sha256 stringlengths 64 64 | language stringclasses 28
values | size int32 1 491k | lines int32 1 23.2k | content stringlengths 1 200k |
|---|---|---|---|---|
99eb8a4420ec26b47de0b6d81955e18968b152a68f887ff7f5dc176790db187c | MATLAB | 46,627 | 1,118 | %% Open ephys data analysis
% First run "load_open_ephys_binary.m" to extract data for each recording,
% then modify and run "Extract_and_save_20211021.m" to organize the data format
% then load the data and stimulus timestmaps
clear;clc;
[fileName pathName]=uigetfile('*.mat','Select .mat file',...
'D:\Data\... |
8bfc38e514d4d8f7c8e4643fc694a24d2d6ee91962f689dd2ddd82551b84cd36 | MATLAB | 46,916 | 1,082 | function [header,Aout,cmap] = scim_openTif(varargin)
%% function [header,Aout,cmap] = scim_openTif(varargin)
% Opens a ScanImage TIF file, extracting its header information and, if specified, stores some/all of image contents as output array Aout if specified.
% By default, Aout, if specified for output, is of size Mx... |
92e53adc167e8edf01b1495c78006dd36a8909660f5b08af207775075524a42c | MATLAB | 47,124 | 766 | function SpecificMod_USVsAndDLC_25072023(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFiles.Video2B... |
c2cb7998b0fb58c64f1f945a26995ce685e376cc272725428d66448cdf899d97 | MATLAB | 47,433 | 1,132 | function varargout = fipgui(varargin)
% FIPGUI MATLAB code for fipgui.fig
% FIPGUI, by itself, creates a new FIPGUI or raises the existing
% singleton*.
%
% H = FIPGUI returns the handle to a new FIPGUI or the handle to
% the existing singleton*.
%
% FIPGUI('CALLBACK',hObject,eventData,handles,... |
09969b12b3123d1e0d8e35ee7cd48b10a79ad184750c4e44b450b0b2e057cd41 | MATLAB | 50,479 | 1,036 | %% AlphaAnalysis.m
% Pre-stimulus alpha analysis, following Wang et al. (2026, Communications
% Psychology). Tests whether pre-stimulus alpha power differs before trials
% whose actual visual-auditory phase difference matched their nominal
% condition vs trials where it didn't, and whether alpha relates to
% subsequent... |
5c21853bd0c96adabcd220b45d3928394161b858989adf668b4e706d738cbe09 | MATLAB | 50,747 | 722 |
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = ICC_SMC_Neuro(e, w, f_e, f_i, duration)
% Solves the combined ICC and SMC model with neurotransmission. See ICC_SMC_Neuro_Explanation.txt for a key to variable names.
% INPUTS
% e: 1 x 5 array of effector component weighting values in sequence
% [kiAno1, k... |
6d7b7a83f253517d669108ec596cb1b95f10fdd0ee9440e06faa8950f0ed5d1a | MATLAB | 51,801 | 1,184 | function [stats,varargout]=mes2way(X,group,esm,varargin)
% ** function [stats,varargout]=mes2way(X,group,esm,varargin)
% computes measures of effect size for samples in a factorial two-way
% design and places the results in output structure stats. A summary table
% including the effect size measures and two-way ANO... |
fe04f0fa838d41e98cc3d9e85be6e4257ba06134342b317eaa2622208e35a766 | MATLAB | 51,852 | 1,132 | %==========================================================================
% This script examines the following topics:
% (1) Rate of ripples during different trial phases.
% (2) Relationship between ripple rates, memory, and experience (separately
% for the different trial phases).
% (3) Development of ripples ov... |
8ed4059350b7e3faacbe1cb62b54ddc051a7d64206ef105ddd86949a2255a5c2 | MATLAB | 52,165 | 736 |
function [VOI, STATES, ALGEBRAIC, CONSTANTS] = ICC_SMC_Neuro_Tvar(f_e, f_i, duration)
% Solves the combined ICC and SMC model with neurotransmission using the fitted weights
% and scaling constants but applying sitmulation only between 120 - 180 s.
% INPUTS
% f_e: excitatory stimulation frequency in doma... |
226b0255fe80e121f2d615272aea9ca602082a909089bae66878ab798b502f59 | MATLAB | 52,338 | 866 | function SpecificMod_SniffAndVideoChambers_16022023(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllData... |
930f1437c7e2ccac2a69977b942242f7c064298dba54a8eb197803c9aceac71f | MATLAB | 52,374 | 1,048 | % Estimate CSD speed through neuropil
csdWave = cell(1,Nexpt);
for x = intersect(xFiber, xSlope) %xSlope %intersect(xFiber, xCSD)
%[csdBout{x}(expt(x).csd), csdStat{x}, csdParam(x)] = PeriCSD(runInfo{x}(expt(x).csd), Tscan{x}{expt(x).csd}, loco{x}(expt(x).csd), deform{x}(expt(x).csd), fluor{x}(expt(x).csd), def... |
1a296834a38998e5ec799a511bf0a3e471efbf4bf286a7e257ce5bf66c8d65a6 | MATLAB | 53,057 | 1,451 | function [d,si,h]=abfload(fn,varargin)
% ** function [d,si,h]=abfload(fn,varargin)
% loads and returns data in ABF (Axon Binary File) format.
% Data may have been acquired in the following modes:
% (1) event-driven variable-length (currently only abf versions < 2.0)
% (2) event-driven fixed-length or waveform-fixed len... |
035ab9e0d1eae19c0d947f2b346ad17b08ba36c36b5c798ac7ca59a2a1f6bdf5 | MATLAB | 53,249 | 1,050 | %==========================================================================
% This script investigates the MTL-wide effects of hippocampal ripples
% including cross-correlations and time-frequency power analyses.
%
% Lukas Kunz, 2023
%==========================================================================
% start
c... |
55e3b1540ff900799009f5ce740493b364177d010b756b1a51af3cd856ac022c | MATLAB | 54,270 | 948 | function out = LK_CoactivityDuringRipples_Function_20230317(cfg)
%
% LK_CoactivityDuringRipples_Function_20230317 computes the coactivity
% between object cells and place cells during ripples. The coactivity is
% tested for different ripple conditions.
%
% The coactivity is estimated via a z-score (Sosa et al., Neuron,... |
5e6ce2370a6387bd5971ecb1c3c648f0ddde3b6c415aa7f7375db6f89c719f87 | MATLAB | 57,058 | 793 | function SpecificMod_SpikesMEAandVideoChambers_20032022(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDa... |
761b61254094d541e3af7c6c83177e7fe357e8f07c954db4e450e8abbb58d254 | MATLAB | 57,341 | 1,369 | function 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.e... |
81bfe906f5be6a26ade15aa89474ff522a5c88d822dd5fda090286382ac368cb | MATLAB | 58,547 | 1,398 | function data = TDTbin2mat_Sri(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.
%
% da... |
2cabbc2bb51c9beb876af356f2cf4d594a80adb9b7a25c8efc69f14ad48f1342 | MATLAB | 62,676 | 1,451 | function varargout = spm_results_ui(varargin)
% User interface for SPM/PPM results: Display and analysis of regional effects
% FORMAT [hReg,xSPM,SPM] = spm_results_ui('Setup',[xSPM])
%
% hReg - handle of MIP XYZ registry object
% (see spm_XYZreg.m for details)
% xSPM - structure containing specific SPM, di... |
4fc0c9ceee0bcfac0f0eda8c28418392df7afe99e80c96c9dd1711f3f7452beb | MATLAB | 64,585 | 1,173 | minStillDur = 120;
stillClip = 30; % clip the first few seconds of stillness to guard against residual locomotion-associated activity
stillChunkDur = 60;
maxMissingFrac = 0.1; % exclude epochs of stillness where the median ROI is missing at least this much data
minFluorDur = 1;
minScaleDur = 0.2;
minZ = 2.5;
... |
3119e3bffd8e5c750c793a72ab13e4bb5e727b5c29513f77b3b581d4b6a7dc62 | MATLAB | 65,622 | 1,076 | function SpecificModAccelerometer_29032020(AllDataFiles,AllParameters,app)
%TRACKMICEPOPULATIONSUMMARY Summary of this function goes here
% The aim of this function is to summarize the results of several rodents extracted by the software TrackRodent.
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
... |
ce03a30b9d361090276168b5aaa20953a06d0565d03ee07a2cbe18a58d51c20c | MATLAB | 66,036 | 1,527 | function varargout = old_tfce_results_ui(varargin)
% User interface for SPM/PPM results: Display and analysis of regional effects
% FORMAT [hReg,xSPM,SPM] = tfce_results_ui('Setup',[xSPM])
%
% hReg - handle of MIP XYZ registry object
% (see spm_XYZreg.m for details)
% xSPM - structure containing specific S... |
955daad6884274de497885c28884a4baaaae9b2bb40d49e9e76b10e7a68046f6 | MATLAB | 66,384 | 1,048 | function SpecificMod_USVsAndVideoChambersAndFree_28042022(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(All... |
a7a56fe852530623095fbb5ab209b5c228baddcabf8aee2d1096a2c681578955 | MATLAB | 68,052 | 2,697 | load('E:\learningAnalysis\summaryManyMice_includingOldEnvBadMoreMice\indicesAllNewCueThresh.mat');
load('E:\learningAnalysis\summaryManyMice_includingOldEnvBadMoreMice\corrAllFOVs.mat');
load('E:\learningAnalysis\summaryManyMice_includingOldEnvBadMoreMice\dfofSigNormAllFOVs.mat');
i=indicesAllNewCueThresh.GridIdx;... |
5b7beb20535e2ff15abf65e4d29ac33cccf7a51cee8b51f180802d3a2a9b5dfe | MATLAB | 70,064 | 1,649 | function 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.e... |
dc2732b7a60250507f3556e5a250dd7c0909cbbcf746e83ea30499bcae76d70e | MATLAB | 70,895 | 1,169 | function SpecificMod_SpikesNPandVideoChambers_19032023(AllDataFiles,AllParameters,app)
%%% SpecificModSpikesClustersNPDuringChambersInteractions_CheckBox
%%% SpecificModSpikesNPDuringChambersInteractionsBoutTimeEditBox
%%% SpecificModSpikesNPDuringChambersInteractionsBoutDurEditBox
NumOfFiles=[ length(A... |
73fa3ad15b47f5c174719d3c255e04f945cf9a344226a222f4fc67e87ec34130 | MATLAB | 81,045 | 1,354 | % ----------------------------------------------------------------------------------------------
% -- Title : Kernel Alignment
% -- Project : VocalMat - A Tool for Automated Mouse Vocalization Detection and Classification
% --------------------------------------------------------------------------------------... |
afb25edbbea81d6d8aad8e48e6dd6a47221632a4d0799f3dafd103b4a74225fc | MATLAB | 81,053 | 1,360 | %clear all; close all
all_correlations=[];
dist_centroids_all=[];
%work_dir = 'Z:\test\Combined_Trpv1_Control';
cd(work_dir)
% list = list_dir;
show_plots = 1;
group_animals=1;
%if you want to combine all the animals all the same group and then compare
%groups
if group_animals==1
keyword{1} = 'Control'; keyword{... |
42e8965c012c339acebc88647259b3224ed3ff9dc6e9cf1e4c15741038010155 | MATLAB | 82,713 | 1,342 | clear all; close all
all_correlations=[];
dist_centroids_all=[];
% addpath(genpath('../'))
work_dir = 'Z:\test'; cd(work_dir)
list = dir;
isdir = [list.isdir].';
list_dir = list(isdir,:); list_dir(1:2)=[];
% list = dir('Control_2nd*');list2 = dir('Agrp_2nd*');
% list3 = dir('Agrp_1st*'); list4 = dir('Agrp_2nd*');
% li... |
a73cb36c97e25e2d0729124514ec0c1c243069fcffe734fa0a4b0a04ca4c0b8c | MATLAB | 86,298 | 1,440 | function SpecificMod_LFPandSniff_07052020(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFiles.Video2... |
fb3886834c6bde043758c62bbe273453c34fb3f9c2b2bb405e7cf6c37975a812 | MATLAB | 88,365 | 1,380 | function SpecificMod_LFPandManuallyDefinedEvents_26052020(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(All... |
9f709000de2acbc32fb22ec4308fbe327c0812a3978e16615d280730c9ebcea0 | MATLAB | 90,126 | 2,130 | function varargout = cat_spm_results_ui(varargin)
% User interface for SPM/PPM results: Display and analysis of regional effects
% FORMAT [hReg,xSPM,SPM] = cat_spm_results_ui('Setup',[xSPM])
%
% hReg - handle of MIP XYZ registry object
% (see spm_XYZreg.m for details)
% xSPM - structure containing specific... |
2be80606a25d10b8158c2596bbb8c88b4f0a80a8e6cd6dc330b383d3365e1b5a | MATLAB | 91,215 | 1,531 | function SpecificMod_SpikesAlone_03052020(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFiles.Video2... |
327a9ab3baef10118019cb4e358f181a00dd7619fee1fae607968f5ae9861ac7 | MATLAB | 96,200 | 1,450 | function SpecificMod_AccAndVideoChambers_18032021(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFile... |
0ab5764133521c492a03cf30f2d481b84172522a7773bc2c62121dc5c94e54f0 | MATLAB | 103,881 | 1,682 | % initialize the GUI
%
% the TREES toolbox: edit, visualize and analyze neuronal trees
% Copyright (C) 2009 Hermann Cuntz
clear cgui
% special gui related global structure containing all handles and variables
global cgui
% initializing colors of GUI-elements
cgui.NColor.text = [.7 .7 .7 ];
cgui.NColor.btext... |
aa7d711bb895d7fbbd487f62d88bb79dc701eae3997be8b807c68a6917449a63 | MATLAB | 104,201 | 1,656 | function SpecificMod_LFP_NP_Alone_13072023(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFiles.Video... |
c3b44356f7a9c0569d4a05650ca51e25e61ae29b6123e04f0b73967c2491a8ca | MATLAB | 106,998 | 4,925 | %compareing good and bad in different aspects
%% compare run by run consistency: use sig: run by run to mean
load('E:\learningAnalysis\summaryManyMice_includingOldEnvGoodMoreMice\corrAllFOVs.mat');
G=corrAllFOVs;
load('E:\learningAnalysis\summaryManyMice_includingOldEnvBadMoreMice\corrAllFOVs.mat');
B=corrAllFOV... |
955aa4b201c65ff40c357aae1fdee9692a3f22efe17ebfeba2eda92070b9a7e9 | MATLAB | 107,459 | 1,567 | function SpecificMod_LFP_NP_AndVideoChambers_02072023(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllData... |
6548fb2b9f8610f90ac6ea8c565cc7453623cb8f79fb3758199eb5b06a5eff97 | MATLAB | 115,944 | 1,916 | function SpecificModVideoChamber_04032020(AllDataFiles,AllParameters,app)
%TRACKMICEPOPULATIONSUMMARY Summary of this function goes here
% The aim of this function is to summarize the results of several rodents extracted by the software TrackRodent.
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
... |
a44ce7ac72bfb8fe71cbc37f2ab53ba4bd049eaaf5d0f7f31ce7e941ca2b32dc | MATLAB | 139,812 | 4,115 | function tfce_estimate_stat(job)
% main TFCE function for estimating TFCE statistics
%
% FORMAT tfce_estimate_stat(job)
% job - job from tbx_cfg_tfce
%
% job fields:
% data
%
% nproc
% 0 - no multi-threading
% x - number of processors for multi-threading
%
% nuisance_method
% method to deal wit... |
6faf2bb6c49acdeaef938ae707687bf25893109f4bfb8c61908e9d0faa38f01e | MATLAB | 149,104 | 2,411 | function cfg = data2bids(cfg, varargin)
% DATA2BIDS is a helper function to convert MEG, EEG, iEEG or MRI data to the Brain
% Imaging Data Structure. The overall idea is that you write a MATLAB script in which
% you call this function multiple times, once for each individually recorded data
% file (or data set). It wi... |
ed2c2feefbecdc2d38f1e8fb6ffb6543bd8a07811e8f64a5fc88d716ee853795 | MATLAB | 157,311 | 2,249 | function SpecificMod_LFPAndVideoChambers_30062021(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFile... |
ba7542150d0d37ce32d7c03cb122d18034d91cf0f4d11f2c1606a985dbeeca51 | MATLAB | 161,794 | 2,447 | function [out, origminterf,tree] = t2n(neuron,tree,options,exchfolder,server)
% t2n ("Trees toolbox to Neuron") is to generate and execute a NEURON
% simulation with the morphologies in tree, and parameters in the structure
% neuron. This is the main function.
% The output-file(s) of the NEURON function are read and tr... |
63e58c6366f85598b26672bdded8c474e3b1a240e59d21bf5a0f029ff7daef6a | MATLAB | 162,845 | 3,773 | %Analysis of context-dependent firing: it's a version of
%placefieldanalyzer_short for a delayed spatial alternation dataset.
%Dependencies are the same except two additional functions: pyrIntSep.m and
%placefieldidentifierrRH.m
%location of data
Rsessions = {'e14_2m2_201017','e14_2m2_201019','e15_13f1_220117','... |
845f2d06b98e027a077c78bc47c597b9636e51513c51c74142a1f29d6d844373 | MATLAB | 163,429 | 2,627 | function SpecificMod_LFPAlone_31032020(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFiles.Video2Beh... |
92c1768706a05cfb9e2308bb981d4f2f1b194b9715f892fad797247cb09feb19 | MATLAB | 168,800 | 3,833 | % This script analyzes preprocessed data generated by the CellExplorer
% framework (Petersen et al., 2021, Neuron). It can be run on the dataset
% containing recordings of dorsal CA1 activity during a continuous
% alternation task. The dataset can be found in the Buzsaki Lab Databank:
% https://buzsakilab.com/wp/pr... |
1615f144d78ab1048616120c58aa424c61f6bdd22d5ce1c54759df7a93ecb427 | MATLAB | 176,261 | 6,757 | %put all corr together
foldersAll={};
% foldersAll{1}='E:\ID20201118\findCells\allCellsWith1210\analyzeCells';
% foldersAll{2}='E:\ID20210206\findCells\loc1\subsetOfFOVsWithAnotherOldNo11\analyzeCells';
% foldersAll{3}='E:\ID20210206\findCells\loc2\subsetFOVsWithAnotherOldNo11\analyzeCells';
% foldersAll{4}='E:\ID... |
091393c35f85ee1ee488c5a06bfcecbc3df665e91ffd918db3de624a47413c4a | MATLAB | 200,000 | 2,726 | function CheckInteractionBetweenMultipleModalities_18112020(AllDataFiles,AllParameters,app)
%%%%%%% This function creates a figure for presntation of the raw behavioral and physiological data.
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDef... |
2930b6d029c2ae09515b51c0d02edcf4ea5f5cf461beff8344984563595914a6 | MATLAB | 200,000 | 5,895 | % COLORCET - Perceptually uniform color maps
%
% Usage 1: [map, descriptorname, description] = colorcet(name)
%
% Usage 2: colorcet (to get a list of all possible colour maps)
%
% Argument:
% name - A string label indicating the colour map to be generated.
%
% names: 'L1' - 'L15' for linear maps
% ... |
372428a8837b7061746870b8c9d1c4ef8d69bfea043b18386ab488a6030336f3 | MATLAB | 200,000 | 3,343 | function SpecificMod_LFPAlone_31032020(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFiles.Video2Beh... |
50b8772dc2ca0b3f6fa9d8ec38bc529db561696dea3f127520c28224290700a0 | MATLAB | 200,000 | 3,551 | % CGUI_TREE User interface to try out TREES package functions.
% (trees package)
%
% cgui_tree (action)
% ------------------
%
% launches a GUI to handle trees. The GUI is segregated in multiple panel
% areas which are handled pretty much separately. These are:
% from top to bottom on the left, editor panels:
% stk_:... |
8e1a5912e0bb9f9e7b6e76847c74cf7016985a450f86b6209dd33f960854582c | MATLAB | 200,000 | 2,718 | function CheckInteractionBetweenSpecificModalities_03022020(AllDataFiles,AllParameters,app)
%%%%%%% This function creates a figure for presntation of the raw behavioral and physiological data.
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedE... |
b03caee20926ac835a724d94002fbd4f82de9288c7923aefc2981e28f7ca9e3e | MATLAB | 200,000 | 2,123 | function SpecificMod_LFPAndSpikes_02082021(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFiles.Video... |
c223d1df967c8be63fb0ce67cff411a09ed66cdae118723c3f8da60e5dfb7ec2 | MATLAB | 200,000 | 2,331 | function SpecificMod_LFPAndSpikesAndVideo_10012022(AllDataFiles,AllParameters,app)
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...
length(AllDataFiles.Video1BehavioralfileList) ...
length(AllDataFil... |
dcb2fc3d41f96cd3d7955e99397c0d27228ef24a4cbe622feaf557ec3772a457 | MATLAB | 200,000 | 5,030 | %This collection of procedures run additional analysis on data generated by the
%placefieldanalyzer_short script plus it generates figures from the output
%of these analyses. This and accompanying scripts were created for the
%manuscript titled
%"Working memory features are embedded in hippocampal place fields."
... |
e8ac4819fa7cf21cdf2156143caa2127a12fc1be7808e69de2f028286f606d4f | MATLAB | 200,000 | 3,290 | function ShowRowDataAllModalities_22012020(AllDataFiles,AllParameters,app)
%%%%%%% This function creates a figure for presntation of the raw behavioral and physiological data.
NumOfFiles=[ length(AllDataFiles.TimeStampsfileList) ...
length(AllDataFiles.ManuallyDefinedEventsfileList) ...... |
e62069b4d499381a2356c486a694322066e04485aa398194051767bb23a3d9d5 | MATLAB | 200,106 | 3,114 | %% Analysis.m
% Trial-level theta/delta measures, sensor weight estimation, visual- auditory phase lag, source-theta combination, merge with behaviour, and diagnostics.
%
% Run order: Preprocessing (once, produces merged cesub-*.mat) -> TIME_TF (setup + time-frequency decomposition, needs a parallel pool) -> this scrip... |
b5e22fa0b9b6ddf45f7bcf649e359631cd93fd0f9183751f9c0ab9d16ed59fb8 | NEURON | 112 | 7 | load_file ("nrngui.hoc")
load_file ("morpho.hoc")
objectvar GC
load_file ("neu_tree.hoc")
neu_tree ("GC.neu") |
ed70ffcb69dad94427bac49a5f767981e577b456b5a2e68b2ed618e9204072a8 | NEURON | 112 | 6 | : 3-D mapping of model geometry
NEURON {
SUFFIX d3
RANGE x, y, z
}
ASSIGNED {x(micron) y(micron) z(micron)}
|
1c32bd0158636fbb0a411fcbe3b2c07026fe06d8a560c453e3bdc357426df94c | NEURON | 126 | 9 | load_file ("nrngui.hoc")
load_file ("GCT.hoc")
objectvar GC
GC = new GC7()
load_file ("neu_tree.hoc")
neu_tree ("GCT.neu") |
9b279cf56b4abf2704afff1d7159e027225fee90d475902309aec605df8334ac | NEURON | 224 | 12 | proc biophys_HL23BN1(){
$o1.delete_axon_BPO()
forsec $o1.all {
insert pas
insert Ih
Ra = 100
cm = 2
e_pas = -83.85905159083714
g_pas = 0.00013276715388485768
gbar_Ih = 4.0286355749662496e-05
}
}
|
c8637bd8b600ba40a7c19fbe02c70776ff2ea5a6cd3cf6ef527ea614fff82cb1 | NEURON | 234 | 11 | /*****************************
TMS simulator for T2N morphologies
GUI for generating parameters
AUTHOR: Nicholas Hananeia
CONTACT: nickhananeia@gmail.com
*******************************/
strdef quasi_file
load_file("GUI.hoc")
GUI()
|
3739e419cd59571b67fc81dbfcaa3f3020d7a7a62bc4853b54ed3f85adce4207 | NEURON | 319 | 22 | proc biophys_HL23MN1(){
$o1.delete_axon(3,1.75,1,1)
forsec $o1.all {
insert pas
Ra = 100
cm = 1
e_pas = -81.5
g_pas = 0.0000232
insert Ih
}
forsec $o1.somatic {
gbar_Ih = 0.0000431
}
forsec $o1.basal {
cm = 1
gbar_Ih = 0.0000949
}
$o1.myelin{
Ra = 100
cm = 0.02
}
}
|
46f1df4a6f5bb16f7a2b861cf64916098dff1447f59425059f234476ed753eaf | NEURON | 423 | 18 | proc biophys_HL23VN1(){
$o1.delete_axon_BPO()
forsec $o1.all {
insert pas
insert Ih
Ra = 100
cm = 2
e_pas = -81.64099928563398
g_pas = 5.640407332265837e-05
gbar_Ih = 7.937538666539732e-05
shift1_Ih = 117.54696999889302
shift2_Ih = 3.460797910265395
shift3_Ih = -49.69676238671805
sh... |
e1a5fdc5390b5677cc7c0fbc7d5949cd68de5b6d73de1fbecd2c3df7c1c2c773 | NEURON | 443 | 26 | proc biophys_HL23PN1(){
$o1.delete_axon(3,1.75,1,1)
forsec $o1.all {
insert pas
Ra = 100
cm = 1
e_pas = -80
g_pas = 0.0000954
insert Ih
}
forsec $o1.somatic {
gbar_Ih = 0.000148
}
forsec $o1.apical {
cm = 2
}
forsec $o1.basal {
cm = 2
gbar_Ih = 0.000000709
}
$o1.distrib... |
424ef539d6bb6613f282e2beb4e0a9dde3e84f9218b87f6221fb25af67842c95 | NEURON | 515 | 17 | /*
* $Id: setpointers.hoc,v 1.4 2008/12/02 22:19:41 ted Exp ted $
* sets up the pointers after the sections have been created
* 2018/05/20 Modified by Aman Aberra
*/
proc setpointers() { local done
getSecRefs() // save coordinates, get section refs, and assign section types
forall {
if (ismembrane("xtra") && ... |
6683b9a1973109cd0a70d9ff3f9c3409d8b32a65f310c54ee4af5d3ed9b6452a | NEURON | 622 | 15 | /*****************************
TMS simulator for T2N morphologies
Main simulation file; execute to run simulation after copying wrapper files
AUTHOR: Nicholas Hananeia
CONTACT: nickhananeia@gmail.com
*******************************/
strdef tmpstr,simfold, quasi_file // temporary string object
objref f, vlist, tvec, se... |
f3676342a320bef67448ee6768c5dc4fc529bf379cc8ba88c9896e0c1fa96398 | NEURON | 655 | 40 | COMMENT
Since this is an electrode current, positive values of i depolarize the cell
and in the presence of the extracellular mechanism there will be a change
in vext since i is not a transmembrane current but a current injected
directly to the inside of the cell.
ENDCOMMENT
INDEPENDENT {t FROM 0 TO 1 WITH 1 (ms)}
NE... |
ca27b216a4c35f706fb3db04ed6908a3215f8d53cb59eb644d3e8b5442936327 | NEURON | 656 | 36 | : $Id: xtra.mod,v 1.4 2014/08/18 23:15:25 ted Exp ted $
: 2018/05/20 Modified by Aman Aberra
NEURON {
SUFFIX xtra
RANGE es : (es = max amplitude of the potential)
RANGE x, y, z, type, order
GLOBAL stim : (stim = normalized waveform)
POINTER ex
}
PARAMETER {
es = 0 (mV)
x = 0 (1) : spatial coords
y = 0 (1... |
4ae5a18e638ee2c6ed28875a8346c0e8392e3a5a191f1a026be6697cb7c12c4f | NEURON | 689 | 36 | : Dynamics that track inside calcium concentration
: modified from Destexhe et al. 1994
NEURON {
SUFFIX CaDynamics_E2
USEION ca READ ica WRITE cai
RANGE decay, gamma, minCai, depth
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = (faraday) (coulombs)
(molar) = (1/liter)
(mM) = (millimolar)
(um) = (mi... |
f49398dbd39e7288235e1bf525feb4e9d13a0cc540c20433e6d9f0395f44a919 | NEURON | 811 | 24 | /*****************************
Location and index exporter
Run this to generate reference files; does no simulation
AUTHOR: Nicholas Hananeia
CONTACT: nickhananeia@gmail.com
*******************************/
strdef tmpstr,simfold, quasi_file // temporary string object
objref f, vlist, tvec, secRef, loc
objref pc,nil,c... |
32daecc2e3a914fd1be035a4d82acc8199bdf013ede42abc516997cf878a986a | NEURON | 862 | 54 | :Comment :
:Reference : : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992), from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
NEURON {
SUFFIX SKv3_1_hay2011
USEION k READ ek WRITE ik
RANGE gbar, gSKv3_1, ik
}
... |
185d695b5a3c0ba0cbc96681135264a9071472d432dbc6717137210023e3dc66 | NEURON | 880 | 61 | :Comment :
:Reference : : Kole,Hallermann,and Stuart, J. Neurosci. 2006, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
NEURON {
SUFFIX Ih_hay2011
NONSPECIFIC_CURRENT ihcn
RANGE gbar, gIh, ihcn
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gb... |
5e26816322fb0f1fc372be3d2e3f5af43ba268d3d171bb040f6859486076ea3b | NEURON | 929 | 58 | TITLE Anomalous rectifier current for RD Traub, J Neurophysiol 89:909-921, 2003
COMMENT
Implemented by Maciej Lazarewicz 2003 (mlazarew@seas.upenn.edu)
ENDCOMMENT
INDEPENDENT { t FROM 0 TO 1 WITH 1 (ms) }
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
}
NEURON {
SUFFIX ar
NONSPECIFIC_CURRENT i
... |
775ebeda822c9c0819a623b9492559e24125ab74d63931633fca1c58f6db543d | NEURON | 930 | 40 | : Dynamics that track inside calcium concentration
: modified from Destexhe et al. 1994 by Hay et al., 2011 https://doi.org/10.1371/journal.pcbi.1002107
NEURON {
SUFFIX CaDynamics_E2_hay2011
USEION ca READ ica WRITE cai
RANGE decay, gamma, minCai, depth
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
FARADAY = ... |
6ac36aa3e113eab67d7d882a6a2b1c9c5e9d52cadae44f763666faa360ccd1c0 | NEURON | 962 | 61 | :Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones
:Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21
: **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**
NEURON {
SUFFIX Im
USEION k READ ek WRITE ik
RANGE ... |
3d971b90042431d18735a52703cf0ac9ede0ea6a650079b20e7f4be7803ed4b6 | NEURON | 980 | 61 | :Reference : : Adams et al. 1982 - M-currents and other potassium currents in bullfrog sympathetic neurones, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
:Comment: corrected rates using q10 = 2.3, target temperature 37 (K. Duecker for duecker_ET_model), orginal 21
NEURON {
SUFFIX... |
cfad4773db518a9330fe2aa4bb2757b651f3316728efb7cd7fe29f2772b20100 | NEURON | 986 | 56 | : SK-type calcium-activated potassium current
: Reference : Kohler et al. 1996
NEURON {
SUFFIX SK_E2
USEION k READ ek WRITE ik
USEION ca READ cai
RANGE gSK_E2bar, gSK_E2, ik, zTau
}
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
(mM) = (milli/liter)
}
PARAMETER {
... |
0764512b6622a9dcbe35b4e98310fec661dbd1fb492551867dd0b2f166e955a7 | NEURON | 992 | 64 | TITLE Calcium dependent potassium channel (small conductance SK)
UNITS {
(molar) = (1/liter)
(mV) = (millivolt)
(S) = (siemens)
(mA) = (milliamp)
(mM) = (millimolar)
}
NEURON {
SUFFIX kcas
USEION ca READ cai
USEION k WRITE ik
RANGE gk,gbar,km,oinf,ik,n,otau
... |
355571a4b1838f1ab756cadb87a68096ba869f5dfcead2b3ba7b541998852ebb | NEURON | 1,010 | 60 | TITLE Na persistent channel
: used in distal oblique dendrites to assist Ca spike initiation
:
: modified to use CVode --Carl Gold 08/12/03
: Updated by YiotaPoirazi 26/1/05
NEURON {
SUFFIX nap
USEION na READ ena WRITE ina
RANGE gnabar,vhalf, K, ina
}
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
... |
5f8c393f4832dd93b828dd37c60b24b3834016cbe1fdb2f704c5d48aa59ddc35 | NEURON | 1,014 | 79 | : Vector stream of events
NEURON {
ARTIFICIAL_CELL VecStim
POINTER ptr
}
ASSIGNED {
index
etime (ms)
ptr
}
INITIAL {
index = 0
element()
if (index > 0) {
net_send(etime - t, 1)
}
}
NET_RECEIVE (w) {
if (flag == 1) {
net_event(t)
element()
if (index > 0) {
net_send(etime - t, 1)
}
}
}
DEST... |
5ea7d2fb8059173935b38e7a568f797ac41b5126beee0652d24c92c92be48725 | NEURON | 1,046 | 61 | : dipole_pp.mod - creates point process mechanism Dipole
:
: v 1.9.1m0
: rev 2015-12-15 (SL: minor)
: last rev: (SL: added Qtotal back, used for par calc)
NEURON {
POINT_PROCESS Dipole
RANGE ri, ia, Q, ztan
POINTER pv
: for POINT_PROCESS. Gets additions from dipole
RANGE Qsum
POINTER Qtotal
}
... |
fa6e2bf02df4f61824846698d3d16ad535db5316b44f931da41a5a1a6bdaa7cd | NEURON | 1,072 | 56 | : SK-type calcium-activated potassium current
: Reference : Kohler et al. 1996, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
NEURON {
SUFFIX SK_E2_hay2011
USEION k READ ek WRITE ik
USEION ca READ cai
RANGE gbar, gSK_E2, ik
}
UNITS {
(mV) = (milliv... |
4cc1a5da9a81ddf6ba04b821b49838ff20e2defb969882a0d81a434582489e48 | NEURON | 1,160 | 73 | :Comment :
:Reference : : Reuveni, Friedman, Amitai, and Gutnick, J.Neurosci. 1993, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
NEURON {
SUFFIX Ca_HVA_hay2011
USEION ca READ eca WRITE ica
RANGE gbar, gCa_HVA, ica
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milli... |
58b8af966bd657b86f9623675a6eae4d9eb6416a5c0f868ba2550ce55065571b | NEURON | 1,178 | 64 | :Comment : "Kv3.2" channel
:Comment : BBP Kv channel, but activation/inactivation vHalf and slope adjusted to fit experimental data.
:Reference : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol.11, no.7,2473-2486 (1992)
:Comment: Adapted by Christopher Currin (2022) to m... |
579cc81ce113557886ebcb54870d25d265f7fdabf78623c1a67de378379b45ff | NEURON | 1,197 | 79 | :Reference :Colbert and Pan 2002
: **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**
NEURON {
SUFFIX NaTa_t
USEION na READ ena WRITE ina
RANGE gNaTa_tbar, gNaTa_t, ina
}
UNITS {
(S) = (siemens)
(mV) = (millivolt)
(mA) = (milliamp)
}
PARAMETER {
gNaTa_tbar = 0.00001 (S/cm2)
}
ASSIGN... |
9d84302d963f8dd649e5e51cad691b72066f2adf21dd449b73bb7cb1ccc2feec | NEURON | 1,197 | 67 | TITLE Calcium low threshold T type current for RD Traub, J Neurophysiol 89:909-921, 2003
COMMENT
Implemented by Maciej Lazarewicz 2003 (mlazarew@seas.upenn.edu)
ENDCOMMENT
INDEPENDENT { t FROM 0 TO 1 WITH 1 (ms) }
UNITS {
(mV) = (millivolt)
(mA) = (milliamp)
}
NEURON {
SUFFIX cat
NONSPECIFIC_CUR... |
21ec22269dd143dbb2d75df94c478434ac813fd13eb8b8a93866e41bf036c5ba | NEURON | 1,213 | 68 | :Comment : LVA ca channel. Note: mtau is an approximation from the plots
:Reference : : Avery and Johnston 1996, tau from Randall 1997
:Comment: shifted by -10 mv to correct for junction potential
:Comment: corrected rates using q10 = 2.3, target temperature 34, orginal 21
: **Modified to use 'celsius' for temperature... |
bb9e8efb7352d4bfee7d47f0dd0ac372ebf2d0a1e2f76385f47dfdd9cb57c25e | NEURON | 1,218 | 68 | :Comment : The transient component of the K current
:Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000
:Comment : shifted -10 mv to correct for junction potential
:Comment: corrected rates using q10 = 2.3,... |
47775ca2fefd36a2a531071602656386ae95407ccd8008875cb39aaa1a23defd | NEURON | 1,235 | 68 | :Comment : The transient component of the K current
:Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
:Comment : shifted ... |
134dc14b13c2a73403cff4702ed10853415b3459697857a13d6092aedb72af80 | NEURON | 1,264 | 77 | COMMENT
**************************************************
File generated by: neuroConstruct v1.3.7
**************************************************
ENDCOMMENT
: This is a NEURON mod file generated from a ChannelML file
: Unit system of original ChannelML file: Physiological Units
COMMENT
Channe... |
ade5a2409a66f4327b43829d0d810dc166aa2c4c0a341200e49775e561d0a7de | NEURON | 1,264 | 77 | COMMENT
**************************************************
File generated by: neuroConstruct v1.3.7
**************************************************
ENDCOMMENT
: This is a NEURON mod file generated from a ChannelML file
: Unit system of original ChannelML file: Physiological Units
COMMENT
Channe... |
55c741a00b9bcd62ff82f6c5594ae983a03df85ad70d2946e867c1eba68ed6f9 | NEURON | 1,274 | 69 | :Comment : LVA ca channel. Note: mtau is an approximation from the plots
:Reference : : original: Avery and Johnston 1996, tau from Randall 1997; adapted from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
:Comment: shifted by -10 mv to correct for junction potential (in Hay et al, 2011)... |
87ec87a2e5bcba2e8fab848b69b4b94d98e58fd1d32c8089e0704899019e5d63 | NEURON | 1,275 | 79 | :Reference :Colbert and Pan 2002
:comment: took the NaTa and shifted both activation/inactivation by 6 mv
: **Modified to use 'celsius' for temperature to correct rates by Aman Aberra**
NEURON {
SUFFIX NaTs2_t
USEION na READ ena WRITE ina
RANGE gNaTs2_tbar, gNaTs2_t, ina
}
UNITS {
(S) = (siemens)
(mV) = (millivol... |
97964616c99c358f03c208002ad8944f6d6e2e714c17b2eeab7d705db58905d3 | NEURON | 1,275 | 66 | :Comment : "Kv3.2" channel
:Comment : BBP Kv channel, but activation/inactivation vHalf and slope adjusted to fit experimental data.
:Comment : Use this mechanism to 'mutate' given proportion of Kv3.2 channels.
:Reference : Characterization of a Shaw-related potassium channel family in rat brain, The EMBO Journal, vol... |
21ccbfc2f32e4bcfd5e376e067fa21011338f220ec542a92d0e92d8fa22b5bc3 | NEURON | 1,305 | 68 | COMMENT
Conceptual model: Delayed rectifier current for
a model of a fast-spiking cortical interneuron.
Authors and citation:
Golomb D, Donner K, Shacham L, Shlosberg D, Amitai Y, Hansel D (2007).
Mechanisms of Firing Patterns in Fast-Spiking Cortical Interneurons.
PLoS Comput Biol 3:e156.
Original impleme... |
3218bba31a2ebcb737d6d2de14e0fc6f97bce47da82190b8c01db95d0c78f0be | NEURON | 1,309 | 79 | :Reference :Colbert and Pan 2002, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
:Comment : corrected rates using q10 = 2.3, target temperature 37 (K. Duecker for duecker_ET_model, fast L5 ET pyr APs), orginal 21
NEURON {
SUFFIX NaTa_t_hay2011
USEION na READ ena WRITE ina
RANGE gba... |
bc6a05e285c133095e1ef77eab8ecd06902655dc3ab8913fcc5457569cf81476 | NEURON | 1,315 | 80 | :Reference :Colbert and Pan 2002, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
:Comment : corrected rates using q10 = 2.3, target temperature 32 (K. Duecker for duecker_ET_model, slower L2/3 pyr APs), orginal 21
NEURON {
SUFFIX NaTa_t_32d_hay2011
USEION na READ ena WRITE ina
RAN... |
9c94a8e47b7b9c2a4e1dfae9b0c78c380061f3ba13bab0b38833fc99612d29f2 | NEURON | 1,332 | 73 | :Comment : The persistent component of the K current
:Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000
:Comment : shifted -10 mv to correct for junction potential
:Comment: corrected rates using q10 = 2.3... |
e9b6bc59d45fc215c5b9a6a9ff7963f06ded0663bd274d009e8801a7ab9ea685 | NEURON | 1,335 | 101 | TITLE CA1 KM channel from Mala Shah
: M. Migliore June 2006
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
}
PARAMETER {
v (mV)
ek
celsius (degC)
gbar=.0001 (mho/cm2)
gk (mho/cm2)
: vhalfl=-40 (mV)
vhalfl=-42 (mV)
kl=-4
: vhalft=-42 (mV)
vhalft=-42 (m... |
9a3e3d4217016f2e5f7c41501b5668700599856e71a1b1f70b609ad4215e248d | NEURON | 1,347 | 72 | :Comment : The persistent component of the K current
:Reference : : Voltage-gated K+ channels in layer 5 neocortical pyramidal neurones from young rats:subtypes and gradients,Korngreen and Sakmann, J. Physiology, 2000, from Hay et al., 2011 PLOS Comp Bio, https://doi.org/10.1371/journal.pcbi.1002107
:Comment : shifted... |
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