Neuroscience Data Integration Through Use of Digital Brain Atlases

Neuroscience Data Integration Through Use of Digital Brain Atlases

By
University of Oslo
Category
Neuroinformatics
Data science
Level
Beginner

With a new generation of three-dimensional digital reference atlases, new solutions for integrating and disseminating brain data are being developed. Digital brain atlases play an important role in several large international projects, including the European Union ICT Future Emerging Technologies Flagship project, the Human Brain Project.This course contains an introduction to currently available reference atlases for mouse and rat brain. It will demonstrate how the 3D brain templates for the reference atlases are acquired, how they are used as a basis for delineating the structures of the brain, how they can be enriched by other data modalities, and how they can be used as a basis for assigning location (coordinate based or semantic) to a wide range of structural and functional data collected from the brain. The course will also outline examples of data system employed to organize neuroscience data collections in the context of reference atlases as well as analytical workflows applied to the data, with opportunities for hands-on exploration of selected tools.

Read more about how digital brain atlases are used in the EBRAINS infrastructure. 

Course Features
Lectures
Tutorials
Videos
Code / Datasets
Lessons of this Course
1
1
Introduction to Neuroscience Data Integration Through Use of Digital Brain Atlases
Duration:
14:02
Speaker:
Trygve Leergard

This lesson provides an introduction to the course Neuroscience Data Integration Through Use of Digital Brain Atlases, during which attendees will learn about concepts for integration of research data, approaches and resources for assigning anatomical location to brain data, and infrastructure for sharing experimental brain research data. 

2
2
Concepts for Sharing and Integration of Neuroscience Research Data
Duration:
30:39
Speaker:
Jan G. Bjaalie

This talk covers the various concepts, motivations, and trends within the neuroscientific community related to the sharing and integration of brain research data. 

3
3
Brain Anatomy in Men and Mice
Duration:
51:30
Speaker:
Nicola Palomero-Gallagher

This lesson focuses on the neuroanatomy of the human brain, delving into macrostructures like cortices, lobes, and hemispheres, and microstructures like neurons and cortical laminae.

4
4
Introduction to EBRAINS Atlas Services
Duration:
27:45
Speaker:
Trygve Leergard

This lesson provides an introduction to the European open research infrastructure EBRAINS and its digital brain atlas resources.

5
5
Assigning Location Parameters to Experimental Data
Duration:
32:18
Speaker:
Ingvild Elise Bjerke

In this lesson, attendees will learn about the challenges in assigning experimental brain data to specific locations, as well as the advantages and shortcomings of current location assignment procedures. 

6
6
Data Integration: WHY, WHAT, HOW?
Duration:
25:41
Speaker:
Trygve Leergard

This lesson covers the inherent difficulties associated with integrating neuroscientific data, as well as the current methods and approaches to do so. 

7
7
The QuickNII Approach: Mapping Customized Atlas Plates Onto Serial Image Data
Duration:
21:08
Speaker:
Maja Puchades

Attendees of this talk will learn about QuickNII, a tool for user-guided affine registration of 2D experimental image data to 3D atlas reference spaces, which also facilitates data integration through standardized coordinate systems. 

8
8
DeepSlice: Using Deep Learning for Histology to Atlas Registration
Duration:
17:30
Speaker:
Harry Carey

This lesson provides an overview of DeepSlice, a Python package which aligns histology to the Allen Brain Atlas and Waxholm Rat Atlas using deep learning.

9
9
Refining Linear Atlas Registration
Duration:
08:50
Speaker:
Maja Puchades

This short talk addresses how to use VisuAlign to make nonlinear adjustments to 2D-to-3D registrations generated by QuickNII. 

10
11
Approaches to Quantifying Labelling in Images, Finding a Way Through the Jungle of Methods
Duration:
35:20
Speaker:
Sharon Yates

This talk aims to provide guidance regarding the myriad labelling methods for histological image data. 

11
12
Quantitative Analysis of Calbindin and Parvalbumin Positive Neurons Across the Rat and Mouse Brain
Duration:
17:16
Speaker:
Ingvild Elise Bjerke

This lesson provides a cross-species comparison of neuron types in the rat and mouse brain. 

12
13
Visions for Neuroscience Data Integration in the Future
Duration:
09:49
Speaker:
Jan G. Bjaalie

This lecture concludes the course with an outline of future directions of the field of neuroscientific research data integration. 

 

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