Brain/MINDS Marmoset Reference Atlas Set

About the Brain/MINDS Marmoset Reference Atlas (BMA)

The current Brain/MINDS Marmoset Reference Brain 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) have been warped to match the ex-vivo MRI data, then mirrored across the sagittal plane. The brain atlas can be used for tasks such as brain region identification and data analysis, such as connectomics.

BMA 2017 Ex Vivo

(Brain Space 1)
v1.0.0
  • Released on November 22, 2017

Atlas 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
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.