CONP Portal | Dataset


BigBrain dataset - Hippocampus Segmentation (derived dataset)
Creators: BigBrain project
Contact: info@bigbrainproject.org
Licenses: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International Public License
Version: 1.0
Modalities: histology
Formats: OBJ GIfTI
Size: 2.8 GB
No of Files: 76
No of Subjects: 1
Input Datasets: bigbrain-datalad
Primary Publication: BigBrain: an ultrahigh-resolution 3D human brain model. Science.
Project Landing Page: https://bigbrainproject.org
Metadata file: DATS.json
Is About: Homo sapiens, adult
Description:
The BigBrain Hippocampus Segmentation dataset contains hippocampus segmentation derived from the BigBrain dataset, a digitized reconstruction of high-resolution histological sections of the brain of a 65 years old man with no history of neurological or psychiatric diseases. The BigBrain dataset is the result of a collaborative effort between the teams of Dr. Katrin Amunts and Dr. Karl Zilles (Forschungszentrum Jülich) and Dr. Alan Evans (Montreal Neurological Institute). For more information please visit the BigBrain Project website [https://bigbrainproject.org]

Dataset README information

README.md

BigBrain Hippocampus Segmentation

BigBrain

The BigBrain is the brain of a 65 year old man with no neurological or psychiatric
diseases in clinical records at time of death. The brain was embedded in paraffin and
sectioned in 7404 coronal histological sections (20 microns), stained for cell bodies.
BigBrain is the digitized reconstruction of the hi-res histological sections
(20 microns isotropic).

Dataset content

This dataset contains hippocampus segmentation from the BigBrain release 2015
published in the BigBrain Project website.

Surfaces are provided for CA1, CA2, CA3, CA4, dendate gyrus, subiculum, and the mid-surface.

Files are organized as follows:

  • JSON/*: a complete model in JSON format (try it with brainbrowser)

  • A3D/*: these are the surface files to use with Atelier3D (you also need to download the full A3D model for the BigBrain volume and place these files in the same base directory for A3D)

  • MNI-obj/*: surfaces in MNI-OBJ format

  • wavefront-obj/*: surfaces in WaveFront-OBJ format

  • stl/*: surfaces in STL format

  • gii/*: surfaces in GIfTI format

Reference and more information

Hippocampus segmentation

DeKraker, J., Lau, J.C., Ferko, K.M., Khan, A.R., Kohler, S., "Hippocampal subfields revealed through unfolding and unsupervised clustering of laminar and morphological feaures in 3D BigBrain", NeuroImage, Feb 1 2020 (DOI 10.1016/j.neuroimage.2019.116328).

The BigBrain

The BigBrain dataset is the result of a collaborative effort between the
teams of Dr. Katrin Amunts and Dr. Karl Zilles (Forschungszentrum Jülich)
and Dr. Alan Evans (Montreal Neurological Institute).

Amunts, K. et al.: "BigBrain: An Ultrahigh-Resolution 3D Human
Brain Model", Science (2013) 340 no. 6139 1472-1475, June 2013.
https://www.sciencemag.org/content/340/6139/1472.abstract

For more information please visit the BigBrain Project website.

Download Using DataLad

CircleCI status

The following instructions require a basic understanding of UNIX/LINUX command lines. A subset of open datasets on the Portal are also available through a browser-based download button. The instructions below regard dataset download with the use of DataLad. To install DataLad on your system, please refer to the install section of the DataLad Handbook .

Note: For maximum compatibility with conp-dataset, the CONP recommends versions 3.12+ of Python, 10.20241202+ of git-annex, and 1.1.4+ of datalad.

1) Initiate the CONP dataset

Run the following command in the directory where you want the CONP dataset (conp-dataset) to be installed:

2) Install the BigBrain_Hippocampus_Segmentation dataset

To install the BigBrain_Hippocampus_Segmentation dataset, run the following commands to move into the "projects" subdirectory under the "conp-dataset" directory (created in the previous step) and run datalad install:

3) Download data from the BigBrain_Hippocampus_Segmentation dataset

Now that the dataset has been installed, go into the BigBrain_Hippocampus_Segmentation dataset directory.

The files visible after installing the dataset but before downloading (in the next step) are symbolic links and need to be downloaded manually using the datalad get command:

If you run datalad get * command, all the files available in the dataset directory will be downloaded.


For more information on how DataLad works, please visit the DataLad Handbook documentation.