The Belgian INCF node presents:
INCF-sponsored summerschool 2013: Imaging the brain at multiple scales: how to integrate multi-scale structural information?
This page contains a copy of the official summerschool website, and was last updated January 28, 2013
The improvement of imaging techniques over the last decades has provided neuroscientists with means to investigate the relations between the structure and the 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) and 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).
The aim of this course is to provide training in several aspects of imaging techniques which are applicable in Connectomics. Obtaining abundant data poses several challenges for the storage, processing, and sharing/communication infrastructures. 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.
In order to build and operate such infrastructure, neuroscientists need to be aware of the different imaging techniques, the corresponding image processing methods and (open-source) software and the different methods to extract the connectivity from the experimental data, the existing solutions to store and manipulate large scales datasets and the methods to reference their data into the existing standard atlases.
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
the standard image processing techniques,
the methods used for extracting the brain connectivity and
the current solutions for storing, manipulating and annotating large image datasets.
These theoretical presentations will be supported by practical examples using open-source software and publicly available datasets wherever possible.
One of the main challenges in the emerging fields of Connectomics and Neuroinformatics is the implementation of interoperable platforms enabling the integration of multi-scale structural information into a common framework in order to gain a better understanding and visualization of brain structures at all the presented scales. The course will be concluded by a final day demonstrating different atlasing solutions for multi-scale data integration.
International renowned scientists in each field, working on advanced methodologies and software development enabling the assembly of different connectomes will be contributing to this course. Several widely used open-source software (ImageJ/Fiji, TrakEM2, vIST/e, …), 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 by the different speakers during the course. As the topics covered by the course are broad and advanced, we organized the course to provide optimal interactions between the participants and the invited speakers, with the aim to foster collaborations and cross-fertilization of ideas.
