sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
346d9abfdb1e327f66c32e409a322b9c4fcd26e091b3e02bac3638ca98230388 | MATLAB | 66,504 | 2,256 | function [zmaps omaps cost] = mri_b1map_sliceselect(yy, alpha, varargin)
%function [zmaps omaps cost] = mri_b1map_sliceselect(yy, alpha, [options])
%|
%| Estimate "B1+ map" for each of ncoil coils
%| from sequence of reconstructed images with ntip different nominal tip angles.
%| Model:
%| todo
%| in
%| yy [nx ny nmea... |
c5edc7cef64fc14de4849167cb5f454c9646a8f8769f15e30b4b3ca46bc3bb30 | MATLAB | 66,552 | 1,362 | % function MAP_fig_1_multi(mname,config)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% ################################################################# %% DESCRIPTION
% Script to analyse data for:
% Grieves et al. (2020)
% Quantification of firing rate map procedures
%
% This script
% NO... |
8ab52489d30e904a7e45e9ae47356745ae108ddc28553a7fb6463293c2a6979d | MATLAB | 66,593 | 1,368 | function dartel = tbx_cfg_dartel
% Configuration file for toolbox 'Dartel Tools'
%_______________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% John Ashburner
% $Id: tbx_cfg_dartel.m 7155 2017-08-17 10:55:05Z john $
if ~isdeployed, addpath(fullfi... |
4628c1505e370639f90d0167385ca79afe007ea2cb7f903d5509c6db0c273ea0 | MATLAB | 66,642 | 1,310 | %PlotBinFirRate.m
% This function plots firing rate from BinFirRate.mat as color plot and average trace.
% structure of input file:
% bfa{animal, day}.bft{trial}(cell,bin_id) : binned frequency for each
% bfa{animal, day}.bpt{trial}(3, bin_id) : binned position (x, y, vel) for each trial
% bfa... |
9f8b76694a63feed20b0ef0a4a581509efd9390f32769a968c8e8bbd8c1b94ff | MATLAB | 66,694 | 1,315 | %PlotBinFirRate.m
% This function plots firing rate from BinFirRate.mat as color plot and average trace.
% structure of input file:
% bfa{animal, day}.bft{trial}(cell,bin_id) : binned frequency for each
% bfa{animal, day}.bpt{trial}(3, bin_id) : binned position (x, y, vel) for each trial
% bfa... |
09bfb57f27f56cefbb4dd02e333bc810cc0f007967277a7cdcbd5b463cacbea9 | MATLAB | 68,050 | 1,445 | function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1>
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export_fig ... -c[<v... |
7712949d3f7cd023b7f275cd3320335df11ae123e01359e72ab36772616939b4 | MATLAB | 69,253 | 1,638 | unction data = TDTbin2mat(BLOCK_PATH, varargin)
%TDTBIN2MAT TDT tank data extraction.
% data = TDTbin2mat(BLOCK_PATH), where BLOCK_PATH is a string, retrieves
% all data from specified block directory in struct format. This reads
% the binary tank data and requires no Windows-based software.
%
% data.ep... |
799a8cefffde8bd913ba23b4c9e2d659668907fe4a55a57f4c0d4d74fe1bc7c2 | MATLAB | 70,690 | 1,663 | % topoplot() - plot a topographic map of a scalp data field in a 2-D circular view
% (looking down at the top of the head) using interpolation on a fine
% cartesian grid. Can also show specified channnel location(s), or return
% an interpolated value at an arbitrary scalp locat... |
73920cb9139350838db0ba767d12862c3c77e1859cb43594a2958b6657cf9496 | MATLAB | 70,787 | 1,666 | % topoplot() - plot a topographic map of a scalp data field in a 2-D circular view
% (looking down at the top of the head) using interpolation on a fine
% cartesian grid. Can also show specified channnel location(s), or return
% an interpolated value at an arbitrary scalp locat... |
bb5dd7e41ff9d3e2d26dcbc39721f88c7efa0b2da7bf7597f3d0081776f38778 | MATLAB | 74,026 | 1,654 |
classdef ksGUI < handle
% GUI for kilosort
%
% Purpose is to display some basic data and diagnostics, to make it easy to
% run kilosort
%
% Kilosort by M. Pachitariu
% GUI by N. Steinmetz
%
% TODO: (* = before release)
% - allow better setting of probe site shape/size
% - a... |
1fee991924b4e9445244b14ec9857b890eac5da75688221877e6f852c9fe8b9f | MATLAB | 74,332 | 1,918 | classdef Supervisors < 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... |
93606ded91ffb5dbd4bd95c15aad820700a5291f186a43ce483de4ada5a4f9e4 | MATLAB | 74,538 | 1,625 | function [type] = ft_filetype(filename, desired, varargin)
% FT_FILETYPE determines the filetype of many EEG/MEG/MRI data files by
% looking at the name, extension and optionally (part of) its contents.
% It tries to determine the global type of file (which usually
% corresponds to the manufacturer, the recording syst... |
551259c58172e2aa7fcb1a6479e0fc698f499a7d8b6b34d5f13446fc22930e1c | MATLAB | 75,134 | 1,298 | function Pooled_animals_analysis(PATH,show_plot,save_plot,reanalysis,overwrite)
% PATH = 'Z:\Arturo\_Marie_Data\D1Npas-Arturo\Rotarod\DeepLabCut and calcium data\GPe-SNr\ACC';
spltpath = strsplit(PATH,'\');
spltnames = strsplit(spltpath{end-1},'-');
data_names = cell(1,2);
data_names{1} = spltnames{1};
data_names... |
960356c6758077aeb227cb787d7fc5d5a7725aef28a3f4303d0aad56482038ce | MATLAB | 76,335 | 1,798 | function varargout=spm_conman(varargin)
% Contrast manager: GUI for defining valid contrasts
% FORMAT varargout=spm_conman(varargin)
% - An embedded callback, multi-function function
% - For detailed programmers comments,
% see format specifications in main body of program (below user help)
%_______... |
6bd5e5e172a75c8a94d33f5c480ba60051e7f98244a558f186101afc60ce6174 | MATLAB | 76,440 | 2,045 | classdef Args < 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 ... |
74fa67f3d30cd7e48b54ec20699aff43d767afc87ccde64e3da85b90c9aa3150 | MATLAB | 79,273 | 1,861 | function varargout = cfg_util(cmd, varargin)
% This is the command line interface to the batch system. It manages the
% following structures:
% * Generic configuration structure c0. This structure will be initialised
% to an cfg_repeat with empty .values list. Each application should
% provide an application-speci... |
5e3313771209a6320aa8aa1a0150b3ec1fcaf8750ba17d91c41f31bdf4659d96 | MATLAB | 80,452 | 2,146 | classdef MDS< 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(Constant)
NO_MATCH_CLR=[.99 .99 .99];
CLR_EDGE_NORMAL=[.88 .... |
5d2258d5e3a2973b6a4f0300a59a51dc3bc25e7e2eb98a30e3bb6664d8f87c99 | MATLAB | 80,468 | 1,981 | function out = spm_dicom_convert(Headers,opts,RootDirectory,format,OutputDirectory,meta)
% Convert DICOM images into something that SPM can use (e.g. NIfTI)
% FORMAT out = spm_dicom_convert(Headers,opts,RootDirectory,format,OutputDirectory)
% Inputs:
% Headers - a cell array of DICOM headers from spm_dicom_headers... |
9d06ddfe47c41cc8ffdd147537ccccc997754503857c399a2c8ab76d07268b86 | MATLAB | 80,787 | 1,999 | %%
clc; clear all; close all;
dataLoc = 'C:\Users\kmfo8\Dropbox\Rutgers\Firestein Lab\MEA papers -- addl experiments\EXP for BDNF + glu\Glutamate cell death, BDNF treatment\v3 (final) of analysis\';
%
% load([dataLoc,'cellDeathPixelData.mat']);
% load([dataLoc,'cellDeathNucleiData_blindUnblind.mat']);
%
% blin... |
0fe0184eba9ccceefbcadda71930281677e4356b845f0980f0c59866d3c54943 | MATLAB | 81,235 | 1,921 | function [nidmfile, prov] = spm_results_nidm(SPM,xSPM,TabDat,opts)
% Export SPM stats results using the Neuroimaging Data Model (NIDM)
% FORMAT [nidmfile, prov] = spm_results_nidm(SPM,xSPM,TabDat,opts)
% SPM - structure containing analysis details (see spm_spm.m)
% xSPM - structure containing inference details... |
7679c79279a551bbc7786462e08590aaa852c0c4cc5df4050957408c725ec509 | MATLAB | 81,525 | 2,046 | classdef QfTable < handle
% Class for Hi-D matching with merging of data subsets using QFmatch or
% F-measure or both.
%
% This produces a visual table and histogram of dissimilarities and
% overlaps between subset matches.
%
% The function getAverages answers the question of overall goodness by
% returning... |
90cd59e21dea24403513a17b3d7f353b3d4052b56f47d7d56cfe84306f0875f6 | MATLAB | 82,132 | 2,029 | function [varargout] = spm_eeg_review_callbacks(varargin)
% Callbacks of the M/EEG Review facility
%__________________________________________________________________________
% Copyright (C) 2008 Wellcome Trust Centre for Neuroimaging
% Jean Daunizeau
% $Id: spm_eeg_review_callbacks.m 7269 2018-02-28 15:53:43Z vladimi... |
96c175212e23b28cc16d29cbd0743800283dda2248734f35b98745893747907c | MATLAB | 82,552 | 2,331 | function varargout = FieldMap(varargin)
% FieldMap is an SPM Toolbox for creating field maps and unwarping EPI.
% A full description of the toolbox and a usage manual can be found in
% FieldMap.man. This can launched by the toolbox help button or using
% `spm_help FieldMap.man`. The theoretical and practical principles... |
ea0153b9069f5e315bbbe9ff2fbe3e5bfd315b55a642eba8c6571a2953896583 | MATLAB | 83,915 | 1,332 | function [reduction, umap, clusterIdentifiers, extras]=run_umap(varargin)
%%RUN_UMAP reduces data matrices with 3+ parameters down to fewer parameters using
% the algorithm UMAP (Uniform Manifold Approximation and Projection).
%
% [reduction,umap,clusterIdentifiers,extras]=RUN_UMAP(csv_file_or_data,...
% 'NAME1',... |
e3df3cefce848ff5e14bc9ada6d1f717edb4e92fdbde8e1d527fc6e0e50c18c0 | MATLAB | 84,071 | 2,330 | 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... |
73e2c505cb15093695525014e4c701d9ed7651757523bc519bf50508e0f6ec1e | MATLAB | 85,400 | 2,404 | 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... |
06f0746935254db19ad2fbe1f9308cd818e533d6e8b3b660cefddcf60bdb4cf7 | MATLAB | 86,468 | 2,411 | 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... |
0812776e721701149695943eb0741efd7f49793d4471bf32f2c5bc84d7539acc | MATLAB | 87,199 | 2,291 | function varargout = spm_orthviews(action,varargin)
% Display orthogonal views of a set of images
% FORMAT H = spm_orthviews('Image',filename[,area[,F]])
% filename - name of image to display
% area - position of image {relative}
% [left, bottom, width, height]
% F - figure handle
% H - han... |
7731372441568a9e7ff7c41d7ea44976c7a4b0a55e02cf3503b3b821d7655b20 | MATLAB | 87,523 | 2,604 | %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% %
% 'The Representation of Priors and Decisions %
% in the Human Parietal Cortex' %
% T.R. Marsha... |
f115314b89820036bb17785327224b72939d807f18cd15d8c5dd8c9817027024 | MATLAB | 89,231 | 2,170 | function [varargout, OutputNiiFilenameDK] = dicm2nii(src, dataFolder, varargin)
% DICM2NII converts dicom files into NIfTI or img/hdr files.
%
% DICM2NII(dcmSource, niiFolder, outFormat, MoCoOption, subjName)
%
% The input arguments are all optional:
% 1. source file or folder. It can be a zip file, a folder ... |
764112c3bcc99b2b67dfda55179f5d345f68cd5dc98dbb8b209f27d3e0fabbc9 | MATLAB | 89,253 | 2,172 | function NiiFname = dicm2nii_DKU(src, dataFolder, varargin)
% DICM2NII converts dicom files into NIfTI or img/hdr files.
%
% DICM2NII(dcmSource, niiFolder, outFormat, MoCoOption, subjName)
%
% The input arguments are all optional:
% 1. source file or folder. It can be a zip file, a folder containing dicom
% ... |
52ca80fa42d24b73bf627c51c12666a68e5043f9f8ccbec1d1c3ac7ea4dce6d2 | MATLAB | 89,776 | 2,387 | function varargout = spm_input(varargin)
% Comprehensive graphical and command line input function
% FORMATs (given in Programmers Help)
%_______________________________________________________________________
%
% spm_input handles most forms of interactive user input for SPM.
% (File selection is handled by spm_select... |
c3a225da08ad57a57b4693d00cf3de3fff37ee1fd0701762a30ac85fba764f55 | MATLAB | 89,953 | 2,093 | classdef UmapUtil < 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 Junior... |
0465b4428d49d33a336079a4ffd5530bd7c299e045fa92539ad2201e51cbe736 | MATLAB | 91,630 | 2,728 | function varargout = fixerrorsgui(varargin)
% TRX = FIXERRORSGUI(SEQS,MOVIENAME,TRX,ANNNAME,PARAMS,[LOADNAME])
% SEQS: array of suspicious sequences
% MOVIENAME: name of movie
% TRX: positions of flies over time
% ANNNAME: name of annotation file
% PARAMS: parameters used to determine suspicious sequences
% LOADNAME: p... |
e4d67a9aaf29f2932551f60a5b1ff15860b55a8e9eb13a64ed648857b7c6df1d | MATLAB | 94,322 | 1,902 | function individual_session_analysis(trace_directory,trace_name,show_plot,save_plot,done,overwrite)
%% LOAD THE CORRECT FILE AND CREATE RESULT FOLDER
load([trace_directory,'\',trace_name])
tmp = strsplit(trace_directory,'\');
session_name = tmp{end};
if exist(strcat(trace_directory,'\results'),'dir') == 0
... |
7a054c18359043f6419a684279c09985d799cb3900e8e44609ca23ccae30b51b | MATLAB | 94,887 | 2,323 | function [event] = ft_read_event(filename, varargin)
% FT_READ_EVENT reads all events from an EEG, MEG or other time series dataset and
% returns them in a common data-independent structure. The supported formats are
% listed in the accompanying FT_READ_HEADER function.
%
% Use as
% [event] = ft_read_event(filename,... |
23545d2407f1de4c00baf2654dfd415389ea7e1f80a59ff7fe708c8599f00c47 | MATLAB | 95,399 | 2,311 | classdef Density < handle
% AUTHORSHIP
% Software Developers: Rachel Finck,
% Connor Meehan <connor.gw.meehan@gmail.com>
% Stephen Meehan <swmeehan@stanford.edu>
%
% ORIGINAL PUBLICATION
% http://cgworkspace.cytogenie.org/GetDown2/demo/dbm.pdf
%
% PUBLICATION ... |
b3d1fa785f477dc207fca3abcc283d7701a5aae56f8eaad838c962087a38baec | MATLAB | 96,507 | 2,274 | function plot_theta_vs_replay(bayesian_control,rest_option,time_chunk_size,time_window)
% Code for quantifying and plotting the relationship between theta sequence
% and awake replay and sleep replay
% Input:
% bayesian_control - Use 'all' for analysing first exposure data using first
% exposure template and re-expo... |
a3b9475387faab15a6202b85703ce890ea1b047ba93dbb8bec4f68b01a018800 | MATLAB | 96,782 | 2,737 | classdef File
% 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
% University License: BSD 3 clause
%TODO ..... |
113ed554c1c6bd81334566edd997637f3868d63f3ba9fcac4af0daab41f7fc95 | MATLAB | 97,056 | 1,694 | %pipeline for analysing FM-stimulus+tACS data
clear
close all
clc
%DEFINE DIRECTORIES
MAINdir = uigetdir (); %main path to raw data, e.g., '/Users/yuranny.cabral/Documents/gapDetectionProject/tACS/DATA'
BEHdir = fullfile(MAINdir, 'Beh'); %raw beh data
EEGdir = fullfile(MAINdir, 'tACS'); %raw eeg data (for tACS si... |
f0b0102b6273783fcfeb9ed42e031a916a4c8c9724c9bab127b822b170d5f479 | MATLAB | 98,070 | 2,615 | classdef FlowJoWsp < handle
% EXAMPLES
%
% 1. Run UMAP on "Eliver" demo FlowJo workspace for live singlets in
% sample all_3-3.fcs. Compare the manual gating subsets to the UMAP
% data islands using basic UMAP reduction.
%
% run_umap('all_3-3.fcs/Sing*/Live*@https://storage.googleapis.com/cytog... |
5b24a2fbf95ef9bcf253cb18d213014812a5a125cdfbd45ddb2e72dee149145d | MATLAB | 99,390 | 1,304 | %% organize and normalize data by MEA
clc; clear all;
normNotes = {}; % *** added 2019-09-03
N = 0;
% *** change each time! *** %
% chooseData = 0; %glu only
% chooseData = 1; %BDNF dose response
chooseData = 2; %glu injury + BDNF recovery
% *** change each time! *** %
if chooseData==0
dataDir = 'C:... |
9fca8acc8913810945b3808690755cba1b570e218aef24624d8cd4bfb6712ed8 | MATLAB | 100,139 | 1,683 | % DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT: OPEN FIELD WITH OPTO STIM:
% Marie_FP_IndivData_extraction
% Closed loop experiment based on dFF threshold or motor bout.
% also calculates average speed and average rotations (in the stim epoch
% extracts FP data and behavioral data
% generates and s... |
bdb6669375867e8b435c37f098bfc1bcd0ef56dc0fd7709a79f826c071bef45f | MATLAB | 101,557 | 1,641 | function CALIPR_Philips_Cord_FullProcess(fulldat_names)
%%%%%%%
% Input is a cell array containing strings with the full path to the .raw data file to be processed
% Example:
% fulldat_names = {...
% '/home/bizon/Research/MWI_Development/CALIPR/CALIPR_Publication_Share/CALIPR_Code/test_calipr_repro_c05_calip... |
da2aa9908d556eb9c0fdf84955d3a284e021ae3d6a45a86c308a5acb09d5ea69 | MATLAB | 102,795 | 3,135 | function REAVER_GUI
%%%%% Start: Get Initial "Values"
if true
% Get the screen size. The first two values are the position ( always
% (1,1) so unneeded )
screenSize = get( 0 , 'ScreenSize' ) ;
screenSize(1:2) = [] ;
% Find the greatest power of 2 less than the minimum screen dimension
initialAxSizePower = next... |
c7140833e28001728e66b0617cbb3db9bd1474c40b5ea5d388c1cdfa96499866 | MATLAB | 103,101 | 1,688 | function SockeyeCluster_CALIPR_Philips_Cord_FullProcess(fulldat_names)
%%%%%%%
% Input is a cell array containing strings with the full path to the .raw data file to be processed
% Example:
% fulldat_names = {...
% '/home/bizon/Research/MWI_Development/CALIPR/CALIPR_Publication_Share/CALIPR_Code/test_calipr_... |
779d2bb192b60b0cdd51e3b6523dc413355e1ee4769422eea128f3f6f05887c1 | MATLAB | 104,847 | 1,658 | function CALIPR_Philips_Brain_FullProcess(fulldat_names)
%%%%%%%
% Input is a cell array containing strings with the full path to the .raw data file to be processed
% Example:
% fulldat_names = {...
% '/home/bizon/Research/MWI_Development/CALIPR/CALIPR_Publication_Share/CALIPR_Code/test_calipr_repro_c05_calipr_... |
07c1a64298b1a17fd59c544b584c974b8ea49a7348d35c5a90a35f4cb933881a | MATLAB | 106,676 | 1,710 | function SockeyeCluster_CALIPR_Philips_Brain_FullProcess(fulldat_names)
%%%%%%%
% Input is a cell array containing strings with the full path to the .raw data file to be processed
% Example:
% fulldat_names = {...
% '/home/bizon/Research/MWI_Development/CALIPR/CALIPR_Publication_Share/CALIPR_Code/test_calipr_re... |
62594fafcc98b40840c95baff5e009e6087b4fd6ddb16e35f2b417858af044df | MATLAB | 106,705 | 3,555 | function varargout=view3D(varargin)
%VIEW3D Viewer for 3D images
%
% Shows the three orthogonal planes of the volumic image.
% For this viewer we consider matrices to represent 2D or 3D images.
% The viewer can also show the three planes in a 3D view in a separate
% figure (3D slicer).
%
% The planes can be selected b... |
057f8b27650183359f6b516553afb2856bac69b698c73cd239682f8556744e0b | MATLAB | 108,402 | 3,278 | classdef MatBasics
% 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 Univers... |
2695544ec05fb33adc897811d0ecbb9b1f100e4af719821a0c818392a41f295b | MATLAB | 110,272 | 2,882 | classdef QfTree < handle
% Class for building a dendrogram based on QF dissimilarity measurements.
% 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>... |
809f3739700a9e16d3ee0bc0f45c563fe416a942f596812260a9f5a8d891f248 | MATLAB | 113,504 | 2,449 | %% Creating the figures for Movie tuning
clc
addpath(genpath('C:\Users\chinm\Desktop\MovieTuning\ForGithub'));
load('Allen_VVDot_DataSet_ForMovie_v1.mat') ;
ID1=find(contains(DumpNS.Region,'LG') );
ID2=find(strcmp(DumpNS.Region,'VISp') );
ID3=find(strcmp(DumpNS.Region,'VISam') | strcmp(DumpNS.Region,'VISpm') ... |
9cd05c1cab0ac1f687d0bda38afe66ad92898c1aea24bdca2260375440cfd0cd | MATLAB | 115,906 | 2,689 | % trialEstStats_bgluSynchData.m
%
% some taken from bgluSynchData_forRM.m
% some taken from trialEstStats_plot_stats.m
%% ESTIMATION STATS METHOD
%% PART 0 (est) - set colors and load data
clc; clear all; close all;
addpath('C:\Users\kmfo8\Dropbox\Rutgers\Firestein Lab\Manuscript DRAFTS\2022 BDNF MEA pape... |
df90ee923d9242122c3e4ca997b3a93aad345ba67b0c7fe93e8f2345c51a8ff9 | MATLAB | 117,933 | 1,917 | % Marie_FP_IndivData_extraction_GPeSNR_OF
% DATA ANALYSIS PIPELINE FOR FIBER PHOTOMETRY EXPERIMENT: OPEN FIELD GPESNR:
% Marie Labouesse 13 Jan 2022
% need to select the folder in which several animals data exist; in principle could have several sessions per mice but not implemented yet in detail
% extracts FP ... |
56393737ffc552d5c72781f5e2c87e46bd044df509d993dfdd1ddc49f0ad763d | MATLAB | 119,858 | 3,934 | %% Loads data
clear all
close 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\Preprocessed_data\';
WS_path='C:\Users\xscogn... |
4766ba9c3d41b6ea2a2524dcdeb9fb188ae34e533cc7ade5726be17c207e0002 | MATLAB | 119,978 | 2,799 | function plot_theta_vs_replay_log2(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\Analysis\H... |
4bdb431e7d3d09ec4038ef30e954479f0064af0972cbc27d5b8cce9d55bbb438 | MATLAB | 127,682 | 3,140 | classdef SuhEpp < SuhAbstractClass
% AUTHORSHIP
% Primary Developer: Stephen Meehan <swmeehan@stanford.edu>
% Math/Statistics: Connor Meehan <connor.gw.meehan@gmail.com>
% Guenther Walther <gwalther@stanford.edu>
% Primary inventors: Wayne Moore <wmoore@stanford.edu>
% ... |
ab1a89a8c1715a3ce1ebf78859ce245e1d59989c9fdb1033c578878e0d5bc834 | MATLAB | 131,684 | 3,119 | function plot_place_cell_SWR_firing(bayesian_control,rest_option,time_chunk_size,time_window)
% Code for quantifying and plotting the place cell firing and participation
% during SWR and theta sequences
% Input:
% bayesian_control - Use 'all' for analysing first exposure data using first
% exposure template and re-e... |
23d7ba6ae6d16fa3034b6c5203ebfe69082f8b6fe3c5770acca8d752d5f665aa | MATLAB | 135,186 | 3,125 | %% part 2a - BGLU - plot est stats by subtracting from control
clc; clear all; close all;
theDir = 'D:\kate_dropbox\Dropbox\Rutgers\Firestein Lab\Manuscript DRAFTS\2022 BDNF MEA paper\figures\data - BDNF GLU injury recovery\revision_0g30gonly_newPlots\data\';%C:\Users\kmfo8\Dropbox
figDir = 'D:\kate_dropbox\Drop... |
b80ee04ccea393c48e5881ec7d69a5b254994760c8b8f74f5e18dd8ffcc4cb8d | MATLAB | 138,351 | 3,227 | % trialEstStats_bgluSynchData.m
%
% some taken from trialEstStats_BGLUsynchData.m
% some taken from plotNetworkParams.m
%% ESTIMATION STATS METHOD
%% PART 0 (est) - set colors and load data
clc; clear all; close all;
myColors(1,:) = [0 0 0]; % black
myColors(2,:) = [0 0 0]; % black
myColors(3,:) = [1 0 ... |
e3326f34665afc418a9dbde1b68cd97ca3c7c4240b959b7f1430d6f06190c523 | MATLAB | 140,317 | 2,615 | function [imageData, alpha] = export_fig(varargin) %#ok<*STRCL1,*DATST,*TNOW1>
%EXPORT_FIG Exports figures in a publication-quality format
%
% Examples:
% imageData = export_fig
% [imageData, alpha] = export_fig
% export_fig filename
% export_fig filename -format1 -format2
% export_fig ... -nocrop
% export... |
48295d4a1ce8844438fabebddf182108d520c0c108b26dbf54c2614792c3e126 | MATLAB | 147,507 | 2,980 | function [handles,levels,parentIdx,listing] = findjobj(container,varargin)
%findjobj Find java objects contained within a specified java container or Matlab GUI handle
%
% Syntax:
% [handles, levels, parentIds, listing] = findjobj(container, 'PropName',PropValue(s), ...)
%
% Input parameters:
% container -... |
43f552375fc10c908222bdeefbc3676af5ba63b0549473d9fac2b548d03f750d | MATLAB | 149,681 | 2,793 | classdef UTExperiment < handle
% We will extrat each rhs segment separately and reference the
% appropriate ADI record for comments
% |--rhs 1--| |---rhs 2---| |------rhs 3------| |--rhs 4--|
% |------ADI 1------| |-ADI 2-| |-----------ADI 3-----------|
% multiple files can be contiguous. If... |
73be5db81f500d18c423d128f7d0a5ccc9bcac0ec51f3468c33fde3e5b9944d5 | MATLAB | 166,162 | 3,430 | function [handles,levels,parentIdx,listing] = findjobj(container,varargin) %#ok<*CTCH,*ASGLU,*MSNU,*NASGU>
%findjobj Find java objects contained within a specified java container or Matlab GUI handle
%
% Syntax:
% [handles, levels, parentIds, listing] = findjobj(container, 'PropName',PropValue(s), ...)
%
% Input par... |
59f3dbf84bc897cd5cf6c89674aa14460b3a1a21fbe4ba87b24c9c49fc268443 | MATLAB | 167,443 | 3,451 | function [handles,levels,parentIdx,listing] = findjobj(container,varargin) %#ok<*CTCH,*ASGLU,*MSNU,*NASGU>
%findjobj Find java objects contained within a specified java container or Matlab GUI handle
%
% Syntax:
% [handles, levels, parentIds, listing] = findjobj(container, 'PropName',PropValue(s), ...)
%
% Input par... |
24d27fbe6d3c4afa6d11ed5987c95bd0cf33d8f6af298064b910040829e2b543 | MATLAB | 167,994 | 4,233 | classdef QfHiDM < handle
% Class for Hi-D matching with merging of data subsets using QFMatch or
% F-measure or both.
%
% t prefix is data set #1 (previously referred to as teacher or training set)
% s prefix is data set #2 (previously referred to as student or test set)
% QF Algorithm is described in
% h... |
18d9bdb6f15b69e96dd4a8f5ac7c15d48e848ac2d877474494ce8c5fefcfb142 | MATLAB | 169,409 | 4,214 | classdef FlowJoTree < 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
%
%FlowJoTree.GetData is the primary module for integrating MATLAB
% functionality ... |
f58de8ef2339824ad80e61780a7a371c0c50d1d25f7e7835e8209e2a9a95af3a | MATLAB | 173,240 | 2,054 | %Run all analysis for the paper
%Created by LIDIA RIPOLL SANCHEZ, for L.Ripoll-Sanchez et al. 2023, Neuron
% project 21/11/2023
%Builds the neuropeptide network and gets degree and rich club measures for
%it, it also performs the dimensionality reduction analysis to obtain the
%mesoscale structure, compares the differ... |
2994eecd4bb40517e740490229fbfa73da3b9af724990ef293a10ca9117c988c | MATLAB | 176,636 | 3,784 | classdef SuhRunUmap < handle
%SuhRunUmap aims to make the old run_umap more readable. It became
% unreadable between May 2019 and October 2021 due to rapid addition of
% easy end-user features and arguments ... a typical feature creep.
%
% The method for achieving readability is subsetting related code into
% function ... |
07b6fab1e61cb487a91d151532f59ab79b03a31dcf98458c8fa1acc7c0cc3b7a | MATLAB | 200,000 | 4,219 | classdef MotionAnalyser < matlab.apps.AppBase
% Properties that correspond to app components
properties (Access = public)
MotionAnalyserUIFigure matlab.ui.Figure
ImportMenu matlab.ui.container.Menu
ImportXYMenu matlab.ui.container.M... |
40096791df1fb1f913c1e029887c4f993d3132c74fff4320c082e4b7cb8a0cbd | MATLAB | 200,000 | 5,603 | classdef Gui
% 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(Constant)
SCALE_FNCS={@xlim, @xlabel , @Gui.XTick;...
@ylim, @yla... |
74feec6021e8c18d61fb1bdf770526f6e47d7ecb1e19edc7d982e80a17aa708b | MATLAB | 200,000 | 4,376 |
function varargout = vesGraphValidate(varargin)
% VESGRAPHVALIDATE MATLAB code for vesGraphValidate.fig
% VESGRAPHVALIDATE, by itself, creates a new VESGRAPHVALIDATE or raises the existing
% singleton*.
%
% H = VESGRAPHVALIDATE returns the handle to a new VESGRAPHVALIDATE or the handle
% tov
% ... |
bd5b8c0ea9abba2d278863ef449864de7860a6e154473859038908bca031d169 | MATLAB | 200,000 | 4,288 |
function varargout = vesGraphValidate(varargin)
% VESGRAPHVALIDATE MATLAB code for vesGraphValidate.fig
% VESGRAPHVALIDATE, by itself, creates a new VESGRAPHVALIDATE or raises the existing
% singleton*.
%
% H = VESGRAPHVALIDATE returns the handle to a new VESGRAPHVALIDATE or the handle
% tov... |
3a110241ab2a8fdce3166e6699dcc65135a459b71c33cd790315c8c9e1f8634e | Mathematica | 160,411 | 3,152 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 11.3' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
152fc43f260d4aaf1c3fbeb7ecd98e31dd16d8fa51ed40f1a3adeac65c1fe020 | Mathematica | 200,000 | 3,559 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 10.0' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
2f83a871f3cefa94989aee93569cab2fdae83f0fb055b2183eef36c28607922f | Mathematica | 200,000 | 3,604 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 10.4' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
63c6e9921dbe675d01ed9623e7efcbba94c8cb0968de6a18de8820e126f09a16 | Mathematica | 200,000 | 3,474 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 10.4' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
ae291c0f0a67565c9c75177faa6c6a5e073850c879e01100b9c4fdeef94a8598 | Mathematica | 200,000 | 3,474 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 10.4' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
c7ad5fd1d52c4b4f906670154381d3a931e92e1e45da4208530e2dd65fb338e5 | Mathematica | 200,000 | 3,484 | (* Content-type: application/vnd.wolfram.mathematica *)
(*** Wolfram Notebook File ***)
(* http://www.wolfram.com/nb *)
(* CreatedBy='Mathematica 10.4' *)
(*CacheID: 234*)
(* Internal cache information:
NotebookFileLineBreakTest
NotebookFileLineBreakTest
NotebookDataPosition[ 158, 7]
NotebookDataLengt... |
821296effaea4c9149883b164da19fcf229af696164e1e875e1e5e78131622c3 | NEURON | 32 | 3 | NEURON {
POINT_PROCESS pp
}
|
28cfd86efcf3394f079bff0959831bebfacda58e70b6813e64a53b5a0ffc265f | NEURON | 68 | 6 | NEURON {
SUFFIX function_table
}
INCLUDE "function_table.inc"
|
3bde74406055e5a750c506c1884629a1ef91dd7341cc7069791d580dec213317 | NEURON | 70 | 7 | NEURON {
SUFFIX example
}
FUNCTION f(x) {
f = at_time(x)
}
|
3d2868836a92ed8a77bf880b79c5aa353e3a420454f3ed384c5b18aeb9bd06d6 | NEURON | 81 | 6 | NEURON {
ARTIFICIAL_CELL art_function_table
}
INCLUDE "function_table.inc"
|
57f818f1eced02d010ff7c96f0370e1e9e60e4f86c14ac060645a0c27bf30f84 | NEURON | 81 | 7 | NEURON {
SUFFIX nothing
}
FUNCTION forty_three() {
forty_three = 43.0
}
|
c13cf8480391c1ec3954a958104d3158a4e8973358de5aedc41556dbe82ec421 | NEURON | 81 | 6 | NEURON {
POINT_PROCESS point_function_table
}
INCLUDE "function_table.inc"
|
35f8a0e6200623c92c592262875bb9b60077383b6ccea5d1cbbf382f73e05370 | NEURON | 92 | 12 | NEURON {
SUFFIX src
GLOBAL gbl
}
PARAMETER {
param = 123.0
}
ASSIGNED {
gbl
}
|
b6f4a5666e8cfda548165fe91c5fa1f32bc6ac06240fb0da780d0d7c84c2605d | NEURON | 93 | 11 | NEURON {
SUFFIX constant_mod
}
CONSTANT {
a = 2.3
}
FUNCTION foo() {
foo = a
}
|
769136380e268cd1e0c3291d7750e0e7ef10c3f8c45813dd01b12e48316698d5 | NEURON | 104 | 11 | NEURON {
SUFFIX parameter
}
PARAMETER {
gbl = 42.0
}
FUNCTION get_gbl() {
get_gbl = gbl
}
|
6429c9868610ac1556fc4e1b8a3c8fe83ad32a66224890d182566910a9fdd050 | NEURON | 108 | 12 | NEURON {
SUFFIX write_cao
USEION ca WRITE cao
}
ASSIGNED {
cao
}
INITIAL {
cao = 1124.0
}
|
7be650451e4b585422c01b2adcd56dbdc7114d040346a4c51921bf5fd670220c | NEURON | 108 | 12 | NEURON {
SUFFIX write_eca
USEION ca WRITE eca
}
ASSIGNED {
eca
}
INITIAL {
eca = 1124.0
}
|
8fded3d3691053f002e2d066d5a93efd47345048fb3446a5fdf372d0504d4310 | NEURON | 108 | 12 | NEURON {
SUFFIX write_cai
USEION ca WRITE cai
}
ASSIGNED {
cai
}
INITIAL {
cai = 1124.0
}
|
a19e945556f2b745fd2c772e0ffbf7b8e952bac718de9ee86767e02fd7883dbc | NEURON | 110 | 9 | NEURON {
SUFFIX random_variable
RANDOM rng
}
FUNCTION negexp() {
negexp = random_negexp(rng)
}
|
e925a3f00a002c24d2355d4b92036fd4aa259e7b711772a162aae6382241ca8e | NEURON | 111 | 7 | NEURON {
SUFFIX compile_only
}
FUNCTION call_nrn_ghk() {
call_nrn_ghk = nrn_ghk(1.0, 2.0, 3.0, 4.0)
}
|
fbcc961fdca600db8c9ef4c1e08db390c7d95da9d51949cdce0c4e7aae6ba74a | NEURON | 116 | 13 | NEURON {
POINT_PROCESS range_parameter
RANGE x, y
}
PARAMETER {
x = 42
y
}
INITIAL {
y = 43
}
|
ab8c2c6a7c58a5473e76fb6f830943c328f1ec83e2b734ba545052a0a40d72a2 | NEURON | 118 | 12 | : The name of this mod file should be `no_suffix`.
NEURON {
RANGE x
}
ASSIGNED {
x
}
INITIAL {
x = 42
}
|
59b5f3491deffd3cb53fbc2d722168f0070dad52fea686f13edeb68890b709bb | NEURON | 119 | 14 | NEURON {
SUFFIX read_eca
USEION ca READ eca
RANGE x
}
ASSIGNED {
x
eca
}
INITIAL {
x = eca
}
|
97539c2d43c86af9c8ca924abaff67305b7cd94bef2ee89d15421ca244a70463 | NEURON | 119 | 14 | NEURON {
SUFFIX read_cai
USEION ca READ cai
RANGE x
}
ASSIGNED {
x
cai
}
INITIAL {
x = cai
}
|
cd6199787b07e61dc4224067ba2779eb78662636768893821ed20afb8e860cf3 | NEURON | 119 | 14 | NEURON {
SUFFIX read_cao
USEION ca READ cao
RANGE x
}
ASSIGNED {
x
cao
}
INITIAL {
x = cao
}
|
23d6da3d564f5ac662af83384f470b621d4825c9e0cb749b06dd8e106fe8c89d | NEURON | 123 | 14 | NEURON {
SUFFIX globals
GLOBAL gbl
}
ASSIGNED {
gbl
}
FUNCTION get_gbl() {
VERBATIM
_lget_gbl = gbl;
ENDVERBATIM
}
|
a5cdeca9c55412cfd000957990608e93813cf592a50428546cc1fd308dea8d82 | NEURON | 126 | 14 | NEURON {
SUFFIX default_parameter
RANGE x, y, z
GLOBAL a
}
PARAMETER {
a
b = 0.1
x
y = 2.1
z
}
|
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.