Preparing your data - The data descriptor
This video discusses the importance of providing a data descriptor alongside your data and gives advice on how to prepare such a document for the purpose of sharing data through EBRAINS.
Data
Resources
Preparing your data - Metadata organisation
This video gives an introduction to the importance and benefits of metadata organisation for a neuroscience researcher. It then explains how EBRAINS organises and integrates metadata to provide an easy and user-friendly service.
Data
Preparing your data - Data organisation
This video outlines the importance of data organisation and best practices.
Data
What is open data and EBRAINS data sharing?
This video gives an overview of open data and how to share data on EBRAINS.
Data
Anterogradely labeled axonal projections from the orbitofrontal cortex in rat
The project was initiated to determine the projections of the orbital frontal cortex (OFC) to the parahippocampal region in the rat, using the anterograde tracers biotinylated dextran amine (BDA) and Phaseolus vulgaris-leucoagglutinin (PHA-L).
Brain atlases
Semiquantitative overview of efferent projections from the orbitofrontal, posterior parietal and insular cortices in rat
This dataset contains a brain-wide overview of the efferent neural projections from the orbitofrontal, posterior parietal and insular areas in the rat cerebral cortex.
Brain atlases
QUINT user manual
The QUINT workflow comprises a flexible suite of software designed to support atlas-based quantification of labelled features in series of histological images from mouse or rat brain.
Brain atlases
QUINT workflow tutorial
The QUINT workflow takes you through a series of steps developed to enable researchers to quantify and analyse labelled features in a series of histological images of rodent brain sections within a known atlas space.
Brain atlases
The Virtual Brain: INCF TVB Training Space
In this short series of lectures, participants look at articles using TVB in a clinical context. Specifically, participants will see how TVB can help to predict recovery after stroke and how individual epileptic seizures are simulated. The course lecturers will briefly describe the methods and results achieved in the articles. Using the graphical user interface, participants will replicate the principle ideas of the articles and see how artificial lesions introduced in the connectome alter brain dynamics and how seizures spreading through the brain network can be modelled. All videos use the default TVB dataset, so you can follow each step in your TVB GUI.
Modelling and simulation
TVB on EBRAINS: short videos
Mini-videos explaining The Virtual Brain on EBRAINS.
Modelling and simulation
TVB on EBRAINS: The Virtual Brain integrated workflows on EBRAINS (Long Version)
An explainer video describing the The Virtual Brain tool set integrated into EBRAINS supercomputing resources. The tool set includes everything you need for brain simulation - processing pipelines, example datasets, multi-scale simulating tools and learning resources to help you get started.
Modelling and simulation
TVB on EBRAINS: The Virtual Brain integrated workflows on EBRAINS (Short Version)
A short explanatory video about the TVB ecosystem on the EBRAINS infrastructure. Learn about the range of TVB tools available, such as simulators, pipelines, super computing backends, fast TVB, and learning resources.
Modelling and simulation
Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain
Densities and numbers of calbindin and parvalbumin positive neurons across the rat and mouse brain. 2021, iScience. https://doi.org/10.1016/j.isci.2020.101906
Brain atlases
Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images
Nutil: A Pre- and Post-processing Toolbox for Histological Rodent Brain Section Images. Front. Neuroinform. 2020,14:37. https://doi.org/10.3389/fninf.2020.00037
Brain atlases
Navigating the Murine Brain: Toward Best Practices for Determining and Documenting Neuroanatomical Locations in Experimental Studies
Navigating the murine brain: towards best practices for determining and documenting neuroanatomical locations in experimental studies. Frontiers in Neuroanatomy. 2018 Nov 2; 12: article 82. https://doi.org/10.3389/fnana.2018.00082
Brain atlases
QUINT: Workflow for Quantification and Spatial Analysis of Features in Histological Images From Rodent Brain
QUINT: Workflow for quantification and spatial analysis of features in histological images from rodent brain. Front Neuroinform. 2019 Dec 3;13:75. https://doi.org/10.3389/fninf.2019.00075.
Brain atlases
Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool
Spatial registration of serial microscopic brain images to three-dimensional reference atlases with the QuickNII tool. PLosONE, 2019, 14(5): e0216796. https://doi.org/10.1371/journal.pone.0216796
Brain atlases
Waxholm Space atlas of the Sprague Dawley rat brain.
Papp E.A., Leergaard T.B., Calabrese E., Johnson G.A., Bjaalie J.G. (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386. https://doi.org/10.1016/j.neuroimage.2014.04.001
Brain atlases
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