Anatomy for Beginners

• Nicola Palomero-Gallagher (Institute of Neuroscience and Medicine INM-1, Research Centre Jülich, Jülich, Germany)

The goal of this course is to familiarize scientists with no, or only very little, knowledge about brain anatomy with major brain structures and their functions. You will learn about the landmarks used by anatomists to navigate through the brain, and the functions they are involved in. Most importantly, you will have a chance to search for these structures yourselves. By the end of the course you will not only be familiar with terms such as lobes, gyri, diencephalon, hippocampus or visual cortex, but you will also be able to find these structu

Collaborative segmentation and analysis of histological data on the Web using MicroDraw

• Nicolas Traut (Institut Pasteur)
• Katja Heuer (Institut Pasteur)
• Roberto Toro (Institut Pasteur)

High resolution histological data provides a unique perspective on the cellular structure of the brain. Histological data is available for a large number of species, and the possibility of staining for particular aspects of the tissue allows the researcher to formulate an extremely rich range of questions. It presents, however, several challenges which make its analysis difficult. In particular, the data is affected by various types of artefact, and the subtle differences that distinguish one structure from the other require a well trained human eye. In addition, scanned at very high resolution, the file sizes involved become difficult to manipulate. These may be in part the reasons why the expert segmentation of histological material is often performed by a single researcher. MicroDraw is an online tool for the collaborative segmentation of high-resolution histological data. MicroDraw uses deepzoom to enable rapid access to high-resolution data without limits in image size. Images can be manipulated in any Web browser, in computers, tablets or even smart phones. MicroDraw provides a growing number of tools for vectorial annotation, which allow us to segment data at any resolution. MicroDraw greatly simplifies distributed collaboration, by providing researchers access to the same dataset independently of the computer where the data is hosted. MicroDraw provides simple tools for the definition of collaborative projects, and helps coordinate access to data and results. Finally, MicroDraw implements a RESTful API, which allows researchers to programmatically query the segmentations performed in a project and use sophisticated image analysis tools for their analysis. In this tutorial we will show how to encode data and host it to make it accessible. We will use the BigBrain data as an example. We will then show how to visualise data and annotate it using the different vectorial annotation tools. We will show how to create a project to centralise a set of annotations. Finally we will show how to query that data using a Python script, display the data obtained and compute some simple measurements. MicroDraw is open source and we invite you to contribute to its development either as a user or as a developer.

BigBrain data processing with CBRAIN and DataLad

• Tristan Glatard (Concordia University)
• Shahbaz Memon (Jülich Super Computing Centre, Forschungszentrum Juelich GmbH)
• Morris Riedel (Jülich Supercomputing Centre, Forschungszentrum Jülich)
• Natacha Beck (McGill University)
• Bryan Caron (McGill University)

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. 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.

Working with BigBrain in the EBRAINS atlas ecosystem

• Timo Dickscheid (Institute of Neuroscience and Medicine (INM-1), Forschungszentrum Jülich)

The EBRAINS multilevel human brain atlas integrates maps that capture different facets of human brain organization into a common framework. It is defined across multiple reference spaces, where BigBrain represents the micrometer level. The atlas links cytoarchitectonic areas with ultra-high resolution BigBrain data, complements them with maps of fibre architecture and functional organization, and links them to a growing set of multimodal data features associated to brain regions. EBRAINS atlas services are designed as an online framework that can be accessed interactively using an online viewer, as well as in a programmatic fashion through structured Python and http interfaces. This tutorial will give a tour of the recent status of EBRAINS atlas services, and discuss some future directions.

Integrating BigBrain with MRI using The BigBrain Warp

• Casey Paquola (INM-1, Forschungszentrum Jülich)

The BigBrain Warp is a toolbox for multi-modal integration of BigBrain, composed of a centralised repository of BigBrain related transformations and scripts to easily move between histological and MRI spaces. In this session, we'll walkthrough the toolbox and guide short tutorials on how to use BigBrain in the context of structural and functional MRI.