Every Step from Experiment to Insight
Launch into the Platform
with Your Region of Interest
Cerebellum
Examine sub-structures of the cerebellum
Find cerebellum in Allen Human Brain Atlas Microarray
Explore cell types in the cerebellum:
- >100k cells in adult human (snRNA-seq)
Find related areas in the:
Cerebral cortex
Examine sub-structures of the cerebral cortex
Find cerebral cortex in Allen Human Brain Atlas Microarray
Explore cell types in the cerebral cortex:
- >1.3M cells in adult human (snRNA-seq)
Find cortical areas in the:
- Allen Human Brain Atlas ISH
- Developing Human Brain Atlas ISH
- Developing Human Brain Atlas Transcriptome
- Aging, Dementia and TBI dataset
- Autism dataset
Explore cell types in cortical areas:
- >2.7M cells in adult human w/ AD (snRNA-seq)
- >302 cells in adult human w/ AD (spatial transcriptomics)
- 1.7M cells in adult human w/ Parkinsons (single nucleus and PolyA RNA-seq)
- 128 cell types with multi-modal features in adult primary motor cortex
- Additional morphologic reconstructions and electrophysiology recordings
Cerebral nuclei
Examine sub-structures of the cerebral nuclei
Find cerebral nuclei in Allen Human Brain Atlas Microarray
Explore cell types in the cerebral nuclei:
- >250k cells in adult human (snRNA-seq)
Find related areas in the:
Hypothalamus
Examine sub-structures of the hypothalamus
Find hypothalamus in Allen Human Brain Atlas Microarray
Explore cell types in the hypothalamus:
- >130k cells in adult human (snRNA-seq)
Find related areas in the:
Midbrain
Examine sub-structures of the midbrain
Find midbrain in Allen Human Brain Atlas Microarray
Explore cell types in the midbrain:
- >248k cells in adult human (snRNA-seq)
Find related areas in the:
Thalamus
Examine sub-structures of the thalamus
Find thalamus in Allen Human Brain Atlas Microarray
Explore cell types in the thalamus:
- >340k cells in adult human (snRNA-seq)
Find related areas in the:
White matter
Examine white matter in the forebrain, midbrain, and hindbrain
Find white matter in Allen Human Brain Atlas Microarray
Find related areas in the:
Medulla oblongata
Examine sub-structures of the medulla
Find medulla in Allen Human Brain Atlas Microarray
Explore cell types in the medulla:
- >85k cells in adult human (snRNA-seq)
Find related areas in the:
Pons
Examine sub-structures of the pons
Find pons in Allen Human Brain Atlas Microarray
Explore cell types in the pons:
- >200k cells in adult human (snRNA-seq)
Find related areas in the:
Cerebellum
We currently don't have resources to highlight for this region of interest. Contact us if you're interested in adding your data on the Brain Knowledge Platform to enhance its data coverage.
Medulla oblongata
We currently don't have resources to highlight for this region of interest. Contact us if you're interested in adding your data on the Brain Knowledge Platform to enhance its data coverage.
Midbrain
We currently don't have resources to highlight for this region of interest. Contact us if you're interested in adding your data on the Brain Knowledge Platform to enhance its data coverage.
Pons
We currently don't have resources to highlight for this region of interest. Contact us if you're interested in adding your data on the Brain Knowledge Platform to enhance its data coverage.
Cerebral cortex
Explore cell types in cortical areas:
- 94 cell types with multi-modal features in adult primary motor cortex (Marmoset)
Find cortical areas in:
Hypothalamus
We currently don't have resources to highlight for this region of interest. Contact us if you're interested in adding your data on the Brain Knowledge Platform to enhance its data coverage.
Cerebellum
Examine sub-structures of the cerebellum
Find cerebellum in Allen Mouse Brain Atlas ISH
Explore cell types in the cerebellum:
- >560k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >320k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the cerebellum
Cortical subplate
Examine sub-structures of the cortical subplate
Find cortical subplate in Allen Mouse Brain Atlas ISH
Explore cell types in the cortical subplate:
- >XXXk cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >XXXk from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the cortical subplate
Hippocampal formation
Examine sub-structures of the hippocampal formation
Find hippocampal formation in Allen Mouse Brain Atlas ISH
Explore cell types in the hippocampal formation:
- >480k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >140k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the hippocampal formation
Hypothalamus
Examine sub-structures of the hypothalamus
Find hypothalamus in Allen Mouse Brain Atlas ISH
Explore cell types in the hypothalamus:
- >490k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >38k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the hypothalamus
Isocortex
Examine sub-structures of the isocortex
Explore cell types in the isocortex:
- > 2M cells from adult mouse (scRNA-seq and spatial transcriptomics)
- 281K cells from aged mouse (scRNA-seq)
- 116 cell types with multi-modal features in adult primary motor cortex
- Additional morphologic reconstructions and electrophysiology recordings
Browse genetic tools that label parts of isocortex
Medulla
Examine sub-structures of the medulla
Find medulla in Allen Mouse Brain Atlas ISH
Explore cell types in the medulla:
- >340k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >81k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the medulla
Midbrain
Examine sub-structures of the midbrain
Find midbrain in Allen Mouse Brain Atlas ISH
Explore cell types in the midbrain:
- >640k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >100k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the midbrain
Olfactory areas
Examine sub-structures of the olfactory areas
Find olfactory areas in Allen Mouse Brain Atlas ISH
Explore cell types in the olfactory areas:
- >350k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >170k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the olfactory areas
Pallidum
Examine sub-structures of the pallidum
Find pallidum in Allen Mouse Brain Atlas ISH
Explore cell types in the pallidum:
- >180k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >25k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the pallidum
Pons
Examine sub-structures of the pons
Find pons in Allen Mouse Brain Atlas ISH
Explore cell types in the pons:
- >280k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >43k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the pons
Striatum
Examine sub-structures of the striatum
Find striatum in Allen Mouse Brain Atlas ISH
Explore cell types in the striatum:
- >500k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >140k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the striatum
Thalamus
Examine sub-structures of the thalamus
Find thalamus in Allen Mouse Brain Atlas ISH
Explore cell types in the thalamus:
- >490k cells from adult mouse (scRNA-seq and spatial transcriptomics)
- >130k from adult mouse (spatial transcriptomics)
Browse genetic tools that label parts of the thalamus
Fiber tracts
Examine sub-structures of the fiber tracts
Explore cell types in the fiber tracts:
- >78k cells from adult mouse (spatial transcriptomics, coronal)
- >112k from adult mouse (spatial transcriptomics, sagittal)
Get Started and Get Help
Access tutorials and how-to resources to get you started using data and tools in the Brain Knowledge Platform.
Access documentation for the Brain Knowledge Platform's data and tools.
Use community forum to get your questions answered by the Allen Institute or others in the community.