This page provides an overview of what a mouse brain atlas is and which atlases we have available

What is a mouse brain atlas

A mouse brain atlas segments a brain into structures by assigning each image element with a unique label. Below shows an example of the mouse brain atlas created by Dorr et.al. [1]

Ex-vivo atlases

Most ex-vivo mouse brains of adult mice are very similar in terms of their shape and contrast. However, over time with changes made to the scanner, and perfusion protocols for instance, some differences have occurred in among others what kind of contrast is visible in the cerebellum and whether or not the lateral ventricle is present. For this reason we have a couple of atlases for ex-vivo mouse brains in order to have a proper atlas for most scans.

Dorr-Steadman-Ullmann-Richards-Qiu-Egan (40 micron, DSURQE)

This is the most complete atlas we have. Uses the following atlases / segmentations:

• Dorr et.al., 2008, High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice.
• Steadman et.al., 2014, Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas.
• Ullmann et.al., 2013, A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.
• Richards et.al, 2011, Segmentation of the mouse hippocampal formation in magnetic resonance images.
• Shannon Egan (2015) – added olfactory bulb segmentation based on data from the Allen Brain Institute
• Lily Qiu et.al, 2018 – Mouse MRI shows brain areas relatively larger in males emerge before those larger in females

Details on this atlas:

This atlas has 180 structures defined (most have both left and right labels; 356 labels in total), which means that you can not load the labels in the current version of Display, as only 256 different label values are supported. You can use itksnap to load this atlas:

itksnap  \
--main /hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/ex-vivo/DSURQE_40micron_average.mnc \
--segmentation /hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/ex-vivo/DSURQE_40micron_labels.mnc \
--labels /hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/mappings/DSURQE_40micron_itksnap_mapping.txt

Example slices:

Dorr-Steadman-Ullmann-Richards-Egan (40 micron, DSURE)

Uses the following atlases / segmentations:

• Dorr et.al., 2008, High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice.
• Steadman et.al., 2014, Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas.
• Ullmann et.al., 2013, A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.
• Richards et.al, 2011, Segmentation of the mouse hippocampal formation in magnetic resonance images.
• Shannon Egan (2015) – added olfactory bulb segmentation based on data from the Allen Brain Institute

Details on this atlas:

Dorr-Steadman-Ullmann-Richards (40 micron, DSUR)

Uses the following atlases:

• Dorr et.al., 2008, High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice.
• Steadman et.al., 2014, Genetic effects on cerebellar structure across mouse models of autism using a magnetic resonance imaging atlas.
• Ullmann et.al., 2013, A segmentation protocol and MRI atlas of the C57BL/6J mouse neocortex.
• Richards et.al, 2011, Segmentation of the mouse hippocampal formation in magnetic resonance images.

Details on this atlas:

Dorr 2008 on the Male-Female atlas (MAIN / ORIGINAL)

The original atlas we use was create by Adrienne Dorr [1], and created on an average of 40 adult C57Bl/6J mice. Details on this atlas:

Example slices from the anatomical MR and labels:

Dorr 2008 on the Crawley BTBR atlas

Derived from [1]. Details on this atlas:

Example slices from the anatomical MR and labels:

Dorr 2008 on the MWM atlas

Derived from [1]. Details on this atlas:

Example slices from the anatomical MR and labels:

Dorr 2008 on the NRXN1a atlas

Derived from [1]. Details on this atlas:

Example slices from the anatomical MR and labels:

Dorr 2008 on the GAMT atlas

Derived from [1]. Details on this atlas:

Example slices from the anatomical MR and labels:

Dorr 2008 on the Rett atlas

Derived from [1]. Details on this atlas:

Example slices from the anatomical MR and labels:

Dorr 2008 on the VVW Sert atlas

Derived from [1]. Details on this atlas:

Example slices from the anatomical MR and labels:

In-vivo t2 MRI atlases

This atlas is based on the male-female atlas [1], and was manually adjusted after an initial non-linear registration.

Example slices from the anatomical MR and labels:

In-vivo Manganese-enhanced magnetic resonance imaging (MEMRI) atlases

Version 2

This atlas is based on the male-female atlas [1], and was created directly using a mincANTS registration between the two of them. Some of the differences with version 1:

• contains the same labels (left and right) and numbering of labels as the male-female atlas
• the atlas is padded to avoid potential cutoffs in the cortex

Example slices from the anatomical MR and labels:

References

[1] A.E. Dorr, et al, High resolution three-dimensional brain atlas using an average magnetic resonance image of 40 adult C57Bl/6J mice, NeuroImage, vol 42, Aug. 2008, pp. 60-69