...
- 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 areaet.al, 2018 – Mouse MRI shows brain areas relatively larger in males emerge before those larger in females
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 |
| Resolution | 40 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:
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- 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 |
| Resolution | 40 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)
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- 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 |
| Resolution | 40 micron |
| Notes | /hpf/largeprojects/MICe/tools/atlases/Dorr_2008_Steadman_2013_Ullmann_2013_Richards_2011_40micron/notes_on_DSUR_atlas |
| Version | 1 (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 |
| Resolution | 30 micron |
| Notes | The information about the olfactory bulbs is not fully present |
| Version | 1 |
Example slices from the anatomical MR and labels:
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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 |
| Resolution | 56 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:
...
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 |
| Resolution | 30 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 |
| Resolution | 56 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:
...
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 |
| Resolution | 56 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 |
| Resolution | 56 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 |
| Resolution | 56 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:
...
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 |
| Resolution | 125 micron |
| Notes | this atlas is derived from the atlas from [1] The mapping is different from the ex-vivo mapping:
Errors (among potential others...):
|
Version | 1 |
Example slices from the anatomical MR and labels:
In-vivo Manganese-enhanced magnetic resonance imaging (MEMRI) atlases
...
- 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 |
| Resolution | 125 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 |
| Version | 1 |
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