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...
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...
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...
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,...
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.
Cytoarchitecture is defined as the spatial organization of neuronal cells in the brain, including the arrangement of cells into layers and columns with respect to cell density, orientation and presence of certain cell types. It allows to subdivide the brain into cortical areas and subcortical nuclei, which are indicators for connectivity and function. Consequently, cytoarchitectonic areas...
The visual system of mammals is comprised of parallel, hierarchical specialized pathways. Different pathways are specialized in so far as they use representations that are more suitable for supporting specific downstream behaviours. In particular, the clearest example is the specialization of the ventral (“what”) and dorsal (“where”) pathways of the visual cortex. These two pathways support...
For the detection of neuronal cell bodies in 1-micron BigBrain data we propose a conceptually simple framework called Contour Proposal Network (CPN). The CPN detects and segments possibly overlapping cells by fitting closed contours using a fixed-sized representation based on Fourier Descriptors. State-of-the-art object detection architectures can be used as backbone networks, forming a...
The medial geniculate nucleus (MGB) is part of the metathalamus and plays an important role in processing auditory information. Previous maps of the human brain did not include subdivisions of the MGB – limiting their use for data integration, modelling and simulation. Here we aim at overcoming this limitation by creating cytoarchitectonic maps of the MGB in the BigBrain (Amunts et al., 2013) ...
The nucleus ventralis intermedius (VIM) of the thalamus is located in the ventral part of the ventrolateral posterior thalamus and exhibits increased connectivity especially with the dentate nucleus of the cerebellum and the primary motor cortex through the dentato-rubro-thalamic tract. Selective lesioning of the VIM is a well-established neurosurgical target for the treatment of patients with...
The current state of reconstruction of BigBrain2 is presented, describing
the brain of a 30 year old anonymous male donor. As for the original BigBrain,
cell-body stained histological coronal sections were digitized and
reconstructed in 3D. Sections are first repaired at 20 microns in-plane
resolution to correct for manipulation artifacts, then aligned to the MRI
serving as the...
Mapping the microscopical organization of the human brain provides an important basis for multimodal brain atlases, and is indispensable for linking functional, physiological, connectivity, molecular, or genetic properties to their cellular correlates. The BigBrain (Amunts et al., 2013) is a 3D model of a complete human brain at microscopic resolution, constructed from more than 7000...
We present a 3D reconstruction pipeline for 2D autoradiographs that will allow for the creation of the first ever set of ultra-high resolution (50𝜇m). The 3D atlases for 20 different neurotransmitter binding sites in the human brain. This pipeline was designed to overcome significant challenges in the data, including: non-linear deformations in the brain tissue, intensity variations between...
Given the usefulness of the BigBrain high resolution histological volume, it would be very valuable to have a similar public domain resource for the macaque. Isotropic high resolution data to build such a resource is not currently available, but as an initial step we present a histological volume based on the NIH Blueprint Non-Human Primate (NHP) Atlas [1], acquired by the Allen Institute and...
Ex-vivo high-resolution MRI of brain tissue can provide morphological and microstructural information. MR images can also serve as undistorted references for the reconstruction of digitized histology, immunohistochemistry, or clearing techniques. Small-bore scanners, equipped with powerful gradients systems and operating at ultra-high magnetic fields present the optimal conditions for ex-vivo...
How does our brain give rise to brain function, cognition and behaviour? Understanding the fundamental features of brain networks (‘the connectome’) and linking the different levels and scales of brain connectivity to each other is key in tackling this challenge. We will start by discussing the organization of brain networks and network theories of how 'principles of wiring’ may shape...
Background. Complex behaviours benefit from parallel distributed processing in multiple brain networks. The roles of certain networks are well-defined, while others remain elusive. Arguably, none are so elusive as the default mode network (DMN); a distributed set of brain regions that decrease in activity during many externally oriented tasks. Revealing the cytoarchitectural composition...
Analysis of histological data requires sophisticated methods and tools. In the past, research teams have aimed at producing tool packages covering all researchers’ needs. Such large packages can quickly become unwieldy: difficult to maintain and complex to use. Web technologies allow for a powerful alternative: focused micro-services. Instead of a single, overly complex tool, users can rely on...
Connections and interactions among neurons manifest as patterned neural activity and adaptive behaviour. Ascending projections from the brainstem and subcortical nuclei have a modulatory effect on the electrical potential - and therefore the excitability and firing rate - of cortical neurons (Shine 2019). These modulatory influences are coordinated by overlapping and heterogeneous...
Extensive research over the past three decades have been revolutionary by conceptualizing a neuron-glial paradigm which aims at describing the mutual dependence between glial and neuronal processes at multiple spatiotemporal scales. However, glial contributions to large-scale functional neuronal network organization remain mysterious due to the lack of empirical and theoretical frameworks...
Segmentation of the human cerebellar cortex from histological data has been considered a challenge due to its convoluted structure, and the numerous artifacts caused by sectioning or staining. The high resolution BigBrain model (Amunts et al., 2013) enables to overcome the lack of detail occasioned by the limited number of sections in existing datasets, and the large BigBrain data is ideal for...
Reference brain cortical surfaces derived from various structural pipelines enable integration of multimodal data into a standard space. In the absence of a common framework across structural pipelines, high profile surface atlases created within FreeSurfer (fsaverage) or Human Connectome Project (fs_LR) are not available in standard reference frames like the MNI152 or the 3D-reconstructed...
Magnetic resonance imaging (MRI) studies show that the majority of the T1-weighted contrast stems from myeloarchitecture, but cytoarchitecture still has an impact on the signal. Many cortical MRI markers are thought of as being driven mostly by myelin. Here, we compare the spatial organization and age effects of cortical thickness (CT) to 3 measures of cortical microstructure (gray-white...
We propose a 3D surface extraction benchmarking tool to evaluate the performance of 3D model extraction methods from 2D discrete label maps. We have used one geometrical and one anatomical model as references. The anatomical model is selected from the BigBrain hypothalamus atlas (Jones et al. in prep).
3D triangular meshes are used as ground truth 3D surfaces. These contain various...
The expansion of the cerebro-cerebellar system may be a primary driving factor behind primate cognitive evolution. Due to extensive connectivity to cognitive parts of the neocortex, the cerebellum is thought to support cognition analogous to its role in motor functions. Using an extensive MRI dataset (34 primates; 65 specimens) we found that cerebellar and...
The cerebral cortex consists of distinct layers with unique properties and functions. Previous work has shown that the laminar architecture of cortical regions varies in a spatially ordered fashion along a ‘‘sensory-fugal’’ axis, with decreasing laminar differentiation from the unimodal to transmodal areas. Indeed, the “Structural Model” proposes that the isocortex can be divided into regions...
Brain structure scaffolds intrinsic function, supporting cognition and ultimately behavioral flexibility. To evaluate the association between structure and function we assessed whether regions with similar microstructure would also be functionally connected in humans and macaques. This microstructural profile similarity approach has been previously developed in the big brain (Paquola, 2018)....
In current neuroimaging analyses the hippocampus is typically modelled as a subcortical volume, but it is actually made up of a folded archicortical mantle, or ‘ribbon’. Representing the hippocampus as such can be leveraged to enable qualitatively new analyses, such as registration, despite inter-individual differences in gyrification and folding structure, through topological alignment....
In recent years, three-dimensional polarized light imaging (3D-PLI) has opened new avenues for measuring and analyzing nerve fiber orientations in postmortem brains at the micrometer scale. The raw data consists of 18 or 9-channel images, while common derived formats include transmittance, retardation, inclination and computed fiber orientation maps. These measurements are highly detailed and...
