ToolConnect: a functional connectivity toolbox for in vitro networks
Nowadays, the use of in vitro reduced models of neuronal networks to investigate the interplay between structural-functional connectivity and the emerging collective dynamics is a widely accepted approach. In this respect, a relevant advance for this kind of studies has been given by the recent intr...
Main Authors: | , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2016-03-01
|
Series: | Frontiers in Neuroinformatics |
Subjects: | |
Online Access: | http://journal.frontiersin.org/Journal/10.3389/fninf.2016.00013/full |
id |
doaj-f6c8cbacb1a84e93a65feb4df1d25497 |
---|---|
record_format |
Article |
spelling |
doaj-f6c8cbacb1a84e93a65feb4df1d254972020-11-25T00:04:02ZengFrontiers Media S.A.Frontiers in Neuroinformatics1662-51962016-03-011010.3389/fninf.2016.00013167726ToolConnect: a functional connectivity toolbox for in vitro networksVito Paolo Pastore0Daniele ePoli1Aleksandar eGodjoski2Sergio eMartinoia3Sergio eMartinoia4Paolo eMassobrio5University of GenovaUniversity of GenovaUniversity of GenovaUniversity of GenovaConsiglio Nazionale delle Ricerche (CNR)University of GenovaNowadays, the use of in vitro reduced models of neuronal networks to investigate the interplay between structural-functional connectivity and the emerging collective dynamics is a widely accepted approach. In this respect, a relevant advance for this kind of studies has been given by the recent introduction of high-density large-scale Micro-Electrode Arrays (MEAs) which have favored the mapping of functional connections and the recordings of the neuronal electrical activity. Although several toolboxes have been implemented to characterize network dynamics and derive functional links, no specifically dedicated software for the management of huge amount of data and direct estimation of functional connectivity maps has been developed. TOOLCONNECT offers the implementation of up to date algorithms and a user-friendly Graphical User Interface (GUI) to analyze recorded data from large scale networks. It has been specifically conceived as a computationally efficient open-source software tailored to infer functional connectivity by analyzing the spike trains acquired from in vitro networks coupled to MEAs. In the current version, TOOLCONNECT implements correlation- (cross-correlation, partial-correlation) and information theory (joint entropy, transfer entropy) based core algorithms, as well as useful and practical add-ons to visualize functional connectivity graphs and extract some topological features. In this work, we present the software, its main features and capabilities together with some demonstrative applications on hippocampal recordings.http://journal.frontiersin.org/Journal/10.3389/fninf.2016.00013/fullfunctional connectivityin vitroneural networksMicro-Electrode Arraysmulti-threadingcorrelation algorithms |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Vito Paolo Pastore Daniele ePoli Aleksandar eGodjoski Sergio eMartinoia Sergio eMartinoia Paolo eMassobrio |
spellingShingle |
Vito Paolo Pastore Daniele ePoli Aleksandar eGodjoski Sergio eMartinoia Sergio eMartinoia Paolo eMassobrio ToolConnect: a functional connectivity toolbox for in vitro networks Frontiers in Neuroinformatics functional connectivity in vitro neural networks Micro-Electrode Arrays multi-threading correlation algorithms |
author_facet |
Vito Paolo Pastore Daniele ePoli Aleksandar eGodjoski Sergio eMartinoia Sergio eMartinoia Paolo eMassobrio |
author_sort |
Vito Paolo Pastore |
title |
ToolConnect: a functional connectivity toolbox for in vitro networks |
title_short |
ToolConnect: a functional connectivity toolbox for in vitro networks |
title_full |
ToolConnect: a functional connectivity toolbox for in vitro networks |
title_fullStr |
ToolConnect: a functional connectivity toolbox for in vitro networks |
title_full_unstemmed |
ToolConnect: a functional connectivity toolbox for in vitro networks |
title_sort |
toolconnect: a functional connectivity toolbox for in vitro networks |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Neuroinformatics |
issn |
1662-5196 |
publishDate |
2016-03-01 |
description |
Nowadays, the use of in vitro reduced models of neuronal networks to investigate the interplay between structural-functional connectivity and the emerging collective dynamics is a widely accepted approach. In this respect, a relevant advance for this kind of studies has been given by the recent introduction of high-density large-scale Micro-Electrode Arrays (MEAs) which have favored the mapping of functional connections and the recordings of the neuronal electrical activity. Although several toolboxes have been implemented to characterize network dynamics and derive functional links, no specifically dedicated software for the management of huge amount of data and direct estimation of functional connectivity maps has been developed. TOOLCONNECT offers the implementation of up to date algorithms and a user-friendly Graphical User Interface (GUI) to analyze recorded data from large scale networks. It has been specifically conceived as a computationally efficient open-source software tailored to infer functional connectivity by analyzing the spike trains acquired from in vitro networks coupled to MEAs. In the current version, TOOLCONNECT implements correlation- (cross-correlation, partial-correlation) and information theory (joint entropy, transfer entropy) based core algorithms, as well as useful and practical add-ons to visualize functional connectivity graphs and extract some topological features. In this work, we present the software, its main features and capabilities together with some demonstrative applications on hippocampal recordings. |
topic |
functional connectivity in vitro neural networks Micro-Electrode Arrays multi-threading correlation algorithms |
url |
http://journal.frontiersin.org/Journal/10.3389/fninf.2016.00013/full |
work_keys_str_mv |
AT vitopaolopastore toolconnectafunctionalconnectivitytoolboxforinvitronetworks AT danieleepoli toolconnectafunctionalconnectivitytoolboxforinvitronetworks AT aleksandaregodjoski toolconnectafunctionalconnectivitytoolboxforinvitronetworks AT sergioemartinoia toolconnectafunctionalconnectivitytoolboxforinvitronetworks AT sergioemartinoia toolconnectafunctionalconnectivitytoolboxforinvitronetworks AT paoloemassobrio toolconnectafunctionalconnectivitytoolboxforinvitronetworks |
_version_ |
1725431413375762432 |