Blue Brain data
Published April 4, 2024 | Version v1
Dataset Open

BlueBrainHeadModels

Authors/Creators

  • 1. ROR icon École Polytechnique Fédérale de Lausanne

Contributors

  • 1. ROR icon Foundation for Research on Information Technologies in Society

Description

Input data used to create a finite element head model aligned to the BBP rat somatosensory cortex model. Associated with the github repo BlueBrain/BlueBrainHeadModels and with the paper "BlueRecording: A pipeline for the efficient calculation of extracellular recordings in large-scale neural circuit models"

In this datset, we include the SIGMA atlas (https://www.nitrc.org/projects/sigma_template), which is licensed under a noncommerical license. 

The file Waxholm_Atlas.nii.gz, and Waxholm_Atlas_Labels.nii, Waxholm_Atlas_Mask.nii, and Waxholm_Atlas_Labels.nii in align_waxholm_to_neurorat.zip, are derivations of the Waxholm Rat Brain atlas v3 (RRID:SCR_017124;  Papp et al. 2014, Osen et al., 2019). It is licensed under a CC-BY 4.0 license.

The file Paxinos_Watson_Atlas.nii.gz is a digitization of the Paxinos Watson atlas created, as described in Supplementary Materials A of (Bolanos-Puchet et al. 2024), by aligning, rasterizing and interpolating the individual slices obtained from the CD-ROM distributed with (Paxinos and Watson 2007)

The file Neurorat.nii.gz, and the files NeuroRatLabels.nii and NeurRat_MRI.nii in align_waxholm_to_neurorat.zip, are adaptations of the  ViZOO NeuroRat (150g) model V4.0 (DOI: 10.13099/VIP91106-04-1, https://itis.swiss/virtual-population/animal-models/animals/neurorat/)

 

Files

align_waxholm_to_neurorat.zip

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Additional details

Dates

Submitted
2024

References

  • S. Bolanos-Puchet, A. Teska, J. B. Hernando, H. Lu, A. Romani, F. Schuermann, and M. W. Reimann, "Enhancement of brain atlases with laminar coordinate systems: Flatmaps and barrel column annotations," bioRxiv, 2024. [Online]. Available: https://www.biorxiv.org/content/early/2024/02/23/2023.08.24.554204
  • G. Paxinos and C. Watson, The rat brain in stereotaxic coordinates (6th ed). Academic Press/Elsevier, 2007.
  • Osen KK, Imad J, Wennberg AE, Papp EA, Leergaard TB (2019) Waxholm Space atlas of the rat brain auditory system: Three-dimensional delineations based on structural and diffusion tensor magnetic resonance imaging. NeuroImage 199, 38-56. DOI: 10.1016/j.neuroimage.2019.05.016
  • Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386. DOI: 10.1016/j.neuroimage.2014.04.001