795 (Aug 2023)

Data Release v795 (August 23, 2023) is the first quarterly release of 2024.

This version ADDS the following tables

The following tables from previous versions are included:

The following tables have been REMOVED (removed tables still available in version 661):

# report timestamp metadata on the version of interest
client.materialize.get_version_metadata(795)['time_stamp']
datetime.datetime(2023, 8, 23, 8, 10, 1, 404268, tzinfo=datetime.timezone.utc)

Automated Cell types

Soma and nucleus model

Table name: aibs_metamodel_celltypes_v661

This table contains the results of a hierarchical classifier trained on features of the cell body and nucleus of cells. This was applied to most cells in the dataset that had complete cell bodies (e.g. not cut off by the edge of the data), detected by nucleus_detection_v0, with small-objects and multi-soma errors removed. The model was run with cell-based features as of version 661 of the dataset. For more details, see (Elabbady et al. 2025). In general, this does a good job, but sometimes confuses layer 5 inhibitory neurons as being excitatory:

The key columns are:

AIBS Soma Nuc Metamodel Table
Column Description
id Soma ID for the cell
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
classification-system One of excitatory_neuron or inhibitory_neuron for detected neurons, or nonneuron for non-neurons (glia/pericytes).
cell_type One of several cell types, detailed below
Tip

This is a reference table on nucleus_detection_v0, and can be indexed by the same nucleus id.

The cell types in the table are:

AIBS Soma Nuc Metamodel: Cell Type definitions
Cell Type Subclass Description
23P Excitatory Layer 2/3 cells
4P Excitatory Layer 4 cells
5P-IT Excitatory Layer 5 intratelencephalic cells
5P-ET Excitatory Layer 5 extratelencephalic cells
5P-NP Excitatory Layer 5 near-projecting cells
6P-IT Excitatory Layer 6 intratelencephalic cells
6P-CT Excitatory Layer 6 corticothalamic cells
BC Inhibitory Basket cell
BPC Inhibitory Bipolar cell. In practice, this was used for all cells thought to be VIP cell, not only those with a bipolar dendrite
MC Inhibitory Martinotti cell. In practice, this label was used for all inhibitory neurons that appeared to be Somatostatin cell, not only those with a Martinotti cell morphology
NGC Inhibitory Neurogliaform cell. In practice, this label also is used for all inhibitory neurons in layer 1, many of which may not be neurogliaform cells although they might be in the same molecular family
OPC Non-neuronal Oligodendrocyte precursor cell
astrocyte Non-neuronal Astrocyte
microglia Non-neuronal Microglia
pericyte Non-neuronal Pericyte
oligo Non-neuronal Oligodendrocyte 
# Standard query
client.materialize.query_table('aibs_metamodel_celltypes_v661')

# Content-aware query
client.materialize.tables.aibs_metamodel_celltypes_v661(id=example_nucleus_id).query()

For more on how to interpret the table, see Annotation Tables.

Dendritic features and connectivity motifs

Table name: aibs_metamodel_mtypes_v661_v2

Excitatory neurons and inhibitory neurons were distinguished with the soma-nucleus model (Elabbady et al. 2025), and subclasses were assigned based on a data-driven clustering of the neuronal features. Inhibitory neurons were classified based on how they distributed they synaptic outputs onto target cells, while exictatory neurons were classified based on a collection of dendritic features.

This was applied to most detected neurons in the dataset that had complete cell bodies (e.g. not cut off by the edge of the data), detected by nucleus_detection_v0, with small-objects and multi-soma errors removed. The model was run with cell-based features as of version 661 of the dataset.For more details, see (Schneider-Mizell et al. 2025).

Note that all cell-type labels in this table come from a clustering specific to this paper, and while they are intended to align with the broader literature they are not a direct mapping or a well-established convention.

For a more conventional set of labels on the same set of cells, look at the manual table allen_v1_column_types_slanted_ref. Cell types in that table align with those in the aibs_metamodel_celltypes_v661.

The key columns are:

Allen Motif-type (mtype) Table
Column Description
id Soma ID for the cell
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
classification-system excitatory or inhibitory
cell_type One of several cell types, detailed below
Tip

This is a reference table on nucleus_detection_v0, and can be indexed by the same nucleus id.

The cell types in the table are:

Cell Type Subclass Description
L2a Excitatory A cluster of layer 2 (upper layer 2/3) excitatory neurons
L2b Excitatory A cluster of layer 2 (upper layer 2/3) excitatory neurons
L3a Excitatory A cluster of excitatory neurons transitioning between upper and lower layer 2/3
L3b Excitatory A cluster of layer 3 (upper layer 2/3) excitatory neurons
L3c Excitatory A cluster of layer 3 (upper layer 2/3) excitatory neurons
L4a Excitatory The largest cluster of layer 4 excitatory neurons
L4b Excitatory Another cluster of layer 4 excitatory neurons
L4c Excitatory A cluster of layer 4 excitatory neurons along the border with layer 5
L5a Excitatory A cluster of layer 5 IT neurons at the top of layer 5
L5b Excitatory A cluster of layer 5 IT neurons throughout layer 5
L5ET Excitatory The cluster of layer 5 ET neurons
L5NP Excitatory The cluster of layer 5 NP neurons
L6a Excitatory A cluster of layer 6 IT neurons at the top of layer 6
L6b Excitatory A cluster of layer 6 IT neurons throughout layer 6. Note that this is different than the label “Layer 6b” which refers to a narrow band at the border between layer 6 and white matter
L6c Excitatory A cluster of tall layer 6 cells (unsure if IT or CT)
L6CT Excitatory A cluster of tall layer 6 cells matching manual CT labels
L6wm Excitatory A cluster of layer 6 cells along the border with white matter
PTC Inhibitory Perisomatic targeting cells, a cluster of inhibitory neurons that target the soma and proximal dendrites of excitatory neurons. Approximately corresponds to basket cell
DTC Inhibitory Dendrite targeting cells, a cluster of inhibitory neurons that target the distal dendrites of excitatory neurons. Most SST cells would be DTC
STC Inhibitory Sparsely targeting cells, a cluster of inhibitory neurons that don’t concentrate multiple synapses onto the same target neurons. Many neurogliaform cells and layer 1 interneurons fall into this category
ITC Inhibitory Inhibitory targeting cells, a cluster of inhibitory neurons that preferntially target other inhibitory neurons. Most VIP cells would be ITCs 
# Standard query
client.materialize.query_table('aibs_metamodel_mtypes_v661_v2')

# Content-aware query
client.materialize.tables.aibs_metamodel_mtypes_v661_v2(id=example_nucleus_id).query()

Dendritic features and connectivity motifs of V1 column

Table name: allen_column_mtypes_v2

This table contains the anatomical cell type clusters (m-types) for the Minnie columnar sample described in (Schneider-Mizell et al. 2025).

The key columns are:

Allen Motif-type (mtype) Table
Column Description
id Soma ID for the cell
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
classification-system excitatory or inhibitory
cell_type One of several cell types, detailed in the reference
Tip

Consider using aibs_metamodel_mtypes_v661_v2 instead, which is the same model run across the entire dataset.

For more on how to interpret the table, see Annotation Tables.

Manual Cell types

manual cell typing outside V1 column

Table name: allen_minnie_extra_types

This is a table to store extra manual cell typing that the Allen Insitute has done outside the column, in relation to several papers including: (Elabbady et al. 2025), (Schneider-Mizell et al. 2025), (Gamlin et al. 2025), and (Bodor, Agnes L. et al. 2023).

Allen Extra Manual Cell Types Table
Column Description
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
classification-system aibs_coarse_neuronal,aibs_coarse_excitatory, 'aibs_coarse_excitatory,aibs_coarse_inhibitory| |cell_type| One of several cell types, depending on theclassification-system`
Tip

This working table is only available from materialization version 795

Publication: Bodor et al.

L5 extratelencephalic cells

Table name: l5et_column

All the Layer 5 extratelencephalic cells in the V1 column used for (Bodor, Agnes L. et al. 2023)

The key columns are:

Bodor et al. L5ET
Column Description
id Soma ID for the cell
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
Tip

This is a reference table on nucleus_detection_v0, and can be indexed by the same nucleus id.

L5 pyramidal tract cells

Table name: bodor_pt_cells

Pyramidal tract Layer 5 cells used for (Bodor, Agnes L. et al. 2023)

The key columns are:

Bodor et al. L5PT
Column Description
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
classification-system is layer5_pt for all entries in the table
cell_type brain area of the cell body, one of: primary visual cortex v1 or higher visual areas hva

Targets of L5 PT cells

Table name: pt_synapse_targets

Target classification of a subset of downstream synaptic partners of PT cells in the bodor_pt_cells table, used for (Bodor, Agnes L. et al. 2023).

The key columns are:

Bodor et al. L5PT Targets
Column Description
id Soma ID for the cell
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
classification-system One of excitatory, inhibitory, error.
cell_type Subclass label or none
Tip

This is a reference table on synapses_pni_2, and can be indexed by the same synapse id.

Proofread targets of L5 PT cells

Table name: bodor_pt_target_proofread

A proofread collection of numerically strong BC and MC targets downstream of the L5-ET cells in the bodor_pt_cells table, used for (Bodor, Agnes L. et al. 2023).

The key columns are:

Bodor et al. L5PT Targets, proofread
Column Description
id Soma ID for the cell
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the cell nucleus
classification-system proofread_inhib_target for all entries.
cell_type Inhibitory subclass, one of: BC or MC
Tip

This is a reference table on nucleus_neuron_svm, and can be indexed by the same nucleus id.

Count of cell edits

Table name: cell_edits_v661

A count of how many proofreading edits were made to each cell, one entry for every nucleus that had a valid id, calculated at v661.

The key columns of are:

Cell edit at v661
Column Description
id Soma ID for the cell
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the nucleus
group_id The number of edits at v661
Tip

This is a reference table on nucleus_detection_v0, and can be indexed by the same nucleus id.

This working table is only available from materialization version 795

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References

Bodor, Agnes L., Schneider-Mizell, Casey M., Zhang, Chi, Elabbady, Leila, Mallen, Alex, Bergeson, Andi, Brittain, Derrick, et al. 2023. “The Synaptic Architecture of Layer 5 Thick Tufted Excitatory Neurons in the Visual Cortex of Mice.” bioRxiv. https://doi.org/10.1101/2023.10.18.562531.
Elabbady, Leila, Sharmishtaa Seshamani, Shang Mu, Gayathri Mahalingam, Casey M. Schneider-Mizell, Agnes L. Bodor, J. Alexander Bae, et al. 2025. “Perisomatic Ultrastructure Efficiently Classifies Cells in Mouse Cortex.” Nature 640 (8058): 478–86. https://doi.org/10.1038/s41586-024-07765-7.
Gamlin, Clare R., Casey M. Schneider-Mizell, Matthew Mallory, Leila Elabbady, Nathan Gouwens, Grace Williams, Alice Mukora, et al. 2025. “Connectomics of Predicted Sst Transcriptomic Types in Mouse Visual Cortex.” Nature 640 (8058): 497–505. https://doi.org/10.1038/s41586-025-08805-6.
Schneider-Mizell, Casey M., Agnes L. Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Leila Elabbady, Clare Gamlin, et al. 2025. “Inhibitory Specificity from a Connectomic Census of Mouse Visual Cortex.” Nature 640 (8058): 448–58. https://doi.org/10.1038/s41586-024-07780-8.