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aqua

An event-based tool for analyzing and quantifying calcium or glutamate imaging data

bhtsne

Barnes-Hut t-SNE

brick

a general-purpose Matlab toolbox

caiman-matlab

Complete Matlab pipeline for large scale calcium imaging data analysis

cellsort

This toolbox includes routines for using principal component analysis (PCA) and independent component analysis (ICA) to extract cellular signals from imaging data sets. A full description and validation of the method is provided in the paper, "Automated Analysis of Cellular Signals from Large-Scale Calcium Imaging Data," Neuron, 63:747 (2009): http://tinyurl.com/cellsort

connectomicspcv

Set of tools for the connectomics post challenge verification

connectomicsperspectivespaper

Code, datasets and tools used for the perspectives paper

cotete.jl

Continuous-Time Event-based Transfer Entropy

deepinterpolation

esp32-camera

export_fig

A MATLAB toolbox for exporting publication quality figures

fpa

Fiber photometry analysis

hamamatsuorcatools

Set of tools to work with files created with Hamamatsu Orca cameras and their software (Hokawo and HCImage)

helpertools

common functions for everyday (personal) MATLAB use

jidt

JIDT: Java Information Dynamics Toolkit for studying information-theoretic measures of computation in complex systems

jsonlab

JSONLab: a native JSON/UBJSON/MassagePack encoder/decoder for MATLAB/Octave

micropython

MicroPython - a lean and efficient Python implementation for microcontrollers and constrained systems

netcal

NETwork CALcium analysis

neurondyn

Simulates neuronal culture dynamics using a modified Izhikevich model

neurondyngenmatlab

Matlab tools for neurondyn and neurongen

neurongen

Generates realistic neuronal networks using arbitrary geometrical patterns as a substrate

neurongm

oasis_matlab

papercite

Bibtex plugin for wordpress

sessionmanager

Simple MATLAB session manager to handle different sets of open editor files and paths.

simkernel

SimKernel controls parameter scans and iterations for any given C++ code

spikes

spike extraction from calcium signals (Deneux et al., 2016)

te-causality

Generalized Transfer Entropy program for model-free connectivity analysis.

tensortools

Fitting and visualizing tensor decompositions in Python