sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
2dc5fea6ec34b10acf7b34b886bfd5cfb515348084342dae5dd18525434fb363 | MATLAB | 3,279 | 97 | function calibrateScanners_Callback(obj,~,~)
% Initiate the proces of calibrating the scanners with the camera
%
% zapit.gui.main.controller.calibrateScanners_Callback
%
% Purpose
% The scanners and camera must be calibrated with respect to each other. This
% method does this.
if nargi... |
dd5de6ec0ab9e3c8d35ddf16c3a5a6869dc3951a65fe15b3659280df121882c0 | MATLAB | 3,284 | 87 | function varargout = plot(self, objPI, varargin)
%plot - Plot a figure
%
% plot(OBJ, OBJ_PI) plots the default figure for the CalcMeasureROIs
% object OBJ using the ProcessedImg object OBJ_PI.
%
% plot(OBJ, OBJ_PI, AX, FIG_NAME) plots the figure on the specified axes
% handles AX, and the particular figure spec... |
6f90524f5d8349cabbf22141bbebb7385689f0908d87ea827f0c4bcd05f4ae40 | MATLAB | 3,289 | 128 | cd ..\
load('foldersAllIndvFOV.mat');
cd('dfofTrack');
%%
p=pwd;
folders=foldersAllIndvFOV;
folders=folders([1 2 3 4 5 6 7 8 9]);
allCellsDfof={};
allCellsDfof_sig={};
for n=1:11;
allCellsDfof{n}=[];
allCellsDfof_sig{n}=[];
end
% M=[];
for n=1:length(folders);
disp(n)
for ... |
433798166ef4751fbdab3696448e91d50977900c539e7eb389449f56ce0decfe | MATLAB | 3,295 | 109 | % op_getLW.m
% Jamie Near, McGill University 2014.
%
% USAGE:
% [FWHM]=op_getLW(in,Refppmmin,Refppmmax,zpfactor,suppressPlots);
%
% DESCRIPTION:
% Estimates the linewidth of a reference peak in the spectrum. By default,
% the reference peak is water, between 4.4 and 5.0 ppm. Two methods are
% used to estimate the ... |
8ac235dfdb26b1990e34dda78c6794026a4beeabd80270b23950b85fdd318b7b | MATLAB | 3,302 | 288 | %new version (fixed by Shinya Ito):
%first column = numbering of channels on probe PCB connectors looking from
%the top.
%second column = numbering of channels on head stage amplifiers.
headstagewiring = zeros(256,2);
headstagewiring(1:256,1) = 1:256;
headstagewiring(1:32,2) = 32:-1:1;
headstagewiring(33:64,2) = 64... |
7673fa70e9c9d5854f6673e4e7aa876645665a7d41d84f5d63115afba5fb42b7 | MATLAB | 3,306 | 91 | function make_mex()
%make_mex - Compile relevant C, C++, and MATLAB functions into MEX files
%
% make_mex() compiles relevant C, C++, and MATLAB functions included with
% this package into MEX files using the InstallMex utility function (for
% C and C++ files) and the MATLAB coder (for MATLAB functions).
%
% Be... |
3d7fbd16d6c85e43ae801e7fd806ab3f0f6b9f54375e2a8abe483b35e0cef1a2 | MATLAB | 3,307 | 104 | % this code will read all the gaze files from the trials and covernt them
% to the image coordinate.
clear
close all force
imSize = [733, 977];
pix2deg = 34.910;
hWB = waitbar(0,'checking the trials ...');
load a0_3_0_extractingTheMorphingDataFromAnalyze1
%load tirals info
load('a0_0_bhv2trialStrct.mat');
I = arra... |
d1881565ffe21b12bd2a38f73cc40d6128ca4f45c66bbcbf462d4e6c5823de36 | MATLAB | 3,310 | 131 | % SYN_TREE Steady-state synaptic electrotonic signature of a tree.
% (trees package)
%
% syn = syn_tree (intree, ge, gi, Ee, Ei, I, options)
% ---------------------------------------------------
%
% Calculates the steady state potentials with a given synaptic input.
%
% Input
% -----
% - intree ::integer: inde... |
8afa581201a5d7bbeb612c9825ff131bf76e9652b96fa40dc45498dd9df2706c | MATLAB | 3,311 | 140 | %%
clear; close all; clc
good = 1;
bad = 0;
use = bad;
if use
cd('Z:\SNM\labMembers\YG\data\learningAnalysis\summaryManyMice_includingOldEnvGoodMoreMice\commonUniqueCells')
outFolder = 'Z:\SNM\labMembers\TM\Novelty_Analysis\clusterMan\good';
else
cd('Z:\SNM\labMembers\YG\data\learningAnalys... |
a84558972bc64d1bbfb91ef29bd9adc6ac2d40239b813ccf6eadbd8188596645 | MATLAB | 3,316 | 180 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
b817285f69c9adb2c36843a17a11d63a6c66916df4a2a6631cc2030f880637b0 | MATLAB | 3,318 | 133 | %rf_hs.m
%Jamie Near, McGill University 2020. Based on old code from 2007.
%
% USAGE:
% [RF,FM,mv,sc]=rf_hs(N,n,tbw,Tp,trunc,thk)
%
% DESCRIPTION:
% this funciton creates a GOIA gradient modulated adiabatic pulse, using
% the method of gradient modulated offset-independent adiabaticity as first
% described by Tannus... |
484f87a7fe1fc60c0fe37c172d16b4988fad4b5f49b16776dd7eb6276fdc954d | MATLAB | 3,321 | 123 | dblist=dir('*_data_*.mat')
minrelaxdur=0.03; %minimal duration of the relaxed/silent phase_MU
twin=0.5; %timewindow in second
BurstTiming_CTL=[];
BurstTiming_WK7=[];
%temporary
for k=1:length(dblist)
load(dblist(k).name)
%%EXTRACTING DATA
%stim timebase
sttemp=[];
c_st=1;
for s=1:50:length(stim.time... |
32b28915d63077c82cf3756a2d9d8041b04c9cd341d37c3c313d60da8997e2b6 | MATLAB | 3,331 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
4b4dcd7e377c0faa448969ffa79f7f6b8dd0ec7bcd97e9033898295eedbc1218 | MATLAB | 3,331 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
51db3aa681fbc84f1e01d4966a18e69cd80f7ed56cb48a1f76c046bb66a20c40 | MATLAB | 3,331 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
e2f7915dcac4aec425608db31f2d177c4a0abc61c6e62aba37be08483cc50e55 | MATLAB | 3,331 | 100 | function softwareTimedVoltage
% Example showing software-timed analog input using the Vidrio dabs.ni.daqmx wrapper
%
% function vidrio.AI.softwareTimedVoltage
%
% Purpose
% Describes how to do software-timed analog input using Vidrio's dabs.ni.daqmx wrapper
% This is unbuffered or "on demand... |
02e2d7a125c842d5d96175d59fe73617adb493526b2d1f202b16933116a2c3f7 | MATLAB | 3,332 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
dcc7cd85a53e01a493af54c74bf8271ab8c46e42326a0670b10f98c91b7a2bb1 | MATLAB | 3,332 | 105 | % SWC_TREE Export tree to swc-format.
% (trees package)
%
% [name path] = swc_tree (intree, name)
% -------------------------------------
%
% Exports a tree to the swc-format, a matrix with 7 columns:
% [inode R X Y Z D/2 idpar]
% node index inode is usually from 1..N and idpar is the direct parent
% index. The root... |
11085964177aa25275893259ac922b3dbec358f1c718a3e2fc5bf309b48cee61 | MATLAB | 3,334 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
17769346262d9d7aadbd3df82a51a6f2fb1669b5847ac9b8b8c2a5f8fd23d29e | MATLAB | 3,334 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
5a306863576206f962904e1a916afdd65fed306f472b0ebaea854c7ef56864f6 | MATLAB | 3,335 | 92 | clearvars
clc
close all
%% parameters
allNeurons=[1]; %Add neuron number here
amplitudes=[0 20 50 100 200];
conditions = {'ACSF','BQCA', 'TD'};
preStimDuration = .1;
postStimDuration = .1;
%% loading And Filtering Data
cd '\\researchdata.anu.edu.au\\...' %specify the directory to load files
window=0.05;
... |
9c31c7d4789274824e77d98431da063089691c59060c974ffc8694bddfb1f8be | MATLAB | 3,335 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
77756dac1e4ccd5d7da2a2072e29c29d4aac3a9738d604274e16ce3d88d532c0 | MATLAB | 3,337 | 182 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
450303648803204bc1349e4e7ff6693cb6c0b30863a668496a744abcacfb3b36 | MATLAB | 3,338 | 89 | function mv_print_classification_info(cfg, X, clabel, X2, clabel2)
% Prints information regarding the classification procedure, including the
% cross-validation procedure and the dimensions of the input data. This
% function is called by mv_crossvalidate, mv_classify_across_time, and
% mv_classify_timextime.
%
% Usage:... |
791d99a7a3276caf94991a1e99c8bb2aa55e3f6c4294c161b56e919ced1b1fe8 | MATLAB | 3,340 | 82 | function [job, data] = TF_prepare_generic_data(job, data)
% [job, data] = TF_prepare_generic_data(job, data)
%
% Add aggregated TF-domain data sets per subject across conditions, per
% condition across subjects, and both.
% Creates data sets that are only dependent on the conditions used for
% aggregation; NOT on con... |
d4e6e4775c443edd3dcc196802c4f9f31f4c58df9b0258f210f0980fd0020427 | MATLAB | 3,340 | 182 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
98f5a9fe5aa285a5d431c82420c62d52552d0a90ce43971df08ec2767ff7c02c | MATLAB | 3,347 | 76 | function [final_tform, align_vol] = OptoAlign_rigid(ref_vol, z_ref)
%
Nz = size(ref_vol,3);
if nargin == 1, z_ref = round(Nz/2); end
%temp_ref = ref_vol(:,:,z); figure; %temp_trim = [0,0]; % y, x
metric = registration.metric.MeanSquares;
optimizer = registration.optimizer.RegularStepGradientDescent;
imVi... |
070a679df38d495dd1a96f5cdb7577a91f44259b9e8719788aca51120c5f914d | MATLAB | 3,350 | 100 | %sim_megapress.m
%Jamie Near, McGill University 2014.
%
% USAGE:
% out=sim_megapress(n,sw,Bfield,linewidth,sys,taus,refoc1Flip,refoc2Flip,editFlip)
%
% DESCRIPTION:
% Simulate the MEGA-PRESS sequence with instantaneous localization and
% editing pulses. Provides the ability to specify the flip angle of each
... |
1fb76e0929944f3fb09ddb092d12fc888d5d12cddfe664f453851b9525f433d3 | MATLAB | 3,353 | 94 | function data = edf2fieldtrip(filename)
% EDF2FIELDTRIP reads data from a EDF file with channels that have a different
% sampling rates. It upsamples all data to the highest sampling rate and
% concatenates all channels into a raw data structure that is compatible with the
% output of FT_PREPROCESSING.
%
% Use as
% ... |
a9acf0d6f54239d84ca725ba06a39a11114abc847c029813b228b22e5ee4bcab | MATLAB | 3,356 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
219c518ead906cbdf1de75ae26e403987b23321180a6bfc1a659c1e704aa22ef | MATLAB | 3,357 | 94 | function simulateCombSimpleModel(baseModel, outFilename, fracA, TNM, TNG, TAM, TAG, statUtil, mobUtilN, mobUtilA)
% simulateCombSimpleModel
%
% Generates a combined model from the params supplied and runs a simulation.
% The fluxes of glycolysis, mitochondrial respiration, and both are then extracted
% for both ne... |
49050bb3d10771d661aebbb37d3001b16938c283433b38cc0498d0552ba5688a | MATLAB | 3,357 | 125 | % mv_crossvalidate unit test
rng(42)
tol = 10e-10;
mf = mfilename;
% Generate data
nsamples = 100;
nfeatures = 10;
nclasses = 2;
prop = [];
scale = 1;
do_plot = 0;
[X, clabel] = simulate_gaussian_data(nsamples, nfeatures, nclasses, prop, scale, do_plot);
%% accuracy on test set should be lower than on training set
c... |
65a33725e26252a0e9ed4994a46df464c8d4b10090e7d8097c27912c4a9ea3cb | MATLAB | 3,365 | 182 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
0a435c92c3bdef32d0294cbf5d3b564eb96413a411aad985b7fdf9ed764d4dad | MATLAB | 3,368 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
3c4b66f7fef766963e99192a3ef0e278e225f30441370c901ff58bf86c4e0df2 | MATLAB | 3,370 | 182 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
3668894d653d3dd407c4c0b32b0bd80d62e18b33141168dcb5ae869d7030cc23 | MATLAB | 3,371 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
516b5f394899a2fd07aa1999f5f4ea7869bba7b99acb40a3541ab0a9241abc3e | MATLAB | 3,373 | 130 | function figureS1(dataFolder)
if(nargin<1)
error('Path to data required as input argument. Data can be downloaded from link in README file.');
end
for i = 1:11
render_neuron_morphology(i,dataFolder);
end
end
function fig = render_neuron_morphology(mType,dataFolder)
mTypes ={'L23... |
ad7b608ff3a53381f5216471cef4bcfe78814a1b711402fcf4ad6091e3c5dbbb | MATLAB | 3,373 | 125 | clear all
% Define PB and FB angles
thetaRight = -[67.5 112.5 157.5 157.5 -157.5 -112.5 -112.5 ...
-67.5 -22.5 -22.5 22.5 67.5];
thetaLeft = -[-67.5 -22.5 22.5 22.5 67.5 112.5 112.5 ...
157.5 -157.5 -157.5 -112.5 -67.5];
thetaFB = -((0:30:330) + 15);
% Parameters from data fit
a = 29.2... |
7785db6cda7effc2caf4981622ddcae5a28344e354be862e6d2e771c654c0afc | MATLAB | 3,374 | 90 | function[RowShifts,ColumnShifts,ZShifts] = InterpolateZshift(ReferenceVolumes, Volume, WidthCorr)
% COMPUTEZSHIFTINTERPOLATE: calculate Z shifts
%
% Inputs:
% ReferenceVolumes -- 4D matrix of uint16 or other, dim (x,y,z/n,t)
% Volume -- 2D matrix of doubles, dim (z,t)
% WidthCorr -- 2D matrix of d... |
b0faabef82a9c77772a9443b6efb4dd8597c0efb09b9b2caf89724631e7f37ef | MATLAB | 3,374 | 77 | function controlVal = laser_mW_to_control(obj,mW)
% Convert a desired value in mW to a control voltage for the laser
%
% function controlVal = zapit.pointer.laser_mW_to_control(mW)
%
% Purpose
% The user will request a laser power in mW at the sample. If a calibration curve has
% been genera... |
cfe94a670f6828a7a564b6b6d50f04d6009070e08103e17b4251b0282b5cbc14 | MATLAB | 3,377 | 97 | function self = detect_sigs(self, objPI, tracesNorm, frameRate, roiNames)
%detect_sigs - Detect the signals
%
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% This program is free software: you can redistribute it and/or modify
% it under the terms of the GNU General Public License as publ... |
437c58d79b98c818cd4a2c2e557d805a71733f76bdb39d9d6d71ada7f97f4e96 | MATLAB | 3,378 | 133 | load('foldersAllIndvFOV.mat');
fieldD={};%day by day distribution
fieldDA={};%day by day distribution and amplitude
p=pwd;
for n=1:11;
fieldD{n}=[];
fieldDA{n}=[];
for m=1:length(foldersAllIndvFOV);
cd(foldersAllIndvFOV{m}{n});
load('PValueClassifier_KY2_6_sig\al... |
d62ac7f536ff58fcab2b7aff77072e348e7c773699bf78bb9d6822dc3edee2cb | MATLAB | 3,378 | 102 | function TFplot(job, data, zlim, yScale)
% TFplot(job, data, zlim, yScale)
%
% Creates time-frequency plot (2D heat map) contasting two conditions.
%
% INPUTS:
% job = cell with relevant fields for plotting settings,
% required fields:
% .TFtiming = vector of 2 scalars, start and end tim... |
a258f2c6175e528915d49adfd89c6debc005a6b084481bac6915a29ca148add1 | MATLAB | 3,379 | 93 | function varargout = plot(self, objPI, varargin)
%plot - Plot a figure
%
% plot(OBJ, OBJ_PI) plots the default figure for the CalcDetectSigs
% object OBJ using the ProcessedImg object OBJ_PI.
%
% plot(OBJ, OBJ_PI, AX, FIG_NAME) plots the figure on the specified axes
% handles AX, and the particular figure speci... |
4364990dbd8347919732719494449704cf4f7a7402f773ee785c2f4b6364126c | MATLAB | 3,380 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
d40c5506bc5722b90004809ca695958c913925c302f7affcd09a9a1d927d5ee7 | MATLAB | 3,380 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
4de01abeb60573a2cb40f786b9a626d0a70ac4af0f0c353dfb0ed0e5637561d8 | MATLAB | 3,381 | 96 | function img = resize_img(img, szImg, varargin)
%resize_img - Convenience function to resize an image, with warnings
%
% IMG = resize_img(IMG, [NUMROWS NUMCOLS]) resizes the image IMG so that
% it has the specified number of rows and columns.
%
% IMG = resize_img(IMG, [NUMROWS NUMCOLS], METHOD) specifies a method... |
aa4c74d84d2cda3a605d1dad9df493ed6e5a1337e1329de327d0be37a3ff0fbb | MATLAB | 3,383 | 106 | function [lambda, fntwrk, gmf, ixAMPAmf] = solve_gALL_lambda_fntwrk_iX(sx, sy, x0ini, xx0ini)
% Solves MF & LS equations for synaptic conductances, instability growth
% rate, and oscillation frequency given external and population firing
% rates.
%
% External and population rates are passed through
% global ... |
cf2d28705a3ec3d68626cf9aa3a3a4f40b523c68826793342d18d5e89838ad5a | MATLAB | 3,383 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
556658b696caf3b6b1c37286a3353f8313dc21b37209b18f8e803339802c5e8c | MATLAB | 3,390 | 116 | clear
close all force
warning on
imSize = [733, 977];
imSizeCent = fix([733, 977]/2);
pix2deg = 34.910;
y1 = imSizeCent(1)+(-130:70);
x1 = imSizeCent(2)+(-120:0);
y2 = imSizeCent(1)+(-130:70);
x2 = imSizeCent(2)+(0:120);
%load tirals info
load('a0_0_bhv2trialStrct.mat', 'dataExp');
load('a0_3_0_extractingTheMorphing... |
65cc3b23c6ba83a4286547acb924b09782d8c4f43d237c7c6afd379a02015e92 | MATLAB | 3,391 | 91 | function [MM, bgCh] = assemble_mixmat(img, maskFPBG)
%assemble_mixmat - Assemble the mixing matrix based on masked regions
%
% MM = assemble_mixmat(IMG, MASKS) assembles a mixing matrix MM for the
% image IMG using the exclusive fluorophore regions identified using
% MASKS.
% IMG must be an MxNxCxP image array,... |
70234545b2658b42f9070da53eeebcbfe81f9c9cfccf5ec5325c017594d56a71 | MATLAB | 3,395 | 90 | %% Note Filter Example
%
% <html>
% Import streaming EEG data into Matlab using TDTbin2mat <br>
% Filter around behavioral events that were timestamped by the user
% using the Run-time Notes feature in Synapse <br>
% Plot each occurrence in a subplot organized by Note type <br>
% Good for sleep scoring and behav... |
06285c08df3ce227c35fd6c9f33c2c35476e7ad481a1ab191461ea1c56ae5d88 | MATLAB | 3,397 | 90 | %% Note Filter Example
%
% <html>
% Import streaming EEG data into Matlab using TDTbin2mat <br>
% Filter around behavioral events that were timestamped by the user
% using the Run-time Notes feature in Synapse <br>
% Plot each occurrence in a subplot organized by Note type <br>
% Good for sleep scoring and behav... |
222a8a8c72c3914d1d95abf613a046f7350021891727dcf7413126f417820b94 | MATLAB | 3,399 | 92 | % folder of the raw video
dir_video='..\..\demo\data\';
% folder of the GT Masks
dir_GTMasks=fullfile(dir_video,'GT Masks\');
% name of the videos
list_Exp_ID={'YST_part11';'YST_part12';'YST_part21';'YST_part22'};
fs=10; % frame rate
before=15; % number of frames before spike peak
after=60; % number of frame... |
462c0770de2a6409db6f7b27f1dd21cce220d4e0ff5a5aa7b03f27801efe9944 | MATLAB | 3,401 | 58 | function periBout = GetBoutData( boutScans, T, loco, deform, fluor, deformVars, periParam ) % , isCSD
Nbout = numel(boutScans);
periBout = struct('Nbout',Nbout, 'dur',nan(1,Nbout), 'scan',[], 'Nscan',nan(1,Nbout), 'iso',[], 'T',[], 'Tstart',nan(1,Nbout), 'Tstop',nan(1,Nbout), 'preScan',[], 'boutScan',[], 'postScan'... |
a94de0f213095926ccfaf2871642ff81c24a8dbcd681052eef7e2230dcf755c3 | MATLAB | 3,402 | 106 | function [All, outVars] = defineDistanceTypes(All, outVars)
numExps = numel(All);
for ind = 1:numExps
pTime =tic;
fprintf(['Processing Experiment ' num2str(ind) '...']);
if isfield(All(ind).out.exp, 'dataToUse')
dataToUse = All(ind).out.exp.dataToUse;
else
disp(['ind ' num2str(ind)... |
6078dd3df59ed177a6578bc58b400e5158653dd110347daa7c0661e60b55533d | MATLAB | 3,404 | 110 | % fida_depCheck.m
% Jamie Near, Sunnybrook Research Institute 2024.
%
% USAGE:
% [flist,plist]=fida_depCheck(in);
%
% DESCRIPTION:
% Returns the full list of file dependencies and matlab product dependencies
% within a particular FID-A toolbox (or within all FID-A toolboxes).
%
% INPUTS:
% in = The name of the FID-... |
e51a33c6f037eb0e63f38250e31c869067efce620f2e7c658ec21e296e427512 | MATLAB | 3,405 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
8375fbbbdcde02218250e6727823ecebc9b0e4954727ee0d48a175d8d427c6a9 | MATLAB | 3,406 | 102 | function [ephysWaveform,scaleFactor] = filterForEphys(obj,inputWaveform)
% Filter the laser waveform for ephys: turning square waves into sinusoids
%
% function ephysWaveform = zapit.stimConfig.filterForEphys(obj,inputWaveform)
%
% Purpose
% By default the laser is gated by a square wave which i... |
6859c6e603d5f272e46eed7c51c3422d83a45a95c634fd66fc34a9d5fe43f402 | MATLAB | 3,407 | 74 | function success = loadStimConfig(obj,pathToConfig)
% Load a stim config and add as property
%
% success = zapit.pointer.loadStimConfig(pathToConfig)
%
% Purpose
% Load a stim config file and attach it as a zapit.stimConfig
% to zapit.pointer.stimConfig and set up the parent property.
%
... |
165540bdde55ecd66a92c98b617a0436989d069d23c05460af2dd593c1a74bef | MATLAB | 3,408 | 140 | close all force
%
clear
load('a0_0_bhv2trialStrct.mat')
%}
NImage{2} = [...
2
4
5
6
8
10
12
13
17
18
19
20
26
29
35
];
NImage{1} = [...
7
11
25
27
38
39
40
47
49
53
56
60
9
22
28
41
42
... |
aac902831263236613d2a63778334317521dc4de143b86f3ffdc136f8b220a99 | MATLAB | 3,414 | 93 | function [totModel] = buildSimpleAstroNeuronModel(baseModel, fracA, TNM, TNG, TAM, TAG, statUtil, mobUtilN, mobUtilA)
% buildSimpleAstroNeuronModel
%
% Generates a combined model having one astrocyte model and one neuron model.
% The models can exchange lactate. Glucose is administered via the neuron model (untagged)
%... |
806be20d5eae221c782d9ca418b38077dbde39fc61642d944b2141ff9fe3042a | MATLAB | 3,423 | 113 | % CYL_TREE Cylinder coordinates of all segments in a tree.
% (trees package)
%
% [X1, X2, Y1, Y2 ,Z1, Z2] = cyl_tree (intree, options)
% -----------------------------------------------------
%
% OR (if only one output):
%
% M = cyl_tree (intree, options)
% ------------------------------
%
% Uses the adjacency m... |
8715395f0303fca788b88d98f98bae98dd233f8611327e43ef90685abdb19147 | MATLAB | 3,424 | 84 |
Nz = size(ref_vol,3);
z_ref = round(Nz/2);
metric = registration.metric.MeanSquares;
optimizer = registration.optimizer.RegularStepGradientDescent;
imView = imref2d(size(ref_vol,[1,2]));
%temp_ref = ref_vol(:,:,z); figure;
temp_trim = [0,0]; % y, x
dX = zeros(Nz,1); dY = zeros(Nz,1);
blank_tform = im... |
6608b4260d8ba557c15a4da32d63d394239f06700ebd6b037278ffafddf42c8f | MATLAB | 3,425 | 72 |
load('Fig3DoubleDissociationEffect')
for ntp = 1:49
[h,p(ntp),dc,stats] = ttest2(-AMY_structure.real_t_val_aro(ntp,:) , -AMY_structure.real_t_val_discrimination(ntp,:) ,'tail', 'right') ; %
t_val(ntp) = stats.tstat ;
end
h = p<=0.05;
[labeledA, numRegions] = bwlabel(h , 8);
for n_cluster = 1:numRe... |
f81951dba3043b1b1c70e0aac3f6c4877cc2e690ae55ac0ffb84d84ba6225502 | MATLAB | 3,430 | 102 | function [lambda, fntwrk, gN] = solve_gNMDA_lambda_fntwrk(xvar, yvar, sync, nuX0, g0, omega0, xx0ini)
% Solves MF & LS equations for population firing rates, instability growth rate,
% and oscillation frequency given conductances and external firing rate.
%
% Population rates are passed through global variable s... |
65e0e09dca99f062aeb6004234d0ab0c808e0cf507af30beb4d24b2a2adee838 | MATLAB | 3,431 | 100 | function [loglik] = EEGfMRIPav_cbm_mod04(parameters,subj)
% Standard Q-learning model with delta learning rule and with Go bias and
% instrumental learning bias.
% ----------------------------------------------------------------------- %
%% Retrieve parameters:
% 1) Feedback sensitivity:
nd_rho = parameters(1);... |
5e2cce4ff56f9e540bcb1dbac5a2d6fd1df0255ef19dbdba2371b0bdf7195b93 | MATLAB | 3,440 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
fd2d49dd41b8a5e02c5a4d430e7fad4003e494457e3c9b763f2a0f7c8c99364f | MATLAB | 3,442 | 98 | function [ph_filt_signals, amp_filt_signals] = filt_signalsWAV(sig1,sig2,...
Fs, ph_freq_vec, amp_freq_vec, measure, width)
% function [ph_filt_signals, amp_filt_signals] = filt_signalsWAV(sig1,sig2,...
% Fs, ph_freq_vec, amp_freq_vec, measure, width)
%
% Returns cell arrays 'ph_filt_signals' and 'amp_filt_signals'... |
ec1466e90d90f03ce1f81b4c0d3648e831f0bc234ee5fe68c17c6486a75f0558 | MATLAB | 3,443 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
0aba4fdd167798969c57173b287b7a2e8bf7e6b02bbd5b18c04a7c416de748db | MATLAB | 3,447 | 133 | function [Y,Nsum] = moving_average(X,F,DIM)
%MOVING_AVERAGE Smooths a vector through the moving average method.
%
% Syntax:
% [Y,Nsum] = moving_average(X,F,DIM);
%
% Input:
% X - Vector or matrix of finite elements.
% F - Window semi-length. A positive scalar (default 0).
% DIM - If DIM=1: smo... |
6ad8dd9e6552e8d11723e5f9e9409848451e251765f3a8982cc2b5f303663015 | MATLAB | 3,459 | 110 | function tfce_progress(action,varargin)
% Display progress and remaining time
% FORMAT tfce_progress('Init',n_iterations,process_name,iteration_name)
% Initialises progress tool
%
% FORMAT tfce_progress('Set',value)
% Sets iteration.
%
% FORMAT tfce_progress('Clear')
% Clears the progress output and prints processing t... |
e9d66f806fc2ed07c0c930fc8cc0df274565c6f0e2e6fb0e6942730d97a79d65 | MATLAB | 3,459 | 95 | function [m]=mesh_extract_points(m,chunk_points_logical,varargin)
% Returns a mesh which contains only the selected points (i.e., nodes)
% and affected simplices and data.
% USAGE: [m] = MESH_EXTRACT_POINTS(m,chunk_points_logical)
% Mirko Windhoff, 2009
% updated by Alexander Opitz, 2016
% modified by Ivan... |
853e72cc7725e8ccacce570810ab33bd2450fcf4032f22558b1d8180634316ba | MATLAB | 3,460 | 82 | %% READ ME:
%
% Written by Zachary Sanger, M.S.
% University of Minnesota
% Biomedical Engineering Department
% May 16th, 2023
% INPUTS: This code requires a path which defines the location for whatever folder your data
% is stored. Filename can be changed to a structure if you plan to load
% multiple ".json" files.... |
c27aa167d30b6a149ac098e8c43aa484b24e58800765b7149c7a7387310ded4f | MATLAB | 3,478 | 128 | classdef testCamera < handle
% zapit.testCamera
%
% Barebones class to test the camera stream to be used in the optostim box
%
% e.g.
% C = zapit.testCamera
%
% % Now stop and start the video
% C.stopVideo
% C.startVideo
%
%
% Rob Campbell - SWC 2022
% The foll... |
aaedf038801be9e47be2c89a3aa10a312e55fce1478f7067339e51f659178cf9 | MATLAB | 3,480 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
edc8a87719d1fbc96d9e4f5da7ad0aeed1087b4612e11fcdc21a57773e35c028 | MATLAB | 3,481 | 112 | %% Load data
load('demo_data');
%%
%% PLOTTING INTRACRANIAL ELECTRODES AND DATA
%%
%% First we will plot the brain (the right hemisphere):
% You can rotate the brain with the 3D rotation tool (selected by default).
% Since you are also rotating the light source, it needs to be manually
% reset. To do this, de-selec... |
8902ee3f90cd4daac1e0b3d616fa06b0c2eb7ec8a294e7301e129932b8d3d149 | MATLAB | 3,483 | 181 | %first column = channel number on probe. Convention is ch. 1 is at top left of PCB
%and number wrap around in counter-clockwise fashion.
%second column = x coordinate, horizontal distance to reference electrode in microns. Convention is
%for reference electrode to be at bottom left corner of array when array
%points... |
0756e63594c5f7559b2beee50371e6b49f85da13ec45d3b055497523559753b0 | MATLAB | 3,485 | 129 | % SCALE_TREE Scales a tree.
% (trees package)
%
% tree = scale_tree (intree, fac, options)
% ----------------------------------------
%
% Scales the entire tree by factor fac at the location where it is (NEW!).
% If fac 3-tupel scaling factor can be different for X, Y and Z. By
% default, diameter is also scaled (as ... |
fbd3436b7614a445f826d169914a502111bae401c8d042f50c936a0995efc6c4 | MATLAB | 3,486 | 31 | %% To extract the voltage from 32 channels and timestamps for stimuli for experiment 20211021
Record1_data_20211021 = load_open_ephys_binary('D:\Data\optogenetics\Open Ephys\DataFiles\max_ephys1_2021-10-21_16-34-10\Record Node 110\experiment1\recording1\structure.oebin','continuous',1);
Record1_stim_20211021 = load... |
d972bf54edd1e6e3a9e3817eab487f72654224deb9356e9369811516577d7d8b | MATLAB | 3,488 | 107 | % PETERS_TREE Calculates candidate synapses oftwo trees.
% (trees package)
%
% syn = peters_tree (intree1, intree2, spinedis, synapsedis, options)
% -----------------------------------------------------------
%
% Finds putative synapses of two trees. Loops through all nodes of tree2 to
% find all nodes of tree1 closer... |
0ffff528b01e7f00cac7445a6ba25040a34619dc366349c3e2d5eb833a8457c7 | MATLAB | 3,494 | 112 | lambda_E = @(p) pdf('logn',p,log(0.5),1);
lambda_I = @(p) pdf('logn',p,log(2.5),1);
tauE = @(p) pdf('unif',p,1,3.5);
tauI = @(p) pdf('unif',p,5,20);
gE = @(p) pdf('unif',p,0.2e-3,2e-3);
gI = @(p) pdf('unif',p,0.2e-3,2e-3);
erev = @(p) pdf('unif',p,-75,-45);
gleak = @(p) pdf('unif',log10(p),-5,log10(0.005));
t1 = 10.^... |
b59bf154878cec76bc99c09e645c03e183deb636f7a93e5a7a434bb9016f489e | MATLAB | 3,498 | 102 | function val_nuisance
% Calibration of the three strategies for nuisance variables.
%
% Draper-Stoneman permutes the effects of interest in the design, Freedman-Lane
% permutes the data after residualising it against the nuisance variables, and
% Smith orthogonalises the effects of interest against the nuisance space b... |
f5cd2f5fbb7b1e4af67fea172b26e2b2edacb8631727fedc4e4d58dbd9eb47d8 | MATLAB | 3,498 | 111 | % PRUNE_TREE Prunes short branches.
% (trees package)
%
% tree = prune_tree (intree, radius, region, options)
% -------------------------------------------
%
% Cleans tree of terminating segment smaller than radius. If two sub
% branches are smaller, then the shorter one is deleted first.
%
% Input
% -----
% - intree... |
8fd9f84fac54716cad74ac13f546679ef9d99e283241918b9606e63c8c4edf00 | MATLAB | 3,499 | 130 | function [proj] = KMAproject(labeled,unlabeled,test,ALPHA,options)
% Kernel manifold alignment
%
% Usage : [eigenvectors,eigenvalues] = KMA(Labeled,Unlabeled,NumDomains,options)
%
% Inputs:
%
% - labeled: structure with labeled data [1,NumDomains].
% each cell has X (n1 x dim1) and Y (n1 x 1) fi... |
97e78e6c450dbd8eaf2c839a7f46a723cf316b1cb692b1362f6163ae293a6e55 | MATLAB | 3,499 | 99 | function varargout = plot(self, varargin)
%plot - Plot a figure
%
% plot(OBJ) plots the default figure for each element of OBJ.
%
% plot(OBJ, H_FIG, FIG_NAME) plots the figure on the specified figure
% handle(s) H_FIG, and the particular figure specified by FIG_NAME.
% FIG_NAME must be one of the following:
%
%... |
2fea20cf92ed6e57f1a366bf0010b475aeef63eebaf10199ddb586db183694cd | MATLAB | 3,502 | 91 | function edges = GetEdges(inputIm, varargin)
% edges =[ leftEdge, rightEdge, topEdge, bottomEdge ]
IP = inputParser;
addRequired( IP, 'inputIm', @isnumeric )
addParameter( IP, 'max', [300, 300, 150, 150], @isnumeric )
addParameter( IP, 'minInt', 2000, @isnumeric ) %
addParameter( IP, 'show', false, @islogical... |
68bfd0d1895514770f84115b485e6fd1c32be58e250ca6f43341492c1b403205 | MATLAB | 3,503 | 120 | % LOADDIR_STACK load images from a folder into a stack structure.
% (trees package)
%
% [stack path] = loaddir_stack (path, options)
% --------------------------------------------
%
% Loads all images from a directory to an image stack. Images must have the
% same size. But no file error handling.
%
% the stack struc... |
a0d6de1932d7ac9d087c32bd418f243ec5c6ec9c9e37ee8ef48b4aa5edbc3c80 | MATLAB | 3,504 | 87 | classdef SbxWriter < handle
% A class to write SBX files, which keeps track of the current position
properties
path = [];
curframe = 1;
info = [];
fid = [];
end
methods
function obj = SbxWriter(path, info, extension, force)
% Path for savin... |
df3336afb298b5fd79d8b0a30db76dd367e0277c90e879aad91658b02ae1eab8 | MATLAB | 3,505 | 72 | function normalizeImage_cuda(roundnum,do_downsample)
%TODO: The CUDA Version of normalization still needs to be improved. See normalizeImage.m
% for reference. -DG 2020 09 09
loadParameters;
src_folder_name = params.colorCorrectionImagesDir;
dst_folder_name = params.normalizedImagesDir;
channe... |
34c623e85544a0ac96bcac31564c6ae4c757a1e8d39f1d7dcade5da7431c07a9 | MATLAB | 3,506 | 113 | function varargout = calibrateScanners(obj)
% Calibrate scanners with camera: conduct an affine transform to calibrate camera and beam
%
% function varargout = zapit.pointer.calibrateScanners()
%
% Purpose
% Moves beam sequentially across a series of locations and records the intended vs
% a... |
bd8b105484f308ea894f33936d53c6549dd86e0ca645b3073d703cd53defe213 | MATLAB | 3,507 | 93 | function [totModel] = buildSimpleAstroNeuronModel(baseModel, fracA, TNM, TNG, TAM, TAG, statUtil, mobUtilN, mobUtilA)
% buildSimpleAstroNeuronModel
%
% Generates a combined model having one astrocyte model and one neuron model.
% The models can exchange lactate. Glucose is administered via the neuron model (untagge... |
562fe127930621522b72d94ac3f60958773a8a185cc39434986dad6eb44d0b2a | MATLAB | 3,515 | 127 | function val = read_stats(dir,save)
val = 0;
printdocs = 1;
beta = [];
load(strcat(save,'/train_stats.mat'));
fileID = fopen(strcat(save,'/train_alphabet.txt'),'r');
tok = textscan(fileID, '%s');
fclose(fileID);
fileID = fopen(strcat(save,'/train_target_alphabet.txt'),'r');
label = textscan(fileID, '%s');
fclose(file... |
2820605332b222271158deb43480c4e783949310135cf44556f72a5049643da0 | MATLAB | 3,519 | 101 | function plot_imgs_sub(self, objPI, hAxes, varargin)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% 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 Foundation, either versio... |
1d71c7b1bd1de91585154b7ec46cf902d0e3c450dbc1d4c5daf124e4e9d37ba7 | MATLAB | 3,522 | 83 | % Compute segregation measures based on Chan et al. (2014) PNAS paper
% Both global and network-level measures are created
% Function files required:
% 1) systemsegregation.m: computes the system segregation measures given the network assignment and FC matrix
% 2) mat2col.m: converts the 2D FC matrix to a vector colum... |
965ae7fd123b9ab9151fbb403b816fed6f395e55a36f31a06fdaa2867c07b14a | MATLAB | 3,522 | 118 | function varargout = plot_default(self, objPI, ~, varargin)
%plot - Plot a figure
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% 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 Softw... |
fc55f7e5ecc0ccb587c60ce08326ff9c916c67895e552ab28fee13314ccf5799 | MATLAB | 3,525 | 134 | function [respvolTotal,timeVector, rawTotal] = getRespCompSliceTR(inputImage,s,TR,interpolationFactor)
imSize = s(1:3);
imIndex = 0:19:38;
respvolTotal = zeros(size(inputImage));
rawTotal = zeros(19,s(4));
for ii = 1:19
inputSG = squeeze(inputImage(:,:,imIndex + ii,:));
imSizeSG = size(inputSG,1:3);
... |
977c5694bc140250a7fc2f5cd77fb88a57dc29f52980f8c541603aa904a53eec | MATLAB | 3,537 | 112 | function [objID, objZoom, pxSize, experimenter, channels] = parseOME(self)
% Copyright (C) 2017 Matthew J.P. Barrett, Kim David Ferrari et al.
%
% 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 Fou... |
0c68f160dc888f5fc9aca809f010bfe11ab74c5608342f10d064f348e87b2de9 | MATLAB | 3,540 | 113 | function prop = parsepropval(prop, varargin)
%PARSEPROPVAL2: Parse property/value pairs and return a structure.
% Manages property/value pairs like MathWorks Handle Graphics functions.
% This means that in addition to passing in Property name strings and
% Values, you can also include structures with appropriately n... |
1ce469f50edc64fef8258b92b09933d71c0f492aea65615f4eb5a0c3db06da3e | MATLAB | 3,541 | 106 | function maskFPsBG = select_fp_masks(img, nFPs)
%select_fp_masks - Select masks for fluorophore and background regions
%
% MASKS = select_fp_masks(IMG, N_FP) displays the multichannel image
% and prompts to select N_FP regions, each one containing exclusively a
% single fluorophore, as well as a mutual background... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.