Supplementary material for the release of the “Extremely Brilliant Brain” (EBB), a 7.72 μm/voxel 3D volume of a whole adult human brain acquired using Hierarchical Phase-Contrast Tomography (HiP-CT)[see note].
The associated manuscript is available as a preprint on bioRxiv: https://www.biorxiv.org/content/10.64898/2026.01.27.702076
The data (EBB & MRI) can be downloaded from the BioImage Archive (BIA)[see note] following the Brain Imaging Data Structure (BIDS) specification[see note]: https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD1939
The EBB data itself can be downloaded from the Human Organ Atlas (HOA) data portal[see note] as series of JPEG2000 files at different voxel sizes: https://human-organ-atlas.esrf.fr/datasets/2270234369
The data is also replicated on a Google Cloud Storage[see note] bucket for streaming to Neuroglancer[see note]. Some files had to be converted to a format that is compatible with Neuroglancer, using the scripts that are provided.
Interactive figures are available in the subfolder.
The Python scripts are available in the subfolder.
Besides, this work has required the use of a few Python tools:
| Repository | Usecase |
|---|---|
stack-to-chunk |
Conversion of a series of 2D images to a 3D volume stored as an OME-Zarr |
ngregister |
Register with an affine transform using a set of hotkeys within Neuroglancer (optimal for large multiscale dataset) |
cardiotensor |
Compute the structure tensor field in a 3D volume |
ngretrieve |
Download a crop of the dataset that can be picked with a Neuroglancer annotation layer |
ngpointstobox |
Change a set of annotations into one annotation that is their bounding box in a Neuroglancer state |
ngvolbox |
Replace a volume layer with an annotation layer that is its bounding box |
segment_properties_for_neuroglancer |
Generate the segmentation properties for the Neuroglancer precomputed format to add metrics and a colormap to the segmentation layer |
freesurfer |
Suite of processing tools for 3D imaging data, initially focused on MRI and the NIfTI file format |
FastSurfer |
Deep learning-enabled segmentation toolbox |
hippunfold |
Hippocampus parcellation toolbox |
tiff_to_nifti |
Convert a TIFF file to a NIfTI file with the necessary header |
This work is licensed under Creative Commons Attribution 4.0 International
A copy of the license is available in the repository.
Notes
- Hierarchical Phase-Contrast Tomography (HiP-CT): https://mecheng.ucl.ac.uk/hip-ct/ | https://www.nature.com/articles/s41592-021-01317-x
- BioImage Archive: https://www.ebi.ac.uk/bioimage-archive/
- Brain Imaging Data Structure (BIDS): https://bids.neuroimaging.io/
- Human Organ Atlas (HOA): https://human-organ-atlas.esrf.fr/
- Google Cloud Storage: https://cloud.google.com/storage
- Neuroglancer: https://neuroglancer-docs.web.app/ | https://github.com/google/neuroglancer