List of Maps

This is a complete list of maps available in the neuromaps_mouse package.

Psychedelic drug activation maps (aboharb2025)

Regional brain activation maps following administration of various psychedelic compounds and controls, measured via whole-brain imaging.

Each file contains activation values for a single treatment condition: psychedelics (5-MeO, 6-F-DET, Ketamine, MDMA, Psilocybin), antidepressant controls (ASSRI, CSSRI), and saline control.

Available files

Description

Format

Key

5-MeO

tabular

('aboharb2025', '5meo', 'allenccfv3', 'region')

6-F-DET

tabular

('aboharb2025', '6fdet', 'allenccfv3', 'region')

ASSRI

tabular

('aboharb2025', 'assri', 'allenccfv3', 'region')

CSSRI

tabular

('aboharb2025', 'cssri', 'allenccfv3', 'region')

Ketamine

tabular

('aboharb2025', 'ket', 'allenccfv3', 'region')

MDMA

tabular

('aboharb2025', 'mdma', 'allenccfv3', 'region')

Psilocybin

tabular

('aboharb2025', 'psi', 'allenccfv3', 'region')

Saline

tabular

('aboharb2025', 'sal', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('aboharb2025', '5meo', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/aboharb2025

# region mapping files
# source-aboharb2025_regionmapping.csv

Cell type density atlas (ero2018)

A Cell Atlas for the Mouse Brain (Ero et al., 2018).

Provides density estimates of major cell types across Allen CCFv3 brain regions, derived from single-cell RNA sequencing and in situ hybridization data.

Available files

Description

Format

Key

Density of cell types

tabular

('ero2018', 'celldensity', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('ero2018', 'celldensity', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/ero2018

# region mapping files
# source-ero2018_regionmapping.csv

IBL behavioral and electrophysiology maps (ibl2025)

Regional brain maps from the International Brain Laboratory (IBL) reproducible brain-wide mapping pipeline.

Includes behavioral task performance metrics and electrophysiology summary statistics mapped to Allen CCFv3 regions.

Available files

Description

Format

Key

Behavioral task

tabular

('ibl2025', 'behtask', 'allenccfv3', 'region')

Electrophysiology

tabular

('ibl2025', 'ephys', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('ibl2025', 'behtask', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/ibl2025

# region mapping files
# source-ibl2025_regionmapping.csv

Brain microvasculature (ji2021)

Brain microvasculature has a common topology with local differences in geometry that match metabolic load (Ji et al., 2021).

Whole mouse brain microvasculature imaged, reconstructed, and analyzed at sub-micrometer resolution. Includes data from Ji et al. (2021), Kirst et al. (2020), and Todorov et al. (2020).

Each file contains region-level tabular data characterizing microvascular network properties across Allen CCFv3 regions.

Available files

Description

Format

Key

Ji 2021

tabular

('ji2021', 'ji2021', 'allenccfv3', 'region')

Kirst 2020

tabular

('ji2021', 'kirst2020', 'allenccfv3', 'region')

Todorov 2020

tabular

('ji2021', 'todorov2020', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('ji2021', 'ji2021', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/ji2021

# region mapping files
# source-ji2021_regionmapping.csv

High-resolution connectome model (knox2018)

A high-resolution data-driven model of the mouse connectome (Knox et al., 2018).

Provides region-by-region connectivity matrices at the Allen CCFv3 parcellation. Each matrix is asymmetric: rows are source regions and columns are target regions. Available for both ipsi- and contralateral projections, in connection density and connection strength variants, each with normalized versions.

Available files

Description

Format

Key

Connection density (contralateral)

matrix

('knox2018', 'conndencontra', 'allenccfv3', 'region')

Connection density (ipsilateral)

matrix

('knox2018', 'conndenipsi', 'allenccfv3', 'region')

Connection strength (contralateral)

matrix

('knox2018', 'connstrcontra', 'allenccfv3', 'region')

Connection strength (ipsilateral)

matrix

('knox2018', 'connstripsi', 'allenccfv3', 'region')

Normalized connection density (contralateral)

matrix

('knox2018', 'normconndencontra', 'allenccfv3', 'region')

Normalized connection density (ipsilateral)

matrix

('knox2018', 'normconndenipsi', 'allenccfv3', 'region')

Normalized connection strength (contralateral)

matrix

('knox2018', 'normconnstrcontra', 'allenccfv3', 'region')

Normalized connection strength (ipsilateral)

matrix

('knox2018', 'normconnstripsi', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('knox2018', 'conndencontra', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/knox2018

# region mapping files
# source-knox2018_regionmapping.csv

Allen Mouse Brain Atlas gene expression (lein2006amba)

Allen Mouse Brain Atlas (Lein et al., 2006) — regional gene expression data aggregated across sagittal and coronal sections.

For each section type (sagittal, coronal), three expression metrics are provided: energy, density, and intensity. Each file is a region-by-gene matrix where rows are Allen CCFv3 regions and columns are genes (see feature mapping file for gene names).

This is a large dataset; files are compressed (.csv.gz).

Warning

This is a very large dataset, and may take a long time to download.

Available files

Description

Format

Key

Expression energy of sagittal slices

tabular

('lein2006amba', 'sagittalenergy', 'allenccfv3', 'region')

Expression energy of coronal slices

tabular

('lein2006amba', 'coronalenergy', 'allenccfv3', 'region')

Expression density of sagittal slices

tabular

('lein2006amba', 'sagittaldensity', 'allenccfv3', 'region')

Expression density of coronal slices

tabular

('lein2006amba', 'coronaldensity', 'allenccfv3', 'region')

Expression intensity of sagittal slices

tabular

('lein2006amba', 'sagittalintensity', 'allenccfv3', 'region')

Expression intensity of coronal slices

tabular

('lein2006amba', 'coronalintensity', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('lein2006amba', 'sagittalenergy', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/lein2006amba

# region mapping files
# source-lein2006amba_regionmapping.csv

# feature mapping files
# source-lein2006amba_genemapping.csv

Cell-type-specific functional connectivity (mandino2025)

Cell-type-specific functional connectivity matrices from Mandino et al. (2025), combining calcium imaging and fMRI.

Files are organized by modality (calcium imaging: cal prefix, fMRI: fmri prefix), cell type (PV, VIP, SLC, SOM, glia), and whether global signal regression was applied (gsr = with GSR, nogsr = without GSR).

For example, calpvallgsr is the calcium imaging PV cell matrix with GSR. Each file is a region-by-region connectivity matrix. Region mappings differ between modalities.

Available files

Description

Format

Key

Calcium imaging PV with GSR

matrix

('mandino2025', 'calpvallgsr', 'allenccfv3', 'region')

Calcium imaging PV without GSR

matrix

('mandino2025', 'calpvallnogsr', 'allenccfv3', 'region')

Calcium imaging VIP with GSR

matrix

('mandino2025', 'calvipallgsr', 'allenccfv3', 'region')

Calcium imaging VIP without GSR

matrix

('mandino2025', 'calvipallnogsr', 'allenccfv3', 'region')

Calcium imaging SLC with GSR

matrix

('mandino2025', 'calslcallgsr', 'allenccfv3', 'region')

Calcium imaging SLC without GSR

matrix

('mandino2025', 'calslcallnogsr', 'allenccfv3', 'region')

Calcium imaging SOM with GSR

matrix

('mandino2025', 'calsomallgsr', 'allenccfv3', 'region')

Calcium imaging SOM without GSR

matrix

('mandino2025', 'calsomallnogsr', 'allenccfv3', 'region')

Calcium imaging glia with GSR

matrix

('mandino2025', 'calgliaallgsr', 'allenccfv3', 'region')

Calcium imaging glia without GSR

matrix

('mandino2025', 'calgliaallnogsr', 'allenccfv3', 'region')

fMRI PV with GSR

matrix

('mandino2025', 'fmripvallgsr', 'allenccfv3', 'region')

fMRI PV without GSR

matrix

('mandino2025', 'fmripvallnogsr', 'allenccfv3', 'region')

fMRI VIP with GSR

matrix

('mandino2025', 'fmrivipallgsr', 'allenccfv3', 'region')

fMRI VIP without GSR

matrix

('mandino2025', 'fmrivipallnogsr', 'allenccfv3', 'region')

fMRI SLC with GSR

matrix

('mandino2025', 'fmrislcallgsr', 'allenccfv3', 'region')

fMRI SLC without GSR

matrix

('mandino2025', 'fmrislcallnogsr', 'allenccfv3', 'region')

fMRI SOM with GSR

matrix

('mandino2025', 'fmrisomallgsr', 'allenccfv3', 'region')

fMRI SOM without GSR

matrix

('mandino2025', 'fmrisomallnogsr', 'allenccfv3', 'region')

fMRI glia with GSR

matrix

('mandino2025', 'fmrigliaallgsr', 'allenccfv3', 'region')

fMRI glia without GSR

matrix

('mandino2025', 'fmrigliaallnogsr', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('mandino2025', 'calpvallgsr', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/mandino2025

# region mapping files
# source-mandino2025_cal_regionmapping.csv
# source-mandino2025_fmri_regionmapping.csv

Homogeneous and voxel-scale connectivity models (nathan2026)

Connectivity matrices from Nathan et al. (2026) providing two complementary models of mouse brain connectivity.

The homogeneous model (hom) is a linear connectivity model via constrained optimization and linear regression, similar to Oh et al. (2014).

The voxel-scale model (vox) from Knox et al. (2018) performs Nadaraya-Watson regression to infer voxel-to-voxel connectivity, splitting the source space into 12 major brain divisions to prevent influence from adjacent divisions. The voxel-scale results are then regionalized into Allen CCFv3 regions.

Files are further organized by:

  • Laterality: ipsi (ipsilateral) or contra (contralateral)

  • Quality: orig (original methods) or qc (carefully QC-ed experiments providing a refined connectome)

  • Resolution: 211 (regions from Oh et al., 2014) or 291 (regions from Knox et al., 2018)

Each resolution has its own region mapping file (r211, r291).

Available files

Description

Format

Key

Homotopic ipsilateral QC at 211 region resolution

matrix

('nathan2026', 'homipsiqc211', 'allenccfv3', 'region')

Homotopic ipsilateral QC at 291 region resolution

matrix

('nathan2026', 'homipsiqc291', 'allenccfv3', 'region')

Homotopic ipsilateral original at 211 region resolution

matrix

('nathan2026', 'homipsiorig211', 'allenccfv3', 'region')

Homotopic ipsilateral original at 291 region resolution

matrix

('nathan2026', 'homipsiorig291', 'allenccfv3', 'region')

Homotopic contralateral QC at 211 region resolution

matrix

('nathan2026', 'homcontraqc211', 'allenccfv3', 'region')

Homotopic contralateral QC at 291 region resolution

matrix

('nathan2026', 'homcontraqc291', 'allenccfv3', 'region')

Homotopic contralateral original at 211 region resolution

matrix

('nathan2026', 'homcontraorig211', 'allenccfv3', 'region')

Homotopic contralateral original at 291 region resolution

matrix

('nathan2026', 'homcontraorig291', 'allenccfv3', 'region')

Voxelwise ipsilateral QC at 211 region resolution

matrix

('nathan2026', 'voxipsiqc211', 'allenccfv3', 'region')

Voxelwise ipsilateral QC at 291 region resolution

matrix

('nathan2026', 'voxipsiqc291', 'allenccfv3', 'region')

Voxelwise ipsilateral original at 211 region resolution

matrix

('nathan2026', 'voxipsiorig211', 'allenccfv3', 'region')

Voxelwise ipsilateral original at 291 region resolution

matrix

('nathan2026', 'voxipsiorig291', 'allenccfv3', 'region')

Voxelwise contralateral QC at 211 region resolution

matrix

('nathan2026', 'voxcontraqc211', 'allenccfv3', 'region')

Voxelwise contralateral QC at 291 region resolution

matrix

('nathan2026', 'voxcontraqc291', 'allenccfv3', 'region')

Voxelwise contralateral original at 211 region resolution

matrix

('nathan2026', 'voxcontraorig211', 'allenccfv3', 'region')

Voxelwise contralateral original at 291 region resolution

matrix

('nathan2026', 'voxcontraorig291', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('nathan2026', 'homipsiqc211', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/nathan2026

# region mapping files
# source-nathan2026_r211_regionmapping.csv
# source-nathan2026_r291_regionmapping.csv

Mesoscale structural connectome (oh2014)

A mesoscale connectome of the mouse brain (Oh et al., 2014).

Provides weighted connectivity strength, p-values, and projection distances for both ipsi- and contralateral projections across Allen CCFv3 regions.

Original source: Supplementary Table 3.

Available files

Description

Format

Key

Weighted ipsilateral strength index

matrix

('oh2014', 'wipsi', 'allenccfv3', 'region')

P values for wipsi

matrix

('oh2014', 'pvalipsi', 'allenccfv3', 'region')

Weighted contralateral strength index

matrix

('oh2014', 'wcontra', 'allenccfv3', 'region')

P values for wcontra

matrix

('oh2014', 'pvalcontra', 'allenccfv3', 'region')

Distance (mm) for ipsilateral projections

matrix

('oh2014', 'distipsi', 'allenccfv3', 'region')

Distance (mm) for contralateral projections

matrix

('oh2014', 'distcontra', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('oh2014', 'wipsi', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/oh2014

# region mapping files
# source-oh2014_regionmapping.csv

ABC Atlas MERFISH cell types and gene expression (yao2023abca)

Mouse whole-brain transcriptomic cell type atlas from the Allen Brain Cell Atlas (Yao et al., 2023), MERFISH dataset (C57BL6J-638850).

Gene expression files (*mean) are region-by-gene matrices averaged at three hierarchical levels: division (divi), structure (stru), and substructure (subs). imp prefix indicates imputed expression values.

Cell type files (*ct*) are region-by-cell-type matrices at four classification levels: class, subclass, supertype, cluster, each at the three hierarchical region levels.

Each hierarchical level uses its own region mapping file. Separate feature mapping files are provided for measured and imputed gene sets.

This is a large dataset; files may take a long time to download.

Warning

This is a very large dataset, and may take a long time to download.

Available files

Description

Format

Key

Average regional gene expressions at the division level

tabular

('yao2023abca', 'divimean', 'allenccfv3', 'region')

Average regional gene expressions at the structure level

tabular

('yao2023abca', 'strumean', 'allenccfv3', 'region')

Average regional gene expressions at the substructure level

tabular

('yao2023abca', 'subsmean', 'allenccfv3', 'region')

Average imputed regional gene expressions at the division level

tabular

('yao2023abca', 'impdivimean', 'allenccfv3', 'region')

Average imputed regional gene expressions at the structure level

tabular

('yao2023abca', 'impstrumean', 'allenccfv3', 'region')

Average imputed regional gene expressions at the substructure level

tabular

('yao2023abca', 'impsubsmean', 'allenccfv3', 'region')

Cell type (class) at the division level

tabular

('yao2023abca', 'divictclass', 'allenccfv3', 'region')

Cell type (class) at the structure level

tabular

('yao2023abca', 'structclass', 'allenccfv3', 'region')

Cell type (class) at the substructure level

tabular

('yao2023abca', 'subsctclass', 'allenccfv3', 'region')

Cell type (subclass) at the division level

tabular

('yao2023abca', 'divictsubclass', 'allenccfv3', 'region')

Cell type (subclass) at the structure level

tabular

('yao2023abca', 'structsubclass', 'allenccfv3', 'region')

Cell type (subclass) at the substructure level

tabular

('yao2023abca', 'subsctsubclass', 'allenccfv3', 'region')

Cell type (supertype) at the division level

tabular

('yao2023abca', 'divictsupertype', 'allenccfv3', 'region')

Cell type (supertype) at the structure level

tabular

('yao2023abca', 'structsupertype', 'allenccfv3', 'region')

Cell type (supertype) at the substructure level

tabular

('yao2023abca', 'subsctsupertype', 'allenccfv3', 'region')

Cell type (cluster) at the division level

tabular

('yao2023abca', 'divictcluster', 'allenccfv3', 'region')

Cell type (cluster) at the structure level

tabular

('yao2023abca', 'structcluster', 'allenccfv3', 'region')

Cell type (cluster) at the substructure level

tabular

('yao2023abca', 'subsctcluster', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('yao2023abca', 'divimean', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/yao2023abca

# region mapping files
# source-yao2023abca_division_regionmapping.csv
# source-yao2023abca_structure_regionmapping.csv
# source-yao2023abca_substructure_regionmapping.csv

# feature mapping files
# source-yao2023abca_merfish_genemapping.csv
# source-yao2023abca_imputed_genemapping.csv

ABC Atlas Zhuang-ABCA gene expression (zhang2023abca)

A molecularly defined and spatially resolved cell atlas of the whole mouse brain (Zhang et al., 2023, Zhuang-ABCA MERFISH).

Gene expression files are region-by-gene matrices averaged at three hierarchical levels: division (divi), structure (stru), and substructure (subs). Each level uses its own region mapping file.

This is a large dataset; files may take a long time to download.

Warning

This is a very large dataset, and may take a long time to download.

Available files

Description

Format

Key

Average regional gene expressions at the division level

tabular

('zhang2023abca', 'divimean', 'allenccfv3', 'region')

Average regional gene expressions at the structure level

tabular

('zhang2023abca', 'strumean', 'allenccfv3', 'region')

Average regional gene expressions at the substructure level

tabular

('zhang2023abca', 'subsmean', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('zhang2023abca', 'divimean', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/zhang2023abca

# region mapping files
# source-zhang2023abca_division_regionmapping.csv
# source-zhang2023abca_structure_regionmapping.csv
# source-zhang2023abca_substructure_regionmapping.csv

# feature mapping files
# source-zhang2023abca_merfish_genemapping.csv

Brain synaptome architecture (zhu2018)

Architecture of the Mouse Brain Synaptome (Zhu et al., 2018).

Provides synaptic type density measurements across Allen CCFv3 brain regions, characterizing the molecular and cellular composition of synapses throughout the mouse brain.

Available files

Description

Format

Key

Synaptic type density

tabular

('zhu2018', 'typedensity', 'allenccfv3', 'region')

How to use

# fetch a specific annotation
fetch_annotation(('zhu2018', 'typedensity', 'allenccfv3', 'region'))

# file location
# $MOUSEMAPS_DATA/zhu2018

# region mapping files
# source-zhu2018_regionmapping.csv