List of Maps
This is a complete list of maps available in the neuromaps_mouse package.
synaptome (zhu2018)
Full description
Architecture of the Mouse Brain Synaptome
zhu2018-typedensity-allenccfv3-region
Description: Synaptic type density
Format: tabular
How to use
# get annotation
fetch_annotation(source='zhu2018', desc='typedensity', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/zhu2018
# file name
# source-zhu2018_desc-typedensity_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-zhu2018_regionmapping.csv
zhu2018-similarity-allenccfv3-region
Description: Synaptic similarity
Format: matrix
How to use
# get annotation
fetch_annotation(source='zhu2018', desc='similarity', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/zhu2018
# file name
# source-zhu2018_desc-similarity_space-allenccfv3_res-region_matrix.csv
# region mapping file
# source-zhu2018_regionmapping.csv
References
structural connectome (oh2014)
Full description
A mesoscale connectome of the mouse brain
oh2014-wipsi-allenccfv3-region
Description: Weighted ipsilateral strength index
Format: matrix
How to use
# get annotation
fetch_annotation(source='oh2014', desc='wipsi', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/oh2014
# file name
# source-oh2014_desc-wipsi_space-allenccfv3_res-region_matrix.csv
# region mapping file
# source-oh2014_regionmapping.csv
oh2014-pvalipsi-allenccfv3-region
Description: P values for wipsi
Format: matrix
How to use
# get annotation
fetch_annotation(source='oh2014', desc='pvalipsi', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/oh2014
# file name
# source-oh2014_desc-pvalipsi_space-allenccfv3_res-region_matrix.csv
# region mapping file
# source-oh2014_regionmapping.csv
oh2014-wcontra-allenccfv3-region
Description: Weighted contralateral strength index
Format: matrix
How to use
# get annotation
fetch_annotation(source='oh2014', desc='wcontra', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/oh2014
# file name
# source-oh2014_desc-wcontra_space-allenccfv3_res-region_matrix.csv
# region mapping file
# source-oh2014_regionmapping.csv
oh2014-pvalcontra-allenccfv3-region
Description: P values for wcontra
Format: matrix
How to use
# get annotation
fetch_annotation(source='oh2014', desc='pvalcontra', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/oh2014
# file name
# source-oh2014_desc-pvalcontra_space-allenccfv3_res-region_matrix.csv
# region mapping file
# source-oh2014_regionmapping.csv
References
cell type density (ero2018)
Full description
A Cell Atlas for the Mouse Brain
ero2018-celldensity-allenccfv3-region
Description: Density of cell types
Format: tabular
How to use
# get annotation
fetch_annotation(source='ero2018', desc='celldensity', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/ero2018
# file name
# source-ero2018_desc-celldensity_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-ero2018_regionmapping.csv
References
Allen Mouse Brain Atlas (lein2006amba)
Full description
Allen Mouse Brain Atlas
lein2006amba-sagittalenergy-allenccfv3-region
Description: Expression energy of sagittal slices
Format: tabular
How to use
# get annotation
fetch_annotation(source='lein2006amba', desc='sagittalenergy', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/lein2006amba
# file name
# source-lein2006amba_desc-sagittalenergy_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-lein2006amba_regionmapping.csv
lein2006amba-coronalenergy-allenccfv3-region
Description: Expression energy of coronal slices
Format: tabular
How to use
# get annotation
fetch_annotation(source='lein2006amba', desc='coronalenergy', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/lein2006amba
# file name
# source-lein2006amba_desc-coronalenergy_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-lein2006amba_regionmapping.csv
References
ABC Atlas (MERFISH-C57BL6J-638850) (yao2023abca)
Full description
Mouse whole-brain transcriptomic cell type atlas (Hongkui Zeng)
yao2023abca-divimean-allenccfv3-region
Description: Average regional gene expressions at the division level
Format: tabular
How to use
# get annotation
fetch_annotation(source='yao2023abca', desc='divimean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/yao2023abca
# file name
# source-yao2023abca_desc-divimean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-yao2023abca_division_regionmapping.csv
yao2023abca-strumean-allenccfv3-region
Description: Average regional gene expressions at the structure level
Format: tabular
How to use
# get annotation
fetch_annotation(source='yao2023abca', desc='strumean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/yao2023abca
# file name
# source-yao2023abca_desc-strumean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-yao2023abca_structure_regionmapping.csv
yao2023abca-subsmean-allenccfv3-region
Description: Average regional gene expressions at the substructure level
Format: tabular
How to use
# get annotation
fetch_annotation(source='yao2023abca', desc='subsmean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/yao2023abca
# file name
# source-yao2023abca_desc-subsmean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-yao2023abca_substructure_regionmapping.csv
yao2023abca-impdivimean-allenccfv3-region
Description: Average imputed regional gene expressions at the division level
Format: tabular
How to use
# get annotation
fetch_annotation(source='yao2023abca', desc='impdivimean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/yao2023abca
# file name
# source-yao2023abca_desc-impdivimean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-yao2023abca_division_regionmapping.csv
yao2023abca-impstrumean-allenccfv3-region
Description: Average imputed regional gene expressions at the structure level
Format: tabular
How to use
# get annotation
fetch_annotation(source='yao2023abca', desc='impstrumean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/yao2023abca
# file name
# source-yao2023abca_desc-impstrumean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-yao2023abca_structure_regionmapping.csv
yao2023abca-impsubsmean-allenccfv3-region
Description: Average imputed regional gene expressions at the substructure level
Format: tabular
How to use
# get annotation
fetch_annotation(source='yao2023abca', desc='impsubsmean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/yao2023abca
# file name
# source-yao2023abca_desc-impsubsmean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-yao2023abca_substructure_regionmapping.csv
References
ABC Atlas (Zhuang-ABCA) (zhang2023abca)
Full description
A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Xiaowei Zhuang)
zhang2023abca-divimean-allenccfv3-region
Description: Average regional gene expressions at the division level
Format: tabular
How to use
# get annotation
fetch_annotation(source='zhang2023abca', desc='divimean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/zhang2023abca
# file name
# source-zhang2023abca_desc-divimean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-zhang2023abca_division_regionmapping.csv
zhang2023abca-strumean-allenccfv3-region
Description: Average regional gene expressions at the structure level
Format: tabular
How to use
# get annotation
fetch_annotation(source='zhang2023abca', desc='strumean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/zhang2023abca
# file name
# source-zhang2023abca_desc-strumean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-zhang2023abca_structure_regionmapping.csv
zhang2023abca-subsmean-allenccfv3-region
Description: Average regional gene expressions at the substructure level
Format: tabular
How to use
# get annotation
fetch_annotation(source='zhang2023abca', desc='subsmean', space='allenccfv3', res='region')
# file location
# $MOUSEMAPS_DATA/zhang2023abca
# file name
# source-zhang2023abca_desc-subsmean_space-allenccfv3_res-region_tabular.csv
# region mapping file
# source-zhang2023abca_substructure_regionmapping.csv
References