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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 (2016) – added the medial amygdala and medial preoptic area

Details on this atlas:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/ex-vivo/DSURQE_40micron_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/ex-vivo/DSURQE_40micron_labels.mnc
Mapping of labels to structures (csv)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/mappings/DSURQE_40micron_R_mapping.csv
Mapping of label for itksnap (txt)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/mappings/DSURQE_40micron_itksnap_mapping.txt
Resolution40 micron
Notes/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Qiu_2016_Egan_2015_40micron/notes_on_DSURQE_atlas
Version

1 (23 August, 2016)

External link to files (MINC)http://repo.mouseimaging.ca/repo/DSURQE_40micron/
External link to files (NIFTI)http://repo.mouseimaging.ca/repo/DSURQE_40micron_nifti/

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:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Egan_2015_40micron/ex-vivo/DSURE_40micron_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Egan_2015_40micron/ex-vivo/DSURE_40micron_labels.mnc
Mapping of labels to structures (csv)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Egan_2015_40micron/mappings/DSURE_40micron_R_mapping.csv
Mapping of label for itksnap (txt)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Egan_2015_40micron/mappings/DSURE_40micron_itksnap_mapping.txt
Resolution40 micron
Notes/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_Egan_2015_40micron/notes_on_DSURE_atas
Version

1 (20 July, 2016)

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:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_40micron/ex-vivo/DSUR_40micron_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_40micron/ex-vivo/DSUR_40micron_labels.mnc

Mapping of labels to structures (csv)none (this atlas contains "TODO" labels, use either the DSURE or the DSURQE atlas)
Mapping of label for itksnap (txt)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_40micron/mappings/DSUR_40micron_itksnap_mapping.txt
Resolution40 micron
Notes/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_40micron/notes_on_DSUR_atlas
Version1 (21 September, 2015)

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:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_labels.mnc
Mapping of labels to structures (csv)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_mapping_of_labels.csv
Mapping of labels to structures (pdf)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_mapping_of_labels.pdf
Resolution30 micron
NotesThe information about the olfactory bulbs is not fully present
Version1

Example slices from the anatomical MR and labels:

Dorr 2008 on the Crawley BTBR atlas

Derived from [1]. Details on this atlas:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_Crawley_BTBR_v1_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_Crawley_BTBR_v1_labels.mnc
Mapping of labels to structures (csv)same as male-female mapping
Mapping of labels to structures (pdf)same as male-female mapping
Resolution56 micron
Notes

this atlas is derived from the atlas from [1] and version 1 contains inaccuracies

Version

1

Example slices from the anatomical MR and labels:

Dorr 2008 on the MWM atlas

Derived from [1]. Details on this atlas:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_MWM_v1_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_MWM_v1_labels.mnc
Mapping of labels to structures (csv)same as male-female mapping
Mapping of labels to structures (pdf)same as male-female mapping
Resolution30 micron
Notes

this atlas is derived from the atlas from [1] and version 1 contains inaccuracies

Version

1

Example slices from the anatomical MR and labels:

 

Dorr 2008 on the NRXN1a atlas

Derived from [1]. Details on this atlas:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_NRXN1a_v1_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_NRXN1a_v1_labels.mnc
Mapping of labels to structures (csv)same as male-female mapping
Mapping of labels to structures (pdf)same as male-female mapping
Resolution56 micron
Notes

this atlas is derived from the atlas from [1] and version 1 contains inaccuracies

Version

1

Example slices from the anatomical MR and labels:

Dorr 2008 on the GAMT atlas

Derived from [1]. Details on this atlas:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_GAMT_v1_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_GAMT_v1_labels.mnc
Mapping of labels to structures (csv)same as male-female mapping
Mapping of labels to structures (pdf)same as male-female mapping
Resolution56 micron
Notes

this atlas is derived from the atlas from [1] and version 1 contains inaccuracies

Version

1

Example slices from the anatomical MR and labels:

 

Dorr 2008 on the Rett atlas

Derived from [1]. Details on this atlas:

 Information
MR anatomy file /hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_Rett_v1_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_Rett_v1_labels.mnc
Mapping of labels to structures (csv)same as male-female mapping
Mapping of labels to structures (pdf)same as male-female mapping
Resolution56 micron
Notes

this atlas is derived from the atlas from [1] and version 1 contains inaccuracies

Version

1

Example slices from the anatomical MR and labels:

 

Dorr 2008 on the VVW Sert atlas

Derived from [1]. Details on this atlas:

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_VVW_Sert_v1_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/ex-vivo/Dorr_2008_on_VVW_Sert_v1_labels.mnc
Mapping of labels to structures (csv)same as male-female mapping
Mapping of labels to structures (pdf)same as male-female mapping
Resolution56 micron
Notes

this atlas is derived from the atlas from [1] and version 1 contains inaccuracies

Version

1

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.

 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/in-vivo-t2/Dorr_2008_on_in-vivo-t2_version_1_SIGNIFICANT_ERRORS_average.mnc

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/in-vivo-t2/Dorr_2008_on_in-vivo-t2_version_2_SIGNIFICANT_ERRORS_labels.mnc
Mapping of labels to structures (csv)/hpf/largeprojects/MICe/tools/atlases/Dorr_2008/in-vivo-t2/Dorr_2008_on_in-vivo-t2_mapping_of_labels.csv
Resolution125 micron
Notes

this atlas is derived from the atlas from [1]

The mapping is different from the ex-vivo mapping:

  • the stratum granulosum of the hippocampus is combined with the dentate gyrus of the hippocampus to form a single label
  • the fundus of the striatum is combined with the striatum to form a single label

Errors (among potential others...):

  • the right striatum is off around zslice 36
  • both hippocampi are off around zslice 33
  • the corpus callosum is off around zslice 48

Version

1

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
 Information
MR anatomy file/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013/in-vivo-MEMRI_90micron//

Label file

/hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013/in-vivo-MEMRI_90micron//
Mapping of labels to structures (csv)same as male-female mapping
Resolution125 micron
Notes

this atlas is derived from the atlas from [1] and contains inaccuracies because no manual adjustments have been performed. Given that the contrast in these brains is different from ex-vivo MRI (in the hippocampus and cerebellum for instance) the labels there are not correct

Version1

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