choose a iiject {'NY742', 'NY717', 'NY749'} -- we don't have iiject brains other than these but MNI should work for all Ss
Sj = 'NY717';
% get paths ... |
688f011c8a577e814f5faaa237f3788c7beccd9ba2bd5b068d06f58857ac75d6 | MATLAB | 23,481 | 904 | function st = ct_geom(type, varargin)
%function st = ct_geom(type, varargin)
%|
%| Create the "CT geometry" structure that describes the sampling
%| characteristics of a cone-beam CT system (axial or helical).
%| (Use sino_geom() for 2D fan-beam or parallel-beam systems.)
%|
%| in
%| type 'fan' multi-slice fan-beam -... |
7512b2eeac072feccfe703462ed95d7b2a1d99244384e47e1c5be3ac69bbb047 | MATLAB | 23,546 | 497 | clear
clc
%bayesreg
%J Ruffle j.ruffle@ucl.ac.uk
%%
%configure paths
addpath('/home/jruffle/Documents/MATLAB/bayesreg');
addpath('/home/jruffle/Documents/MATLAB/bayesreg/examples');
%%
%%for your given survival outcome, 12, 24 36 month etc.,
nsamples = 1e5;
burnin=1e5;
model_results = table;
df = readtable('p... |
4ece0df7655191ccff5d6b861a2faa619cd4924255454eb363d2c9933f7255a4 | MATLAB | 23,561 | 532 | function total = touchBuffer(duration,varargin)
% !!! This function should only be used in experiments that require a
% touchscreen as input-device, if the paradigm could also be implemented
% with input-keys use keyBuffer instead. !!!
% This buffer terminates if a specified number of inputs on "good keys" or "bad
% k... |
9534c6edb3d03456e6feca35e0dfd801d7a45f15334468f9641e765386763573 | MATLAB | 23,566 | 665 | % function [gcbf,cbfdat] = perf_resconstruct_3D (Filename, FieldStrength, ASLType, FirstimageType, SubtractionOrder, SubtractionType, ThreshFlag, threshold, CBFFlag, MeanFlag, Delaytime, Labeltime, Slicetime, T1b, PASLMo, optionPCA, ASLscaling, M0scaling, diffs)
%
% This MATLAB function is to reconstruct the raw perf... |
dd8111ee0a740da6a0201811df16566a0a1c72652a713dde8084e41a9cd856ae | MATLAB | 23,621 | 600 | function varargout = Coregister(varargin)
% COREGISTER MATLAB code for Coregister.fig
% COREGISTER, by itself, creates a new COREGISTER or raises the existing
% singleton*.
%
% H = COREGISTER returns the handle to a new COREGISTER or the handle to
% the existing singleton*.
%
% COREGISTER('CALL... |
33c30ea32783f6408862283339c68212fc4283b56b9eeca71fa0a35979fabf7b | MATLAB | 23,736 | 565 | %cdf plots, sawtooth plots, avg chunks of 5 trials september 4,2011
%chunk1 2 6
%chunk2 7 11
%chunk3 12 16
%chunk4 17 21
%chunk5 21 25
%absolutes_for16_rms05.m mlp 4/22/2009
%rm332_development_rms05.m mlp 3/22/2004
%this is similar to rm332_corrected and RM316_analysis however, will extra... |
45b21437b4d64547b8cff3e415cb36df36b371bceb787334e31826ef31cf6a07 | MATLAB | 23,763 | 590 | function varargout = spm_bms_display(BMS,action)
% Display results from BMS Maps
% FORMAT spm_bms_display(BMS,action)
%
% Input:
% BMS - BMS containing details of excursion set
% action - 'Init' (Initialise)
% 'do_plot' (plot voxel results)
% 'save' (save results as NIfTI image)
% 'overlay... |
583de3bc3c6fa858e3825c7e85c30287afa4e1bbf591235346ce7b55c3154c21 | MATLAB | 23,835 | 554 |
function compare_run_sleep_replay(bayesian_control)
% MH 2022
% Runs correlations and linear regression comparing awake replay on track with the subsequent sleep session. Compares it usimg both absolute number
% of events and rate of events. Comparisons are run within track (e.g. awake replay on T1 vs POST1 T1 sleep r... |
0bbfe1d7a588abf1d0d391a7b29bada63ea9ace91a4bc6232b9fd948b5b4f84a | MATLAB | 23,860 | 501 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% ################################################################# %% DESCRIPTION
% Script to analyse data for:
% Grieves et al. (2020)
% Quantification of firing rate map procedures
%
% This script
% NOTE: This script is dependent on graphtest... |
223ad1a279c5491296d1e41dcfe35378e3d9f68150ab288f63b27633356021f6 | MATLAB | 23,949 | 570 | function Swarm(x, y, varargin)
% Updated SymphonicBeeSwarm
% Produces a distribution of points akin to a beeswarm, violin, or box and whisker
% Swarm(x, y, varargin)
% Only supports a single group at a time as this reduces ambiguity in matrix dimensions.
% First check x & y for validity
if isnumeric(x) && all(size(x) ... |
a66459dfde0058f332ca8c4e740c2be49a4d713174b2d9f927ec775769afbb45 | MATLAB | 24,003 | 644 | classdef ColorsByName <handle
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Copyright (c) 2022 The Board of Trustees of the Leland Stanford Jun... |
3bef2844ea3f51ec6a81ef0367440289ecfe3544ecbb6b5a5f9190d4ca2d228a | MATLAB | 24,007 | 580 | % function [phaseCongruency, or, M, m]=myphasecong3(varargin)
%
% This function is a revised version of Kovesi's phasecong3.m.
% Please "type myphasecong3" for detailed information.
%
%
% Z. Liu @NRCC[ July 31, 2006]
% PHASECONG2 - Computes edge and corner phase congruency in an image.
%
% This function calculates t... |
53e7d3cfc009eb1b5310a0aa5cc602428e5243c8f070e520e14e3d1af3f0a07f | MATLAB | 24,135 | 627 | function BHV02a_RL_model(SBJ,proc_id,model_id)
%% Run reinforcement learning (RL) model on single SBJ behavior
% for specific combination of model regressors and conditions
% Plots and saves:
% design matrix (SBJ_modelID_design.png)
% correlation matrix between regressors (SBJ_modelID_design_corr.png)
% violin ... |
b20705b904aa4148505cb49032389fb5781e2188347f48bffd47a99c4fe4971c | MATLAB | 24,158 | 631 | % POP_VIEWPROPS See common properties of many EEG channel or component
% Creates a figure containing a scalp topography or channel location for
% each selected component or channel. Pressing the button above the scalp
% topopgraphies will open pop_prop_extended for that component or
% channel. If pop_viewprops... |
d93e4b28af97776e01a9f8cef8d968a3835b93d3a0161942650336ae1998fa4c | MATLAB | 24,271 | 710 | classdef RetinalMap < handle
properties
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% Simulation ID and directories used
simName = 'default';
dataPath = 'SAVE';
figurePath = 'FIGS';
simID = 0;
timeStamp = 0;
%%%%%%%%%%%%%%%%%%%%%%%... |
9096756818d02a1e06ed01ec675764eea752201ac81b6daa66f526cc83f9770b | MATLAB | 24,276 | 623 | function [D, D_eye] = preprocess_dataset(datadir, exname, varargin)
% first written by J. Yates, 2021
% modified by Bharath Talluri, Dec 2021
% Modified for sharing by Bharath Talluri, Dec 2022
% Preprocess dataset will take all of the files in an experiment folder,
% time-align them for each trial and then bin and ma... |
f6e23af975c90e0f8f50dd8f4d87518cb05761cbd13d8ee5644a090a91b595ef | MATLAB | 24,463 | 431 | function natsortfiles_test()
% Test function for NATSORTFILES.
%
% (c) 2014-2023 Stephen Cobeldick
%
% See also NATSORTFILES TESTFUN_NSX ARBSORT_TEST NATSORT_TEST NATSORTROWS_TEST
fnh = @natsortfiles;
chk = testfun_nsx(fnh);
%
c2s = @(c)struct('name',cellstr(c));
rmf = @(s)rmfield(s,setdiff(fieldnames(s),'n... |
5641c502d7db46dfeb4379a6de91c59824a91d089bf08c635b4eec919c036fc1 | MATLAB | 24,485 | 444 | function raster_plot_replay_times(state)
% Plot replay times as raster plot for all sessions
% Loads 'extracted_replay_plotting_info.mat'
% INPUT:
% track: being 1 - for 16 runs,2 - for short exposures,3 - for re-exposure to track 1, or 4 - for re-exposure to track2
% state: 'sleep' for plotting only SLEEP replay (thus... |
a6a93d50d09c6d551420d5dd4126f240c27157a2daa896f797ba1d7657fe940b | MATLAB | 24,545 | 574 | close all;
clear;
load('U:\rg-yoshida\Yoshida_lab_shared_folder\Shared Data\Antonio\In vivo data\Babak\preliminary analysis\Space_bin\Space_bin_filt30Kalman.mat')%no return trajetories from T and goal
load('U:\rg-yoshida\Yoshida_lab_shared_folder\Shared Data\Antonio\In vivo data\Babak\preliminary analysis\Space_... |
fbd58330cce94d1d54be12430a9df3eefe0536499d8b4292e45ae9efbb70ea73 | MATLAB | 24,894 | 391 | function plot_diff_proportion_cum_replay_periods(epoch,multievents,bayesian_control)
% Plots difference in number of cumulative replay events between trackd over sleep periods for each protocol.
% Histogram is calculated as the sum of cumulative replay event times across tracks & each experiment (always within a protc... |
2ae073b6f04718ba1b6353a18b7e3c904e64c36481a1884a37566410e36b223a | MATLAB | 24,934 | 646 | function [accum, varargout] = CircularHough_Grd(img, radrange, varargin)
%Detect circular shapes in a grayscale image. Resolve their center
%positions and radii.
%
% [accum, circen, cirrad, dbg_LMmask] = CircularHough_Grd(
% img, radrange, grdthres, fltr4LM_R, multirad, fltr4accum)
% Circular Hough transfo... |
ab5b922e1e7b943dde2448fc7fc26abc873df03727af6fafe6ce780f3b78ea39 | MATLAB | 24,968 | 505 | % Created by A. Benitez Andonegui, M. Luehrs
% Modified by A. Vorreuther
%%%%% include these %%%%%
% mainPath: path where all participant data is stored. assumed directory format is:
% mainPath > P01 > run 1
% > run 2
% > ...
% ... |
432eae50f586195f2036e526ff9416e51a14ae7bdd7ece40ac252b56e0277fc9 | MATLAB | 25,077 | 666 | function varargout = ZSlicer(varargin)
% ZSlicer MATLAB code for ZSlicer.fig
% ZSlicer, by itself, creates a new ZSlicer or raises the existing
% singleton*.
%
% H = ZSlicer returns the handle to a new ZSlicer or the handle to
% the existing singleton*.
%
% ZSlicer('CALLBACK',hObject,eventData,... |
d95136b2d9878fb6ee9cdd021fa9a1b8b1e99faaa1bc8238c79cf2c333775da4 | MATLAB | 25,093 | 466 | % Marie_FP_PooledData
% Marie Labouesse, marie.labouesse@gmail.com - Feb 2021
% 1- POOLED DATA
% load matlab spaces generated in: Marie_FP_IndivData_extraction
% puts individual trials into one big matrix (all mice together): PooledINDIV
% calculates the mean of individual trial trajectories aligned to specific ... |
0ada8f14d2eb70eef5f5eadeaa1b5aa632ba5c784463278bd6f73eb5cc8ee9ae | MATLAB | 25,110 | 812 | %% - Figure 5c
% this script rungs additional analysis required for the plots of figure
% 5c.
%%
clear
close all;
ft_defaults;
%% -SUBJECTS - %%
% ID 18 missing because of LP at 50Hz
subjects = {'OSL13', 'OSL14', 'OSL17', 'OSL21', 'OSL24', 'OSL26', 'OSL27', 'OSL28', ...
'OSL29', 'OSL30', 'OSL31', 'OSL32', 'OSL3... |
a90f20d3363961b3e6d44f2686e1dadbd1ae762440b0c62205d271bfac2d28f3 | MATLAB | 25,127 | 611 | function [D, D_eye] = preprocess_dataset(datadir, exname, varargin)
% first written by J. Yates, 2021
% modified by Bharath Talluri, Dec 2021
% Modified for sharing by Bharath Talluri, Dec 2022
% load and preprocess raw data
% Preprocess dataset will take all of the files in an experiment folder,
% time-align them fo... |
f881d9ab520f41e0e31797fe6fb92edb24db80414cf145d1be93fba11321a577 | MATLAB | 25,172 | 840 | function [cond_tr_avg_all_cp] = perm_test_for_GLM(betas_sj,time_idx,chanlabels,EEGdir)
keyboard;
cl = cbrewer('div','RdBu',100);
% average frequent and rare trial conditions
for r = 3%1:length(time_idx)
% frequent averaged
freq_avg_sj = mean(betas_sj{r}(:,:,:,1:2),4);
% short averaged
short_avg_sj ... |
b48856ab004e761139db53b752c4f73de54dc8315c6e29b70e5d11987d05b49f | MATLAB | 25,196 | 515 | % Created by A. Benitez Andonegui, M. Luehrs
% Modified by A. Vorreuther
%%%%% include these %%%%%
% mainPath: path where all participant data is stored. assumed directory format is:
% mainPath > P01 > run 1
% > run 2
% > ...
% ... |
a3949e0227326c8120b5b2eeec7cec4622267a43e8a3865d2ffe849881fb55fa | MATLAB | 25,230 | 1,004 | function Sim=getSim(Sim)
% comments here
% last change: 2014/04/02 by PS
%references:
% Henkelman1993 MT agar parameters
% R. M. Henkelman, X. Huang, Q. S. Xiang, G. J. Stanisz, S. D. Swanson, and M. J. Bronskill, Magn Reson Med 29, 759–766 (1993).
%Singh2011 gagcest and cartilage
% A. Singh, M. Haris, K. Cai, V. B.... |
0af71fc6e1bdff6797062be9c932da65690430d5ba9e9f2187cf3846e396f234 | MATLAB | 25,292 | 706 | % Script to plot Figure 5, calculate statistics reported, and save data to
% Excel spreadsheets that are then imported into the Source Data file. For
% saving the data for panels d and f in Source Data, there is separate
% code.
% Kit Longden 2023.
addpath ../../src/Shared_functions/
% Data parameters
frate = 6.147;
... |
3bf669549a40aa30195f1ebca9d19fbb90caae5355f49e5fd690937f92f3e546 | MATLAB | 25,335 | 566 | function [outSig,spikeTimings,spikeProbs, outStruct] = SBLIF_model(insig, varargin)
%S-BLIF model (version 1.0.0) for electrically stimulated auditory nerve fiber
%
% Usage: [outSig,tSpk,Prob_blif] = SBLIF_model(insig)
%
% Input parameters:
% insig : signal used to electrically stimulate the AN fib... |
8b68e272029c56dc2600566bbdc8fdf315dfb3e25ffce5e2bd47d811366e4e99 | MATLAB | 25,336 | 655 | classdef Radio
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Copyright (c) 2022 The Board of Trustees of the Leland Stanford Junior University;... |
7b65c543891fda7f2a98c4ba4357257d5d8b24b1b4b2da5d3f84e0d366296e2d | MATLAB | 25,394 | 493 | classdef ParamEstimationModel
properties
% Original graph if for synthetic data, for real data empty matrix
graph
% training and Validation samples
XTrain, XVal
% Struct array for the estimated graphs form structural learning
% with different p... |
7f12efeb5b34c007cde3bafa96d918e74483c2afecb72d437ca649744f7eb064 | MATLAB | 25,433 | 583 | %% Calculates the COM for data, shuffling and TW using a bin size of time_bin_size
clear all
close all
dpath='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
% Params
pixel_size_new=1.18185;
pixel_size_old=1.78211;
num_clus_discr=10;
N_sh=500;
sf=7.73;
count=0;
data=load('C:\Users\xscogno\MATLAB\Flavio2\Waves\Se... |
3619f898da7d7ae4cf9791ac99d86386ada5d1fec2450a08e931c282ad19f863 | MATLAB | 25,449 | 408 | function plot_sleep_replay_temporal_effect(bayesian_control,rest_option,time_chunk_size,time_window)
if ~isempty(bayesian_control)
load('X:\BendorLab\Drobo\Lab Members\Marta\Analysis\HIPP\Chapter 2\Raw_replay_analysis\extracted_time_periods_replay_excl.mat')
path = 'X:\BendorLab\Drobo\Lab Members\Marta\An... |
ece9fdeacd9f8a97eeb95acbd9f9d45517927c2f41be5b3800ffbd5c6a98690d | MATLAB | 25,457 | 726 | classdef LabelLegendRoi < handle
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Copyright (c) 2022 The Board of Trustees of the Leland Stanford Junior University; Herzenberg Lab
% License: BSD 3 clause
properties(SetAccess=private)
xyData;
javaLegend;
bt... |
8b6cb50565d9eaba14079aa380e8fcd8b731ce0228b304bef810235a84e03b78 | MATLAB | 25,471 | 590 | classdef RegisterStack < handle
properties (SetAccess = private)
% View related properties
fig
% Display axes
axesStack
stackView
axesReference
referenceView
axesTransform
transformView
% GUI control... |
98b7bc084226780daa4b946a92667ad9cc75d3fca85636fad1458c29419717a9 | MATLAB | 25,490 | 704 | function [VO,M] = pm_segment(VF,PG,flags)
% Segment an MR image into Gray, White & CSF.
%
% FORMAT VO = pm_segment(PF,PG,flags)
% PF - name(s) of image(s) to segment (must have same dimensions).
% PG - name(s) of template image(s) for realignment.
% - or a 4x4 transformation matrix which maps from the image... |
f90cfe77fff288cf89ae6d0c9ed9f6a78842b71494fb1432dc5e0ed31dcbd5c3 | MATLAB | 25,497 | 469 | %makeData2struct_allVars.m
clc; clear all; close all;
% recording parameters
fs = 20000;
totalTime = 300; %sec
numIts = totalTime*fs;
totalElecs = 64;
% *** change each time! *** %
% chooseData = 0; %glu only
% chooseData = 1; %BDNF dose response
chooseData = 2; %glu injury + BDNF recovery
% *** change e... |
c05b60f6c3c30564fab6686c7abb57e2b2f03be9fb916516e7400017c0485329 | MATLAB | 25,517 | 827 | clear all
close all
dbeh_path='C:\Users\xscogno\MATLAB\Flavio2\Waves\Tracking data\';
rec_data_path = 'C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_spikes='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_sorting='C:\Users\xscogno\MATLAB\Flavio2\Waves\Sorting\';
dpath='C:\Users\xscogno\MATLAB\F... |
25012314a4daabd5ad2c3c41ed6b2c2d8e063fbb2d31406cb093c648059624a0 | MATLAB | 25,526 | 630 | %% Script to visualize data
% Works for both actual and simulated results
%% User settings
num_replicates = 1000;
update_confusion_matrix_for_each_trial = false;
pause_length = 0.05;
pvalue_threshold = 0.05;
rolling_window_size = NaN; % If NaN, then won't use a rolling widnow.
%% Define some useful things
combin... |
4331c5676b0bc2c65f811ce335b58f5c0b32f754ef31985159d2ac517481f810 | MATLAB | 25,526 | 573 | %% Script to create output for Fig. 4 - parameter comparisons between Young, healthy Elderly, MCI combined
% Zilong Ji, UCL, 2022 zilong.ji@ucl.ac.uk
% Fits the model on all of the groups and run a two-way Anova
% (group*condition) on Young Controls, Elderly Controls and MCI
% Output: for each parameter fitted by the m... |
eee123681b6d2c9e838da698ae007355e0dfc015838dc0640247b3160d1efe54 | MATLAB | 25,575 | 709 | classdef Hermaphrodite
%HERMAPHRODITE Hermaphrodite related data.
methods (Static)
%% Utility functions.
function is_neuron = isNeuron(name)
%ISNEURON Is this a neuron name?
is_neuron = ...
~isempty(find(strcmp(name, Neurons.Hermaphrodite.getNeurons()),1)... |
9b3554473a818af7e1018692bc75bc898317ad15620d7c426f853d2ac3594553 | MATLAB | 25,624 | 453 | function normalise = spm_cfg_normalise
% SPM Configuration file for toolbox 'Old Normalise'
%__________________________________________________________________________
% Copyright (C) 2005-2012 Wellcome Trust Centre for Neuroimaging
% $Id: spm_cfg_normalise.m 7155 2017-08-17 10:55:05Z john $
if ~isdeployed, addpath(f... |
1033e721bd8303e2036e1155ca2097f9a0b62435148a758e6a9b3ccd5fdf102d | MATLAB | 25,626 | 508 | % main script for analyzing micro-electrode array (MEA) data %%%%%%%%%%%%%%
% 5/12/2016 combined this main function with GetSpikePoints for feeding %%%
% into WaveClus analysis. %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 6/16/2021 needed to change the way the raw data was accessed: this %%%%%%
% version (_... |
3cbeba5644b8db84086092dac243b846505b7b1e74aaf9db4e9c1dec66d2e910 | MATLAB | 25,737 | 597 | classdef RegisterStack < handle
properties (SetAccess = private)
% View related properties
fig
% Display axes
axesStack
stackView
axesReference
referenceView
axesTransform
transformView
% GUI control... |
614da837590a9e43a99362b99bd2df161d5b941028d329c5d48425e4a212cfcc | MATLAB | 25,821 | 511 | % Created by A. Benitez Andonegui, M. Luehrs
% Modified by A. Vorreuther
%%%%% include these %%%%%
% mainPath: path where all participant data is stored. assumed directory format is:
% mainPath > P01 > run 1
% > run 2
% > ...
% ... |
83e5f80c83cdb4a2b1e2a47f2a65df143c04b3614c177f9079c09f16db9ca598 | MATLAB | 25,861 | 732 | %EXPORT_FIG Exports figures suitable for publication
%
% Examples:
% im = export_fig
% [im alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -native
% export_fig ... -m<val>
% export_fig ... -r<val>
% export_fig ... -a<val>
% ... |
859d690d00e8b3d835f01092ea532c69aedbe8917ec8b421037c938c875e96bc | MATLAB | 25,923 | 511 |
function population_vector_analysis(computer,bayesian_option,plotting_option,save_option)
% Marta Huelin_January 2020
% Computes population vectors for each track exposure (taking raw firing rate from bayesian place fields) and computes correlation between
% different tracks. Plots correlations as cumulative frequency... |
890e019accc3970b54eeb5bfa8f4aca20a7039c4afd7a4bac7aa8960fa8ef96c | MATLAB | 25,977 | 672 | classdef UMAP_extra_results < handle
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Copyright (c) 2022 The Board of Trustees of the Leland Stanf... |
8dd65486cf301f961f487d1f993cbded6ea2ef458658eecb447195a6749d5e7d | MATLAB | 26,020 | 1,228 |
% Code responsible for generated the behavior data displayed in "Ciliary
% localization of a light activated neuronal GPCR shapes behavior", PNAS,
% 2023
% Written and annotated by Amy Winans
% Notes:
% 1) It is recommended to run this script section by section in order. The
% first section generates the workspace t... |
face57d9d03dc3db8a1e30d37c54020a1a7bf41ec0a4f535609095d688ed88e2 | MATLAB | 26,060 | 417 | function plot_diff_cum_replay_periods(epoch,bayesian_control)
% Plots difference in number of cumulative replay events between trackd over sleep periods for each protocol.
% Histogram is calculated as the sum of cumulative replay event times across tracks & each experiment (always within a protcol),
% and averaged (div... |
d4a9bbe794bf5a8fe5734c8f1cc9c18ae7b76097f84fc50a540ffed04b7c7f38 | MATLAB | 26,137 | 638 | %% indicate variables
tic
for iSubj = 1
disp(iSubj)
clearvars -except iSubj
close all;
subj_list = {'39' '44' '57' '63' '66' '84' '85' '87'};
subj = subj_list{iSubj}
% adjust theses
removeERP = 'yes';
cue_responsive = 'yes';
lock = 'onset'; % 'response' %'... |
57bd2cad9e7917e96201c512faf8730d7d2266b841eb6d2a93d6d1f31819c4fc | MATLAB | 26,153 | 505 | function firing_rate_population_vector_analysis(computer,bayesian_option,save_option)
% Marta Huelin_February 2020
% Computes a variation of population vector analysis between matrices for the same type of comparisons used in the population_vector_analysis.m code (meaning,
% between same track exposures and between dif... |
9d575b04ea1819ef8d96dd9b1c1c6c73009fb71e9e171fc999be6acfde7b2465 | MATLAB | 26,159 | 729 | %% Figure 3e & f (right panel)
% this script rungs additional analysis required for the plots of figure
% 3e & 3f.
%%
clear
ft_defaults
%% - SUBJECTS - %%
% ID 18 missing because of LP at 50Hz
subjects = {'OSL13', 'OSL14', 'OSL17', 'OSL21', 'OSL24', 'OSL26', 'OSL27', 'OSL28', ...
'OSL29', 'OSL30', 'OSL31', 'OSL... |
df5cd15ce95e30461434e7482d56d7944b2988e14b42315b92fe6ab9b059198e | MATLAB | 26,201 | 424 | function replayBG(modality, data, BW, scenario, saveName, varargin)
% function replayBG(modality, data, BW, scenario, saveName, varargin)
% Core function of ReplayBG. Can be used to identify ReplayBG model on the
% given data or to "replay" specific scenarios specified by the given data.
%
% Inputs:
% - modality: (r... |
5238ca3f4cef7db7a49c2db1b806a4e6c5a8ff1ec5e8e672d47bf30623779d86 | MATLAB | 26,348 | 597 | function analyze_SI_unimodal_Fig4_Sfig7
rootdir = 'C:\TKlab_agingPFC\';
cd(rootdir)
load SI_unimodal
figure( ...
'Position', [0 100 1450 550], ...
'PaperOrientation', 'landscape', ...
'PaperUnit', 'inches', ...
'PaperPosition', [0 3 ... |
c455e5df9d44769fc91e461066695442288341cb039acb03e450c6076e554ba5 | MATLAB | 26,352 | 672 | clear all
close all
dbeh_path='C:\Users\xscogno\MATLAB\Flavio2\Waves\Tracking data\';
rec_data_path = 'C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_spikes='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_sorting='C:\Users\xscogno\MATLAB\Flavio2\Waves\Sorting\';
dpath='C:\Users\xscogno\MATLAB\F... |
7a20998062f0e79bcb61ecd4751899de20ff5f092a85f449fae892f6a5a314e4 | MATLAB | 26,387 | 934 | clear all
close all
dbeh_path='C:\Users\xscogno\MATLAB\Flavio2\Waves\Tracking data\';
rec_data_path = 'C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_spikes='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_sorting='C:\Users\xscogno\MATLAB\Flavio2\Waves\Sorting\';
dpath='C:\Users\xscogno\MATLAB\F... |
f3f4d99eddda0f435ad0e94ca1079fb806db605d62058f0570ba85f4a8dca360 | MATLAB | 26,610 | 891 | classdef StringArray < handle
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Copyright (c) 2022 The Board of Trustees of the Leland Stanford Jun... |
d770659b6276df64c5949cff1bd0d49e20df0bafe37f828e1654925966c95335 | MATLAB | 26,637 | 612 | function initWindow(screenNum, rotation)
% Initializes a Window for displaying stimuli using the OTBR Toolbox.
% The function initWindow optionally takes the display number as argument
% to place the stimulus window on the correct monitor.
%
% Tip: When testing the toolbox it is helpful to use two monitors
% (one for c... |
6ca6a222151fb07d8011e119f72226e3e15188da77395d7b0462626cd177defe | MATLAB | 26,686 | 686 | clear all; close all; clc
tic
subj = '87' % 84, 85, 87
lock = 'onset'
downsample = 'yes'
ref = 'LM'%'WM' 'LM'[];
clinical = 'yes'
select_chan = 3 % 1: get specified chans indicated by chan_name 3: gets all chans
normalization = 3% 1 = entire task 2 = prestim
norm = {'entire_recording' 'prestim' 'cond_spec_prestim'}... |
50208e2a78a92ff7df5313b58b1980a6ac6da81924ca07550a9f1d4e2cbcef00 | MATLAB | 26,701 | 613 | timelockCondition = 'buttonPress';
reference = 'LMRM';
csdFlag = 0;
rtFlag = 0;
baseline = 0;
faFlag = 1;
subjectList = [16, 18:21, 24, 26, 27, 28, 29, 31, 33, 34, 35, 42, 43, 47, 50, 51, 52, 54, 55, 57, 58];
%subjectList = [58];
numberSubjects = length(subjectList);
options = continuous_RDK_set_options('iMac');
fo... |
0c5121aeb4decd9cf13762765aeaedbdbfdce4e681ae3c1cd7b269568282ee40 | MATLAB | 26,732 | 621 | %% Script to create output for Fig. 4 - parameter comparisons between MCI positive and MCI negative
% Zilong Ji, UCL, 2022 zilong.ji@ucl.ac.uk
% Fits the model on all of the groups and run a two-way Anova
% (group*condition) on MCI positive and MCI negative
% Output: for each parameter fitted by the model output one bo... |
9ee3b7b9161571f0b395018f092993f698cc0986c407a7852bfb60b5d5afd617 | MATLAB | 26,760 | 829 | %% Load data
clear all
close all
dbeh_path='C:\Users\xscogno\MATLAB\Flavio2\Waves\Tracking data\';
rec_data_path = 'C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_spikes='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_sorting='C:\Users\xscogno\MATLAB\Flavio2\Waves\Sorting\';
dpath='C:\Users\xs... |
e73a5e8f9d7e54532c1509e1824108db4e1664b0d2e4025e52dabbeabdcc3823 | MATLAB | 26,763 | 689 | %% Correlation VS distance on tissue and distance on ring
clear all
rec_data_path = 'C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_spikes='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_sorting='C:\Users\xscogno\MATLAB\Flavio2\Waves\Sorting\';
dpath='C:\Users\xscogno\MATLAB\Flavio2\Preprocesse... |
7cc484558757071e0cb40d5b5b4beb698cc0397d4bbcc23e8474eb4be36e78a2 | MATLAB | 26,823 | 484 | function DK_NNLS(T2Data, matmask, Resol, TE, TR, T2Range, spwin, nT2, nCores, nThreads, FAE_in_fin_step, RegType, nSpatIter, Size_DSW, Overlap_DSW, SpatRegOpt, SpatRegSetAlpha, SpatReg_Init_FA, SpatReg_Init_T2)
% clear DataFolder DataFileName WOR MaskFileName Spatial_ProcessMode RegTag1 MatPriorityTag Capsule1 muS... |
8588a1a5cae217382cdac170671269684a437a0971d4df4ce90177ccc495cbab | MATLAB | 26,836 | 643 | function [synthFlys,state,nTurn,spdAll,curvAll,phiAll,dSpk,allAng,lambda_CW,...
lambda_Stop,dfSmooth,fSmooth,tt_baseline] = RunAndTumbleKNNLinFilter(self,params)
% get basic parameters
originalFs = self.fs;
fs = params.LLFfs;
len = ceil(params.len*params.LLFfs/params.fs);
totFly = params.totFly;
posInit = params.po... |
fab67349e171560e4565dcd3f7095e31aeea383884446d992498cbdd347184a9 | MATLAB | 26,856 | 560 | % % 01-02-2019
% % Elias Scheer
% %
% % with tracking some code copied from
% % \MATLAB2016b\toolbox\vision\visiondemos\multiObjectTracking.m
% % and from Ev Yemini's segWorm_stuff\ComputerVision functions for
% % segmentation
% objective: track worms as they hang out in lawns of bacteria and
% occasionally leave. ext... |
c771b9e0c504a6dc8df11f651a6ac5fad30be2f4b46aa05a9d87a0a07b67c5cb | MATLAB | 26,877 | 761 | classdef Male
%MALE Male related data.
methods (Static)
%% Utility functions.
function is_neuron = isNeuron(name)
%ISNEURON Is this a neuron name?
is_neuron = ...
~isempty(find(strcmp(name, Neurons.Male.getNeurons()),1));
end
function is_... |
b50f7277f14d725045e5b4046f59836e600ac19d8889ab5c6b292f6327c6cab4 | MATLAB | 26,914 | 599 | function [D] = spm_eeg_review_uis(D,objects)
% GUI of the M/EEG Review facility
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Jean Daunizeau
% $Id: spm_eeg_review_uis.m 6070 2014-06-26 20:53:39Z guillaume $
% POS = get(D.PSD.h... |
cbf20c09195247e710ac2195facf83a9956dda6645dd59cdeb7cfbe05c73f7e9 | MATLAB | 26,974 | 589 | function spm_image(action,varargin)
% Image and header display
% FORMAT spm_image
% FORMAT spm_image('Display',fname)
%__________________________________________________________________________
%
% spm_image is an interactive facility that allows orthogonal sections from
% an image volume to be displayed. Clicking the... |
a335b33aabc8e9089702e099023cdecb0d05cf0c3d8402e371d3e575e74c02ee | MATLAB | 27,000 | 526 | % fixMontage.m
%
% Purpose:
% Fix montage of PSG data based on information from the accessory files (ie xml).
% Usually this is needed to build the correct referential montage, or to filter signals.
% This step is needed for compumedics edf files, which are stored as unreferenced channels.
%
% Usage:
% [MINFO,MTS]=fi... |
b4312ba8b91f6ee45b0fd2461f13ecd98a04d8f3879989e7c1d431f755100cd3 | MATLAB | 27,035 | 491 | function DK_nii_NNLS(T2Data, matmask, Resol, TE, TR, T2Range, spwin, nT2, nCores, nThreads, FAE_in_fin_step, RegType, nSpatIter, Size_DSW, Overlap_DSW, SpatRegOpt, SpatRegSetAlpha, SpatReg_Init_FA, SpatReg_Init_T2)
% clear DataFolder DataFileName WOR MaskFileName Spatial_ProcessMode RegTag1 MatPriorityTag Capsule1... |
35852de9371258c20e5e673003b30ec74334ff983d063336f524ca76291536bc | MATLAB | 27,128 | 944 | clear all
close all
dbeh_path='C:\Users\xscogno\MATLAB\Flavio2\Waves\Tracking data\';
rec_data_path = 'C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_spikes='C:\Users\xscogno\MATLAB\Flavio2\Preprocessed_data\';
dpath_sorting='C:\Users\xscogno\MATLAB\Flavio2\Waves\Sorting\';
dpath='C:\Users\xscogno\MATLAB\F... |
2e114fa45adff06c20a038e461e20f4b165d17acfd4096c4bc94dc66a93b7958 | MATLAB | 27,233 | 695 | function [idx, C, sumD, D] = kmeans(X, k, varargin)
%KMEANS K-means clustering.
% IDX = KMEANS(X, K) partitions the points in the N-by-P data matrix
% X into K clusters. This partition minimizes the sum, over all
% clusters, of the within-cluster sums of point-to-cluster-centroid
% distances. Rows of X corres... |
938dd935d9e3e654f00b1123587ecb5dae9f5cd67024a0e2e06490b3d6395d79 | MATLAB | 27,241 | 695 | function [idx, C, sumD, D] = mymatlabkmeans(X, k, varargin)
%KMEANS K-means clustering.
% IDX = KMEANS(X, K) partitions the points in the N-by-P data matrix
% X into K clusters. This partition minimizes the sum, over all
% clusters, of the within-cluster sums of point-to-cluster-centroid
% distances. Rows of ... |
5b395d64331ca88732f719db93ae45911ad136a9e345d42a96a981189fb11bb2 | MATLAB | 27,243 | 873 | function spm_dcm_peb_review(PEB, DCM)
% Review tool for DCM PEB models
% FORMAT spm_dcm_peb_review(PEB,DCM)
%
% PEB - PEB model to review
% DCM - (Optional) A single DCM or cell array of DCMs. Data is used to
% enhance the GUI.
%
%__________________________________________________________________________
% Copyr... |
7dcbb0483a1937893afea1363a08cf213f1c861b052c11416da2a0602ae86f57 | MATLAB | 27,250 | 744 | function mondichNRexpt
% normalization reweighting experiment with mon and dichoptic presentation
% code based on surround suppression experiment from 2014
% this version for ViewPixx, 36 pix/cm dot pitch
% four conditions - 5Hz component, 7Hz component, both mon, dichoptic
% DHB 1/3/20
clear
close all;
pID = inputd... |
57ec2879ea448e39751f83e18f0ad70096dd4b6445cbdeb1073e876bae52d36a | MATLAB | 27,251 | 579 | classdef PhysioData < dynamicprops
properties
% comments % comments structure
inputfile
% record_meta % record meta data
% channel_meta
% stimchans % cell array of stim channel records
% toffset % vector of length record_meta
ecg % raw ecg sign... |
02d944343998ad05b2849681dfbbf1e4121be1174fde54e5487b78993636ecca | MATLAB | 27,352 | 619 | function plot_theta_vs_replay_backup(bayesian_control,rest_option,time_chunk_size)
if ~isempty(bayesian_control)
path = 'X:\BendorLab\Drobo\Lab Members\Marta\Analysis\HIPP\Chapter 2\Raw_replay_analysis\Bayesian Controls\Only first exposure';
path2 = 'X:\BendorLab\Drobo\Lab Members\Marta\Analysis\HIPP\Chapter 2\Ra... |
ce15b803a323dcaa8084a663135aef894d3f42dac183f86a60ce8f753b8354a7 | MATLAB | 27,400 | 563 | function dishRig4()
% Etho View Protocol
% Rev. Jun 06 2012
% Mar 01 2013: New protocols (appear suddenly & grow nearby).
% Mar 06 2013: Further modified.
% Dec 08 2014: Color of the dot changed from brown to grey.
%%% =========== CONSTANTS AND PARAMETERS =================
screenDim = [1024 768]; % Vertical
tankR = ... |
10b756a3831af04cc2e4271f18fbf03bd17aa96611e0a1fecc26fcc998c0a73d | MATLAB | 27,425 | 575 | % Script to plot Figure 3, calculate statistics reported, and save data to
% Excel spreadsheets that are then imported into the Source Data file.
% Kit Longden 2023.
addpath ../../src/Shared_functions/
% Load isoluminance crossing points (cp) responses to opposing motion
% ---------------------------------------------... |
a8ed24eff0a07714f75026d2b68be89837084748fe9d13c338d749e5586a15cc | MATLAB | 27,531 | 463 | % Script to save Figure 5d data to Excel spreadsheets that are then
% imported into the Source Data file.
% Kit Longden 2023.
% Data parameters
frate = 6.147;
N_frames = 47;
dt = 1/frate;
t = (0:dt:dt*(N_frames-1))-3;
% Load data that is plotted in Figure 5d
load ../../results/Figure_5/Medulla_cells_looming_UV_disc... |
378cbd6ccb049f258fde37329255876df60f6a817ea41583c0d875678f3fdcf4 | MATLAB | 27,602 | 446 | % Plot single cell correlation between laps between exposures
% Marta Huelin
% Loads extracted data for each protocol session and for all rats, and calculates the difference in specific parameters (e.g. centre of mass)
% between the last laps of the first exposure and each lap in the second exposure.
% INPUT:
% 'pa... |
363544a2f991c4d45a20494bd0af9747dd3e936b31268817940bf486c58f5faa | MATLAB | 27,696 | 295 | % DECODING ERROR FOR BAYESIAN DECODING
% Marta Huelin_2019
% Calculates decoding error between real position and the bayesian decoded position.
% INPUTS:
% estimated_position: structure witht the matrix and information of the position decoded.
% place_fields: structure. place fields as a template for decoding... |
266ba976e7a8aa34b1cded39f8d53a028ae525d5cacb659440294a524c915184 | MATLAB | 27,700 | 717 | function [idx, C, sumD, D] = weightedkmeans(X, k, varargin)
%KMEANS K-means clustering.
% IDX = KMEANS(X, K) partitions the points in the N-by-P data matrix
% X into K clusters. This partition minimizes the sum, over all
% clusters, of the within-cluster sums of point-to-cluster-centroid
% distances. Rows of ... |
d06c472b976e554623578b3f7e0c152a32b289da40d429bce285d78a5f24e47f | MATLAB | 27,789 | 455 | % Plot single cell correlation between laps between exposures
% Marta Huelin
% Loads extracted data for each protocol session and for all rats, and calculates the difference in specific parameters (e.g. centre of mass)
% between the laps 13 to 16 from the re-exposure and each lap in the first exposure.
% INPUT:
% '... |
db58f72edb9f31e788915f4a4a37b8063d745e662703bde3b4d228645f67f233 | MATLAB | 27,870 | 667 | % PLOT AWAKE REPLAY PROPERTIES ON TRACK
% MH 2021
% Extracts and plots information about each awake replay event on track - duration,
% bayesian bias (loaded)
% Protocol structure loaded is as follows: each row is a protocol (e.g. protocol(x)) and each column contains information about replay events on
% each track (e... |
6c647292827927143dab390ab2439de7c6b462b704ff7a0d046347d4e3b4723b | MATLAB | 28,007 | 770 | function [D] = spm_eeg_review_switchDisplay(D)
% Switch between displays in the M/EEG Review facility
%__________________________________________________________________________
% Copyright (C) 2008-2015 Wellcome Trust Centre for Neuroimaging
% Jean Daunizeau
% $Id: spm_eeg_review_switchDisplay.m 7221 2017-11-16 14:25... |
49fdbbb82ec33e540060dc4673bb2cda635782951f2439bb2e7578671a8cc78b | MATLAB | 28,021 | 628 | function [idxbest, Cbest, sumDbest, Dbest] = fun_kmeans2(X, k, distance,...
emptyact, reps, start,Xmins,Xmaxs,CC,online,...
display, maxit,useParallel, RNGscheme,...
wasnan,hadNaNs,varargin)
% KMEANS uses a two-phase iterative algorithm to minimize the sum... |
63ee28198b2de1a1233c71c58574c86098631e1328c3a499a9ba76e6208c9b3a | MATLAB | 28,028 | 479 | % function MAP_generate_maps
%% >>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>> DESCRIPTION
% MAP_generate_maps script to analyse data for:
% Grieves et al. (2020) Quantification of firing rate map procedures
% This script is dependent on graphtest for inputs and data
%
% USAGE:
% MAP_generat... |
6a8d28f2786963de186b5813bee1e41cfe004475162c33bdabdd26df5bfe7016 | MATLAB | 28,066 | 817 | function out = spm_deformations(job)
% Various deformation field utilities
% FORMAT out = spm_deformations(job)
% job - a job created via spm_cfg_deformations.m
% out - a struct with fields
% .def - file name of created deformation field
% .warped - file names of warped images
%
% See spm_cfg_deformation... |
2391ed5ed19da98fd2a6a5e2a2b8be152b88577e62f903f24ff9188bef6f5ddb | MATLAB | 28,115 | 973 | function pot = potential_fun(ptype, delta, param, varargin)
%function pot = potential_fun(ptype, delta, param, varargin)
%|
%| Define roughness penalty potential functions (as strum).
%|
%| The penalty will have the form
%| R(x) = sum_k w_k * potential_k([Cx]_k, delta_k)
%| where w_k is provided elsewhere, not here!
%... |
b2b0af793296dba4bf80800d9f684f554d0f27d9ec1ec0132d6f9c177cdb5d3b | MATLAB | 28,204 | 954 | % this script takes behavioural data created with step_1_read_in_behav_data
% and calculates integration kernels leading up to a button press and
% fitting an exponential to it
%% add paths
addpath(genpath('/Users/maria/Documents/Matlab/cbrewer'))
addpath('/Users/maria/Documents/MATLAB/raacampbell-shadedErrorBar-9b19a... |
e5cf5f0cab7b09e38e313eb0e9ce78897e1b02ab095190fe12c4acf69fe74345 | MATLAB | 28,315 | 748 | %
% This code reproduce the main results of the article 'The evolution of
% information transmission in mammalian brain networks' - Alessandra
% Griffa, Mathieu Mach, Julien Dedelley, Daniel Gutierrez-Barragan,
% Alessandro Gozzi, Gilles Allali, Joanes Grandjean, Dimitri Van De Ville,
% Enrico Amico.
%
%
% Alessandr... |
37982017d5b94a71b1e9097825a56d6d2b3d4c1a6a282ac4c427740f34c2b1e9 | MATLAB | 28,333 | 521 | function [sig_cells,areasSternberg] = NWB_calcSelective_SB(nwbAll, all_units, params)
%NWB_CALCSELECTIVE Takes the output of NWB_SB_extractUnits and runs
%selectivity tests for the sternberg task. Optionally plots trial aligned
%spikes
if isfield(params,'rateFilter') && params.rateFilter > 0
rateFilter = par... |
49c8149d263ab150b81f299aecf66f7f23ddf6b8ba54a9ede6d050b96c1bc18d | MATLAB | 28,421 | 719 | classdef SuhJsonSplitter<SuhModalSplitter
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math Lead & Secondary Developer: Connor Meehan <connor.gw.meehan@gmail.com>
% Bioinformatics Lead: Wayne Moore <wmoore@stanford.edu>
% Copyright (c) 2022 The Board of Trustees of the Leland S... |
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