sha256 stringlengths 64 64 | language stringclasses 27
values | size int32 1 491k | lines int32 1 21.8k | content stringlengths 1 200k |
|---|---|---|---|---|
54cb8f9a54169c858c4999930c03f12360af330ebebbfab8016fffddc22e36f2 | MATLAB | 7,261 | 183 | % From the paper of Brenner, Benjamin, et al.
% "Quantifying nanoscopic alterations associated with mitochondrial dysfunction using three-dimensional single-molecule localization microscopy."
% Biomedical optics express 15.3 (2024): 1571-1584.
% https://github.com/FOIL-NU/Mitochondria
% TU Delft
% Grussmayer Lab
%
% ... |
51d1377970288ada9063d832b675c2478b0af26bf9e0d228ddb668304e756a0a | MATLAB | 7,404 | 235 | function plotADCandB0Values(project_directory, project_name, subject_list, roi_patterns, voxel_size, adc_map);
%%
% Inputs:
% project_directory
% project_name
% subject_list
% roi_patterns
% voxel_size
% adc_map
%%
% Process the first subject only
subject_code = subject_list(1).name;
subjPath = fullfile... |
927e7722597e85d6525b968bd3c8ac657c5b074b1e289f3f7f5fe2041b0d74a4 | MATLAB | 7,504 | 458 |
%%
%model normal learning
%plot auditory vs. spatial weight
load model_chem_control.mat
rmsd_all=[];
for qq=27
% for qq=[7 10 12 16 22 23 24 25 27]
load mod2lp_control_result
parm_results2=parm_results;
parm_results2(:,2:4)=parm_results2(:,2:4)/10e7;
qq=parm_results... |
60413e21ef847c473c90e6abb7655ae6b7bb5005fc7a41ec6ab777ed8dc64c5b | MATLAB | 7,576 | 203 | function [xshifts, yshifts] = track_subpixel_wholeframe_motion_fft_forloop(movref, refframe)
%save the size of the movie
z = size(movref, 3);
xshifts=zeros(1,z);
yshifts=zeros(1,z);
% It is safer to use the square root of the fluorescence intensities to
% minimize the effect of bright calcium transients. Not necessa... |
6c1a2a15c25ea0697368697994f746bc96c318ffb7bb327fde5e1c04a2f6acc0 | MATLAB | 7,587 | 167 | clear; clc; close all;
%% PARAMETERS
projPath = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\';
scriptsPath = 'R:\- Gorter\- Personal folders\Fultz, N\scripts\csfdonuts_lydiane\';
centralDataPath = 'R:\- Gorter\CSF_STREAM\Data\';
physioConditions = {'cardiac', 'resp','random'};
physioFolders = {'... |
035cdec511e199515182c6aacea36f76f14472873c2f0de7bad84e1de41b7ab3 | MATLAB | 7,610 | 241 | function plotADCandB0Values(project_directory, project_name, subject_list, roi_patterns, voxel_size, adc_map);
%%
% Inputs:
% project_directory
% project_name
% subject_list
% roi_patterns
% voxel_size
% adc_map
%%
% Process the first subject only
subject_code = subject_list(1).name;
subjPath = fullfile... |
1a8cb6b322a1867d30d6c047e87ff772f276e0f68ce1ca2766ca0e96078fb714 | MATLAB | 7,645 | 157 | %% plotting Concentric Circles lydianes way
% csf donut protocol
% nina fultz january 2026
% n.e.fultz@lumc.nl
%% goals:
clear
clc
%%
% defining paths
project_directory = 'R:\- Gorter\- Personal folders\Fultz, N\';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project_directory, 'scri... |
4f087c502fa300e31ae270a0984fc3faf3a038004598f80605b64ea3c3d71a9c | MATLAB | 7,669 | 202 | %% READLISTDATA Reads a Philips .LIST/.DATA file pair
%
% [DATA,INFO] = READLISTDATA(FILENAME)
%
% FILENAME is a string containing a file prefix or name of the .LIST
% header file or .DATA binary file, e.g. RAW_001 or RAW_001.LIST or RAW_001.DATA
%
% DATA is an N-dimensional array holding the raw binar... |
638c17b79d1fc3e4e782eef8dc826caac48c022540ee3349473a3ff68be7b5b8 | MATLAB | 7,670 | 243 | function [rec_data, fileToRead1, par_data, par_txt] = import_parrec_special_WT2_LH( in_type, name_filter, filename)
%%
% [rec_data, par_data, par_txt] = import_parrec()
% Imports data from the specified file
% FILETOREAD1: file to read
% Maarten Versluis: read PAR / REC files
DELIMITER = ' ';
if (nargin... |
a14e3aad8280bae971a6171e1d29c1f7de4b1dfacdb51d9c0a9c116eba01cb5f | MATLAB | 7,707 | 242 | function [rec_data, fileToRead1, par_data, par_txt] = import_parrec_special_WT2_LH( in_type, name_filter, filename)
% [rec_data, par_data, par_txt] = import_parrec()
% Imports data from the specified file
% FILETOREAD1: file to read
% Maarten Versluis: read PAR / REC files
DELIMITER = ' ';
if (nargin == 4... |
930099a356b48a0d4eb857abf8df66e140e2c41a423dbee4044c907676665eb1 | MATLAB | 7,775 | 209 | function [corrected, xshift, yshift] = correct_translation_singleframe(moving, ref, isRefPrecalcd, movingFullSize)
% Translate a single frame to match a reference, using subpixel FFT
% registration.
if nargin < 4
movingFullSize = moving;
end
% Find shifts:
if nargin<3 || ~isRefPrecalcd
ref_fft = zeros(size(re... |
631791e5ed5c613ca6f7b9192cad870e920e7eb07491879a4e04d2ba3603e317 | MATLAB | 8,086 | 208 | % csf donut protocol for CAA patients
% nina fultz january 2026
% n.e.fultz@lumc.nl
%% goals:
clear
clc
%%
% defining paths
project_directory = 'R:\- Gorter\- Personal folders\Fultz, N\';
project_name = 'csfdonuts_lydiane'
scripts = fullfile(project_directory, 'scripts', project_name);
%... |
b8fd5c44e65598de303b5f07621c6998e6f09c06f926bb1b5405161b647fb3e4 | MATLAB | 8,174 | 244 | function group_outfile = ft_group_wPLI(subjList, cond, freqLabel, varargin)
% ft_group_wPLI
% Group-level aggregation of subject-wise wPLI matrices (single-band files).
%
% INPUTS
% subjList : cell array of subject IDs
% cond : condition label
% freqLabel : band label used in filenames (e.g., 'alpha','be... |
3692070651ae0fe6d4e29b522eaddff742edb8212196d9812c07855b28fed37c | MATLAB | 8,178 | 178 | clear; clc; close all;
%% PARAMETERS
projPath = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\';
scriptsPath = 'R:\- Gorter\- Personal folders\Fultz, N\scripts\csfdonuts_lydiane\';
centralDataPath = 'R:\- Gorter\CSF_STREAM\Data\';
physioConditions = {'cardiac', 'resp','random'};
physioFolders = {'... |
fec1cf2efc9d49cc806ca89e95dcad7d4ba31f9f8d494d44d5092aadaad42f8f | MATLAB | 8,208 | 244 | function group_outfile = ft_group_wpli(subjList, cond, freqLabel, varargin)
% ft_group_wpli
% Group-level aggregation of subject-wise wPLI matrices (single-band files).
%
% INPUTS
% subjList : cell array of subject IDs (e.g., {'A0102','A0174',...})
% cond : condition label (e.g., 'EMG2' or 'EMG3')
% freqL... |
711755c7fd90feb7a09574f83f84897e0fa1be30db6ac4b5ee8fad4a2753c5e8 | MATLAB | 8,396 | 282 |
function [x,fval,exitflag,output] = fminsearchbnd(fun,x0,LB,UB,options,varargin)
% FMINSEARCHBND: FMINSEARCH, but with bound constraints by transformation
% usage: x=FMINSEARCHBND(fun,x0)
% usage: x=FMINSEARCHBND(fun,x0,LB)
% usage: x=FMINSEARCHBND(fun,x0,LB,UB)
% usage: x=FMINSEARCHBND(fun,x0,LB,UB,options)
% ... |
082a632bd785b8a63bb8f65afc5194c05fd38aab073b344ad39bfabc687e4cd1 | MATLAB | 8,492 | 235 | function [ADC_all_phases, FA_all_phases] = DTIphases_to_niftis(projPath, subject_code, ...
subjOriginalData, physio);
% goal: convert DTI maps to niftis
subjPath = [projPath, subject_code, '\'];
%% Paths
regDir = fullfile(subjPath, 'reoriented');
adc = fullfile(subjOriginalData);
anatF... |
da5bae8b0bacf4283c6b6b14251e389155e68a6ce7b284c5e9d6671aeca5840a | MATLAB | 8,588 | 292 | function [aligned, dpxAl, dpyAl, B] = doLucasKanadeSPMD(stackFull, ref, isGpu)
% Parts of the Lucas Kanade motion correction code were obtained from
% https://xcorr.net/2014/08/02/non-rigid-deformation-for-calcium-imaging-frame-alignment/
% and/or are originally based on the method published in:
% Greenberg, David S.... |
9f5079fa7df7a4517b17d066c241841adcb6717f9b72b691f1df3cfc72b09d37 | MATLAB | 8,630 | 256 | function group_outfile = ft_group_psi(subjList, cond, freqLabel, varargin)
% ft_group_psi
% Group-level aggregation of subject-wise PSI matrices (single-band files).
%
% INPUTS
% subjList : cell array of subject IDs
% cond : condition label
% freqLabel : band label used in filenames (e.g., 'alpha','bet... |
0a57d1a65ef806d9271738d523c9f48354dd447f0399f1cb279f81dae8455edd | MATLAB | 8,634 | 220 | function b0_segmentation(project_directory, project_name, subject_code, scripts);
%edited by Nina Fultz, originally from Madda Debiasi
%
GENERALDIR = fullfile(project_directory, project_name);
savingdir = fullfile(project_directory, project_name, subject_code, 'reg');
reoriented = fullfile(project_directory, projec... |
761722affe71882bda618c2bacd34bd4819ec66239efc786a25e395f38cc2741 | MATLAB | 8,668 | 211 | function [blinkpsf_clean, blinkpsf_noisy] = bgGen_Cam(blink_clean, Cam, Grid, Optic, subseq, useGPU)
%
% Inputs:
% Cam struct
% Qgain scalar, # of electrons per incoming photon
% readout scalar, root mean square (randn between 0 and 1 -> ...
% multiply by readout noise)
% therma... |
7a9f4554c909b9fab76dc271dbac8ff52a9a00e088835b74a52d229205b9a298 | MATLAB | 8,675 | 256 | function group_outfile = ft_group_psi(subjList, cond, freqLabel, varargin)
% ft_group_psi
% Group-level aggregation of subject-wise PSI matrices (single-band files).
%
% INPUTS
% subjList : cell array of subject IDs (e.g., {'A0102','A0174',...})
% cond : condition label (e.g., 'EMG2' or 'EMG3')
% freqLabe... |
e553ab60ac58d150c5b4d0b45c46e9f75ecf5f635faa246fe313c40cd8402d53 | MATLAB | 8,678 | 300 | function out = threeRegionSim(params)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% out = threeRegionSim(params)
%
% Generates a simulated dataset with three interacting regions. Ref:
%
% Perich MG et al. Inferring brain-wide interactions using data-constrained
% recurrent neural netwo... |
2ece06b9986772f1abd1e1f902c9d0de2f10de2aee161f9f7ba4da1e5163a84f | MATLAB | 8,772 | 211 | % fdr_bh() - Executes the Benjamini & Hochberg (1995) and the Benjamini &
% Yekutieli (2001) procedure for controlling the false discovery
% rate (FDR) of a family of hypothesis tests. FDR is the expected
% proportion of rejected hypotheses that are mistakenly rejected
% (i.e... |
55b19a14cd4888f85a541fcca67ed6cde5c0b70b40f75eb85e07fb2ee20ee9e5 | MATLAB | 8,859 | 603 | function info = metaImageInfo(fileName, varargin)
%METAIMAGEINFO Read information header of meta image data
%
% INFO = metaImageInfo(FILENAME)
% Read and decodes the information stored in metaimage header file.
%
% Metaimage header files are text files containing parameters name/value
% pai... |
977764c0b7826beea4c4baa1169ba2019d0e8a3eecdfe8172447fa25059d01e2 | MATLAB | 8,916 | 184 | %% XMLRECPARSEXML Convert a Philips XMLREC XML file to a structure
%
% [INFO] = XMLRECPARSEXML(XMLFILENAME)
%
% INFO is a structure containing the tag information within the XML file
% XMLFILENAME.
%
% INFO = XMLRECPARSEXML(XMLFILENAME,'waitbar',true)
%
% Dislpays a waitbar while the XML tags are b... |
1af500d417267ce58cbd6f722327cdc26aae41621f5c2da44c3db76868142855 | MATLAB | 9,235 | 284 | function wpli_outfile = ft_wPLI_singleSub(subj, cond, freqLabel, freqRange, varargin)
% ft_wPLI_singleSub
% Compute subject-level debiased wPLI for one subject/condition/frequency band.
%
% Expects ROI time series saved by the beamformer/ROI step:
% roi_timeseries_<cond>_<freqLabel>.mat containing
% roi_data :... |
789b9adead96ca3f6d06251d9d62cbfe1941338d9c493a12c9b5e4a0977d9c2d | MATLAB | 9,351 | 191 | function movStruct = lKFast_affineSlow_memMap(...
obj, movStruct, scanImageMetadata, movNum, opMode)
% movStruct = withinFile_withinFrame_lucasKanade(obj, movStruct, scanImageMetadata, movNum, opMode)
% finds/corrects in-frame motion with an algorithm that takes into account
% that images are acquired by raster sca... |
fdcb174ceb95c80a0a9f057a0830952f44376ea6b5ea34468098258ae83ab7aa | MATLAB | 9,459 | 195 | function movStruct = lucasKanade_affineReg(...
obj, movStruct, scanImageMetadata, movNum, opMode)
% movStruct = withinFile_withinFrame_lucasKanade(obj, movStruct, scanImageMetadata, movNum, opMode)
% finds/corrects in-frame motion with an algorithm that takes into account
% that images are acquired by raster scanni... |
489c52baa5eff0339525b0320f60965916b4627a1926e98369b71f1e7d49b2be | MATLAB | 9,805 | 244 | function createGui(sel, acq, img, sliceNum, channelNum, smoothWindow, excludeFrames)
% Constructor method for the selectRoisGui class. See selectROIs.m for
% usage.
%% For debugging:
% assignin('base', 'sel', sel);
%% Create GUI data structure:
% Initialize properties:
sel.acq = acq;
sel.slice = sliceNum;
% Set up r... |
4ab95cbbb621521b70e80a18eaa20ece75aac7d6a484491524ae47867ccccd1b | MATLAB | 9,892 | 252 | function psi_outfile = ft_PSI_singleSub(subj, cond, freqLabel, freqRange, varargin)
% ft_PSI_singleSub
% Compute subject-level PSI (Phase Slope Index) for one subject/condition/frequency band.
% Expects ROI time series saved by ft_Beamformer_extractROI:
% roi_timeseries_<cond>_<freqLabel>.mat with roi_data [nROI x n... |
a72f3488f257cc1d74a82009a3edbd6fa43939a18c25626a2cc794ba794e8e18 | MATLAB | 9,893 | 252 | function psi_outfile = ft_PSI_singleSub(subj, cond, freqLabel, freqRange, varargin)
% ft_PSI_singleSub
% Compute subject-level PSI (Phase Slope Index) for one subject/condition/frequency band.
% Expects ROI time series saved by ft_Beamformer_extractROI:
% roi_timeseries_<cond>_<freqLabel>.mat with roi_data [nROI x n... |
8a66bab7b352bfadc5b50ccacc3ebc95c4592e47fa4a50ae6a0b484424947002 | MATLAB | 10,325 | 217 | function movStruct = withinFile_withinFrame_lucasKanade(...
obj, movStruct, scanImageMetadata, movNum, opMode)
% movStruct = withinFile_withinFrame_lucasKanade(obj, movStruct, scanImageMetadata, movNum, opMode)
% finds/corrects in-frame motion with an algorithm that takes into account
% that images are acquired by ... |
d2f1070508bc33e5074bd61ac77e8b15a0240ff83453bae82d71197b629d7e2f | MATLAB | 10,329 | 334 | clear; clc;
%% plot to show csf mobility ring around vessel and then SAS - M1 and M2
% Define paths
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project_directory, 'scripts');
addpath(genpath(fullfile(scripts, 'Violinplot-Matlab-master')));
addpath... |
1e4ceecff884ce895f909c4ecc435b35d2b58f9bf925560354327badcc04ead2 | MATLAB | 10,371 | 313 | function [out] = trainMultiRegionRNN(activity,params)
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%
% Trains a data-constrained multi-region RNN. The RNN can be used for,
% among other things, Current-Based Decomposition (CURBD). Ref:
%
% Perich MG et al. Inferring brain-wide interaction... |
1d67b36d13198108cb1d776b1960aef2795aaca596f1330a3bd883bad8cf5437 | MATLAB | 10,408 | 214 | %% Script 1: Extract and Save Table for 4 Target Predictors Only
clear all;
close all;
% --- 1. Define Paths and Settings ---
run grabSubiculumCells.m % Loads the 'cellNum' structure
figsFolder = 'D:\Paper\CodesToUpload\PredictPlateaus';
% Analysis Parameters
speedThreshold = 0.05;
preEventDurationSec =... |
6cb014cf4c6cf4d9ea49a59b75137cde24234628c885204400a0d002882071e3 | MATLAB | 10,556 | 339 | clear; clc;
%% plot to show csf mobility ring around vessel and then SAS - M1 and M2
% Define paths
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project_directory, 'scripts');
addpath(genpath(fullfile(scripts, 'Violinplot-Matlab-master')));
addpath... |
0cd0f7a581f798e73d93822078f57be114a5982c77bf1bfae85a78a3bac428c2 | MATLAB | 10,557 | 265 | function [varargout] = textAnalysis(data,varargin)
% textAnalysis Perform text cleaning and first-step clustering to compute a similarity matrix
%
% similarityAll = textAnalysis(data) cleans participant-generated text
% responses and runs the first step of the two-stage semantic
% categorization analysis. T... |
c6f9908dee5957314d124d2cb0bfd993c55cdc78c47850cba80fad6dc98a6d1d | MATLAB | 10,853 | 214 | function analyzePlateauDistributions(data_struct, plotting)
% ANALYZEPLATEAUDISTRIBUTIONS Spatial distribution of dendritic plateaus
% relative to reward, with behaviour-matched control anchors.
%
% Rewards are first grouped into distinct track locations (so recordings with
% a reward-location shift are handled automa... |
c3a5b289d8044f9bb0ebc29b630c53eab14c3ad451715e7c1927514816893340 | MATLAB | 10,873 | 267 | %% WRITEPARREC Write a Philips PARREC image file
%
% [SUCCESS] = WRITEPARREC(FILENAME,DATA,INFO)
%
% FILENAME is a string containing a file prefix or name of the PAR header
% file or REC data file, e.g. SURVEY_1 or SURVEY_1.PAR or SURVEY_1.REC
%
% DATA is an N-dimensional array holding the image data.
... |
4b2590b229c57871fd772a49f9d39b3f89578d3931f3a2b37f36537eee6b0400 | MATLAB | 10,980 | 291 | function ft_Beamformer_extractROI(subj, cond, freqBand, freq_label, varargin)
% ft_Beamformer_extractROI
% LCMV beamforming on preprocessed trials and extraction of ROI time series
% from a warped MNI sourcemodel (10 mm). Includes a QC gate: requires >=MinTrials
% after cleaning; otherwise writes an empty .mat and a QC... |
9cf3f9a4b0ae8e6a6ebca2ad50a255a1e28b7f28907d48ae1c04444ab4652235 | MATLAB | 11,583 | 225 | %% Plot all electrodes from all patients on brain -- project to closest pial surface within anatomical region
clc; clear; close all;
main_path = '/Users/am4611/Dropbox/Research/ChickenSyntax/analysis/R/task ECoG comparisons/electrode wilcox tests and brain plots/output/';
%% Colors
colors_lightest = readtable('/Users... |
496ebe80981be8387915a8e65eff4c0315da17652f3904e769ea901cae3655e7 | MATLAB | 12,013 | 271 | function movStruct = lucasKanade_plus_nonrigid(...
obj, movStruct, scanImageMetadata, movNum, opMode)
% movStruct = withinFile_withinFrame_lucasKanade(obj, movStruct, scanImageMetadata, movNum, opMode)
% finds/corrects in-frame motion with an algorithm that takes into account
% that images are acquired by raster sc... |
003d9ac5b2769efa8c1d755f37e8d96a234d1a26078486cd624c3589ce8c03b9 | MATLAB | 12,066 | 328 | function ft_CBPT_ROI2ROI_EMG2vsEMG3(method, varargin)
% ft_CBPT_ROI2ROI_EMG2vsEMG3
% Cluster-based permutation test (CBPT) for ROI×ROI connectivity (EMG2 vs EMG3),
% for either wPLI (undirected) or PSI (directed), across arbitrary frequency labels.
%
% EXPECTED INPUT FILES PER SUBJECT
% <InDir>/<subj>/<method>_EMG2_<... |
9a05cdd028e5d926897c40c40e5a00bee0e9e28bb5e39dde420977be1780e914 | MATLAB | 12,261 | 304 | classdef fastBSpline
%fastBSpline - A fast, lightweight class that implements
%non-uniform B splines of any order
%
%Matlab's spline functions are very general. This generality comes at
%the price of speed. For large-scale applications, including model
%fitting where some components of the mode... |
a4246ac0b0281b7af6a347db138900dca3b755a02763239cb2785b144ad91b9d | MATLAB | 12,267 | 401 | clear; clc;
%% plot to show csf mobility ring around vessel and then SAS - M1 and M2
% Define paths
project_directory = '/exports/gorter-hpc/users/ninafultz/';
project_name = 'csfdonuts_lydiane';
scripts = fullfile(project_directory, 'scripts');
addpath(genpath(fullfile(scripts, 'Violinplot-Matlab-master')));
addpath... |
33fb3b5ed545ee255a56595a22bc31a7b550c465a4323bc1145a7d465ae2a222 | MATLAB | 12,280 | 333 | function ft_CBPT_ROI2ROI_EMG2vsEMG3(method, varargin)
% ft_CBPT_ROI2ROI_EMG2vsEMG3
% Cluster-based permutation test (CBPT) for ROI×ROI connectivity (EMG2 vs EMG3),
% for either wPLI (undirected) or PSI (directed), across arbitrary frequency labels.
%
% This script is written to be NN-/repo-friendly:
% - no hard-coded i... |
bfa6541fa72feb5e8c55b6af2db3cc02d6c9f4c3e30e3f125a80b73c7178025c | MATLAB | 12,643 | 251 | %% Using the Acuisition2P class:
%
%% -----Setup-------
% All software in the acq2P package has been extensively tested on Matlab
% 2014b. Using earlier versions may cause bugs and will certainly degrade
% appearance.
% You will need a number of functions from the harveylab helper functions
% repository, so I suggest ... |
27538e655f0214b5353d0017645f480f0bea5e1dcbad9c435fa4fcbadc1f43d2 | MATLAB | 12,845 | 210 | %% Using the ROI selection tool
% This guide explains how to use the ROI selection tool contained within the acq2P framework
% The tool is designed to work optimally with a dual-monitor setup,
% although that is not strictly necessary. You will want a mouse with a
% scroll wheel too. And if your data (specifically, th... |
01ba276beb09cb4750124f9730655877cd8bb41537f8740153dfc0c8847784a1 | MATLAB | 13,664 | 301 | function movStruct = lucasKanade_plus_nonrigid_memMap(...
obj, movStruct, scanImageMetadata, movNum, opMode)
% movStruct = withinFile_withinFrame_lucasKanade(obj, movStruct, scanImageMetadata, movNum, opMode)
% finds/corrects in-frame motion with an algorithm that takes into account
% that images are acquired by ra... |
714324f93b3a17b98c0df35e0dd84bc7f79594ecda5442e65e8cb8f8f3e6f438 | MATLAB | 13,958 | 406 | clear; clc; close all;
%% PARAMETERS
projPath = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\';
scriptsPath = 'R:\- Gorter\- Personal folders\Fultz, N\scripts\csfdonuts_lydiane\';
centralDataPath = 'R:\- Gorter\CSF_STREAM\Data\';
physioConditions = {'cardiac', 'random'};
physioFolders = {'Cardiac... |
508bac530a833d1406f119d3f0e289173ec662c330e81f602ca0a9175c112934 | MATLAB | 17,376 | 453 | clear; clc; close all;
%% PARAMETERS
projPath = 'R:\- Gorter\- Personal folders\Fultz, N\csfdonuts_lydiane\';
scriptsPath = 'R:\- Gorter\- Personal folders\Fultz, N\scripts\csfdonuts_lydiane\';
centralDataPath = 'R:\- Gorter\CSF_STREAM\Data\';
physioConditions = {'cardiac', 'random'};
physioFolders = {'Cardiac... |
1b97c0a98bf6d1d312bb3a501e12509fed33236500a9bf5d231e43087cd11021 | MATLAB | 17,839 | 445 | function [ img ] = fourierInterpolation( img, itp_fac, mirrorMode )
% USAGE: [ img ] = fourierInterpolation( img, itp_fac, padding )
% Interpolation of a 2D or 3D input image using zero padding in the Fourier
% domain. The input data can be mirrored along the lateral/axial or both
% dimensions to make the borders perio... |
4689860c808be0d0726416bb6f3f988c79047edd1da8644f26ecb699b2205e60 | MATLAB | 18,082 | 518 | %% FEM Code for the No Tunnelling Calcium Model
% Clear everything to ensure an empty environment before running
clear all
close all
clc
% Track the run time for the simulation
tic
% Load the No Tunnelling Calcium Model's mesh data
load("Mesh_no_tunnel.mat")
% [ER_p,ER_e,ER_t], [Cyto_p,Cyto_e,Cyto_t], inter_bound_p... |
0ede9e2b881717dc52843f23746ba9e746dae6073357fa01e10a14f4cb51a673 | MATLAB | 18,565 | 1,090 |
%Compare 3 three models
% use 39 control animal behavior data
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%
%One animal example
load model_chem_control.mat
rmsd_all=[];
for qq=10
load mod2lp_control_result
parm_results2... |
7b1dfaa2cbf946ab37365371175c4466bd8122ff63396822684159386743eca2 | MATLAB | 18,836 | 530 | %% FEM Code for the Less Tunnelling Calcium Model
% Clear everything to ensure an empty environment before running
clear all
close all
clc
% Track the run time for the simulation
tic
% Load the Less Tunnelling Model's mesh data
load("Mesh_less_tunnel.mat")
% [ER_p,ER_e,ER_t], [Cyto_p,Cyto_e,Cyto_t], inter_bound_p
%... |
8da23b42390c91e636a732cab7ec21bd8113cf092a8363a7da4ddf9abc27e942 | MATLAB | 21,317 | 557 | function [emitter_dist, mask, Param] =...
dataGen(Grid, Fluo, Pattern, plotfig, saveParam)
% Function that generates a mask and random emitter locations based on
% called pattern shape and parameters
%
% Inputs:
% Grid struct
% pxsize scalar, size of pixels [nm]
% pxnum integer, amou... |
c56f51d2a951c00ad9768412b96b66199e32c3daa2c75d21b176b7c149b4e980 | MATLAB | 22,644 | 556 | %% ========== MAIN SCRIPT: aggregate per-cell results across locations ==========
%==== Setup ====
% Set this to the folder that contains one subfolder per recorded cell. Each
% cell subfolder must contain extractedVals/final_allInclusive4_2groups/counts_20ms*.mat
% produced by analyzePlateauDistributions.
mainFolder =... |
1c5aeeee8fed33e5aeaba74de12a16230ad95eb595de1b95b65badcef4afe837 | MATLAB | 23,085 | 454 | function extract_all_pooled_plateau_v3_anchors(main_folder)
% EXTRACT_ALL_POOLED_PLATEAU_V3_ANCHORS
%
% Builds the per-event plateau database used by the clustering/spatial
% analysis. Walks every recording subfolder of MAIN_FOLDER, detects plateau
% events from the Vm trace, and for each event stores shape/amplitude
%... |
571ac9878ba8c921746007a24eef7ffc43e732f2c96c590142f753e54ce35b78 | MATLAB | 23,092 | 527 | %% LOADLABRAW Load a Philips LABRAW file
%
% [DATA,INFO] = LOADLABRAW(FILENAME)
%
% FILENAME is a string containing a file prefix or name of the LAB
% hexadecimal label file or RAW data file, e.g. RAW_001 or RAW_001.LAB or RAW_001.RAW
%
% DATA is an N-dimensional array holding the raw k-space data.
%
... |
36c886ee0ca2017895a749b298452ba2054a9091566d3be668cb8b90c262e153 | MATLAB | 24,453 | 448 | function plateau_clustering_analysis_v3_anchors(main_folder)
rng(1);
%% ====================================================================
%% SECTION 1: SETUP & CONFIGURATION
%% ====================================================================
if nargin < 1
main_folder = uig... |
56d60e5235f26a5dbd40779576f9a4afdb148e5034aeccec55756662fdeba3ad | MATLAB | 25,777 | 705 | %% LOADPARREC Load a Philips PARREC image file
%
% [DATA,INFO] = LOADPARREC(FILENAME)
%
% FILENAME is a string containing a file prefix or name of the PAR header
% file or REC data file, e.g. SURVEY_1 or SURVEY_1.PAR or SURVEY_1.REC
%
% DATA is an N-dimensional array holding the image data.
%
% INF... |
901a32a475653953fb5528e21841be9e846b6aa0ce891c2c3560a5236227a8ce | MATLAB | 25,887 | 510 | clear
clc
%% MANUAL
patient = 'Patient010';
%% AUTO for a bit, but define bad elecs and trigger channels, etc
% Reset path for testing
restoredefaultpath
%% Load shared paths
addpath('/Volumes/Research/Epilepsy_ECOG/CodeBase/Matlab');
local_path = strcat('/Users/am4611/Dropbox/Research/ChickenSyntax/data/',patient,'... |
fc6465e827fa33ab2a87f8fb11912acb36df7fb1313d1591cbb953d8fe734642 | MATLAB | 29,196 | 605 | function [p, iter_used, corr, failed, settings, xpixelposition, ypixelposition, data_corrected, template_sampled] = ...
correct_scanned_imaging(data,template_image,subrec,data_extra_channels,frame_list,settings,isbidirec,est_p,pregauss,leftexclude)
%correct_scanned_imaging
%
%Corrects horizontal motion artifacts in... |
67825836cae915a1ce080b08228c29b86b3393a2dde3390765cd1fad138b541a | MATLAB | 29,879 | 799 | function MJLMselectROIs(obj, img, sliceNum, channelNum, smoothWindow, excludeFrames)
%selectROIs(obj,img,sliceNum,channelNum,smoothWindow)
%all inputs except acquisition object are optional
%
%GUI for sorting through seeds / pixel-pixel correlation matrices to select
%appropriate ROIs for an acquisition. Requires preca... |
62d0d8ff402d38a7c69d68929090ef2e99870d9e1bc754e42b9082fe09a06ac1 | MATLAB | 39,571 | 1,059 | function MJLMselectROIs(obj,img,sliceNum,channelNum,smoothWindow)
%selectROIs(obj,img,sliceNum,channelNum,smoothWindow)
%all inputs except acquisition object are optional
%
%GUI for sorting through seeds / pixel-pixel correlation matrices to select
%appropriate ROIs for an acquisition. Requires precalculated pixel
%cov... |
f1aea97a8e3924f49bed81847849bec535e689361b858ac7bc13ff472e80cc5e | MATLAB | 41,024 | 1,068 | %% LOADXMLREC Load a Philips XMLREC image file pair
%
% [DATA,INFO] = LOADXMLREC(FILENAME)
%
% FILENAME is a string containing a file prefix or name of the XML header
% file or REC data file, e.g. SURVEY_1 or SURVEY_1.XML or SURVEY_1.REC
% DATA is an N-dimensional array holding the image data.
%
% ... |
ca450bf286ac12696e15406c0a228672941c6c84b0af39a9f94de9e85c8eb3d0 | MATLAB | 58,705 | 1,357 | %%%%%%%%
% Author: David Gruskin
% Contact: dcg2153@cumc.columbia.edu
% Project: Heritability of movie-evoked brain activity and connectivity
% Description: This is the main analysis and visualization script for the
% FC component of the HCP 7T ISC heritability project.
%%%%%%%%
% Add paths
% ------------------------... |
bdcb29a3a07ea35807075742a2e4eb9ba85262a3fa5886d63df7e5a0a406ab2a | MATLAB | 104,589 | 2,345 | %%%%%%%%
% Author: David Gruskin
% Contact: dcg2153@cumc.columbia.edu
% Project: Heritability of movie-evoked brain activity and connectivity
% Description: This is the main analysis and visualization script for the
% ISC component of the HCP 7T ISC heritability project.
%%%%%%%%
%% Add and set relevant paths
desktop_... |
e7a9ecaf6b090b878cb523b42ccd9970c42109ef4d2662511a1ad240b8817bb0 | MATLAB | 111,279 | 1,926 | %% PHILIPSDICOMENTRIES Return a structure of information for Philips DICOM entries
%
% [PHILIPS] = PHILIPSDICOMENTRIES
%
% PHILIPS is a structure containing definitions for the PARDEF and IMGDEF
% portions of a Philips PAR header file including the information for the
% associated DICOM entries in an en... |
a5b4beda7a88624159d00ec0c7720636f2da711f37135e6f23b1db5a79da55f5 | MATLAB | 159,623 | 3,228 | %% LOADDICOM Load a Philips DICOM image file
%
% [DATA,INFO] = LOADDICOM(FILENAME)
%
% FILENAME is a string containing the name of a DICOM
% DATA is an N-dimensional array holding the image data.
% INFO is a structure containing details from the DICOM header file
%
% [DATA,INFO] = LOADDICOM([])
%
% ... |
d1a55c0bb9e06e03081f4ac1537d9ec1d3766ffc4051dc8a95a6b2e7f37eae84 | NEURON | 280 | 27 | TITLE Constant current for custom initialization
COMMENT
Taken from NEURON book, Chapter 8
ENDCOMMENT
NEURON {
SUFFIX constant
NONSPECIFIC_CURRENT i
RANGE i, ic
}
UNITS {
(mA) = (milliamp)
}
PARAMETER {
ic = 0 (mA/cm2)
}
ASSIGNED {
i (mA/cm2)
}
BREAKPOINT {
i = ic
}
|
0bcc406fe653a0c97fc4630354e91c6b904d4e7fa8c161c292888c5118284038 | NEURON | 977 | 77 | : Vector stream of events
NEURON {
THREADSAFE
ARTIFICIAL_CELL OldVecStim
RANGE delay
}
ASSIGNED {
index
etime (ms)
space
delay
}
PARAMETER {
::delay = 0.0
}
INITIAL {
index = 0
: delay = 0
element()
if (index > 0) {
net_send(delay + etime - t, 1)
}
}
NET_RECEIVE (w) {
if (flag == 1) {
net_even... |
cb65f5a3b52e1cc9f77ded794ff544b7413686cacb8f55731dd363c0e74e1197 | NEURON | 1,031 | 71 | TITLE NMDA synapse
: from Durstewitz & Gabriel (2006), Cerebral Cortex
NEURON {
POINT_PROCESS NMDA
NONSPECIFIC_CURRENT i
RANGE g, a, b, gNMDAmax, i
RANGE tauD, tauF, util, tcon, tcoff, enmda
}
UNITS {
(uS) = (microsiemens)
(nA) = (nanoamp)
(mV) = (millivolt)
}
PARAMETER {
tcon = 2.3 (ms)
tcoff = 95.0 (ms)
... |
6bbbe0a2b2f2fd90eab301c926b1cb5601cec8a3cf083977983fe2f980e322f2 | NEURON | 1,248 | 59 | TITLE Na persistent channel
COMMENT
used in distal oblique dendrites to assist Ca spike initiation
a typo in the exponential function was pointed out by Michele Migliore and
corrected by Yiota Poirazi on December 4th, 2003
ENDCOMMENT
NEURON {
SUFFIX nap
USEION na READ ena WRITE ina
RANGE gnabar, vh... |
26cf4d7ca815c71152b85d54bd1b16783b39f2ee3c63d643ea7fbeb5826ced5a | NEURON | 1,276 | 62 | TITLE HVAm (R-type) calcium (CA2+) channel with medium threshold for activation
COMMENT
Used in distal dendritic regions, together with calH.mod,
to help the generation of Ca++ spikes in these regions.
Uses channel conductance (not permeability).
Written by Yiota Poirazi on 11/13/00 poirazi@LNC.usc.edu.
ENDCOMMENT
NE... |
f4959f30446f12aebfc0cbcaf0e4b097d133184d4bf1420467baf035b0bf8b0a | NEURON | 1,292 | 64 | TITLE HVAm (R-type) calcium (CA2+) channel with medium threshold for activation
COMMENT
Used in somatic regions.
It has lower threshold for activation/inactivation and slower activation time constant,
than the same mechanism in dendritic regions.
Uses channel conductance (not permeability).
Written by Yiota Poirazi on... |
db6e4565c376177cf2c5546a7b7413e22f35ef07bebad250b39aa419f7a7e878 | NEURON | 1,394 | 61 | TITLE hyperpolarization-activated channel - h current
COMMENT
Used in Pyramidal Cells.
Based on Magee, 1988, J Neurosci, 18:7613-7624, doi: 10.1523/JNEUROSCI.18-19-07613.1998
ENDCOMMENT
NEURON {
SUFFIX h
NONSPECIFIC_CURRENT ih
RANGE ghbar, vhalf, eh, ih, K
}
UNITS {
(mA) = (milliamp)
(mV) = (mil... |
0e6046f5c6b53863ca8850cee4899dba41153e7391b369d0972e41b8c378d29e | NEURON | 1,397 | 71 | TITLE Calcium pump/buffering mechanism
COMMENT
Calcium accumulation into a volume of area*depth next to the
membrane with a decay (time constant tau) to resting level
given by the global calcium variable `cai0_ca_ion`.
Used in Basket, Axoaxonic, Bistartfified, CCK+, VIP+/CCK+, and VIP+/CR+ cells.
Based on Cutsuridis e... |
5ef1191624924c5bd579e9436eae64a2c8bb94e65c69fb1a891fbae766195f0f | NEURON | 1,470 | 81 | TITLE Slow calcium-dependent potassium current (mAHP)
COMMENT
Ca2+-dependent K+ channel medium AHP.
From Moczydlowski and Latorre, 1983, J Gen Physiol, 82: 511-542, doi: 10.1085/jgp.82.4.511
ENDCOMMENT
NEURON {
SUFFIX mykca
USEION ca READ cai
USEION k READ ek WRITE ik
RANGE gkbar, ik
}
UNITS {
(mV) = (millivolt... |
e1d820cbb4551817afbba21a3b4b2ff11bf8758080cbbb17612269899db9640c | NEURON | 1,485 | 68 | TITLE HVA (L-type) calcium channel with low threshold for activation (dendrites)
COMMENT
Used in distal dendrites to account for distally restricted initiation of Ca++ spikes.
Uses channel conductance (not permeability).
Written by Yiota Poirazi, 1/8/00 poirazi@LNC.usc.edu.
ENDCOMMENT
NEURON {
SUFFIX calH
USEION ca... |
0c9118fea284e621fc5a2fb40ac55cc7158ba54722e66f11aceb4c92b5e1ea95 | NEURON | 1,524 | 77 | TITLE Slowly activating potassium current (muscarinic K+ channel)
COMMENT
Potassium channel, Hodgkin-Huxley style kinetics.
Voltage-dependent potassium current (Im) (muscarinic K+ channel)
Slow, noninactivating.
Author: Zach Mainen, Salk Institute, 1995, zach@salk.edu
ENDCOMMENT
NEURON {
SUFFIX km
USEION k READ ek... |
861693637cb1ad1d93bb981a59e31555648601f9967c820841261ac2afe1ab56 | NEURON | 1,563 | 95 | TITLE A-type K+ channel
COMMENT
Original from Klee, et al., 1995, J Neurophysiol, 74, 1892-1895, doi: 10.1152/jn.1995.74.5.1982
modified to account for Dax A Current, Migliore et al., 1997, J. Comput. Neurosci. 7, 5-15, doi: 10.1023/a:1008906225285
modified by Poirazi on 10/2/00 according to Hoffman et al., 1997, Natu... |
1a0d88847bce4fbd60b6b22083951356ddd767cf0e2c8d46a3b9663c5ddb622b | NEURON | 1,597 | 96 | TITLE A-type K+ channel
COMMENT
Original from Klee, et al., 1995, J Neurophysiol, 74, 1892-1895, doi: 10.1152/jn.1995.74.5.1982
modified to account for Dax A Current, Migliore et al., 1997, J. Comput. Neurosci. 7, 5-15, doi: 10.1023/a:1008906225285
modified by Poirazi on 10/2/00 according to Hoffman et al., 1997, Natu... |
942c085cd4a4248d482de2403d6f1ce4664af18e63f5015b1c7c79d8ecad3483 | NEURON | 1,655 | 84 | TITLE Difference of two exponentials
COMMENT
Two state kinetic scheme synapse described by rise time tau1,
and decay time constant tau2. The normalized peak condunductance is 1.
Decay time MUST be greater than rise time.
The solution of A->G->bath with rate constants 1/tau1 and 1/tau2 is
A = a*exp(-t/tau1) a... |
df66c7fe2b702adc883b10f4b8abd8ae0ec8d27b1f48c6e32557d119e2961681 | NEURON | 1,993 | 98 | TITLE HVA (L-type) calcium channel with low threshold for activation (soma)
COMMENT
Used in somatic and proximal dendritic regions.
Uses channel conductance (not permeability).
ENDCOMMENT
NEURON {
SUFFIX cal
USEION ca READ cai, cao WRITE ica
RANGE gcalbar, ica
}
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)
(S)... |
cbdf2d02f6a1b662c59f47e3beb79a8fa538de498fab02320cb1e9edf57c1667 | NEURON | 2,007 | 89 | TITLE standardized kvs channel
COMMENT
Standardized and templated by DendroTweaks.
This NMODL file defines a model for a k ion channel.
ENDCOMMENT
NEURON {
SUFFIX kvs
USEION k READ ek WRITE ik
RANGE gbar, i, vhalf_n, sigma_n, k_n, delta_n, tau0_n, ik, n
}
UNITS {
(mA) = (milliamp)
(mV) = (millivolt)... |
dec33757b5dc8f5c3b95b463a90616fc1a93c9ba2c4cf62694c0e26103cc541e | NEURON | 2,243 | 98 | TITLE Slow calcium-dependent potassium current (sAHP)
COMMENT
Ca2+-dependent K+ current responsible for slow AHP
Sah and Bekkers, 1996, J Neurosci 16:4537-4542, doi: 10.1523/JNEUROSCI.16-15-04537.1996
Differential equations
Model based on a first order kinetic scheme
+n cai <-> (alpha, beta)
Following this ... |
7065a6f76bb8452633908e0a0f56022d056a8282d8c29e8bcaf2e1c84a18b077 | NEURON | 2,246 | 80 | TITLE Calcium Pumping/Buffering
COMMENT
Internal calcium concentration due to calcium currents and pump.
Differential equations.
Decay of internal calcium concentration
The mechanism is taken from: Destexhe et al., 1994, J Comput Neurosci, 1:195-230, doi: 10.1007/BF00961734
This mechanism was published in Destexhe e... |
7942749fab43e3b2a9b245e7a54e46a16aab7e7394c30c88a7046159ce91bca6 | NEURON | 2,586 | 104 | TITLE standardized nas channel
COMMENT
Standardized and templated by DendroTweaks.
This NMODL file defines a model for a na ion channel.
ENDCOMMENT
NEURON {
SUFFIX nas
USEION na READ ena WRITE ina
RANGE gbar, i, vhalf_m, sigma_m, k_m, delta_m, tau0_m, vhalf_h, sigma_h, k_h, delta_h, tau0_h, ina, m, h
}
U... |
49231e15f1163ec1111c2423701c311cf3e3ca9c0fe892f9deccb99554adcd1b | NEURON | 2,714 | 117 | TITLE LVA (T-type) calcium (Ca2+) channel with high threshold for activation
COMMENT
Based on Magee and Johnston, 1995, J Physiol, 487:67-90, doi: 10.1113/jphysiol.1995.sp020862
Used in somatic and dendritic regions.
It calculates I_Ca using conductance (not permeability).
Important:
The T-current does not activate ... |
315ed98d1ffae6e799810d39a9cfb9f793395a561ec0a86ad15734b258bb81e6 | NEURON | 2,735 | 164 | TITLE Vector stream of events
COMMENT
A VecStim is an artificial spiking cell that generates
events at times that are specified in a Vector.
HOC Example:
// assumes spt is a Vector whose elements are all > 0
// and are sorted in monotonically increasing order
objref vs
vs = new VecStim()
vs.play(spt)
// now launch a... |
5ff98593ec4e02a604bd8949d86b3f6d98ebc4c3a146d10bebec1bc801bc00f6 | NEURON | 3,663 | 149 | TITLE HH channel that includes both a sodium and a delayed rectifier channel
COMMENT
accounts for sodium conductance attenuation
Bartlett Mel-modified Hodgkin - Huxley conductances (after Ojvind et al.)
Terrence Brannon-added attenuation
Yiota Poirazi-modified Kdr and Na threshold and time constants,
to make it more... |
6a9f1be5a3c6c8f61efc0e14d8feea4cf8d20b8e54a86919fbce112c2dc880f8 | NEURON | 3,689 | 162 | TITLE HH channel that includes both a sodium and a delayed rectifier channel
COMMENT
accounts for sodium conductance attenuation
Bartlett Mel-modified Hodgkin - Huxley conductances (after Ojvind et al.)
Terrence Brannon-added attenuation
Yiota Poirazi-modified Kdr and Na threshold and time constants,
to make it more... |
0f345df38b1de2b46f450a82e940884a64c91c94d00a1a597f32d87b75ff9344 | NEURON | 3,749 | 143 | TITLE Excitatory Synapse with AMPA/NMDA components
COMMENT
AMPA/NMDA currents: are based on double exponentials of a decay and a rise phase, with a scaling factor
gampa, gnmda: opening/closing states in [0,1]
tau1: rise, tau2: decay
w_ampa/w_nmda: the relevant weights. gampa_max and gnmda_max can be omitted in a la... |
3377dd75a83442f4084accea12c1a87f8e1f0fb8db55ed1e38f9ff222448612e | NEURON | 3,881 | 159 | TITLE HH channel that includes both a sodium and a delayed rectifier channel
COMMENT
accounts for sodium conductance attenuation
Bartlett Mel-modified Hodgkin - Huxley conductances (after Ojvind et al.)
Terrence Brannon-added attenuation
Yiota Poirazi-modified Kdr and Na threshold and time constants,
to make it more... |
27c7de50aeb74372f0c3471970ca8249c08695192e1d2f86133ddcd2b3548b55 | NEURON | 3,951 | 142 | TITLE HH channel that includes both a sodium and a delayed rectifier channel
COMMENT
Original taken from: Bernader, et al., 1991, Proc. Natl. Acad. Sci. USA 88, 11569-11573, doi: 10.1073/pnas.88.24.11569
Accounts for sodium conductance attenuation:
Jung et al., 1997, J. Neurosci. 17, 6639-6647, doi: 10.1523/JNEUROSCI... |
e1938997a67097dbe97521c0eede63d00fe76d35d52f87490fcc3d0caa6636ab | NEURON | 4,034 | 163 | TITLE HH channel that includes both a sodium and a delayed rectifier channel
: and accounts for sodium conductance attenuation
: Bartlett Mel-modified Hodgkin - Huxley conductances (after Ojvind et al.)
: Terrence Brannon-added attenuation
: Yiota Poirazi-modified Kdr and Na threshold and time constants
: to make it ... |
eb581d3884d18d419ac6403b8f10c708463bffa0328a2be83821f1d2cce7bf02 | NEURON | 4,284 | 164 | TITLE Excitatory Synapse with AMPA/NMDA components and Short-Term Plasticity
COMMENT
AMPA/NMDA currents: are based on double exponentials of a decay and a rise phase, with a scaling factor
gampa, gnmda: opening/closing states in [0,1]
tau1: rise, tau2: decay
w_ampa/w_nmda: the relevant weights. gbar_ampa and... |
3a2644343315622e6b8b439feb5d86eeb959fdfe9d5373c1b9316ad3d82d768c | NEURON | 6,098 | 215 | TITLE Excitatory Synapse with Ca concentration and AMPA/NMDA components
COMMENT
Ca2+ diffusion from/to spine/shaft
- if cai_diffused > 0 --> diffusion from the shaft to spine, so cai is decreased via a decrease in ica (ica becomes less negative)
- if cai_diffused < 0 --> diffusion from the spine to shaft, so cai is ... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.