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A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N

Mid-Year Research Report 2015


- Tuesday 18 August -

12:00 - 5:00pm – CIBF ECR WorkshopPullman Cairns International (17 Abbott St, Cairns)

Attendees: CIBF Scholars & Fellows

ECR WorkshopLocation: Boardroom 2

12:00 – 1:00 Lunch

1:00 – 1:15 Introduction – Jason Mattingley

1:15 – 2:45 Facilitating Lab Exchanges – All ECR’s

Introduction to ECR’s, their labs and their projects

2:45 – 3:15 Afternoon Tea

3:15 – 4:00 ECR Committee – All ECR’s

Development of Terms of Reference

Development of programs & outcomes

Voting on committee roles

4:00 – 5:00 Roadmaps For A Successful Science Career – Marta Garrido, Ehsan Arabzadeh, Jason Mattingley, Gary Egan

Round tables with CI’s to discuss career planning, research strategies, recognising opportunities,

overcoming setbacks.

5:00 Close

5:30 - 10:00pm – CIBF Welcome DinnerPullman Reef Hotel Casino (35-41 Wharf St, Cairns)

Attendees: CIBF CI’s, AI’s, Coordinators, Scholars, Fellows, Node Administrators and Advisory Board Members

Welcome DinnerThe Coral Lounge & Pool Deck

5:30 – 6:30 Welcome drinks

6:30 – 10:00 Dinner


- Wednesday 19 August -

9:00 - 5:00pm – CIBF Science MeetingsPullman Reef Hotel Casino (35-41 Wharf St, Cairns)

Attendees: CIBF CI’s, AI’s, Coordinators, Scholars, Fellows, Node Administrators and Advisory Board Members

Main Science MeetingLocation: Urchins 2 & 3

9:00 – 10:30 Introduction and Overview of CIBF Activities

9:00 – 9:20 Welcome and overview of recent CIBF activities, Gary Egan9:20 – 9:40 Operations update, Lisa Hutton9:40 – 9:50 Education and ECR programs, Elizabeth Paton9:50 – 10:00 Gender equity, Elizabeth Paton10:00 – 10:15 The Brain Dialogue, Rachel Nowak10:15 – 10:30 Computation program, Wojtek Goscinski & Pulin Gong10:30 – 11:00 Morning Tea

11:00 – 12:00 Science Session 1 – Systems (human) neuroscience, Chaired by Michael Breakspear

11:00 – 11:15 Rapid information processing in subcortical amygdala pathways, Marta Garrido11:15 – 11:30 Stimulating connections: an effective connectivity brain map, Gary Egan11:30 – 11:45 Understanding human attention, decision-making and prediction using psychophysics, brain

imaging and neural stimulation, Jason Mattingley11:45 – 12:00 Unified Neural Models for Attention, Prediction and Decision, Tahereh Babaie, Peter

Robinson12:00 – 12:30 Science Session 2 – Spatial Systems (atlases), Chaired by Gary Egan

12:00 – 12:15 DTI/MRI atlas of the rat brain, Emma Schofield, George Paxinos12:15 – 12:30 A digital atlas of connections in the marmoset brain, Piotr Majka, Marcello Rosa12:30 – 1:30 Lunch

1:30 – 2:45 Science Session 3 – Circuits & Cells (animal models), Chaired by Paul Martin

1:30 – 1:45 Predictive coding as a theory of integrative brain function, with application to the cortical microcircuit, Michael Ibbotson

1:45 – 2:00 The role of predictive coding in receptive field formation in visual cortex, Hamish Meffen, Michael Ibbotson

2:00 – 2:15 Sensory decision-making in rodents, Ehsan Abrabzadeh & Greg Stuart

2:15 – 2:30 Visual signal processing in thalamocortical loops; predictive coding in attentional circuit, Paul Martin

2:30 – 2:45 Neural circuits that mediate fear learning and extinction, Roger Marek, Pankaj Sah2:45 – 3:30 Science session 4 – Models & Technology projects – Chaired by Peter Robinson



2:45 – 3:00 Computer Modelling of Human Visual System with Applications in Computer Vision, Gary Egan, Arthur Lowery

3:00 – 3:15 Nano Scale Interfaces to Neurons, Stan Skafidas3:15 – 3:30 Real time analysis of network function using an all optical interface, Tim Karle, Steve Petrou3:30 – 4:00 Afternoon Tea

4:00 – 5:00 Wrap up and future directions

4:00 – 4:30 Science program discussion, Gary Egan4:30 – 4:40 Industry engagement, Gary Egan4:40 – 4:50 International collaborations, Lisa Hutton4:50 – 5:00 Concluding comments Gary Egan

5:00 Close


9:00 - 5:00pm – CIBF Node Administration MeetingPullman Reef Hotel Casino (35-41 Wharf St, Cairns)

Attendees: CIBF Management & Node Administrators


9:00 – 10:30 Introduction and Overview of CIBF Activities

9:00 – 9:20 Welcome and overview of recent CIBF activities, Gary Egan9:20 – 9:40 Operations update, Lisa Hutton9:40 – 9:50 Education and ECR programs, Elizabeth Paton9:50 – 10:00 Gender Equity, Elizabeth Paton10:00 – 10:15 The Brain Dialogue, Rachel Nowak10:15 – 10:30 Computation, Wojtek Goscinski & Pulin Gong10:30 – 11:00 Morning Tea

11:00 – 3:30 Node Administration Meeting, Location: Chill out room

11:00 – 11:30 Administration Session 1 – Getting to know you, Lisa Hutton

Informal round table - who we are, what brought us to this role and what we do in the role

11:30 – 12:30 Administration Session 2 – Database & Reporting, Lisa Hutton

Overview of database model: input, instructions & expectations

12:30 – 1:30 Lunch

1:30 – 2:15 Administration Session 3 – Central & Node Staff Responsibilities, Vicki McAuliffe

Review of roles and responsibilities of central theme and node administrators

2:15 – 3:15 Administration Session 4 – Information For Node Administrators, Vicki McAuliffe & Elizabeth Paton

Communication to/ from central theme

Policies & procedures

3:15 – 3:30 Wrap up & Meeting Close

3:30 – 4:00 Afternoon Tea

4:00 – 5:00 Main Meeting, Location: Urchins 2 & 3

4:00 – 5:00 Wrap up and future directions

4:00 – 4:30 Science program discussion, Gary Egan4:30 – 4:40 Industry engagement, Gary Egan4:40 – 4:50 International collaborations, Lisa Hutton4:50 – 5:00 Concluding comments Gary Egan

5:00 Close

5:30 - 10:00pm – CIBF Advisory Board MeetingPullman Reef Hotel Casino (35-41 Wharf St, Cairns)


Attendees: CIBF Advisory Board Members

Location: Wharf Street Boardroom

5:30 – 10:00 Advisory Board meeting & working dinner


TABLE OF CONTENTS

1 Letter from the Director..........................................................................................................................................................22 CIBF Personnel........................................................................................................................................................................3

Chief Investigators (CIs)..............................................................................................................................................................3Partner Investigators (PIs)...........................................................................................................................................................4Associate Investigators (AIs).......................................................................................................................................................4Coordinators................................................................................................................................................................................5Fellows.........................................................................................................................................................................................5Scholars.......................................................................................................................................................................................6Management & Node Administrators...........................................................................................................................................6Advisory Board............................................................................................................................................................................6Centre Contributors - Fellows......................................................................................................................................................7Centre Contributors - Scholars....................................................................................................................................................8

3 CIBF Research projects..........................................................................................................................................................9Project 1: Stimulating connections: an effective connectivity brain map...................................................................................10Project 2: Predictive coding as a theory of integrative brain function, with application to the cortical microcircuit....................12Project 3: The role of predictive coding in receptive field formation in visual cortex.................................................................14Project 4: Brain machine interface tiles.....................................................................................................................................16Project 5: Pedunculotegmental nucleus....................................................................................................................................18Project 6: DTI/ MRI Atlas of the rat brain...................................................................................................................................20Project 7: Real time analysis of network function using an all optical interface.........................................................................22Project 8: Unified neural models for attention prediction and decision......................................................................................24Project 9: Neural signatures of decision making in the primate cortex......................................................................................26Project 10: Nano scale interfaces to neurons............................................................................................................................28Project 11: Sensory decision-making in rodents.......................................................................................................................30Project 12: Understanding human attention, decision-making and prediction using psychophysics, brain imaging and neural stimulation..................................................................................................................................................................................32Project 13: Rapid information processing in subcortical amygdala pathways...........................................................................34Project 14: Computer modelling of human visual system with applications in computer vision................................................36Project 15: A digital atlas of connections in the marmoset brain...............................................................................................38Project 16: Visual signal processing in thalamocortical loops; predictive coding in attentional circuits....................................39Project 17: Neural circuits that mediate fear learning and extinction.........................................................................................40

4 CIBF Strategic initiative projects.........................................................................................................................................41SIP 1: Direct assessment of predictive coding as a theory of Integrative brain function...........................................................42SIP 2: Nexpo system for experimental interface and data visualisation....................................................................................43SIP 4: Predictive coding: Clarity imaging of thalamocortical circuits.........................................................................................44SIP 5: Computing facility for modelling......................................................................................................................................45SIP 6: A custom-designed TMS-compatible headcoil for human brain imaging experiments on attention, prediction and decision-making.........................................................................................................................................................................46

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SIP 9: CLARITY and Viral Vectors to Trace Connections in Attention Pathways.....................................................................47SIP 10: Endocannabinoid modulation of neuronal excitability...................................................................................................48

5 Education...............................................................................................................................................................................496 The Brain Dialogue................................................................................................................................................................507 Neuroinformatics...................................................................................................................................................................528 Gender Equity........................................................................................................................................................................549 Notes......................................................................................................................................................................................55

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1 Letter from the DirectorWelcome to the ARC Centre of Excellence for Integrative Brain Function (CIBF) 2015 Science Meeting! I am delighted to report

that CIBF has continued to develop during the first half of 2015, in both research activities and the number of researchers

associated with the Centre. In the 12 months since the establishment of CIBF in mid 2014, the Centre has become recognised

as a nationally important brain research organisation. During 2015 CIBF has grown substantially with the appointment of 24

Centre (post-doctoral and early career research) Fellows and 10 Centre (post-graduate) Scholars who are supported (either

wholly or in part) from the Centre, as well as 37 fellows and 36 scholars who are contributing to the Centre’s research programs

and activities.

The CIBF 2015 Science Meeting is being held in Cairns in conjunction with the 2015 Australasian Neuroscience Society annual

scientific meeting, and the International Neuroinformatics Coordinating Facility (INCF) 2015 annual congress. The Science

Meeting will include a comprehensive overview of the Centre’s research output that has been achieved over the past year,

together with updates on the experimental and theoretical neuroscience work currently underway, and discussions of the

research plans for the next 12 months.

This year the Science Meeting includes an early career research (ECR) half day program of activities. The Centre’s ECRs,

fellows and scholars are a critical part of the centre’s future as well as the future of brain research in Australia. I am personally

committed to ensuring that CIBF is very active in supporting the next generation of researchers with additional events and

activities throughout the life of the Centre.

The collective research productivity from CIBF in 2014 was substantial with over 49 peer reviewed articles, books and book

chapters published, and over 20 peer reviewed papers have been published to date in 2015. This provides an excellent basis

for discussions at this science meeting that focus on the integration of the research efforts of the four research themes

investigating the three fundamental integrative brain function.

I would like to thank Lyn Beazley, Chair of the CIBF Advisory Board, for her continuing support of CIBF during 2015. I would

also like to thank the advisory board members, and in particular the international members, for their governance and oversight

of the research program and other activities of the Centre. I would also like to acknowledge the hard work of Lisa Hutton, CIBF

Centre Manager, the Central Theme, and the CIBF node administrators who have worked tirelessly over the past few months in

preparation for the science meeting. The success of the meeting will be in no small part due to their stellar efforts.

The CIBF Executive consists of the CIBF Deputy Director, Marcello Rosa, the CIBF Research Theme leaders, Jason

Mattingley, Pankaj Shah, Greg Stuart and Peter Robinson, the Centre Manager, Lisa Hutton, and George Paxinos and Michael

Ibbotson, who meet monthly to oversee the management and development of the Centre. The Executive’s work is ensuring the

successful establishment of an outstanding brain research program across the CIBF multidisciplinary research environment.

Their contributions are ensuring that the scientific goals and broader social outcomes of the Centre are being achieved, and I

sincerely thank them for their invaluable work.

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A key enabling strategy of the Centre has been the establishment of a computational neuroscience and modelling capability.

This consists of access to high performance computing and data storage resources which is co-ordinated by Wojtek Goscinski,

and a repository of computational modelling tools that is being developed by Pulin Gong.

The Centre has developed a highly successful knowledge sharing program, The Brain Dialogue led by Rachel Nowak, and the

Education and ECR program, lead by Ramesh Rajan and supported by Elizabeth Paton, that will be presented during the

Science Meeting. I encourage all CIBF investigators, fellows and scholars to actively engage in these programs.

Director, CIBF

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A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N Personnel

2 CIBF PersonnelChief Investigators (CIs)

Gary Egan

CIBF Director,

Monash University

Marcello Rosa

Deputy Director,

Monash University

Jason Mattingley

CI, Theme Leader -

Brain Systems,

University of

Queensland

Peter Robinson

CI, Theme Leader-

Modelling &

Neurotechnology,

University of Sydney

Pankaj Sah

CI, Theme Leader-

Neuronal Circuits,

University of

Queensland

Greg Stuart

CI, Theme Leader-

Cells & Synapses,

Australian National

University

Ehsan Arabzadeh

CI,

Australian National

University

Marta Garrido

CI,

University of

Queensland

Ulrike Grünert

CI,


Michael Ibbotson

CI,

University of

Melbourne

Arthur Lowery

CI,

Monash University

Paul Martin

CI,


George Paxinos

CI,

University of NSW

Steve Petrou

CI,

University of

Melbourne

Stan Skafidas

CI,

University of

Melbourne

Michael Breakspear

CI,

QIMR Berghofer

Medical Research

Institute

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Partner Investigators (PIs)

Mathew Diamond – International School for Advanced Studies (SISSA), Trieste, Italy

Sean Hill – International Neuroinformatics Coordinating Facility; the Blue Brain Project; the Human Brain Project,

Stockholm, Sweden

Viktor Jirsa – Aix-Marseille University, Marseille, France

G. Allan Johnson – Duke University, North Carolina, USA

David Leopold – National Institute of Mental Health; NIH Neurophysiology Imaging Facility, Maryland, USA

Henry Markram – Brain Mind Institute; the Blue Brain Project; Swiss Federal Institute for Technology (EPFL), Lausanne,

Switzerland

Troy Margrie – MRC National Research Institute of Medical Research, London, UK

Partha Mitra – Cold Spring Harbour Laboratory, New York, USA

Tony Movshon – New York University, New York, USA

Keiji Tanaka – RIKEN Brain Sciences Institute, Wako, Japan

Jonathan Victor – Weill Cornell Medical College, New York, USA

Associate Investigators (AIs)

Derek Arnold – University of Queensland, Brisbane, QLD

Sofia Bakola – Monash University, Melbourne, VIC

John Bekkers – Australian National University, Canberra, ACT

Anthony Burkitt – University of Melbourne; Bionic Vision Australia, Melbourne, VIC

Vincent Daria – Australian National University, Canberra, ACT

Paul Dux – University of Queensland, Brisbane, QLD

Alex Fornito – Monash University, Melbourne, VIC

Geoff Goodhill – University of Queensland, Brisbane, QLD

Ted Maddess – Australian National University, Canberra, ACT

Farshad Mansouri – Monash University, Melbourne, VIC

Nicholas Price – Monash University, Melbourne, VIC

Fabio Ramos – University of Sydney, Sydney, NSW

Olaf Sporns – Indiana University, Bloomington, Indiana, USA

Naotsugu Tsuchiya – Monash University, Melbourne, VIC

Trichur Vidyasagar – University of Melbourne, Melbourne, VIC

Charles Watson – University of New South Wales, Sydney, NSW; Curtin University, Perth, WA

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Coordinators

Sarah Dunlop – Coordinator for Women in Neuroscience, University of Western Australia, Crawley, WA

Pulin Gong – Co-Coordinator for Neuroinformatics and Computer Resources, University of Sydney, Sydney, NSW

Wojtek Goscinski – Co-Coordinator for Neuroinformatics and Computer Resources, Monash University, Melbourne, VIC

Jakob Hohwy – Coordinator for Society and Ethics, Monash University, Melbourne, VIC

Rachel Nowak – Director of the Brain Dialogue, Coordinator for Outreach, Monash University, Melbourne, VIC

Fellows

Romesh Abeysuriya – (Peter Robinson) University of Sydney, Sydney, NSW

Mehdi Adibi – (Ehsan Arabzadeh) Australian National University, Canberra, ACT

Tahereh Babaie – (Peter Robinson) University of Sydney, Sydney, NSW

Gursh Chana – (Stan Skafidas) University of Melbourne, Melbourne, VIC

Shaun Cloherty – (Michael Ibbotson) University of Melbourne, Melbourne, VIC

Calvin Eiber – (Paul Martin) University of Sydney, Sydney, NSW

Yuhong Fu – (George Paxinos) University of New South Wales, Sydney, NSW

Leonardo Gollo – (Michael Breakspear), Queensland Institute of Medical Research, Brisbane, QLD

Sharna Jamadar – (Gary Egan) Monash University, Melbourne, VIC

Tim Karle – (Steve Petrou) University of Melbourne, Melbourne, VIC

Ehsan Kheradpezhouh – (Ehsan Arabzadeh) Australian National University, Canberra, ACT

Sammy Lee – (Ulrike Grünert) University of Sydney, Sydney, NSW

Andy Liang – (George Paxinos) University of New South Wales, Sydney, NSW

Piotr Majka – (Marcello Rosa) Monash University, Melbourne, VIC

Roger Marek – (Pankaj Sah) University of Queensland, Brisbane, QLD

Hamish Meffin – (Michael Ibbotson) University of Melbourne, Melbourne, VIC

Anand Mohan – (Arthur Lowery) Monash University, Melbourne, VIC

Babak Nasr – (Stan Skafidas) University of Melbourne, Melbourne, VIC

Bryan Paton – (Gary Egan) Monash University, Melbourne, VIC

Sander Pietersen – (Paul Martin) University of Sydney, Sydney, NSW

Sivaraman Purushothuman – (Ulrike Grünert) University of Sydney, Sydney, NSW

Emma Schofield – (George Paxinos) University of New South Wales, Sydney, NSW

Guilherme Silva – (Greg Stuart) Australian National University, Canberra, ACT

Dongping Yang – (Peter Robinson) University of Sydney, Sydney, NSW

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Scholars

Natasha Gabay – (Peter Robinson) University of Sydney, Sydney, NSW

Adam Keane – (Peter Robinson) University of Sydney, Sydney, NSW

Xiaochen Liu – (Peter Robinson) University of Sydney, Sydney, NSW

Jessica McFadyen – (Marta Garrido) University of Queensland, Brisbane, QLD

John Palmer – (Peter Robinson) University of Sydney, Sydney, NSW

Mihn-Son To – (Greg Stuart) Australian National University, Canberra, ACT

Rory Townsend – (Peter Robinson) University of Sydney, Sydney, NSW

Gu Yifan – (Peter Robinson) University of Sydney, Sydney, NSW

Natalie Zeater – (Paul Martin) University of Sydney, Sydney, NSW

Iris Zhu – (Marcello Rosa) Monash University, Melbourne, VIC

Management & Node Administrators

Lisa Hutton – Centre Manager, Monash University, Melbourne, VIC

Jessica Despard – Monash University, Melbourne, VIC

Cill Gross – University of Melbourne, Melbourne, VIC

Cindy Guy – University of Sydney, Sydney, NSW

Roxanne Jemison – University of Queensland, Brisbane, QLD

Vicki McAuliffe – Monash University, Melbourne, VIC

Elizabeth Paton – Monash University, Melbourne, VIC

Emma Schofield – University of New South Wales, Sydney, NSW

Danielle Ursino – Australian National University, Canberra, ACT

Advisory Board

Lyn Beazley AO – Chair, (Immediate past Chief Scientist of Western Australia)

Amanda Caples – Government and bio-industry advisory member, (Deputy Secretary Innovation & Technology at

Department of Economic Development, Jobs, Transport and Resources, State Government Victoria)

Ulf Eysel – International scientific advisory member, (Department of Neurophysiology, Ruhr University, Bochum,

Germany)

Allan Jones – International neurotechnology and scientific advisory member, (CEO, Allen Institute for Brain Science,

Seattle, USA)

John Funder – National scientific advisory member, (Honorary Fellow, Hudson Institute of Medical Research,

Melbourne)

David Van Essen – International scientific advisory member, (Director, The Human Connectome Project, Washington

University, St Louis, USA)

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Centre Contributors - Fellows

Ben Allitt – (Marcello Rosa) Monash University, Melbourne, VIC

Duwage Alwis – (Marcello Rosa) Monash University, Melbourne, VIC

Kevin Aquino – (Peter Robinson) University of Sydney, Sydney, NSW

Eleonora Autuori – (Pankaj Sah) University of Queensland, Brisbane, QLD

Corinne Bareham – (Jason Mattingley) University of Queensland, Brisbane, QLD

Oliver Baumann – (Jason Mattingley) University of Queensland, Brisbane, QLD

Konstantinos Chatzidimitrakis – (Marcello Rosa) Monash University, Melbourne, VIC

Luca Cocchi – (Jason Mattingley) University of Queensland, Brisbane, QLD

Bill Connelly (Greg Stuart) Australian National University, Canberra, ACT

Christine Dixon – (Pankaj Sah) University of Queensland, Brisbane, QLD

Hannah Filmer – (Jason Mattingley) University of Queensland, Brisbane, QLD

Maureen Hagan – (Marcello Rosa) Monash University, Melbourne, VIC

Kaori Ikeda – (Greg Stuart) Australian National University, Canberra, ACT

Marc Kamke – (Jason Mattingley) University of Queensland, Brisbane, QLD

Cliff Kerr – (Peter Robinson) University of Sydney, Sydney, NSW

Delphine Levy-Bencheton – (Jason Mattingley) University of Queensland, Brisbane, QLD

James MacLaurin – (Peter Robinson) University of Sydney, Sydney, NSW

Natasha Matthews – (Jason Mattingley) University of Queensland, Brisbane, QLD

Adam Morris – (Marcello Rosa) Monash University, Melbourne, VIC

John Morris – (Pankaj Sah) University of Queensland, Brisbane, QLD

Christopher Nolan – (Pankaj Sah) University of Queensland, Brisbane, QLD

David Painter – (Jason Mattingley) University of Queensland, Brisbane, QLD

Svetlana Postnova – (Peter Robinson) University of Sydney, Sydney, NSW

Parnesh Raniga – (Gary Egan) Monash University, Melbourne, VIC

Margreet Ridder – (Pankaj Sah) University of Queensland, Brisbane, QLD

Susmita Saha – (Michael Ibbostson) University of Melbourne, Melbourne, VIC

Martin Sale – (Jason Mattingley) University of Queensland, Brisbane, QLD

Paula Sanz-Leon – (Peter Robinson) University of Sydney, Sydney, NSW

Somwrita Sarkar – (Peter Robinson) University of Sydney, Sydney, NSW

Peter Stratton – (Pankaj Sah) University of Queensland, Brisbane, QLD

Cornelia Strobel – (Pankaj Sah) University of Queensland, Brisbane, QLD

Robert Sullivan – (Pankaj Sah) University of Queensland, Brisbane, QLD

Fabrice Turpin – (Pankaj Sah) University of Queensland, Brisbane, QLD

Ashika Veghese – (Jason Mattingley) University of Queensland, Brisbane, QLD

Francois Windels – (Pankaj Sah) University of Queensland, Brisbane, QLD

Hsin-Hao Yu – (Marcello Rosa) Monash University, Melbourne, VIC

Elizabeth Zavitz – (Marcello Rosa) Monash University, Melbourne, VIC

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Centre Contributors - Scholars

Sahand Assadzadeh – (Peter Robinson) University of Sydney, Sydney, NSW

Maddu Bhagavathiperumal – (Pankaj Sah) University of Queensland, Brisbane, QLD

Simone Carron – (Marcello Rosa) Monash University, Melbourne, VIC

Tristan Chaplin – (Marcello Rosa) Monash University, Melbourne, VIC

Amanda Davies – (Marcello Rosa) Monash University, Melbourne, VIC

Farah Deeba – (Peter Robinson) University of Sydney, Sydney, NSW

Daina Dickens – (Jason Mattingley) University of Queensland, Brisbane, QLD

Justine Fam – (Ehsan Arabzadeh) Australian National University, Canberra, ACT

Jay Fradkin – (Greg Stuart) Australian National University, Canberra, ACT

Saba Gharaei – (Ehsan Arabzadeh) Australian National University, Canberra, ACT

Andrea Giorni – (Pankaj Sah) University of Queensland, Brisbane, QLD

Michelle Hall – (Jason Mattingley) University of Queensland, Brisbane, QLD

Anthony Harris – (Jason Mattingley) University of Queensland, Brisbane, QLD

Luke Hearne – (Jason Mattingley) University of Queensland, Brisbane, QLD

Sarah Hunt – (Pankaj Sah) University of Queensland, Brisbane, QLD

Gabriel Jones – (Steven Petrou) University of Melbourne, Melbourne, VIC

Rebecca Kotsakidis – (Michael Ibbostson) University of Melbourne, Melbourne, VIC

Thomas Lacy – (Peter Robinson) University of Sydney, Sydney, NSW

Liliana Laskaris – (Stan Skafidas) University of Melbourne, Melbourne, VIC

Conrad Lee – (Ehsan Arabzadeh) Australian National University, Canberra, ACT

Ting Ting Lee – (Stan Skafidas) University of Melbourne, Melbourne, VIC

Matias Maturana – (Michael Ibbostson) University of Melbourne, Melbourne, VIC

Hannan Mazuir – (Greg Stuart) Australian National University, Canberra, ACT

Eli Muller – (Peter Robinson) University of Sydney, Sydney, NSW

James Pang – (Peter Robinson) University of Sydney, Sydney, NSW

Yang Qi – (Peter Robinson) University of Sydney, Sydney, NSW

Nipa Roy – (Peter Robinson) University of Sydney, Sydney, NSW

Chase Sherwell – (Marta Garrido) University of Queensland, Brisbane, QLD

Cooper Smout – (Jason Mattingley) University of Queensland, Brisbane, QLD

Artemio Soto-Breceda – (Michael Ibbostson) University of Melbourne, Melbourne, VIC

Morgan Spence – (Jason Mattingley) University of Queensland, Brisbane, QLD

Shi Sun – (Michael Ibbostson) University of Melbourne, Melbourne, VIC

Susan Travis – (Jason Mattingley) University of Queensland, Brisbane, QLD

Lisa Wittenhagen – (Jason Mattingley) University of Queensland, Brisbane, QLD

Shanzhi Yan – (Pankaj Sah) University of Queensland, Brisbane, QLD

Molis Yunzab – (Michael Ibbostson) University of Melbourne, Melbourne, VIC

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A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N Research Projects

3 CIBF Research projects

Project Lead CI

Stimulating connections: an effective

connectivity brain map

Egan Predictive coding as a theory of integrative

brain function, with application to the cortical

microcircuit

Ibbotson

The role of predictive coding in receptive field

formation in visual cortex

Ibbotson Brain Machine Interface Tiles Lowery Pedunculotegmental nucleus Martin DTI/MRI atlas of the rat brain Paxinos Real time analysis of network function using

an all optical interface

Petrou Unified Neural Models for Attention,

Prediction, and Decision

Robinson Neural signatures of decision making in the

primate cortex

Rosa Nano Scale Interfaces to Neurons Skafidas Sensory decision-making in rodents Stuart/

Arabzadeh Understanding human attention, decision-

making and prediction using psychophysics,

brain imaging and neural stimulation

Mattingley

Rapid information processing in subcortical

amygdala pathways

Garrido Computer Modelling of Human Visual System

with Applications in Computer Vision

Lowery A digital atlas of connections in the marmoset

brain

Rosa Visual signal processing in thalamocortical

loops; predictive coding in attentional circuits.

Martin

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Neural circuits that mediate fear learning and

extinction

Sah

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A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N Research projects

Project 1:

Stimulating connections: an effective connectivity brain map

CIs – Gary Egan, Jason Mattingley, Marta Garrido, Arthur Lowery & Marcello Rosa

Monash University & University of Queensland

Project overviewThis project will develop a unique map of the brain using a novel combination of technologies, including transcranial magnetic

stimulation (TMS). This map will be the basis of key research outputs and will shed new light on existing findings and theories of

neural function and conscious perception. Spanning philosophy, psychology, economics, neuroscience and biological

engineering, the project will depend on the research facilities and resources at Monash Biomedical Imaging (MBI) and the

University of Queensland Centre for Advanced Imaging (CAI).

TMS will be applied comprehensively across the brain with neural activity recorded using magnetic resonance imaging (MRI)

and electroencephalography (EEG). The resulting connectome will allow principled, well-informed application of TMS rather

than the relatively haphazard, piecemeal approach common in the field now. This technologically and scientifically ambitious,

first-of-its-kind connectome will greatly facilitate answering deep questions on the nature of conscious states (perception),

decision-making (economics and healthy living/aging) and general neural function (mental illness and biomedical engineering).

The data and analysis from this project will follow Human Connectome Project acquisition and protocols and be stored in the

INCF open data-share ensuring global impact and access.

This project will provide high-impact outcomes related to the impact of brain stimulation in neuroscience research and mental

illness therapies. The project will deliver impact of multi-scale CIBF research in terms of delivering the first brain stimulation

connectome. The proposed confluence of scientific and technological aspects, unique in Australia, will help to make CIBF a

world leader in these areas of research.

PersonnelCIs: Gary Egan, Jason Mattingley, Marta Garrido, Arthur Lowery & Marcello Rosa

AIs: Jakob Hohwy & Alex Fornito

CIBF Fellows: Bryan Paton & Sharna Jamadar

Project duration2014-2017

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Goals and outcomesOriginal goals Mid 2015 updateTo develop a unique map of the brain

using a novel combination of

technologies including TMS.

The progress to date is (i) the coil was designed in early 2014 in conjunction with an

Australian company (Magnetica) and built over 12 months in 2014-15, (ii) the coil

was installed at MBI in mid 2015, and (iii) the research program utilising the

technology will now commence.

Key infrastructure purchased (>$5,000) TMS compatible MR coil.

OutputsFunding:

Awarded Interdisciplinary Research Support Program grant through Monash University ($120,000).

Further external grant applications are in preparation for submission in late 2015 (ARC LP) and early 2016 (ARC,

NHMRC), based on the TMS compatible magnetic resonance (MR) technology that has been developed.

Key issuesProgress of this project has been somewhat limited due to delays experienced in receiving critical equipment.

14


Project 2:

Predictive coding as a theory of integrative brain function, with application to the cortical microcircuit

CIs – Michael Ibbotson & Michael Breakspear

University of Melbourne & QIMR Berghofer

Project overviewThe theory of predictive coding suggests that a central goal of the sensory brain is to discern the causes underlying the raw

sensory input at the periphery. The notion of causes giving rise to sensory input is captured quantitatively by a generative

model, which describes the probability that a set of causes, c, gives rise to the sensory data, s.

The neural instantiation of the theory of predictive coding maps the hierarchy of a generative model for sensory data onto the

hierarchy of consecutive areas in a sensory pathway. In vision the hierarchy corresponds to the retina, lateral geniculate

nucleus, and multiple cortical areas. The afferent pathway corresponds to inverting the generative model to find the causes

underlying the sensory data. The efferent pathway corresponds to the implementation of the generative model in the forward

direction, mimicking the generative process in nature.

At each stage in the hierarchy, models of predictive coding involve at least two main populations of neurons, which are often

broken down into further subpopulations. One population uses descending projections to predict the hidden causes, at the

previous level in the hierarchy. A second population conveys an error, in the ascending direction, between the local estimate of

the cause, and a top-down estimate of the prediction. The network attempts to minimize the error conveyed by the afferent

projections, which mathematically, leads to defined rules for both neural dynamics and the learning of network parameters. This

learning is based on the statistics of sensory input, for example the presentation of natural scenes in the visual system.

We will test the predictive coding hypothesis of the canonical microcircuit, for which there are several variations. Broadly, the

approach we propose is to measure many of the above properties for a large ensemble of neurons and evaluate if the clusters

obtained experimentally show a correspondence with properties hypothesized for various neural populations in the models. The

focus of the study will be on recording from primary visual cortex because it is comparatively well characterized and due to our

extensive previous experience in this area. Multiple animal models will be used, including marmoset, cat, tree shrew or mouse,

as appropriate. Furthermore, optogenetic approaches are available that permit the manipulation and recording of neural activity

of fine spatial and temporal scales specific to certain cell classes. In parallel, we will undertake computational modelling to

bridge the gap between classic Bayesian-based models of predictive coding and biophysical models of neuronal activity.

PersonnelCIs: Michael Ibbotson & Michael Breakspear

CIBF Fellows: Hamish Meffin & Shaun Cloherty

15



Goals and outcomesOriginal goals Mid 2015 updateCross-species experimental platform for

testing hierarchical models of predictive

coding in the visual stream.

Model of predictive coding implemented.

Developing multielectrode recording technique in visual cortex of mice and cats.

Computational models that link classic

models of hierarchical Bayes to

biophysical models of neuronal activity.

Ongoing.

OutputsPublications:

Cloherty SL, et al, (2015). Contrast-dependent phase sensitivity in V1 but not V2 of macaque visual cortex. J

Neurophysiol. 113: 434-444.

Apollo NV, et al, (2015). Soft, Flexible Freestanding Neural Stimulation Electrodes Fabricated from Reduced Graphene

Oxide. Adv Funct Mater (accepted 9 April 2015).

Meffin H, et al, (2015). Contrast dependence of spatial receptive field structure in primary visual cortex. J Neurophysiol

(accepted with revisions, 1 June 2015).

Lichter SG, et al, (2015). Hermetic diamond capsules for biomedical implants enabled by gold active braze alloys.

Biomaterials. 53:464-74.

Ahnood A, et al, (2015). Ultrananocrystalline diamond-CMOS device integration route for high acuity retinal

prostheses. Biomed Microdevices. 17(3):9952.

Kameneva T, et al, (2015). Spike history neural response model. J Comput Neurosci. 38(3):463-81.

Garrett DJ, et al, (2015). In vivo biocompatibility of boron doped and nitrogen included conductive-diamond for use in

medical implants. J Biomed Mater Res B Appl Biomater. doi: 10.1002/jbm.b.33331. [Epub ahead of print].

Hadjinicolaou AE, et al, (2015). Optimal electrical stimulation of retinal ganglion cells. Trans Neural Syst Rehabil Eng.

23:169-178.

Maturana MI, et al, (2015). The effects of temperature changes on retinal ganglion responses to electrical stimulation.

IEEE Eng Med Biol Soc. (accepted 1 June 2015).

Apollo NV, et al, (2015). Neural stimulation and recording with liquid crystalline graphene oxide fibers. IEEE Eng Med

Biol Soc. (accepted 16 June 2015).

Hadjinicolaou AE, et al, (2015). Prosthetic vision: devices, patient outcomes and retinal research. Clinical and

Experimental Optometry (accepted with revisions, 13 May 2015).

Spencer MJ, et al, (2015). Broadband onset inhibition can suppress spectral splatter in the auditory brainstem. PLoS

One. 10(5):e0126500.

Fox K., et al, (2015). Development of a magnetic attachment method for bionic eye applications. Artifi Organs,

(accepted 9 June 2015).

16


Fox K., et al, (2015). The bionic eye: review of multielectrode arrays, To appear in Handbook of Bioelectronics,

Cambridge Uni. Press. (accepted 20 Feb 2015).

Funding: Awarded a L.E.W Carty Charitable Fund Grant ($46,000).

Key issuesNil to date

Project 3:

The role of predictive coding in receptive field formation in visual cortex

CIs – Michael Ibbotson, Michael Breakspear, Marta Garrido & Marcello RosaUniversity of Melbourne, QIMR Berghofer, University of Queensland, Monash University & New York University

Project overviewPredictive Coding is a theory of brain function that has been hypothesized to explain a wide range of observations including the

hierarchical organization of (sensory) cortex, the architecture of cortical microcircuits, the structure of cortical receptive fields,

single cell integration properties and synaptic plasticity. Here we propose to directly test Predictive Coding theory by combining

multi-electrode array recordings from several consecutive areas in the visual pathway, with a novel information-theoretic

analysis of the space-time dynamics of neural populations. Specifically, our analysis will trace the flow of information through

the visual pathway in space and time, allowing us to evaluate Predictive Coding theory's predictions of where and when

information should flow. An advantage of the approach is that it can be performed without knowledge of the stimuli or the

internal brain states that may be affecting the neural response, and thus may be a powerful tool for analysing the processing

occurring in a variety of brain areas.

PersonnelCIs: Michael Ibbotson, Michael Breakspear, Marta Garrido & Marcello Rosa

PIs: Anthony Movshon.

AIs: Nicholas Price & Trichur Vidyasagar

CIBF Fellows: Hamish Meffin & Shaun Cloherty


Goals and outcomesOriginal goals Mid 2015 updateKnowledge about neural computations Ongoing.

17


performed in the visual geniculo-cortical

pathways.

Knowledge about anatomical and

physiological aspects of neural

processing in the visual pathways.

Experiments commenced rearing mice in novel visual environment to test if cortical

receptive fields of simple cells in primary visual cortex develop according to the

theory of Efficient Coding. Efficient Coding is closely related to Predictive Coding.

Experiments commenced to recover non-linear receptive fields of complex cells in

cat and mouse visual cortex and compare them to predictions of a model of

Efficient Coding of complex cells.

Study demonstrating that receptive fields of complex cells exhibit greater sensitivity

to spatial phase at low compared to high contrast. Manuscript provisionally

accepted at J. Neurophys.

Manuscript on changes in cortical feature map relationships cause by restricted

visual experience submitted to Nature Neurosci.

Development of techniques for massively

parallel electrophysiological recording in

visual cortex.

In development in mouse and cat.

NHMRC grant submitted for the development of new multielectrodes technologies

for chronic cortical recording.

New techniques for data analysis of

complex neural signals.

Developing improved methods for recovering receptive fields to visual stimuli.

Developed new methods for recovering receptive field to electrical stimuli.

Development of the first comprehensive

model of predictive coding in visual

cortex based on experimental findings.

Efficient coding model of primary visual cortex used to predict the development of

cortical receptive fields of simple cells following rearing in novel visual

environments. The predicted receptive fields are dramatically different to those

developed normally, and this will be used to test theories of Efficient Coding in

animal rearing experiment (above).

Complex receptive fields predicted from an Efficient Coding model following rearing

in natural environments.


As per project 2.

Funding: ARC Discovery Grant Application: “Principles of development in the sensory brain”; Status: pending decision in

November 2015.

NHMRC Project Grant Application: “Next generation cybernetics: Long term carbon fibre dual stimulation / recording

electrode arrays for closed loop neural implants”; Status: pending decision in November 2015.

NHMRC Project Grant Application: “Neuro-feedback for improved efficacy of retinal prostheses”; Status pending

decision in November 2015.

New Collaborations: Professor Geoffry Goodhill, Queensland Brain Institute

Dr. David Garrett, University of Melbourne

18



Project 4:

Brain machine interface tiles

CIs – Arthur LoweryMonash University

Project descriptionThis project seeks to develop an enabling technology, providing an 'output' side of a bidirectional brain interface. The 'input side'

will be based on Monash Vision Group’s (MCG) neurostimulation technologies. The eventual aim is to develop stimulation and

recording within one tile, with the same electrodes able to stimulate and record. However, this first project is required to

investigate the interaction of the wireless power transfer with the sensitive electronics required for detecting Na currents, to

develop low-noise amplifiers in a mixed-signal chip, and to develop a method transmitting information from the tile to the

external electronics.

PersonnelCIs: Arthur Lowery

CIBF Fellows: Damien Browne until Qtr 2, 2015


Goals and outcomesOriginal goals Mid 2015 updateDesign for an implantable recording tile,

application-specific integrated circuit

(ASIC) and Distribution Board.

An initial design for an ASIC was developed, including the building blocks for

amplifying, digitizing and wirelessly transmitting the data from tile to external

receiver. This has been put on hold while funds are accumulating.

Manufacture of four tiles. Considerable experience in manufacturing miniaturized hermetically-sealed

19


stimulating tiles as part of MVG’s project. A batch of tiles suitable for First in

Human has been manufactured and the design proven to be successful in bench

and small animal tests. Thus we have the basis for a recording tile – the

electrodes, the hermetic packaging and electronic blocks for powering the tile and

transmitting data.

A simpler electronic approach is being developed based on commercial chip dies.

Prototype recording amplifiers have been built.

Benchtop verification of their operation

using a custom test board.

(Without CIBF funding) MVG has developed methods of testing multi-electrode tiles

that will be used to test the recording tiles. These include a saline baths with XY

positioning for field mapping and sensitive amplifiers that can reject artifacts from

the wireless system. We have discovered that the electronics, when

unencapsulated, is extremely sensitive to saline and de-ionised water; therefore,

unsealed electronic is unlikely to function in an animal.

Delivery to preclinical testing. Not yet reached.

Key infrastructure purchased (>$5,000) A three year license for Synopsys IC design tools has been purchased (before the resignation of the designer)

$39,405.

OutputsNil to date

Key issuesBecause of project costings and the lack of substantial strategic funds to cover them, and also the resignation of one ASIC

designer, the project has had to be delayed (to 2016) until sufficient funds have been accumulated to ensure its completion (i.e.

to cover the costs of people and manufacturing). This delay has the advantage that the project can capitalize on the

development of a proven manufacturing process for implantable times, courtesy of MVG, and can also use the expertise built up

by its engineering and physiology teams. CI Lowery’s efforts have since be re-directed into an alternative project (Research

project 14), as described on page 36.

20


Project 5:

Pedunculotegmental nucleus

CIs – Paul Martin, Greg Stuart, Pankaj Sah, Ulrike Grünert & Ehsan Arabzadeh

University of Sydney, Australian National University & University of Queensland

Project descriptionHere I propose two interesting starting points, Acetylcholine and Noradrenaline.

AcetylcholineThe ‘reticular activating system’ or ‘ascending cholinergic reticular system’ is traditionally considered to mediate arousal. Shute

& Lewis 19671, anatomically distinguished dorsal and ventral tegmental pathways.

- Dorsal tegmental pathway from midbrain tegmentum Cuneiform nucleus to tectum and thalamus: “extensions” go to

thalamic visual centres via medial striate bundle.

- Ventral tegmental pathway from pars compacta of substantia nigra and ventral tegmental area of anterior

mesencephalon and includes amygdala projection

Additionally, there is significant physiological evidence showing that simulating the nucleus basalis and surrounding tegmental

regions produces “activation” of cortex, EEG changes, behavioural activation and arousal noting:

“While the NB likely plays an important role in cortical activation, several neural systems that ascend through the

neuraxis in parallel may contribute to activation under different circumstances. Stimulation of mesopontine

cholinergic nuclei in the brainstem results in cortical activation, an effect that persists even after excitotoxic

lesions of the NB (Steriade et al., 1991). Since mesopontine cholinergic nuclei primarily innervate the thalamus,

this suggests that thalamocortical projections, which may utilize glutamate as a neurotransmitter (Fox and Arm-

strong-James, 1986; Tsumoto et al., 1986; Hicks et al., 1991) contribute to processes of activation. Non-

cholinergic brainstem nuclei such as the locus coeruleus and raphe nuclei that project diffusely to neocortex have

also been implicated in activation (Vanderwolf, 1988; Bet-ridge and Foote, 199 1). How and when these neural

systems contribute to processes of activation are unclear; however, the putative neurotransmitters released by

21


these systems may converge at the cortex onto common cellular mechanisms. That is, norepinephrine, serotonin,

and metabotropic actions of glutamate all can exert some neuromodulatory effects similar to those mediated by

ACh acting at muscarinic receptors (Nicoll, 1988; McCormick, 1989; Baskys, 1992). Thus, final control over

cortical excitability and rhythms may depend on the interplay of several neural systems, of which NB neurons

form the primary source of direct ACh-mediated cortical actions.”

NoradrenalineThe locus coeruleus-noradrenergic system was the first defined neuromodulatory pathway. Whilst we see similar

effects of ACH and NAD, there are to my mind, some very interesting open questions:

• What are the cellular bases of neuromodulation effects?

• Why are there distinct systems for what appear to be similar “activation” properties?

• Do the distinct cholinergic projections have distinct or mutual functions?

• Can we use thalamocortical models to get insight into the distinct properties?

• Has anyone tried optogenetics on these brainstem areas?

We propose that CI Martin & Fellow investigate the effects in thalamus and cortex in marmosets, with the addition of

CI Stuart’s brainstem activation and pharmacology. CI Stuart will also look at the cellular basis of activation in

thalamus amygdala and cortex. CI Arabzadeh will study how noradrenergic inputs can modify sensory coding. CI’s

Sah & Martin will establish in vivo recordings from brainstem together with EEG in behaving rats. CI Grünert will

establish receptor localization and distribution in targets of in response to CI Stuart’s findings.

PersonnelCIs: Paul Martin, Greg Stuart, Pankaj Sah, Ulrike Grünert & Ehsan Arabzadeh

CIBF Fellows: Sander Pietersen


Goals and outcomesOriginal goals Mid 2015 updateImproved understanding of role of

neuromodulators in attention.

No outcomes as yet.

Improved understanding of role of

neuromodulators in decision-making.

No outcomes as yet.

OutputsNil to date

Key issues

22


This project has been placed on hold, with the efforts of lead CI Martin currently re-directed into an alternative project (Research

project 16), as described on page 39.

Project 6:

DTI/ MRI Atlas of the rat brain

CIs – George PaxinosUniversity of New South Wales, Duke University & Curtin University

Project overviewThis project seeks to construct an MRI/ diffusion tensor imaging (DTI) atlas of the rat brain, utilizing the best resolution and

contrast data from partner investigators. This project has used multiple MRI contrasts as though they were different stains of

tissue. Using these methods we were able to detect on the MR images approximately 90% of the structures we identified in our

histological atlas The Rat Brain in Stereotaxic Coordinates. For our work we are identifying the “signature” of each structure of

the brain (when there is one) in the different contrasts we use. This is direct observation and not superimposition of our

histological atlas on the MRI data. Our approach is far more demanding but far more accurate. Many laboratories have

attempted to construct MRI atlases of the rat, but none has produced any detailed atlas as we intend to produce. The proposed

atlas will be of assistance of any project in the consortium that uses MRI/DTI in the rat, and can be viewed as infrastructure

support for the international neuroscience community.

PersonnelCIs: George Paxinos

PIs: G. Allan Johnson

AIs: Charles Watson

CIBF Fellows: Emma Schofield

Project duration

23


2014-2015

Goals and outcomesOriginal goals Mid 2015 updateThe first comprehensive MRI/DTI atlas of

the rat brain. It will be published as a

book and it should be of assistance to

the field of imaging as our histological

atlas was of assistance to histologists.

The book is completed and will be released in July 2015, and will be available

online at: www.amazon.com/MRI-DTI-Atlas-Rat-Brain-ebook/dp/B00YXFP01W.

Individual articles can describe the

"signatures" of structures in the different

contrasts.

Ongoing.

A comprehensive brain ontology (the

logical relations of all structures of the

brain).

Ongoing.


Paxinos, G, Watson, C, Calabrese, E, Badea, A and Johnson, GA, An MRI/DTI Atlas of the Rat Brain, Academic

Press/Elsevier, 2015.

Funding: APP1086083 A 3D Cross-Modality Atlas of the Human Brainstem for Scientists and Clinicians 2015-2017 – Funded

$352,077.00.

APP1086643 High Resolution MRI Atlas of the Rat Brain 2015-2016. Funded $185,932.00.

APP1107308 A High Resolution 3D-MRI Atlas of the Human Forebrain and Cerebellum for Research and Clinical Practice 2016-2019– Application submitted 2015.

Media Engagement: Conversation article: https://theconversation.com/darling-i-love-you-from-the-bottom-of-my-brain-37516

SMH article: http://www.smh.com.au/comment/be-still-my-beating-heart-love-is-on-the-brain-20150213-13c526.html


24

http://www.smh.com.au/comment/be-still-my-beating-heart-love-is-on-the-brain-20150213-13c526.html

https://theconversation.com/darling-i-love-you-from-the-bottom-of-my-brain-37516


Project 7:

Real time analysis of network function using an all optical interface

CIs – Steve Petrou, Ehsan Arabzadeh & Peter RobinsonUniversity of Melbourne, Australian National University & University of Sydney

Project overviewThis project seeks to develop approaches to combine multiscale imaging methods, from MRI tractography, CLARITY imaging

and serial electron microscopy (EM) 3D reconstructions to long and short range circuits in the rodent brain that underlie

decision making and combine with fundamental behavioral analysis using the well studied lemniscal pathway. We have

developed workflows for using high field (16.4T) MRI super-resolution methods and constrained spherical deconvolution

tractography in fixed rodent brains to build mesoscopic level connectomics maps. In the same brains we will process for

CLARITY labelling of genetically defined subsets of neurons and use light sheet microscopy to create higher resolution network

maps of the same circuits imaged with MRI. Finally we will make detailed studies of synapes in the brain regions implicated in

these networks: S1/2 cortical areas are the main target of thalamic projections but recent evidence indicates that some thalamic

projections target other cortical areas potentially to enable isolation of the dominant single sensory input (in this case whisking).

The project seeks to understand structural and then functional basis of signaling. For instance some synapses in this network

are "strong" (PoM) and give massive post synaptic responses, yet the structural correlates and geometries of the boutons and

spines are largely unknown. Serial EM studies will be done initially at Max Planck in Florida and maybe transferred to

Melbourne if a current initiative is successful to acquire this capability.

PersonnelCIs: Steve Petrou, Ehsan Arabzadeh & Peter Robinson

Collaborator: Bert Sakmann

Project duration

25


2014-2017

Goals and outcomesOriginal goals Mid 2015 update"Brain in a dish” All optical interface to

interrogate single neuron and network

function in real time.

We have developed a prototype for narrow field imaging and have

purchased around 80% of the equipment needed for complete

development. Control software has been written in LabView and

Python and the system is working but no yet validated. We have

additional optics design to complete for the wide field imaging mode

including design of a safe method to deliver 6W of red light to excite

the Quasar fluorophore. To this end we are exploring high power

LED solution that provides non-collimated light that is inherently

safer than laser light for this purpose. We are having some setbacks

with the viral delivery of the optopatch construct and are working

towards new approaches.

OutputsFunding:

Awarded: DHB Foundation - "Brain in a dish” $250K Aug 2014- Aug 2015

Requested: Colonial Foundation $3.14M

New Collaborations: Dr Tim Karle, PhD, University of Melbourne (Laser Physicist working on developing the instrument)

Dr Snezana Maljevic, Hertie-Institute for clinical Brain Research, Germany (visiting scientist, Mar-Oct 2015, doing the

biology for this experiment).


26


Project 8:

Unified neural models for attention prediction and decision

CIs – Peter Robinson, Michael Ibbotson, Ehsan Arabzadeh, Jason Mattingley, Pankaj Sah, Paul Martin, Stan Skafidas, Arthur Lowery, Greg Stuart, Marta Garrido, Marcello Rosa, Gary Egan & Michael BreakspearUniversity of Sydney, QIMR Berghofer, University of Queensland, Aix-Marseillies University, Monash University, University of Melbourne & Australian National University

Project overviewThis project will first gather information and insights from Alertness, Prediction, and Decision (APD) leaders and the literature on

current front-running models of these functions (3-6 months). Commonalities of mathematical structure and neural

underpinnings. The above stages will enable a unified model of APD to be formulated that has its foundations in realizable

neural dynamics. It is likely that this model will embody features that are in common with engineering data fusion algorithms,

given the known Bayes-like signal integration that occurs in multimodal sensory tasks, but will be based on neural dynamics

and will reflect actual neural states. A Mark I version of the model will be implemented analytically and numerically using neural-

field, neural-mass, circuit, and other approaches, as appropriate. The first target predictions will be for visual APD with

continuous decision making (as opposed to binary decisions, although these will be investigated later). Tests of analytic and

numerical models will be tested against data from behavioral-imaging data from CIs’ and PIs’ labs and from the literature. A

potential experimental test via visual tracking of an object with a predictable trajectory amid distractors has been outlined and

has received support across APD and for potential human and other animal implementation. This concept lends itself to wider

testing in the area of multimodal sensory integration, other eye-tracking tasks, and in-vivo monitoring of V1 activity. It will be

refined in collaboration with experimentalists with the aims of carrying out direct tests in later years to link predictions to

imaging/recording of brain systems and cellular circuits that are involved. Where possible, we will aim to use outputs from

experiments that are being carried out for other purposes in CIBF. This project will deliver the core modelling and experimental

results to enable testing and further model development to occur in tandem in subsequent years. Initial results from the model

27


will enable new testable predictions and hypotheses to be formulated.

PersonnelCIs: Peter Robinson, Michael Ibbotson, Ehsan Arabzadeh, Jason Mattingley, Pankaj Sah, Paul Martin, Stan Skafidas, Arthur

Lowery, Greg Stuart, Marta Garrido, Marcello Rosa, Gary Egan & Michael Breakspear

PIs: Viktor Jirsa

AIs: Fabio Ramos, Pulin Gong, Alex Fornito, Derek Arnold, Tony Burkitt, Geoff Goodhill, Olaf Sporns & Charles Watson

CIBF Fellows: Dong-Ping Yang, Romesh Abeysuriya & Tahereh Babaie


Goals and outcomesOriginal goals Mid 2015 updateExamination and consolidation of key models in Attention, Prediction and

Decision (APD) to determine the state of the art, and which are compatible

across these three functions.

Well advanced.

Determination of the likely general neural substrates of these models. Underway.

Determination of unified model that can cover APD, likely based on data

fusion ideas. This model will also need to be able to incorporate aspects of

learning and memory, although these will not be targeted in detail until

subsequent years.

Underway.

Formulation of predictions and suitable experiment(s) for testing them.

Initial numerical implementations will be tested against the literature.

Preliminary versions formulated.

Several publications should be forthcoming on the unified modelling,

neural theory developments, and initial comparisons with data from CIs’

and PIs’ labs and from the literature.

Pending.


Abeysuriya, R. G., C. J. Rennie and P. A. Robinson (2015). "Physiologically based arousal state estimation and

dynamics." J Neurosci Methods 253: 55-69.

Zhao, X., J. W. Kim and P. A. Robinson (2015). "Slow-wave oscillations in a corticothalamic model of sleep and wake."

J Theor Biol 370: 93-102.

Townsend, R. G., S. S. Solomon, S. C. Chen, A. N. Pietersen, P. R. Martin, S. G. Solomon and P. Gong (2015).

"Emergence of complex wave patterns in primate cerebral cortex." J Neurosci 35(11): 4657-4662.

Keane, A. and P. Gong (2015). "Propagating waves can explain irregular neural dynamics." J Neurosci 35(4): 1591-

1605.

28


Key issuesThis project has experienced delays in personnel appointments. Much pre-work has been done, and foundations and software

have been developed, but an in-earnest start on the core has only just been made.

Project 9:

Neural signatures of decision making in the primate cortex

CIs – Marcello Rosa, Michael Ibbotson & Arthur LoweryMonash University, University of Melbourne, University of Sydney, RIKEN Brain Science Institute & Cold Spring Harbour Laboratory

Project overviewThis project will investigate the electrophysiological activity of groups of neurones in the prefrontal, parietal and insular cortices

of non-human primates trained to perform complex tasks that involve paying attention to changes in the environment, and

adjusting behavioural choices accordingly. We will use multielectrode techniques to monitor how the information encoded by

trains of action potentials relate to the animal’s behaviours, and how this information can change when certain parts of the

relevant neural circuit are inactivated by lesions or reversible methods (cooling, optogenetics). Isolating the relevant aspects of

neural activity in such changing conditions will require the development of new computational analysis techniques. We will also

address the changes in the neural circuits that underlie the performance of the cognitive tasks, by conducting diffusion tensor

imaging and functional connectivity studies prior to, and after extensive training.

PersonnelCIs: Marcello Rosa, Michael Ibbotson & Arthur Lowery

PIs: Keiji Tanaka & Partha Mitra

AIs: Farshad Mansouri, Nicholas Price, Sofia Bakola, Alex Fornito & Fabio Ramos

Project duration2014 –2017

Goals and outcomesOriginal goals Mid 2015 updateKnowledge about neural computations performed by the No outcomes as yet.

29


association cortex in the context of complex tasks.

Knowledge about anatomical and physiological aspects of

neural plasticity, ranging in time scales from seconds to

years.

No outcomes as yet.

New techniques for massively parallel electrophysiological

recording in behaving animals.

No outcomes as yet.

New techniques for data analysis of complex neural signals. No outcomes as yet.

Better understanding of the inter-relationship between

different types of neural signals.

No outcomes as yet.

Key infrastructure purchased (>$5,000) $25K custom developed touch screens.

OutputsNil to date

Key issuesThis project is still in its infancy with minimal progress to date due to delays in personnel appointments. Due to the delay in this

project, CI Rosa’s efforts will now be re-directed into an alternative project (Research project 15), as described on page 38.

30


Project 10:

Nano scale interfaces to neurons

CIs – Stan Skafidas, Steve Petrou & Peter RobinsonUniversity of Melbourne & University of Sydney

Project overviewThis project aims to design functionalised nanoscale nanowire devices for real time characterisation of electrical and

31


biochemical signals from neurons. This technology will enable the centre’s researchers to interrogate single neurons at the

molecular level in real time providing researchers with measurements at unprecedented spatial scale and temporal resolution.

This will be a valuable tool that will provide new insights into neuronal function for both in vitro and in-vivo applications.

PersonnelCIs: Stan Skafidas, Steve Petrou & Peter Robinson

Collaborator: Mirella Dotorri

CIBF Fellows: Babak Nasr


Goals and outcomesOriginal goals Mid 2015 update

Design of functionalised nanoscale nanowire devices for

real time characterisation of electrical and biochemical

signals from neurons.

Successful demonstration that the surface potential of

functionalized vertical nanowires can be accurately monitored

using a current clamp amplifier in a capacitive regime. (Small,

early View).

Prototype System. No outcomes as yet.

Benchtop Verification. No outcomes as yet.

Delivery of prototype system to enable other CIBF

researchers to undertake new science opening up the

possibilities for new discoveries on how neurons function

at a molecular level. Contemporaneous Electrical and

molecular biochemical signals will be measured.

No outcomes as yet.


B Nasr, G Chana, TT Lee, T Nguyen, C Abeyrathne, GM D’Abaco, M Dottori, E Skafidas (2105); Vertical Nanowire Electrode Arrays as Novel Electrochemical Label-Free Immunosensors; Small; Early View; DOI:

10.1002/smll.201403540; 11 February 2015.

S Harrer, SC Kim, C Schieber, S Kannam, N Gunn, S Moore, D Scott, R Bathgate, E Skafidas, JM Wagner;(2015);

Label-free Screening of Single Biomolecules Through Resistive Pulse Sensing Technology for Precision Medicine Applications; Nanotechnology Vol 26 p 182505.

D Zantomio, G Chana, L Laskaris, R Testa, IP Everall, E Skafidas (2015); Convergent Evidence for MGluR5 in Synaptic and Neuroinflammatory Pathways Implicated in ASD; Neuroscience & Biobehavioural Review; vol 52; pp 172

– 177; DOI: 10.1016/j.neubiorev.2015.02.006; 7 February 2015.

32



Project 11:

Sensory decision-making in rodents

CIs – Greg Stuart & Ehsan ArabzadehAustralian National University, University of Queensland & SISSA

Project overviewOver the last decade, new methods have emerged for the characterisation of neuronal activity at the level of single cells and

neuronal populations. Our strategy is to use these new methods to relate a detailed and quantitative characterisation of animal

behaviour to the underlying cellular and molecular mechanisms at work in the brain. Sensory processing provides a good

setting for such investigation. This project will combine two-photon calcium imaging of single cells and neuronal populations in

vivo with whole-cell and juxta-cellular recording to link neuronal activity with sensory perception in two sensory modalities -

33


whisker touch and vision. Both sensory systems comprise well-studied pathways and have elegant structural organisation.

Visual cortex contains a modular representation of the environment with a topographic map of the visual field and the whisker

area of somatosensory cortex is arranged in a map of cell aggregates (“barrels”) with a one-to-one correspondence with

whiskers. This means that sensory signals are channelled through a restricted population of neurons and can be efficiently

sampled via recording electrodes or imaging, and can be targeted for modulation using optogenetics. The functional circuitry

underlying cortical activity has been extensively studied, but the connection between neuronal activity and sensation and

perception is far from resolved. This project will record sensory-evoked activity in anesthetised and awake (head-fixed) rodents

engaged in a sensory discrimination task. It combines three levels of investigation. At the cellular level we will study synaptic

and dendritic integration of sensory input in single neurons. At the population level we will investigate synergy and redundancy

in coding across the neuronal population, and correlate this with behaviour. Finally, modelling and computational analysis will

be used to provide a framework for interpretation of the data recorded at the cellular and network levels and how this may be

used in decision making.

PersonnelCIs: Greg Stuart & Ehsan Arabzadeh

PIs: Mathew Diamond

CIBF Fellows: Guiherme Silva, Ehsan Kheradpezhouh & Mehdi Adibi


Goals and outcomesOriginal goals Mid 2015 updateDevelopment of the rodent head-fixed set up that

allows precise control of sensory stimuli and behaviour

and simultaneous imaging/recording of neuronal data.

Animal ethics obtained for anaesthetised preparations and is in

process for awake head-fixed.

Correlating neuronal activity (single cell and

population) and behaviour.

PhD student Conrad Lee’s project involves collaborations with PI

Diamond. Manuscript is under preparation. Conrad Lee is scheduled

to present the data at the ANS meeting in Cairns and the SFN

meeting in Chicago, 2015.

Use juxta-cellular recording/labelling to characterise

the role of specific cell types in generating sensory

representations.

Collaboration with AI Linda Richards from QBI. Manuscript in

preparation. Findings are scheduled to be presented at the Japan

Neuroscience Society Meeting (August 2015); ANS meeting in Cairns

and the SfN meeting in Chicago (2015).

Characterise synaptic and dendritic integration of Not yet started.

34


sensory inputs.

Integration of data across multiple levels of

investigation using modelling.

Not yet started.

Key infrastructure purchased (>$5,000) $28,000 (Tissue Slicer, Camera, Stereomicroscope, Illuminator fiber optic LED microscope); $27,700 (Computer

equipment amplifier).

OutputsNil to date


Project 12:

Understanding human attention, decision-making and prediction using psychophysics, brain imaging and neural stimulation

CIs – Jason Mattingley, Marta Garrido, Gary Egan, Michael Breakspear, Michael Ibbotson & Ehsan ArabzadehUniversity of Queensland, Monash University, University of Melbourne, QIMR Berghofer & Australian National University

Project overviewThis project will combine novel behavioural experiments with functional brain imaging (fMRI and EEG) and neural stimulation

(TMS and transcranial direct-current stimulation (tDCS)) to determine the neural circuits responsible for attention, decision-

making and prediction in healthy human participants. The focus will be on characterising how stimulus information from the

external environment (visual, auditory, somatosensory) is filtered on the basis of high level cognitive sets in the service of

35


flexible and adaptive goal-directed behaviour. Across a series of experiments we will focus in particular on how regions of the

prefrontal and parietal cortices coordinate bottom-up and top-down signals during simple selective attention tasks (e.g., spatial

cueing, visual search), decision-making tasks (e.g., probability judgments) and prediction tasks (e.g., oddball detection,

statistical learning). We will apply Bayesian approaches to modelling the functions of these networks, and will endeavor to

understand the underlying neural mechanisms at the level of individual neurons through single-cell recordings carried out in

rodents (collaboration with CI Arabzadeh) and non-human primates (Ibbotson).

PersonnelCIs: Jason Mattingley, Marta Garrido, Gary Egan, Michael Breakspear, Michael Ibbotson & Ehsan Arabzadeh

AIs: Paul Dux, Derek Arnold & Farshad Mansouri


Goals and outcomesOriginal goals Mid 2015 updateA better understanding of the neural circuits involved in

human attention, prediction and decision-making.

Several ongoing projects and publications already produced, as

listed below.

Provide fundamental data for the development of more

effective behavioural interventions for human cognitive

deficits in a range of neurological and psychiatric

conditions.

Not yet addressed – expected to be addressed in later stages of

project.

Provide information to guide the development of human

brain computer interfaces.

Not yet addressed – expected to be addressed in later stages of

project.

Key infrastructure purchased (>$5,000) TMS-compatible MR headcoil.


Painter DR, et al. (2015) Casual involvement of visual area MT in global feature-based enhancement but not

contingent attentional capture. Neuroimage 118:90-102.

Cocchi L, et al. (2015) Dissociable effects of local inhibitory and excitatory theta-burst stimulation on large-scale brain

dynamics. J Neurophysiol 113: 3375-3385.

Filmer HL, et al. (2015) Dissociable effects of anodal and cathodal tDCS reveal distinct functional roles for right parietal

cortex in the detection of single and competing stimuli. Neuropsychologia [Epub ahead of print].

Filmer HL, et al. (2015) Object substitution masking for an attended and foveated target. J Exp Psychol: Hum Percept Perform 41: 6-10.

36


Hall MG, et al. (2015) Distinct contributions of attention and working memory to visual statistical learning and ensemble

processing. J Exp Psychol: Hum Percept Perform [Epub ahead of print].

Hearne L, et al. (2015) Interactions between default mode and control networks as a function of increasing cognitive

reasoning complexity. Hum Brain Mapp [Epub ahead of print].

Painter DR, et al. (2015) Distinct roles of the intraparietal sulcus and temporoparietal junction in attentional capture

from distractor features: an individual differences approach. Neuropsychologia [In press].

Robinson AK, et al. (2015) Olfaction modulates early neural responses to matching visual objects. J Cogn Neurosci 27: 832-841.

Baumann O, et al. (2015) Consensus paper: the role of the cerebellum in perceptual processes. Cerebellum 14: 197-

220.

Dietz MJ, et al. (2014) Effective connectivity reveals right-hemisphere dominance in audiospatial perception:

implications for models of spatial neglect. J Neurosci 34: 5003-5011.

Filmer HL, et al. (2014) Applications of transcranial direct current stimulation for understanding brain function. Trends Neurosci 37: 742-753.

Naughtin CK, et al. (2014) Distributed and overlapping neural substrates for object individuation and identification in

visual short-term memory. Cereb Cortex [Epub ahead of print].

Funding: Cocchi, L., et al. “Selective modulation of neural network activity using focal brain stimulation” NHMRC Project Grant

2016. (APP1099082; Duration - 3 years; Requested - $564,990.00).

Bellgrove, M.A., et al. “An international, multi-site assessment and treatment study of attention deficits in unilateral

spatial neglect” NHMRC Project Grant 2016. (APP1100705; Duration – 5 years; Requested - $1,055,977.00).

Dux, P., et al. Can combined cognitive training and brain stimulation enhance executive function in older adults?

NHMRC Project Grant 2016. (APP1098219; Duration – 5 years; Requested - $1,104,965.00).

Kamke, M., et al. Is it the thought that counts? Investigating the influence of cognitive state on the beneficial effects of

transcranial electrical brain stimulation. NHMRC Project Grant 2016. (APP1107249; Duration – 3 years; Requested -

$621,995.00).

Molenberghs, P., et al. The causes and consequences of social cognitive impairment following stroke: A neuroimaging

investigation. NHMRC Project Grant 2016. (APP1100948; Duration – 4 years; Requested - $836,032.00).

Media Engagement: “Research lays foundations for brain damage study” http://www.qbi.uq.edu.au/content/research-lays-foundations-

brain-damage-study

“Lopsided Brains” in Discovery, The Brain Dialogue website http://www.cibf.edu.au/lopsided-brains


37

http://www.cibf.edu.au/lopsided-brains

http://www.qbi.uq.edu.au/content/research-lays-foundations-brain-damage-study



Project 13:

Rapid information processing in subcortical amygdala pathways

CIs – Marta Garrido, Jason Mattingley, Pankaj Sah, Gary Egan & Michael BreakspearUniversity of Queensland, Monash University & QIMR Berghofer

Project overviewThis project will combine imaging (fMRI and DTI) and electrophysiological recordings in both humans (EEG and

magenetoencephalography (MEG)) and rats (local field potentials (LFP)). The goal is to investigate the role of a putative

subcortical pathway that links thalamus and amygdala directly, the so-called “low-road”, in rapid information processing of

salient, attention-grabbing stimuli, as opposed to a slow cortical route, the “high-road”, which conveys detailed information about

stimuli features onto to higher order regions of the brain. We will test these ideas in a series of experiments using human

neuroimaging data (CI Egan) and modelling approaches (CI Breakspear). We will then validate our findings in an animal model

(CI Sah) to further investigate the circuitry underlying these processes.

PersonnelCIs: Marta Garrido, Jason Mattingley, Pankaj Sah, Gary Egan & Michael Breakspear

AIs: Nao Tsuchiya


Goals and outcomesOriginal goals Mid 2015 updateA better understanding of the human

neural circuits involved in attention

mechanisms that lead to adaptive

decisions.

Several ongoing projects and publications already produced as listed below.

Animal validation of the circuits involved

in attention to behavioural salient stimuli.

Not yet addressed – expected to be addressed in later stages of the project.

An understanding of the relation between

brain structure and function in enabling

attention deployment and rapid decision-

making.

Data Collection completed for study.

38



C. Poch, M.I. Garrido, J.M. Igoa, M. Belichon, I. Garcia-Morales, P.Campo (2015). Time-varying effective connectivity

during visual object naming as a function of semantic demands. J Neurosci 35:8768-76.

W. He, M.I. Garrido, P.F. Sowman, J. Brock, B.W. Johnson (2015). Development of effective connectivity in the core

network for face perception. Human Brain Mapping. 36:2161-73.

S. Dürschmid, T. Zaehle, H. Hinrichs, H.-J. Heinze, J., M.I. Garrido, R. Dolan, R. Knight (2015). Sensory deviancy

detection measure directly within Human Nucleous Accumbens. Cerebral Cortex. Jan 5th : 1-8.

M.J. Rosa, L. Portugal, T. Hahn, A.J. Fallgatter, M.I. Garrido, J. Shawe-Taylor, J. Mourao-Miranda (2015). Sparse

network-based models for patient classification using fMRI. Neuroimage 105:493-506.

M.M. Garvert, K.J. Friston, R.J. Dolan, M.I. Garrido (2014). Subcortical amygdala pathway enables rapid visual

information processing. NeuroImage 102 Pt 2:309-316.

M. Dietz, K.J. Friston, J.B. Mattingley, A. Roepstorff, M.I. Garrido (2014). Effective connectivity reveals right-

hemisphere dominance in audiospatial perception: implications for models of spatial neglect. Journal of Neuroscience 34:5003-5011. Selected by Australian Life Scientist as some of the best Australian research published in May/June 2014.

*G.K. Cooray, M.I. Garrido, L. Hyllienmark, T. Brismar (2014). A mechanistic model of mismatch negativity in the

aging brain. Clinical Neurophysiology 125:1774-1782.

New Collaborations: Wei He, Department of Cognitive Science and ARC, Centre of Excellence in Cognition and Its Disorders, Macquarie

University, NSW, Australia.S. Dürschmid and R Knight, University of California, Berkeley University, CA, USA.

Media Engagement: “Research lays foundations for brain damage study” http://www.qbi.uq.edu.au/content/research-lays-foundations-

brain-damage-study

“Lopsided Brains” in Discovery, The Brain Dialogue website http://www.cibf.edu.au/lopsided-brains


39

http://www.cibf.edu.au/lopsided-brains




Project 14:

Computer modelling of human visual system with applications in computer vision

CIs – Arthur LoweryMonash University

Project overviewIt is hoped that the combined expertise and knowledge of neuroscience within CIBF will guide the direction of the project and

supply sufficient background to enable the work to progress to a publishable standard – i.e. be of great interest to the

neuroscience community.

Also, the extensive background in computer vision and numerical modelling of Profs, Drummond and Lowery will provide new

approaches to understanding existing data and developing efficient software replicas of portions of the human brain. An initial

approach has been to work with Prof. Peter Robinson’s NeuroField code. This models the interactions of populations of cell

types and can predict the spectral and time characteristics for ECG recordings. We are considering modifying this approach to

localise it to a particular section of the brain (e.g. V1), but at the same time, provide more, differentiated, populations

corresponding to the layers of V1 and its striated structure.

Interestingly, the NeuroField approach has similarities to Prof Lowery’s early experience in transmission-line modelling (TLM) of

lasers and electromagnetic fields. TLM was pioneered at Nottingham University by Raymond Beurle, where Lowery did his early

research. Significantly, TLM is extremely computationally efficient, and allowed Lowery to commercialise super-fast laser

simulation tools.

In computer vision (and artificial intelligence), deep convolutional networks (DCN) are capable of self-learning simpler computer

games (like PacMan) with impressive results. One aim is to inform the initial connectivity of DCNs from the human visual

system in order to test whether we can improve them. A related outcome is whether the human visual pathway is in itself

optimum.

Thus, there appears to be a strong synergy between the aims and experience of the members of CIBF and electrical engineers

at Monash. This should create new approaches to understanding the brain, backed by new computational models, and with

outcomes of improved computer vision algorithms and more effective bionic visions systems.

PersonnelCIs: Arthur Lowery

Collaborator: Tom Drummond

40




To develop a greater understanding of the human visual

system, expressed in electrical engineering language (Signal

Processing, Circuit Theory and Software Algorithms).

N/A – new project commenced 2015.

To develop software to enable ‘in-silico’ experimentation to

optimise stimulation of the human visual system for bionic

vision, for example by optimising the location of the

stimulation sites on a probabilistic basis.

To advance the field of computer vision by providing

grounding for bio-inspired computer-vision algorithms, with

an aim of improving algorithmic efficiency by mimicking the

signal processing paths in the human visual system.

OutputsNil to date

41


Project 15:

A digital atlas of connections in the marmoset brain

CIs – Marcello RosaMonash University, Cold Springs Harbour Laboratory, University of Sydney & Nencki Institute

Project overviewThis project will produce the first comprehensive digital map of the connections in a primate brain, and will use advanced

statistical 'data mining' techniques to explore the network characteristics of this system. This will allow new insights on how the

brain works as an integrated system, and will help us to understand how information processing in the brain changes as result

of diseases and normal ageing.

PersonnelCIs: Marcello Rosa

PIs: Partha Mitra

AIs: Pulin Gong, Fabio Ramos & Wojtek Goscinski

CIBF Fellows: Piotr Majka


Goals and outcomesOriginal goals Mid 2015 updateAn integrated web site showing images of sections, 3-dimensional

reconstructions of the brain, and unfolded maps of the cortex from

a large number of experiments involving tracer injections. Free

public access will require registration and use of the material will

be governed by a material transfer agreement, which requires

acknowledgement of the CoE as source of materials.

N/A – new project commenced 2015.

Publications in neuroanatomy and neuroinformatic journals.

Modelling studies attempting to decipher the network properties of

the primate cortex.

OutputsNil to date

42


Project 16:

Visual signal processing in thalamocortical loops; predictive coding in attentional circuits.

CIs – Paul Martin & Ulrike GrünertUniversity of Sydney

Project overviewThe project uses array recordings of thalamic reticular and LGN to look at long timescale effect. We apply turbulence physics

method to lateral geniculate nucleus (LGN) and cross correlate with cortex (V1 and MT). We analyse differential connections of

LGN to V1 and MT.

PersonnelCIs: Paul Martin & Ulrike Grünert

AIs: Pulin Gong


Goals and outcomesOriginal goals Mid 2015 updateOur ultimate goal is three- and four-dimensional analysis of

timing across these subcortical and cortical areas.

Array recordings of thalamic reticular and LGN have begun,

looking at long timescale effects.

AI Gong’s turbulence physics method has been applied to

LGN and cross correlation with cortex (V1 and MT).

Analyses of differential connections of LGN to V1 and MT

have begun.


Townsend RG, et al. (2015). Emergence of complex wave patterns in primate cerebral cortex. J Neurosci, 35 (11),

4657-662.

43


Project 17:

Neural circuits that mediate fear learning and extinction

CIs – Pankaj SahUniversity of Queensland

Project overviewThe key project is using optogenetics coupled with in vitro slice recordings and in vivo behavioural analysis to understand the

neural circuits between the hippocampus, mPFC and amygdala. We are using rats for most behavioural studies as we have

found that behavioural work in mice is much more difficult. For the circuit tracing studies we are using wild type C57Bl6 mice

and three transgenic lines to identify interneurons. First there is a GAD67-EGFP line that marks all interneurons with EGFP. To

identify particular interneuron types we are using PARV-CRE and SOM-CRE lines where cre-recombinase is expressed under

the parvalbumin and somatostatin promoter.

To understand connections between the hippocampus and mPFC and BLA we are using adenoassociated virus to express

channelrhodopsin in the ventral hippocampus using the synapsin promoter to label neurons. For connections between the

mPFC and BLA we are using a lentivirus injected into the IL or PL. To identify particular interneurons we are using AAV to

express td-tomato in specific interneurons. Moreover, we have crossed both CRE lines with the GAD67-EGFP line so that both

labelled interneurons and other non-labelled cohorts can be tested simultaneously.

Finally to understand interneuron connections within the BLA and mPFC we are using a doubly floxed channelrhodopsin

injected into the IL, PL or BLA. Virus is injected into the relevant areas and six week allowed for expression and transport of

channelrhodopsin to the terminals. Brain slices are then prepared and recordings made from pyramidal neurons and

interneurons and 470 nm light used to stimulate afferents. We are defining hippocampal inputs to specific neurons in the IL and

PL, where specific interneuron populations are marked. Similarly we are studying mPFC inputs to the BLA again with

interneurons marked.

PersonnelCIs: Pankaj Sah



44


To identify interneurons and ultimately understand

connections between the hippocampus, mPFC and BLA.

No outcomes as yet.

OutputsNil to date

45


4 CIBF Strategic initiative projects

Strategic Initiative Project Lead CI

Direct assessment of predictive coding as a theory of integrative brain function Ibbotson

Nexpo system for experimental interface and data visualisation Martin

Predictive coding: Clarity imaging of thalamocortical circuits Petrou

Computing Facility for Modelling Robinson

A custom-designed TMS-compatible headcoil for human brain imaging experiments on

attention, prediction and decision-making

Mattingley

CLARITY and Viral Vectors to Trace Connections in Attention Pathways Paxinos

Endocannabinoid modulation of neuronal excitability Stuart

46

A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N Strategic initiative projects

SIP 1:

Direct assessment of predictive coding as a theory of Integrative brain function

CIs – Michael Ibbotson, Marcello Rosa, Paul Martin, Peter Robinson & Michael BreakspearUniversity of Melbourne, Monash University, University of Sydney & QIMR Berghofer

Project overviewPredictive Coding is a theory of brain function that has been hypothesized to explain a wide range of observations including the

hierarchical organization of (sensory) cortex, the architecture of cortical microcircuits, the structure of cortical receptive fields,

single cell integration properties and synaptic plasticity. It proposes that cortical microcircuits perform computations that can be

applied universally to different types of input, regardless of cortical area or modality. Consequently the theory has the potential

to provide a unified view of integrative brain function. A key aspect of the theory describes how bottom-up (afferent) and top-

down (efferent) information interact in local cortical microcircuits, in such a way that only information that was unpredictable,

based on top-down input, is passed up the cortical hierarchy for further processing. In this project we will directly assess this

central hypothesis of predictive coding by recording from three consecutive areas of the visual pathway (LGN, V1 and V2),

measuring the interaction of bottom-up and top-down information at the level of V1 and seeing if it accords with the description

provided by predictive coding. To this end, we are seeking funding to allow the purchase of equipment for high-channel count

electrophysiological recordings from local cortical and thalamic microcircuits across multiple areas of the visual pathway

simultaneously.


The primary outcome is that we will perform the first direct

assessment of the central hypothesis of predictive coding

theory: that only information that is unpredicted, based on

top-down input, is passed up the cortical hierarchy for further

processing.

Simulation of predictive coding model established.

Methods for multi-electrode recording under development

A secondary outcome is that we will have developed a novel

methodology tracking information flow between and within

brain areas over time.

Theoretical framework for tracking information flow identified.

OutputsFunding:

Successful bid for Melbourne Neurosciences Institute Interdisciplinary Seed Funding $20K New Collaborations:

Dr Joseph Lizier (U Syd); Prof Michael Wibral (Goethe University Frankf)

Key issuesDelay in receiving funds

SIP 2:

47


Nexpo system for experimental interface and data visualisation

CIs – Paul Martin, Greg Stuart & Jason MattingleyUniversity of Sydney, Australian National University & University of Queensland

Project overviewWe are developing a license-free stand alone system for high accuracy visual and auditory stimulus generation and massive

data visualization using generic PC / MAC components. Our long-term (strategic) proposal is to badge the system with CIBF

and release it as a freely available public resource.


To develop a licence-free, stand-alone system for high

accuracy visual and auditory Stimulus generation and

massive data visualization using generic PC / MAC

components.

OutputsNil to date

SIP 4:

48


Predictive coding: Clarity imaging of thalamocortical circuits

CIs – Steve PetrouUniversity of Melbourne

Project overviewExperimental validation of the predictions of the predictive coding model requires knowledge of anatomical structures analogous

to the computation elements used within the model. In this aspect of the project we aim to generate short and long range neural

connectivity maps in somatosensory and visual cortices using light sheet imaging of clarity/Scale cleared whole brains of mice.

We have already built a light sheet microscope but require a specialized Clarity objective that is refraction index matched to

Clarity and Scale to eliminate spherical aberrations and provide 8 mm of working distance. This objective costs around $40K

and we are requesting to use our 2014 and 2015 allotment of SI funds to purchase this item in early 2015.


To generate neuronal scale

connectivity maps of

somatosensory and visual

thalamocortical circuits using

glass brain imaging, to provide

connectivity data sets to other

CIs as well as for our own

studies.

Glass Brain A prototype light sheet scope has been built. A small HPC cluster with 1.5TB of

RAM has been deployed at engineering IT and is running our fusion and multi view

deconvolution software system. We are currently exploring software options for automated

neuronal tracing and looking. Once this workflow has been tested we are planning to reach

out to MASSIVE to explore deploying workflow on this super computer cluster. Modifications

to the system to include new refraction index matched objective as well as improvements to

the light sheet design are underway. We have chosen to produce an in toto map of the

rodent olfactory bulb as our first proof of concept project. Marmoset Atlas In addition to this

project we have been working on generating a Marmoset MRI based atlas. A fixed

marmoset brain was prepared for 16.4T imaging at the UQ facility and we will undertake

super resolution tractograhpy and GRE imaging to generate high contrast and resolution

images as the first aim of this study. Scanning has been complete and we are currently

running analysis on the images we have obtained to ascertain whether a second round of

scanning

OutputsPublications

Richards K et al, (2014). Mapping somatosensory connectivity in adult mice using diffusion MRI tractography and

super-resolution track density imaging. Neuroimage. 102 (2):381-92.


49


SIP 5:

Computing facility for modelling

CIs – Peter Robinson & Michael BreakspearUniversity of Sydney & QIMR Berghofer

Project overviewA 96-core high-performance computing facility will be purchased to underpin high-level modelling and data analysis in the CoE.


Provision of adequate on-site computer facilities for the

development, testing and runs of new models & codes.

Equipment has been purchased and is currently operational.

Key infrastructure purchased (>$5,000)• 3 x Dell PowerEdge R360 Servers (Total cost $47,778 - $17,778 USyd contribution)

Outputs Abeysuriya, R. G., C. J. Rennie and P. A. Robinson (2015). "Physiologically based arousal state estimation and

dynamics." J Neurosci Methods 253: 55-69.

Zhao, X., J. W. Kim and P. A. Robinson (2015). "Slow-wave oscillations in a corticothalamic model of sleep and wake." J

Theor Biol 370: 93-102.

Townsend, R. G., S. S. Solomon, S. C. Chen, A. N. Pietersen, P. R. Martin, S. G. Solomon and P. Gong (2015).

"Emergence of complex wave patterns in primate cerebral cortex." J Neurosci 35(11): 4657-4662.

Keane, A. and P. Gong (2015). "Propagating waves can explain irregular neural dynamics." J Neurosci 35(4): 1591-

1605.


50


SIP 6:

A custom-designed TMS-compatible headcoil for human brain imaging experiments on attention, prediction and decision-making

CIs – Jason Mattingley, Gary Egan, Marta Garrido & Michael BreakspearUniversity of Queensland, Monash University & QIMR

Project overviewThis request is for a TMS-compatible headcoil for use in the University of Queensland’s 3 Tesla Siemens magnetic resonance

imaging (MRI) scanner. We will use this piece of equipment across a range of studies aimed at assessing patterns of functional

connectivity within the brain while participants engage in tasks designed to probe specific aspects of attention, prediction and

decision-making.

We will combine both fMRI and TMS to examine the effects of local inhibition or excitation on patterns of activity throughout the

brain. Once in place, we will conduct a number of studies focused on understanding how activity changes throughout the brain

during simple perceptual and cognitive tasks designed to probe specific aspects of attention, prediction and decision-making.

The general approach will be to stimulate higher cortical areas, such as the prefrontal and parietal cortices, and to measure the

influence on activity within sensory processing areas during task performance.


Across separate experiments, to examine the contributions

of the left and right dorsolateral prefrontal cortex and inferior

parietal cortex to information processing within the primary

visual cortex during voluntary focusing of spatial attention.

Equipment is still under construction – expect delivery in late

July 2015.

Key infrastructure purchased (>$5,000)• TMS compatible MR headcoil – Ordered but not yet received

OutputsNil to date


51


SIP 9:

CLARITY and Viral Vectors to Trace Connections in Attention Pathways

CIs – George Paxinos, Ulrike Grünert, Paul Martin & Pankaj SahUniversity of New South Wales, University of Sydney & University of Queensland

Project overviewThis is a collaboration between George Paxinos, Paul Martin, Ulrike Grunert and Pankaj Sah. We propose to establish the

CLARITY and Viral Vectors techniques in connectional work in the mouse, marmoset and human. The visual system from the

retina through the thalamus to the cortex will be investigated. The somatosensory system will be studied through the spinal

cord, brainstem, thalamus and cortex. The visual and auditory pathways linking sensory thalamus to limbic centres will be

investigated in mice, rats and marmosets using CLARITY and Viral Vectors. The anatomy expertise of Paxinos, Grunert and

Martin will be combined with Sah laboratory expertise to target limbic structures for tracer injections. We will consult with Steve

Petrou who has set up the technique. Postdoctoral researchers Huazheng Liang of the Paxinos Laboratory and Sammy Lee of

the Grunert Laboratory will spend approximately 20% of their time working on the project in order to establish the techniques

that will be used by other postdoctoral fellows employed on the core CIBF funds.


To Set up the CLARITY and viral vectors techniques for

three species at three CIBF universities

CLARITY has been successfully implemented in the Paxinos

laboratory by Andy Liang. Along with Sammy Lee, he is using the

retina to test out the method for immunohistochemical staining’s.

They are also using CLARITY to image the visual cortex for which

the first data will be collected next week. The next step will be to

visualize tracer injections in the brain.


Liang H, Schofield E, Paxinos G. Imaging serotonergic fibers in the mouse spinal cord using the CLARITY/CUBIC

technique 2015 Journal of Visualized Experiments (JoVE), Accepted for publication Jun 26 2015 JoVE53673R2.

Funding: ARC DECRA application submitted by CIBF Fellow Huazheng Liang in March

Media Engagement: “Flop when you drop” article on the brain dialogue website

Key issuesIt has been technically difficult to get CLARITY to work on retinal tissue as well as it does in other brain tissue. Researchers are

currently trying an improved method (CUBIC) in an attempt to resolve this. Staining of the visual cortex is expected to be

successful, based on previous experiments on the whole brain, and a result will be available in the middle of July.

SIP 10:

52


Endocannabinoid modulation of neuronal excitability

CIs – Greg Stuart & Ehsan ArabzadehAustralian National University

Project overviewThis proposal will investigate the capacity of endocannabinoids to influence neuronal excitability. “Cannabinoids” are the active

substance found in marijuana, and exert their effect on mood by binding to specific receptors in the brain. Recently, it has been

shown that the same receptors also bind molecules made in the brain itself. We wish to investigate how this “endocannabinoid

system” influences brain activity at the single cell level, as well as during sensory perception and decision-making.


To determine the impact of cannabinoid receptor activation

and inhibition on neuronal excitability, with a specific focus

on dendritic integration.

Preliminary experiments have started


and inhibition on sensory processing in the whisker barrel

system.

Preliminary experiments have started


and inhibition on a decision-making task involving texture

discrimination using the whisker barrel system.

Not yet begun

Key infrastructure purchased (>$5,000)• Remote X, Y & Z control of BX51 microscope by Luigs & Neumann (EUR17,660) – Ordered but not yet received

OutputsNil to date


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5 Education Elizabeth Paton, Ramesh Rajan & Lisa HuttonMonash University

At the heart of CIBF’s education portfolio is our belief that people, be they scientists, students or the public at large, have an

inherent desire to understand the human brain. Our goal is to channel that desire into a life-long interest in the brain, including

encouraging adoption of neuroscience as a profession, especially among people who traditionally haven’t been involved. Whilst

we are developing strategies for communicating brain research to school aged children, the current focus of the CIBF Education

program is on our early career researchers (ECRs).

Early Career Researchers programWe propose to develop a series of programs directed at all ECRs in CIBF-associated laboratories, those funded directly by the

Centre and others working in Chief Investigator labs on related projects. To achieve this we have created a database of all

ECRs in CIBF-associated laboratories, and have subsequently developed a mailing list that will be used as we roll out a series

of initiatives under the CIBF ECR program. Potential initiatives are outlined below, but the ultimate activities undertaken will be

decided and driven by a CIBF ECR committee. The committee will be formed during the ECR forum at Cairns in August, 2015.

ECR website: We have the capacity to create a password-protected website for ECRs in CIBF-associated labs. We

envisage this could be a mechanism for ECRs to identify other ECRs in CIBF-associated labs for future collaborations

and updated regularly with all ECR-related activities, e.g., summaries of ECR video conferences; details of buddy

system; group discussion fora; etc.

Regular video conferences: The aim of these video conferences would be two-fold: (a) to help ECRs get familiar with

each other for future potential collaborations (see above on ECR website service), and (b) to create and foster

discussion on matters identified by ECRs as being of concern for them in developing a career in science or elsewhere.

These may include both general discussion (e.g., surveying ECRs to develop programs for workshops) and specific

themes (e.g., a grant-writing roundtable in mid-Dec/early Jan from 2016 onwards).

ECR workshops: These can include talks, roundtables, small group activities and social occasions, with the aim to

provide useful information on building and sustaining research careers as well as to form connections across nodes

and build stronger support networks.

Mentoring program, buddy systems and lab exchange: Based on the networks developed at the ECR workshops, we

could look to facilitating both formal and informal relationships between CIs and ECRs across labs and nodes. These

could take the form of mentoring programs, buddy systems or laboratory exchanges, exposing ECRs to different ideas

and techniques, building on their existing skill base and creating further potential for more integrative collaboration

within the centre.

The Australian Brain Bee Challenge sponsorship The Australian Brain Bee Challenge is a competition for high school students in year 10 (Australia) to learn about the brain and

its functions, learn about neuroscience research, find out about careers in neuroscience and to dispel misconceptions about

neurological and mental illnesses. CIBF provides sponsorship to allow the National competition winner to represent Australia at

the International competition.

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A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N The Brain Dialogue

6 The Brain DialogueRachel Nowak & Elizabeth PatonMonash University

The Brain Dialogue’s mission is “knowledge sharing with impact”. As a corollary to research impact, knowledge sharing and

engagement with impact should lead to a sustained outcome, such as beneficial changes in policy, industry partnerships, citizen

involvement in science, or cultural enrichment equivalent to engagement with the arts.

The Brain Dialogue’s goals are:

a. Dissemination and exploitation of CIBF results – for industry linkage, cultural enrichment, convergence,

collaboration, and responsible research and innovation

b. Foster discussion of emerging issues – for responsible research and innovation

c. Encourage participation in brain research – for cultural impact, and responsible research and innovation

d. Listen to end-users – for responsible research and innovation

“Responsible innovation and research” is research that aligns with society’s needs and aspirations. The Brain Dialogue

facilitates this through plain-English summaries to help all stakeholders — including researchers — monitor and use CIBF

results as they appear. It also raises awareness about emerging issues in brain research, and involves researchers, policy

makers, and other end-users in discussion of their social and philosophical implications.

Achievements past 6 months: Plain-English summaries for all CIBF research papers; building reputation around this approach to knowledge

dissemination, including organisations seeking to copy approach; and external support, including from ARC

National Library of Australia requested permission to archive The Brain Dialogue website, stating "The National Library has selected your publication for archiving because we have judged it to be an important component of the national documentary heritage. We want it to be available to researchers now and in the future.”

Building an online community of interest through ‘Who’s Dialoguing’. Twitter followers have more than doubled, and include PLOSNeuro, journalists, neuroscientists from around the world;

diverse stakeholders contribute to the Twitter Wall, which hosts online discussions during and following events

Zap My Brain – event discussing use and development of brain stimulation devices for research, clinical, and recreational

purposes (which is not condoned by CIBF and most neuroscientists). We tested three concepts:

That having a home-user on the panel would improve understanding of the issues. It did.

That the audience would value a live demo of TMS. They did.

That the press will cover “discovery” research. They did.

Challenges To more effectively hit goal a) Dissemination and exploitation of CIBF results, we need to disseminate plain-English

summaries faster and wider (which should increase citation rates), increase website traffic, and become a recognised and

trusted authority to a wider range of stakeholders, such as industry, government.

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With the Zap my Brain event, we have developed a partial blueprint for meeting goal b) Foster Discussion of Emerging Issues. One challenge is to increase the impact of these events – potentially through follow-on articles in the lay press and

journals. A second challenge is capacity: brain research is unique among the sciences in the range of issues it raises, and

their potential impact on society. We will need many events, on a range of issues, to have made a meaningful contribution

to responsible research and innovation.

Sharing the love around. Discovery is the quintessential human endeavour but few people get to do it. To meet goal c) Encourage participation in brain research we want to involve non-scientists in research. One option is a citizen science

project — typically researchers use these to access large sample populations; deal with data deluge; and for pattern

recognition and data collection that machines can’t do. (Citizen scientists helped crack the Enigma Code.) Other options

include public data sharing, and engaging with “biohack”/participatory biology communities.

Zap my Brain was our first activity towards goal d) Listen to end-users. It highlighted the challenge of what to do with

end-user knowledge — how do we collect it? Evaluate it? Use it?

Gender diversity on panels/events — The Brain Dialogue is committed to fair gender representation, which introduces

another level of complexity to event design.

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A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N Neuroinformatics

7 Neuroinformatics Wojtek Goscinski & Pulin GongMonash University & University of Sydney

The CIBF neuroinformatics program will focus on a number of proposed projects to coordinate and underpin modeling and data

analysis at CIBF. The key projects to be undertaken are:

(1) To develop an online repository of CIBF models, tools and data, and to support sharing of these resources within

the Centre;

(2) To build a data sharing capability between CIBF and Human Brain Project in the European Union;

And, in collaboration with MASSIVE, as part of the CIBF Affiliate Partnership in MASSIVE:

(3) To provide the CIBF community with dedicated share of the MASSIVE facility; and

(4) To provide CIBF researchers with an Australian mirror of Human Connectome Project data that will be hosted

alongside and accessible from the MASSIVE HPC facility.

CIBF Tools and Data Repository Experimental data and computational models are a major output of the CIBF. The aim is to make these important resources

accessible to relevant researchers of CIBF and thus to facilitate collaborations between different groups, and to publish models

and data more widely where it is possible.

Status:

● Dr Pulin Gong commenced as the Coordinator for Computational Modelling and Data on 1st of July 2015;

● A dedicated file system storage allocation (through RDSI ReDS3) has been allocated to CIBF, providing approximately

100TB of space.

● GitLab instance has been created to publication of models and source code where it’s desirable;

Next steps:

● Undertake a review of data and models across the nodes to establish what can be shared, or made public, and under

what conditions. July-August 2015.

● Commence uploading data and models. August / September onward.

● Link with CIBF website. September / October onward or when relevant.

Data sharing between CIBF and Human Brain Project HBP has expressed interest in CIBF datasets being exposed to the HBP community - in particular marmoset data being

generated at Monash University and University of Sydney - and potentially other data sets.

The proposal is to use the HBP Image Service to expose data from data storage at MASSIVE / Monash.

Status:

● First meeting held to discuss this proposal between CIBF and HBP on 29th June;

● HBP has a prototype Image Service but development has not yet completed;

Next steps:

● HCP to provide information re the Image Service [suggested September onward];

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● CIBF will need to understand [September onward]:

○ how a data set integrates with this service, and what data manipulation will need to be undertaken to support

this;

○ technical requirements of running this service, likely at VicNode.

CIBF Access to MASSIVEThrough funding made available by Monash University, CIBF is now an Affiliate Partner of MASSIVE. This provides dedicated

funding to a share of the facility, proportional to the CIBF contribution.

From 1st of July 2015, CIBF researchers have access to 5.2% of the M1 and M2 computers, which accounts for approximately

1,090,000 CPU-core hours per year. From July 2015 MASSIVE will be procuring additional compute to accommodate this

increased allocation and in the meantime the CIBF share will be allocated from the Monash University share.

Status:

● The facility is available for users from 1st of July and early CIBF adopters have been accessing MASSIVE since the

start of 2015.

● To access, request a project on the MASSIVE website (www.massive.org.au/access) from the Monash University

share and explicitly state this is a CIBF request.

Next steps:

● A communication to CIBF partners to alert them to the open availability of MASSIVE - to be sent out in July 2015.

Australian Human Connectome Project MirrorThis proposal is to create an Australian mirror of HCP data that will be hosted on data storage associated with the MASSIVE

HPC facility and managed by the Victorian Node (VicNode) of the Australian research data infrastructure. The purpose of this

project is:

● Provide access to HCP data to Australian researchers in a coordinated and accessible manner – stored centrally and

alongside tools and services such that researchers do not need to download the data locally;

● Provide researchers access to compute capability for analysis;

● Provide access to recommended HCP tools using the MASSIVE Desktop, so that viewing HCP data can be done

remotely at MASSIVE without the need to copy data locally;

● Ensure access to the latest data made available by the project; and

● Avoid duplication of HCP data on MASSIVE and other Australian HPC systems.

Timeframe: start June and available in August / September 2015.

Status and next steps:

● Monash has meet with Dan Marcus to discuss first steps;

● Monash has allocated required file system space;

● HCP will investigate the best way for MASSIVE to check if scientists have registered with HCP;

● Monash to download HCP packages.

● Make available to researchers (before end of Q3 2015).

Australian National University

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A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N Education

8 Gender EquityElizabeth Paton & Sarah DunlopMonash University

CIBF aims to improve gender diversity in its ranks, and in the wider neuroscience community. We are acutely aware of a current

imbalance in gender distribution within the CIBF and are working to prepare a Gender Equity policy to address this. A snapshot

of the 2014 CIBF statistics on gender balance mirrors the situation at many other research institutes worldwide, and indeed,

across many professional workplaces. These reveal that women are generally under represented and are not progressing to

senior research levels.

The NHMRC announced a new gender equity policy in early 2015 to support the recruitment, retention and progression of

women in health and medical research. Under this new policy all administering institutions are required to update their gender

equity policies to include strategies that:

a) Address the underrepresentation of women in senior positions,

b) Seek to promote and increase women’s participation,

c) Ensure pay equity,

d) Provide flexible and appropriate work arrangements for those with caring responsibilities.

Compliance with these new gender equity standards will be required to ensure continued institutional eligibility for grant funding.

ARC CEO Aidan Byrne “fully backed the principle and was planning a similar announcement”.

Accordingly, Australian academic and research institutions need to implement changes to address the attrition of women at the

early and mid career stage, particularly from science research, and the scarcity of women in senior research leadership

positions.

CIBF initiatives to redress gender inequity include:

Quantifying CIBF’s gender distribution and setting goals to improve gender diversity,

Addressing (unintentional) gender bias in decision-making,

Addressing gender-specific obstacles to career progression,

Pursuing equitable representation of women and men in scientific activities,

Providing a supportive and collegial environment for female and male researchers,

Seeking gender parity for outreach and education programs, and

Developing a grant to support CIBF carers.

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Notes

A R C C E N T R E O F E X C E L L E N C E F O R I N T E G R A T I V E B R A I N F U N C T I O N Notes

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