Magnetic resonance imaging (MRI) and light-sheet fluorescence microscopy (LSFM) are technologies that enable non-disruptive 3-dimensional imaging of whole mouse brains. A combination of complementary information from both modalities is desirable for studying neuroscience in general, disease progression and drug efficacy. Although both technologies rely on atlas mapping for quantitative analyses, the translation of LSFM recorded data to MRI templates has been complicated by the morphological changes inflicted by tissue clearing and the enormous size of the raw data sets. Consequently, there is an unmet need for tools that will facilitate fast and accurate translation of LSFM recorded brains to in vivo, non-distorted templates. In this study, we have developed a bidirectional multimodal atlas framework that includes brain templates based on both imaging modalities, region delineations from the Allen’s Common Coordinate Framework, and a skull-derived stereotaxic coordinate system. The framework also provides algorithms for bidirectional transformation of results obtained using either MR or LSFM (iDISCO cleared) mouse brain imaging while the coordinate system enables users to easily assign in vivo coordinates across the different brain templates.
Folder structure of atlas resources:
Template space | Orientation | Folder name |
MRI (magnetic resonance imaging) | Bregma-lambda at the same level | MRI_space_oriented |
AIBS (Allen Institute of Brain Science) | Original | AIBS_CCFv3_space_original |
AIBS (Allen Institute of Brain Science) | Bregma-lambda at the same level | AIBS_CCFv3_space_oriented |
LSFM (light sheet fluorescence microscopy) | Bregma-lambda at the same level | LSFM_space_oriented |
All | – | Deformation_fields |
All | – | Hierarchy_tree |
All | – | Transform_files_Elastix |
Descriptions of atlas files:
File name | Description |
[mri/ccfv3/ccfv3_orig/lsfm]_temp.nii.gz | Mouse brain template |
[mri/ccfv3/ccfv3_orig/lsfm]_ano.nii.gz | Brain region segmentations |
[mri/ccfv3/ccfv3_orig/lsfm]_tissue_mask.nii.gz | Mask of the brain tissue |
[ccfv3/ccfv3_orig/lsfm]_ventricular_mask.nii.gz | Mask of the ventricular system |
[mri/ccfv3/ccfv3_orig/lsfm]_coords_x.nii.gz | Stereotaxic coordinates for medial-lateral axis |
[mri/ccfv3/ccfv3_orig/lsfm]_coords_y.nii.gz | Stereotaxic coordinates for anterior-posterior axis |
[mri/ccfv3/ccfv3_orig/lsfm]_coords_z.nii.gz | Stereotaxic coordinates for dorsal-ventral axis |
[mri/ccfv3/ccfv3_orig/lsfm]_coords_all.nii.gz | Stereotaxic coordinates of all axis, 4D matrix |
mri_2_ccfv3_orig_deffield.nii.gz | Deformation field for mapping data from the MRI space to the original AIBS CCFv3 space |
ccfv3_orig_2_mri_deffield.nii.gz | Deformation field for mapping data from the original AIBS CCFv3 space to the MRI space |
mri_2_ccfv3_deffield.nii.gz | Deformation field for mapping data from the MRI space to the AIBS CCFv3 space |
ccfv3_2_mri_deffield.nii.gz | Deformation field for mapping data from the AIBS CCFv3 space to the MRI space |
ccfv3_orig_2_lsfm_deffield.nii.gz | Deformation field for mapping data from the original AIBS CCFv3 space to the LSFM space |
lsfm_2_ccvf3_orig_deffield.nii.gz | Deformation field for mapping data from the LSFM space to the original AIBS CCFv3 space |
ccfv3_2_lsfm_deffield.nii.gz | Deformation field for mapping data from the AIBS CCFv3 space to the LSFM space |
lsfm_2_ccfv3_deffield.nii.gz | Deformation field for mapping data from the LSFM space to the AIBS CCFv3 space |
Annotation_info.csv | Hierarchy of the brain region segmentations |
mri_2_ccfv3_orig_transform.nii.gz | Elastix transformation parameters for mapping data from the MRI space to the original AIBS CCFv3 space (to be used together with the respective deformation field) |
ccfv3_orig_2_mri_transform.nii.gz | Elastix transformation parameters for mapping data from the original AIBS CCFv3 space to the MRI space (to be used together with the respective deformation field) |
mri_2_ccfv3_transform.nii.gz | Elastix transformation parameters for mapping data from the MRI space to the AIBS CCFv3 space (to be used together with the respective deformation field) |
ccfv3_2_mri_transform.nii.gz | Elastix transformation parameters for mapping data from the AIBS CCFv3 space to the MRI space (to be used together with the respective deformation field) |
ccfv3_orig_2_lsfm_transform.nii.gz | Elastix transformation parameters for mapping data from the original AIBS CCFv3 space to the LSFM space (to be used together with the respective deformation field) |
lsfm_2_ccvf3_orig_transform.nii.gz | Elastix transformation parameters for mapping data from the LSFM space to the original AIBS CCFv3 space (to be used together with the respective deformation field) |
ccfv3_2_lsfm_transform.nii.gz | Elastix transformation parameters for mapping data from the AIBS CCFv3 space to the LSFM space (to be used together with the respective deformation field) |
lsfm_2_ccfv3_transform.nii.gz | Elastix transformation parameters for mapping data from the LSFM space to the AIBS CCFv3 space (to be used together with the respective deformation field) |