Brain/MINDS Marmoset Reference Atlas Set

About the Brain/MINDS Marmoset Reference Atlas Set (BMA)

This page provides access to the Brain/MINDS 3D Marmoset Brain Atlases. These atlases use different brain shapes as their bases, which we term ‘brain spaces’.

The BMA 2017 Ex Vivo (Space 1) atlas release is a multi-modal Nissl & MRI 3D brain atlas where the Nissl histology data has been normalized to the MRI shape. The brain region annotation is now version 6.2, revised from the Hashikawa et. al (2015). The atlas contains over 200 cortical and sub-cortical annotations per hemisphere and improves upon the work of Hashikawa et al. (2015). State-of-the-art registration algorithms were used to register the different data modalities to one another and to remove noise and artifacts. The original Nissl and parcellation data (for one hemisphere only) were warped to match the ex-vivo MRI data, then mirrored across the sagittal plane.

The BMA 2019 Ex Vivo (Space 2) atlas release builds on previous work and is composed of a population average ex-vivo MRI T2WI contrast with the BMA 2017 Ex Vivo dataset mapped to its shape.The release now includes cortical flat maps for the left and right hemispheres. These can be used for the projection and visualization of data in 2D. In addition, the dataset provides 3D transformation files for mapping between Space 1 and Space 2.

The brain atlases can be used for tasks such as brain region identification for experiment planning, large-scale connectomics and brain simulation. They are being used widely throughout the Brain/MINDS project as a way to integrate heterogeneous data from a wide number of experiments.

BMA 2017 Ex Vivo

(Brain Space 1)
v1.1.0
  • Released on November 22, 2017

BMA 2019 Ex Vivo

(Brain Space 2)
v1.0.0
  • Released on February 4th, 2020
New

Release History

  • BMA 2017 Ex Vivo v1.0.0 : Released on November 22, 2017
  • BMA 2019 Ex Vivo v1.0.0 : Released on February 4th, 2020
  • BMA 2017 Ex Vivo v1.1.0 : Updatedon April 22, 2020.
bminds_atlas_package_v1.1.0/ ├── readme.txt ├── region_hierarchy_v1.0.0.json ├── space_1/ │ ├── readme.txt -info on construction, coordinate systems etc. │ ├── changes.txt │ ├── labelmap/ │ │ ├── sp1_label_512_v1.0.0.nii.gz │ │ ├── sp1_label_116_v1.0.0.nii.gz │ │ ├── sp1_label_grey_v1.0.0.nii.gz │ │ ├── sp1_label_512_3d_slicer_v1.0.0.ctbl │ │ └── sp1_label_512_itk_snap_v1.0.0.ctbl │ ├── contrast/ │ │ ├── sp1_nissl_v1.0.0.nii.gz │ │ └── sp1_ind_mri_exvivo_t2wi_v1.0.0.nii.gz │ ├── flatmap/ │ │ ├── sp1_left_hemi_flatmap_v1.0.0.gii │ │ └── sp1_left_hemi_surface_v1.0.0.gii │ ├── transform/ │ │ ├── space_1_to_space2_warp_v1.0.0.nii │ │ ├── space_1_to_space2_invwarp_v1.0.0.nii │ └── └── space_1_to_space2_affine_v1.0.0.txt ├── space_2/ │ ├── readme.txt │ ├── changes.txt │ ├── labelmap/ │ │ ├── sp2_label_512_v1.0.0.nii.gz │ │ ├── sp2_label_116_v1.0.0.nii.gz │ │ ├── sp2_label_grey_v1.0.0.nii.gz │ │ ├── sp2_label_512_3d_slicer_v1.0.0.ctbl │ │ └── sp2_label_512_itk_snap_v1.0.0.ctbl │ ├── contrast/ │ │ ├── sp2_avg_nissl_v1.0.0.nii.gz │ │ └── sp2_avg_mri_exvivo_t2wi_v1.0.0.nii.gz │ ├── flatmap/ │ │ ├── sp2_left_hemi_flatmap_v1.0.0.gii │ │ ├── sp2_left_hemi_surface_v1.0.0.gii │ │ ├── sp2_right_hemi_flatmap_v1.0.0.gii │ │ └── sp2_right_hemi_surface_v1.0.0.gii │ ├── transform/ └── └── sp2_left_to_right_map.py

Go to package download page:

Package Download
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MRI T2 ex-vivo volume. Version 1.0.
Nissl volume registered to MRI. Version 1.0
Brain region segmentation volume. Version 1.0.
Gray and white matter boundary segmentation volume. Version 1.0.
Mid-cortical boundary segmentation volume. Version 1.0.
Color lookup table for bma-1-regionseg.nii. Version 1.0.
3D Slicer scene file. Version 1.0.