History of BigBrain
what is the BigBrain
BigBrain is a freely accessible high-resolution 3D digital atlas of the human brain, released in June 2013 by a team of researchers at the Montreal Neurological Institute (Canada) and the Forschungszentrum Jülich (Germany) and is part of the European Human Brain Project. The isotropic 3D spatial resolution of the BigBrain atlas is 20 µm, much finer than the typical 1 mm resolution of other existing 3D models of the human brain. In 2014, BigBrain was cited in the top 10 MIT Technology Review.
The 3D model was created from the brain of an unidentified 65-year-old man who died with no known brain pathology. His brain, after being removed from the skull, was first scanned using an MRI machine, then embedded in paraffin.
scanning at 20μm
In April 2004 the brain was sliced into 7,404 sections 20µm thick using a large-scale microtome. After each section was removed, the uncut face was photographed in order to provide an additional reference for removing distortion. The brain sections were placed on large glass slides and then stained for cell bodies using the Merker method, a process that causes the grey matter in the brain to be darkly stained while leaving the white matter uncolored. The stained sections were scanned and digitized using a flatbed scanner at 2400dpi, creating a one terabyte raw record. The acquisition process took about 1,000 hours of labor.
digitally repairing the images
The resulting digital images were then processed by human operators to remove artifacts, and by software to align them with the reference images and with neighboring sections, thereby correcting distortions that inevitably arise during histological processing. The corrected data were then assembled into a three-dimensional computer model with a spatial isotropic 3D resolution of 20 µm. The atlas took five years to complete.
rendering the BigBrain in 3D
In Summer 2017 the first version of the Human Brain Project’s web-based 3D atlas viewer was released. NeHuBa (neuroglancer for human brain atlas) is capable of displaying very large brain volumes, including oblique slicing, a whole brain overview, surface meshes, and maps. It allows to interactively choose difference template spaces and reference parcellations, find brain areas by name or visual selection, and browse additional region-specific multimodal data. The rendering of large volumetric data builds on the open source project Neuroglancer. BigBrain can be directly accessed at https://bigbrain.humanbrainproject.eu
segmentation of the BigBrain
Different approaches are currently being used to trace distinct areas on the BigBrain: manual delineation of brain cortical areas and subcortical structures based on existing atlases, and automatic methods derived from artificial intelligence (machine learning and deep learning) to extract cortical layers or count groups of cells.
sharing the atlas with the world
Users have access to all data: from the raw scanned sections (in order to develop new reconstruction and repair workflows and tools), to the derived data from our own analyses (to be used in different pipelines and analyses). Our online viewers are also available, and the data can be accessed and managed via our neuroinformatics platforms LORIS and CBRAIN.
We are building a community around the BigBrain, and everyone is welcome to join and contribute / collaborate.