Scalable Brain Atlas - Hippocampal atlas by Badhwar, Lerch, Hamel, Sled 2013

Scalable Brain Atlas Coronal3d

Mouse - Hippocampal atlas by Badhwar, Lerch, Hamel, Sled 2013

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About this atlas

Anatomical images (T2-weighted 3D fast spin-echo) of adult C57Bl/6J mouse brains were acquired on a 7.0 Tesla scanner at an isotropic resolution of 32 μm. The hippocampus proper was manually segmented into the CA1, CA2, and CA3 subfields using the average volume generated from 103 independent mouse brain images. A detailed description of this atlas can be found in Badhwar et al., 2013. The non-hippocampal areas are obtained from the whole brain atlas of Dorr et al., 2008, using an automated registration procedure.

Terms of use

The Scalable Brain Atlas does not "own" any of its templates. To ensure that the atlas makers receive proper credit, you must abide by our citation policy.
In brief, always (1) cite each data source that contributed to your analysis, and (2) cite the Scalable Brain Atlas main publication and plugin references where appropriate.

The defining citations for this atlas template are:

Badhwar A, Lerch JP, Hamel E, Sled JG (2013) "Impaired structural correlates of memory in Alzheimer's disease mice" NeuroImage: Clinical 3:290-300. [doi 10.1016/j.nicl.2013.08.017]

Downloads

It is recommended that you download atlas data directly from the original data source. This will give you the most recent version of the data with the highest resolution. In case you can't find the data at the original source, the Scalable Brain Atlas provides selected (downsampled) datasets for your convenience.
The license terms of the original data source apply.

MRI: Average T2-weighted 3D fast spin-echo
- ../../templates/BLHS13/source/badhwar_hippocampal_atlas.nii.gz; filesize 387 MB; shape [420x548x282]
labels: Hippocampal atlas + whole brain regions of Dorr et al. 2008
The label index mapper converts label indices to acronyms, full names, and rgb-values.
- ../../templates/BLHS13/source/bha_labels_sba.nii.gz; filesize 2060 kB; shape [420x548x282]
coronal_svg: Coronal sections of the label volume "bha_labels_sba11411.nii", converted to Scalable Vector Graphics.
Brain regions are color-coded by the RGB to Acronym map, which can be chained with the Acronym to Fullname map.
- ../../templates/BLHS13/source/coronal_svg.zip; filesize 2005 kB
wholebrain_mesh: surface mesh of the entire brain
- ../../templates/BLHS13/wholebrain.x3d; filesize 4889 kB

The Scalable Brain Atlas is developed by Rembrandt Bakker and many contributors with financial support from INCF, Radboud University Nijmegen, and others.
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