Young Researchers Event

Young Researchers Event meets HIBALL: new digital tools to study the brain

25 October 2022 | Zadar, Croatia & online

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About

 

 

© BestofCroatia

By plane

Zadar has a small international airport which has connections to many major European cities. The airport is a 30 min. drive away from the venue. Alternatively, you can also land in Zagreb, which has a bigger airport, and then take a bus from the Zagreb main bus station to Zadar. This ride will take 3 hours.

By car

Zadar is located on the A1 highway. This highway connects the city with major Croatian cities such as Zagreb and Split and also other European countries.

The speed limit in Croatia is 130 km/h on motorways, 90 km/h on open roads and 50 km/h within cities.

In order to use Croatian motorways, you have to pay toll. At the entrance of the motorway, you will get a ticket and at the exit you will have to pay the toll amount. Toll can be paid in Kuna or Euro, as well as by card.

By bus

You can take a bus from Zagreb to Zadar, which will take 3 hours. Alternatively, you can also take a bus from Split to Zadar, which takes 2 hours. Both routes are run by a number of different bus companies. The largest bus operators are Arriva, Croatia Bus and Cazmatrans. Tickets range from 7 to 16€. All busses depart from the main bus terminal (autobusni kolodvor). This is also where you can buy tickets. Bus tickets can also be bought online on getbybus or Vollo.

The venue is located in Petrčane, which is a 15 minute bus ride away from Zadar. The bus stop is a 30 minute walk away from the venue. Alternatively, you can also take a taxi.

As of March 2022, travelers need to show a Green Pass upon entrance. Alternatively, a negative PCR test has to be shown. Travelers have to register their contact details and where they will be staying in Croatia. It is recommended to do this online beforehand.

Face masks are required in indoor spaces, on public transport and taxis. In addition, they also have to be worn outside if you cannot keep a distance of 1,5 meters to other people.

The Adriatic coast region has a Mediterranean climate consisting of hot and dry summers. The winters are cool and rainy. The average temperatures in October are between 12°C and 20°C.

There are a number of accommodations available in Petrčane, as well as Zadar.

Accommodations in Petrčane

Accommodations in Zadar

Language

The official language of Croatia is Croatian, which is written using the Latin alphabet. Especially younger Croatians also commonly speak English.

Currency

The currency in Croatia is the Croatian Kuna (HRK). 1 HRK = 0,13€

Money can be exchanged in banks and post offices. Credit cards are widely accepted in most shops and restaurants. Nevertheless, you should make sure to ask the staff beforehand. Croatian Kuna can also be withdrawn from ATMs, which are readily available.

Time

Croatian is in the Central European Summer Time Zone at the time of the event. This time zone is also referred to as UTC+2. On the 25th of October, Croatia will switch to Central European Time (UTC+1).

Electricity

The standard voltage in Croatia is 230 V. The standard frequency is 50 Hz. Most European countries use the same voltage and frequency.

Please note that the information provided on this site has been obtained from several different sources and therefore the organisers cannot accept any responsibility for errors therein.

The human brain is a multi-level and highly complex system that produces, processes and transmits information in an incomparable manner. The Human Brain Project (HBP) unites researchers and scientists to decode the mechanisms underlying this unique system by investigating the human brain and its diseases with the help of highly advanced ICT tools. As such, the HBP is developing EBRAINS, the new European digital research infrastructure, as a lasting contribution to the global science community, an open source tool that allows scientists and technology experts to seamlessly collaborate, thereby accelerating advancements in the fields of neuroscience, computing and brain-related medicine.

The Helmholtz International BigBrain Analytics and Learning Laboratory (HIBALL) is an HBP Partnering Project that aims to transform the well-known BigBrain model to its next level by reinforcing utilization and co-development of the latest AI and high-performance computing (HPC) technologies for building highly detailed 3D brain models.

HBP and EBRAINS together with the University of Zagreb, School of Medicine and HIBALL invite the entire scientific community, in particular early career researchers, to join the forthcoming Young Researchers Event (YRE), taking place on 25th October in Zadar, Croatia and online. During this one-day free hybrid event, participants can learn more about topics like big data analytics, human brain atlasing and computational neuroscience in interactive plenaries and hands-on workshops. The programme also offers networking opportunities for participants to exchange with peers as well as renowned experts.

This event will take place in conjunction with the 6th BigBrain Workshop - From microstructure to functional connectomics

Registration

REGISTRATION

Registration Deadline: 4 October 2022
Registration is free but mandatory.

We strongly encourage you to also attend the 6th BigBrain Workshop - From microstructure to functional connectomics. Registration for this event is separate.

Registration is mandatory and open until 4 October 2022. Attendance is open to anyone and free of charge.

Registration for on-site participants includes:

  • Admission to all sessions
  • Event material
  • Coffee & lunch break during the event

Registration for online participants includes:

  • Admission to all plenary sessions
  • Event Material

Preliminary Programme & Speakers

This programme is subject to change. Times displayed are in CEST/GMT+2/UTC+2.

09:00 – 10:00

Registration & Welcome Coffee

10:00 – 10:10

Welcome by hosts & HBP

10:10 – 10:30

Introduction to HBP and EBRAINS

10:30 – 11:00

BigBrain data processing with CBRAIN and DataLad

11:00 – 11:30

Postnatal development of the human brain

11:30 – 12:00

Coffee Break

12:00 – 12:20

Introduction to EBRAINS RI I (general/Data)
12:20 – 12:40

Introduction to EBRAINS RI II (Atlases)

12:40 – 13:00

Introduction to EBRAINS RI III (Modelling & Simulation)

13:00 – 13:30

HIBALL activities: international relations

13:30 – 14:30

Lunch Break

14:30 – 15:30

Hands-on sessions iteration I
(find further info on hands-on sessions below)
15:30 – 16:30

Hands-on session iteration II 
(find further info on hands-on sessions below)

16:30 – 17:00

Coffee Break

17:00 – 17:30

Talks by young researchers

17:30 – 18:00

What are you missing in EBRAINS? Feedback and Q&A

18:00

End of the event

 

 

 

Title: BigBrain data processing with CBRAIN and DataLad

Abstract:

This tutorial will provide an introduction to two tools that can be used to process and manage BigBrain-related data: CBRAIN and DataLad.

CBRAIN is a web portal that provides seamless access to high-performance computing clusters, and is a component of the NeuroHub ecosystem of neuroinformatics tools. DataLad is a data integration tool to keep track of distributed datasets. The tutorial will cover the main functionalities of CBRAIN and DataLad, illustrate them on BigBrain data, and demonstrate their interaction.

Tutors (in-person): 

Bryan Caron (McGill University, Canada) 
Tristan Glatard (Concordia, Canada) 
Shahbaz Memon (Forschungszentrum Jülich, Germany) 
Morris Riedel (Forschungszentrum Jülich, Germany) 

Tutors (remote):

Pierre Rioux (McGill University, Canada) 
Serge Boroday (McGill University, Canada) 
Natacha Beck (McGill University, Canada) 

Expected learning outcomes:
In this tutorial participants will learn to use the following infrastructure tools and services for analyzing data in HIBALL:

  • Part 1: DataLad and Boutiques, to access and process BigBrain data through uniform command-line interfaces, including:
    • Finding BigBrain datasets in DataLad
    • Installing and downloading BigBrain datasets
    • Processing BigBrain datasets with Boutiques
    • Uploading derived data to DataLad
  • Part 2: CBRAIN to process BigBrain data on HPC clusters through a web portal, including:
    • Finding BigBrain datasets in CBRAIN
    • Processing BigBrain datasets in CBRAIN
    • Exploring and working with the processing results
    • Downloading and sharing the results

Max. Number of participants: no limit

Preparations & Equipment:

  • Laptop (Windows, Mac or Linux)
  • NeuroHub or CBRAIN account
  • Participants who do not already have a NeuroHub account can obtain one by registering here and selecting ‘Request Account’: https://portal.neurohub.ca/

Title: Using EBRAINS atlas services to explore and analyze the human brain

Abstract:
EBRAINS offers a multilevel atlas of the human brain, which captures different principles of brain organization inside a common framework. It integrates maps and reference brain templates at the microscopic and macroscopic scales, and links them with multimodal data features describing microstructure, connectivity and function. Features are linked semantically to brain regions, or spatially by registration to 3-D reference templates. The multilevel atlas framework can be used interactively with our interactive atlas viewer "siibra-explorer", and as well as through a Python client (siibra-python) which allows to use the atlas for advanced analysis and computational workflows. This hands-on session will present the BigBrain dataset as a microscopic reference brain template, and show how it can be navigated in 3D together with different brain parcellations and other reference spaces. We will use the atlas to discover linked multimodal data features, and show how to use it for reproducible analyses using the Python client.

Expected learning outcome:
The goal of the hands-on session is to provide basic skills to view and download different brain maps along with their metadata, and to access data features linked from different modalities by their anatomical locations in the brain. Participants will learn the basic concepts using the interactive online viewer „siibra-explorer“, and see how these can be translated into exemplary programmatic workflows using siibra-python and Jupyter notebooks. 

Max. number of participants:
25

Preparations & Equipment:
Each user should register for an EBRAINS account in advance to be able to run all provided interactive scripts. A Notebook/PC with internet connection and an up-to-date web browser (Chrome or Firefox recommended) will be needed. 

Title: Introduction to the ENIGMA Toolbox: Surface data visualization and multiscale neural contextualization

Abstract:
Among big data initiatives, the ENIGMA (Enhancing NeuroImaging Genetics through Meta-Analysis) Consortium—a worldwide alliance of over 2,000 scientists diversified into over 50 Working Groups—has yielded some of the largest studies of the healthy and diseased brain. Integration of multisite datasets to assess similarities and differences across brain disorders and to explore brain abnormalities across different biological scales, however, have been limited. In this tutorial, we will introduce the ENIGMA Toolbox, an open-source Python/Matlab ecosystem for (i) accessing 100+ ENIGMA datasets, (ii) visualizing data on brain surfaces, and (iii) contextualizing neuroimaging findings at the microscale (postmortem cytoarchitecture and gene expression) and macroscale (structural and functional connectomes). Our Toolbox tutorial will equip scientists with tools to explore molecular, histological, and network correlates of brain disorders, and perform advanced analytic workflows for multicenter datasets.

Max. Number of participants: no limit

Preparations:
Users should have MATLAB installed and/or python 3.7 (the tutorial will be in both languages at the same time to accommodate the majority of people)

Katrin Amunts did a postdoctoral fellowship at the C. & O. Vogt Institute of Brain Research at Duesseldorf University, Germany. In 1999, she set up a new research unit for Brain Mapping at the Research Center Juelich, Germany. In 2004, she became professor for Structural-Functional Brain Mapping, and in 2008 a full professor at the Department of Psychiatry, Psychotherapy and Psychosomatics at the RWTH Aachen University as well as director of the Institute of Neuroscience and Medicine (INM-1) at the Research Center Juelich. Since 2013, she is a full professor for Brain Research, director of the C. and O. Vogt Institute of Brain Research, Heinrich-Heine University Duesseldorf and director of the Institute of Neuroscience and Medicine (INM-1), Research Center Juelich.
Katrin Amunts is a member of the editorial board of Brain Structure and Function. She is member of the German Ethics Council since 2012, and has been elected as vice chair in 2016. Katrin Amunts is the programme speaker of the programme Decoding the Human Brain of the Helmholtz Association, Germany. She is leading Subproject 2 Human Brain Organization of the European Flagship Project The Human Brain Project (HBP). In 2016, she has been elected as Scientific Research Director and Chair of the Science and Infrastructure Board (SIB) of the HBP. Since 2017 Katrin Amunts is co-speaker of the graduate school Max-Planck School of Cognition and since 2018 she is a member of the International Advisory Council Healthy Brains for Healthy Lives, Canada.
In order to better understand the organizational principles of the human brain, she and her team aim to develop a multi-level and multi-scale brain atlas, and use methods of high-performance computing to generate ultra-high resolution human brain models.

Jan Bjaalie, M.D., Ph.D., is Professor at the Institute of Basic Medical Sciences, University of Oslo, where he leads a team of researchers, data curation scientists, and software developers contributing to the building of the EBRAINS RI, the European distributed research infrastructure for brain and brain-inspired research. He is Infrastructure Director of the EU Human Brain Project, leader of the EBRAINS Data services, special advisor on neuroinformatics for the EBRAINS AISBL, Head of the Norwegian Neuroinformatics Node, and former Head of the Institute of Basic Medical Sciences at the University of Oslo (2009 - 2016). With a strong background in neuroanatomy and neuroscience, he is focused on making scientific research data more accessible and interpretable and on developing advanced brain atlasing tools for brain-wide analysis of multimodal data. In his role as founding Executive Director of the International Neuroinformatics Coordinating Facility (2006 – 2008), he initiated INCF programs on brain atlasing and multi-scale modeling. Professor Bjaalie has been partner and coordinator of several EU projects and has collaborated extensively with leading laboratories in many countries. He is Chief-Editor of Frontiers in Neuroinformatics and has served as member of the Neuroinformatics Committee of the Society for Neuroscience (2004 - 2009) and co-Chair (2018 - 2020) and Chair (2021) of the International Brain Initiative.rate ultra-high resolution human brain models.

Sebastian Bludau graduated with a diploma as a biologist at the Heinrich-Heine University in Duesseldorf and received a PhD in theoretical medicine from the RWTH Aachen University in 2011, where he studied the cytoarchitecture of the frontal pole of the human brain. Subsequently he became post-doc at the INM-1 (Structural and functional organization of the brain) at the Institute of Neuroscience and Medicine at the research center Juelich. Sebastian Bludau’s current research is mainly about the cytoarchitecture of the human brain, the integration of different imaging modalities into high resolution reference spaces, high-throughput optical microscopy and developing and testing of new prototype software for the analysis of histological images.

Andrea Brandstetter is a doctoral researcher at the Architecture and Brain Function group at the INM-1, Institute of Neurosciences and Medicine, Research Center Juelich (FZJ) in Germany.
She develops high-resolution cytoarchitectonic maps of subcortical nuclei in the human brain and works on new methods for quantitative analyses and three-dimensional visualization of these nuclei. Her work contributes to the Juelich Brain and BigBrain atlasses and she is well-connected with researchers in the HIBALL and EBRAINS communities.
She obtained her BSc in Biology and MSc in Zoology at the University of Vienna, Austria.

Timo Dickscheid is a Professor for Microscopic Image Analysis at Heinrich-Heine University Düsseldorf, and head of the "Big Data Analytics" group at the Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich, Germany. He graduated in Computer Science at the University of Koblenz in 2006, and earned his PhD at the University of Bonn in 2011, where he worked on the 3D reconstruction of buildings from images under the supervision of Prof. Wolfgang Förstner. In 2010, he joined Forschungszentrum Jülich as a post-doc to build high-resolution 3D models of the human brain from microscopic images. After accepting a position as the head of Information Technology at the German Federal Institute of Hydrology in Koblenz in 2012, Dickscheid returned back to Jülich in 2014 to build his own research group. Aiming to build a cellular resolution multimodal model of the human brain, his work addresses high throughput microscopy, biomedical image analysis on HPC systems, and neuroinformatics solutions for handling large image datasets. In the Human Brain Project (HBP), Timo is responsible for the development of a publicly accessible multi-level human brain atlas.

Miloš Judaš was born in 1961 (Petrinja, Croatia). He is currently employed at the University of Zagreb School of Medicine as full professor of neuroscience & anatomy (2012-present), director of the Croatian Institute for Brain Research (2015-present), and director of the national Center of Excellence in Basic, Clinical & Translational Neuroscience (2015-present). He also served as Vice-Rector for Science & International Cooperation at the University of Zagreb (2014-2022). Professor Judaš significantly contributed to the development of neuroscience in Croatia, through his involvement in the foundation of the Croatian Institute for Brain Research, the Croatian Society for Neuroscience, the first graduate course in neuroscience (for medical students), and the first Ph.D Study Program in Neuroscience.

Research interest: Human neuroanatomy and human developmental neurobiology; developmental and evolutionary neurobiology of cognition and language; history of neuroscience.

Contact:

Miloš Judaš, M.D., D.Sc.,
Professor of Neuroscience & Anatomy,
Croatian Institute for Brain Research (director),
University of Zagreb School of Medicine,
Šalata 12, 10000 Zagreb, Croatia,
E-mail: mjudas@hiim.hr

Sara Larivière is a CIHR doctoral fellow, fifth-year PhD candidate in the Integrated Program in Neuroscience at Mcgill in Montreal, and a researcher in the Multimodal Imaging and Connectome Analysis (MICA) Laboratory at the Montreal Neurological Institute (MNI) supervised by Dr Boris Bernhardt. Her research focuses on the effects of epilepsy surgery on the brain as well as leveraging big data to study multiscale network alterations in the common epilepsies.

Nicola Palomero-Gallagher, PhD, PD, graduated 1990 from the Sciences Faculty of the Universidad Autónoma of Madrid, Spain. She was a PhD student at the C. & O. Vogt-Brain Research Institute of the Heinrich-Heine University Düsseldorf, Germany, between 1992 and 1999, and received the PhD in 1999. Since 2000 she works at the Institute of Neuroscience and Medicine (INM-1), Research Center Jülich, Germany, where she is a Senior Researcher and Leader of the research group “Rezeptoren”. She is a senior editor of Brain Structure and Function. Her research is centered on the structural (cyto- and fiber-architecture) and molecular (receptor-architecture) organization of the human, non-human primate and rodent cerebral cortex, with particular focus on the cingulate cortex. Her major goal is to understand the cyto- and receptor-architectonic basis of cortical segregation and interareal interactions, with emphasis on their relationship with function.

Scientific Chair

Katrin Amunts | Forschungszentrum Jülich/Heinrich-Heine-Universität Düsseldorf (Scientific Research Director HBP)
 

Programme
Committee

Katrin Amunts | Forschungszentrum Jülich/Heinrich-Heine-Universität Düsseldorf (Scientific Research Director HBP)
Caroline Ernoult | EBRAINS AISBL
Maja A. Puchades | University of Oslo
Paule-J Toussaint | McGill University/HIBALL
Susanne Wenzel | Forschungszentrum Jülich/HIBALL
Goran Sedmak | School of Medicine University of Zagreb
Andrija Štajduhar | School of Medicine University of Zagreb

Local Hosts

Goran Sedmak | School of Medicine, University of Zagreb
Andrija Štajduhar | School of Medicine, University of Zagreb

Supported by



 

In Collaboration with

Venue

Falkensteiner Resort Punta Skala 
23231 Petrčane
Croatia