In this tutorial, you will warp an example MRI scan to MNI ICBM 152 2009c Nonlinear Asymmetric space and analyze a point of the input space in the detailed anatomical context of the EBRAINS Human Brain Atlas.
voluba-mriwarp is a desktop application for aligning human MRI scans to MNI152 template and analyzing brain regions.
voluba is a browser-based tool for interactive alignment of volumes of interest to 3D atlases.
A tutorial on how to anchor partial volumetric data to BigBrain using voluba.
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.
This study includes 40 mice (20 at 6 months(m), 20 at 14 months(m); 2 males and 38 females). Of the mice, 29 are from 14 AD-BXD strains, 2 are the C57B1/6J founder strain, 6 are the F1 B6/DBA/2J (D2) 5XFAD founder strain, and 3 are nontransgenic (Ntg)-BXD.
We present ilastik, an easy-to-use interactive tool that brings machine-learning-based (bio)image analysis to end users without substantial computational expertise.
MeshView is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas based analysis and integration of experimental data and knowledge about the human and rodent brain.
EBRAINS LocaliZoom serial section image viewer provides an intuitive way of navigating high-resolution 2D image series coupled with segmentation overlay, from a web browser.
QuickNII is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas-based analysis and integration of experimental data and knowledge about the human and rodent brain.
VisuAlign is one of several tools developed by the Human Brain Project (HBP) with the aim of facilitating brain atlas based analysis and integration of experimental data and knowledge about the human and rodent brain.
QCAlign was developed to support the use of the QUINT workflow for high-throughput studies
WebAlign is an online tool for spatial registration of histological section images from rodent brains to reference 3D atlases.
WebWarp is an online tool for nonlinear refinement of spatial registration of histological section images from rodent brains to reference 3D atlases.
Here, we review approaches for integrating data describing neural connections and other modalities in rodent brain atlases and discuss how atlas-based workflows can facilitate brainwide analyses of neural network organization in relation to other facets of neuroarchitecture.
Volumetric brain atlases are increasingly used to integrate and analyse diverse experimental neuroscience data acquired from animal models, but until recently a publicly available digital atlas with complete coverage of the rat brain has been missing. Here we present the new Waxholm Space rat brain atlas, a comprehensive open-access volumetric atlas resource.
The mammalian auditory system comprises a complex network of brain regions. Interpretations and comparisons of experimental results from this system depend on appropriate anatomical identification of auditory structures.
Atlases of the rat brain are widely used as reference for orientation, planning of experiments, and as tools for assigning location to experimental data. Improved quality and use of magnetic resonance imaging (MRI) and other tomographical imaging techniques in rats have allowed the development of new three-dimensional (3-D) volumetric brain atlas templates.
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