Deciphering the intimate structure of the brain is one of the grand challenge for Neuroscience. Such endeavor can only be achieved with the development of software infrastructure to efficiently store, manipulate and analyze the large datasets generated by a wide variety of imaging techniques currently available.

With the support of the INCF program for Teaching and Training, the Belgian INCF node and the University of Antwerp are organizing a unique and multi-disciplinary international 5 day training course . The course aims to addresses both the theoretical and practical aspects of cutting-edge image processing techniques used to analyze imaging data at different spatial scales.
In addition, we will provide an introduction to the existing solutions to manage the different types of data and integrate them together in a coherent framework.

This course, proposed by the Belgian, Dutch, French and Polish INCF nodes, is financially supported by INCF, the Belgian INCF node and the Interuniversity Attraction Poles Programme initiated by the Belgian Science Policy Office (IUAP-VII, consortium 11).

Who can attend ?

This course is open to neuroscientists working in fields related to brain imaging or using brain imaging techniques. Particular experience in multi-scale imaging is NOT necessary !

We encourage both early stage (PhD students) and experienced researchers (postdocs and senior researchers) to apply for this course. We will seek balance between early stage and experienced researchers.

Topics in Keywords

  • Electron microscopy
  • Light microscopy
  • Diffusion Tensor Imaging
  • Magnetic Resonance microscopy
  • Image processing
  • Open-source software
  • Data management systems
  • Connectomics
  • Standard digital brain atlases
  • Multi-scale image integration

Confirmed speakers

  • S. MunckKatholieke Universiteit Leuven, Belgium
  • M. HelmstaedterMax Planck Institut, Germany
  • L. WaldHarvard University, MA, USA
  • U. HimmelreichKatholieke Universiteit Leuven, Belgium
  • J. ModersitzkiLübeck University, Germany
  • F. HamprechtHeidelberg University, Germany
  • D. SageEPFL, Switzerland
  • D. ProdanovIMEC, Belgium
  • A. RoebroeckMaastricht University, the Netherlands
  • J. AshburnerUCL, UK
  • M. HawrylyczAllen Institute for Brain Science, WA, USA
  • K. AmuntsForshungszentrum Jülich, Germany
  • V. WedeenHarvard University, MA, USA
  • J. BjaalieUniversity of Oslo, Norway
  • J. GretheUniversity of California San Diego, USA

Why such course?

The improvement of imaging techniques over the last decades has provided neuroscientists with means to investigate the relations between structure and function of the brain at different spatial and temporal scales. Building on these technical developments, the emerging field of Connectomics aims at producing comprehensive maps of neural connections between different brain regions (i.e. connectomes) at different spatial scales (micro-, meso- and macroscales) in different species. To achieve this goal, the field relies on a combination of methodological approaches, notably electron microscopy, two-photon and confocal fluorescence microscopy and non-invasive brain imaging (for example functional Magnetic Resonance Imaging, fMRI; structural MRI; Diffuse Tensor Imaging, DTI).

One of the main challenges in this emerging field is the implementation of interoperable platforms enabling the integration of multi-scale structural information into a common framework.

The design of such infrastructure requires 1- to create data management solutions to store and manipulate large image datasets having heterogeneous spatial resolution, 2- to develop powerful and standardized methods to analyze, extract and manipulate the meaningful information from the experimental data, 3- to define standardized digital brain atlas spaces and 4- to elaborate an infrastructure for mapping the different datasets together in such atlases.

Different technical solutions to address at least some aspects of these problems have been proposed by the Neuroinformatics, the Bioimaging informatics communities and INCF.

In order to build and operate such infrastructure, neuroscientists should be aware of the different imaging techniques, the corresponding image processing methods and (open-source) software, the different methods to extract the connectivity from the experimental data, the existing Neuroinformatics solutions to store and manipulate large scales datasets and the methods to reference their data into the existing standard atlases.

Unfortunately, most of the existing courses in image processing for neuroscientists are offered 1- at local level (universities or research centers), 2-mostly focus on one defined imaging modality and 3- often doesn’t present existing software solution for data management.

What is this course?

With the support of INCF and the INCF program for Teaching and Training, we are providing a unique and multi-disciplinary international short training course (5 days) that addresses both the theoretical and practical aspects of cutting-edge image processing techniques used to analyze imaging data at different spatial scales and provide an introduction to the existing solutions to manage the different types of data and integrate them together in a coherent framework.

This course will focus on 4 different imaging modalities that span multiple spatial scales: electron microscopy, light microscopy, MRI/DTI and MR microscopy. For each of these technical use-cases, we will give an overview of

  1. the standard image processing techniques,
  2. the methods used for extracting the brain connectivity and
  3. the current solutions for storing, manipulating and annotating large image datasets.

The presentations will be supported by practical examples using open-source software and publicly available datasets wherever possible.

The course will be concluded by a day demonstrating different atlasing solutions for multi-scale data integration.

Internationally renowned scientists in each field, working on advanced methodologies and software development enabling the assembly of different connectomes will contribute by giving lectures and hands on sessions. Several widely used open-source software (ImageJ/Fiji, TrakEM2, …), data management systems (the Open Microscopy Environment, Catmaid, LabIS, BIRN, …) and digital atlases framework (scalable brain atlas, Allen Brain atlas, JuBrain, Waxholm space, Digital Atlasing Infrastructure, …) will be represented during the course.

The course aims to provide optimal interactions between the participants and the invited speakers, with the hope to foster collaborations and cross-fertilization of ideas.

Who can attend ?

This course is open to neuroscientists working in fields related to brain imaging or using brain imaging techniques. Particular experience in multi-scale imaging is NOT necessary !

We encourage both early stage (PhD students) and experienced researchers (postdocs and senior researchers) to apply for this course. We will seek balance between early stage and experienced researchers.

How do I apply?

The number of attendees for this course is limited to 50. An application must include:

  1. Scientific abstractThe abstract should not exceed maximally 250 words but no less than 150.The title, author names, affiliations and references are excluded from the word count. Approved applications will be asked to submit a short paper which will bepublished online
  2. Motivation letterApplicants will be asked to submit a motivation letter which should emphasize the following points:
    • relevant skills, experience and qualifications which show that the applicant would be suitable for the course
    • explain what are you expectations of the course and reasons for attendance. For example, including what you can contribute and how you want to apply the knowledge gained during this course to your project.
  3. CVyou should fill in the requested information on the form
  4. Additional documents:
    • For PhD studentsplease provide 2 recommendation letters (max 1 page, 1 from the lab and 1 from a third party)
    • For Postdocsplease provide one recommendation letter from a senior colleague (max 1 page)
    • For senior researchersplease provide one recent reference in the field

Application form will be accessible on the Belgian node portal starting February 15th and will be closed on April 15th 12:00PM GMT.

For more information about how to access the application form and use the system, please use the link that will be provided on February 15th and read carefully the instructions.

Is there a fee?

We are asking for a fair flat fee of 150 euros for each participant in order to cover in part for the organizational costs including lunches and coffee breaks. Dinners, travel and lodging will be at your charge. The payment of the fee will requested after you will receive your acceptation email.

Cancellation policy and refunding

Refund of cancelled registrations will be possible up to 2 months in before the course. After this delay an administrative fee of 75 euros will be charged

When ?

From Monday September 2nd to Friday September 6th 2013

Where?

The course will be held at the following location:

De Grauwzuster building
University of Antwerp
Stadcampus
Lange Sint-Annastraat 7
2000 Antwerp – Belgium

This location is in the city center of Antwerp, surrounded by hotels and restaurants and nearby the Antwerp central train station as shown on the google map below.

The evening lecture on Wednesday will be held at the Elzenveld Hotel:

Elzenveld Hotel
Lange Gasthuisstraat 45
2000 Antwerp – Belgium

How to get to Antwerp?

By plane: Brussels Airport

The easiest way to get to Antwerp by plane is to land at Brussels airport (for more information about the airport, seehttp://www.brusselsairport.be/en/).

From Brussels airport, you can reach Antwerp either by train arriving at Antwerp Centraal train station or by a shuttle bus arriving right next to Antwerp Centraal train station. For more information regarding connections between Brussels airport and Antwerp, see here

By plane: from other major european airports

It is possible to reach Antwerp from London Heathrow, Amsterdam Schipol airport and Paris Charles de Gaulle airport by train (see below) either directly (Schipol-Antwerp) or with a connection at Brussels Zuid/Midi (Heathrow and Charles de Gaulle airport). For more information regarding the connections, please look at the airport websites.

By train: Brussels Zuid and Antwerp Centraal

Belgium is well connected with the major european cities by high-speed train such as the Thalys, the Eurostar and ICE trains which can either arrive directly at Antwerp Centraal station or require a connection at Brussels Zuid/Midi. Connecting trains from Brussels Zuid/Midi to Antwerp Centraal are frequent (between 3 to 4 per hours).

For more information and booking, you can use the SNCB website which will allow you to pay either in Euros or GBP and print your tickets from pdf.

How to get to the course from the train station?


View Larger Map

Hotels in Antwerp

Rates are only valid for reservations directly made to the hotel by phone, fax or e-mail and mentioning the reservation code. After option period reservations at special rates are only possible upon availability.

Walking distance to the congress venue between brackets.

FIRST CLASS

HYLLIT HOTEL ANTWERP**** (10’)

Option on 15 rooms until August 10, 2013
Reservation code: INCF 2013

De Keyserlei 28-30 – 2018 Antwerpen
T +32 3 202 68 00 – F +32 3 202 68 90
www.hyllit.com
deryck@hyllithotel.be
single executive room 139 euro, double executive room 159 euro, incl. breakfast, high speed wifi and free access to indoor swimming pool, sauna, Turkish bath and fitness
Excl. city tax 2,00 euro/pp/night

MIDRANGE

LEONARDO HOTEL ANTWERPEN*** (15’)

Option on 10 rooms until August 10, 2013
Reservation code: INCF 2013

De Keyserlei 59 – 2018 Antwerpen
T +32 3 232 14 43 – F +32 3 233 08 35
www.leonardo-hotels.com
info.antwerpen@leonardo-hotels.com
Standard room single 77 euro – double 87 euro
All rates includes breakfast and wifi. Excl. city tax 1,00 euro/pp/night

BUDGET MINDED

IBIS BUDGET ANTWERPEN CITY CENTER (20’)

Option on 10 rooms until August 10, 2013
Reservation code: INCF 2013

Lange Kievitstraat 145 – 2018 Antwerpen
T +32 3 202 50 20 – F +32 3 202 50 21
www.etaphotel.com
h6192-BO@accor.com
Single room 46 euro, double 61 euro and tripple 67 euro incl. Breakfast and wifi
Excl. city tax 2,00 euro/room/night

Youth hotel PULCINELLA (25’)

Free reservation, no options !

Bogaardeplein 1 – 2000 Antwerpen
T +32 3 234 03 14 – F +32 3 234 10 67
www.vjh.be/jeugdherbergen/antwerpen
antwerpen@vjh.be
21 2-bed rooms
18 4-bed rooms
8 6-bed rooms
From 19,50 euro incl. breakfast, sheets, wifi. Excl. towels (1,50 euro/towel) and welcome stamp for non-members (3,00 euro)

Please note!
Before submitting your application, please make sure to provide all the required information (marked with an orange asterix).
Please also note that you will be able to modify your application until April 15th 2013 12:00PM GMT.

  • Y.  Le Franc – UA, Belgium
  • W. Vanduffel – KUL, Belgium
  • D. Prodanov – IMEC, Belgium
  • J. Sijbers – UA, Belgium
  • R. Bakker – Donders Institute, the Netherlands

  • P. TiesingaDonders Institute, the Netherlands
  • S. MunckKUL, Belgium
  • J.B. PolineCEA, France
  • U. HimmelreichKUL, Belgium
  • P. TomancakMPI Dresden, Germany
  • E. YaksiNERF, Belgium
  • M. BarthDonders Institute, the Netherlands
  • D. WójcikNencki Institute, Poland
  • M. VerhoyeUA, Belgium
  • D. MarinazzoU. Gent, Belgium