1718 (Mar 2026)

Data Release v1718 (March 7, 2026) is the fourth quarterly release of 2025.

This version ADDS the following tables

The following tables have updated status or entries, from VORTEX proofreading and annotations

The following tables from previous versions are included:

Information about the version 1718 release can be queried with the following:

# report timestamp metadata on the version of interest
client.materialize.get_version_metadata(1718)['time_stamp']
datetime.datetime(2026, 3, 7, 8, 10, 1, 190228, tzinfo=datetime.timezone.utc)

Multifeature Cell Type

Table name: cell_type_multifeature_combo

This table contains the results of a hierarchical classifier trained on a combo of dendritic, somatic, and spine features. Full features are used for cells with soma 50 microns from border, labels are propagated to other cells via 20-nearest neighbor in a reduced feature space of properties that had little median variation between cells close and far from dataset edges.

Excitatory subclasses are based on layer and projection class. Excitatory classes might not be physically within the layer in cases where clustering strongly associates cells with a different laminar population. Fine specification, as was in aibs_metamodel_mtypes_v661_v2 is forthcoming.

Inhibitory subclasses are inferred from characteristic proofread exemplars. This expands on the inhibitory classifications in aibs_metamodel_mtypes_v661_v2, combined from morphological characteristics.

Contact Casey Schneider-Mizell for use or questions

The key columns are:

Multifeature-Combo 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:

Multifeature-Combo: Cell Type definitions
Cell Type Subclass Description
L2IT Excitatory Layer 2 (upper layer 2/3) excitatory neurons that have local, intratelencephalic axon
L3IT Excitatory Layer 3 (lower layer 2/3) excitatory neurons that have local, intratelencephalic axon
L4IT Excitatory Layer 4 excitatory neurons that have local, intratelencephalic axon
L5IT Excitatory Layer 5 intratelencephalic cells
L5ET Excitatory Layer 5 extratelencephalic cells, with large somas and thick descending axon
L5NP Excitatory Layer 5 near-projecting cells, with sparse inputs and outputs
L6CT Excitatory Layer 6 intratelencephalic cells
L6IT Excitatory Layer 6 corticothalamic cells
MC Inhibitory Martinotti cells with layer 1 arbors
NMC Inhibitory Non-martinotti cells with dense arbors and dendrite targeting
DTC Inhibitory Dendrite targeting cells that cluster with MCs and NMCs but are not dense like NMCs. Mostly layer 6
ChC Inhibitory Chandelier cells
PV Inhibitory Morpholgical cluster containing proofread cells that are clearly parvalubmin positive non ChCs. Almost entirely basket cells.
ITC Inhibitory Inhibitory targeting cells with a typical preference toward putative SST subclasses
AltBasket Inhibitory AltBasket-Basket cells that cluster with VIP/Sncg cells rather than PV cells
AltDTC Inhibitory Dendrite targeting cells that cluster away from the clear putative SST cells
ITCperi Inhibitory Inhibitory targeting cells that mostly target basket cells, not putative SSTs
L1 Inhibitory Various layer 1 cells, mostly not Neurogliaform
NGC Inhibitory Neurogliaform cells across all layers. 
# Standard query
client.materialize.query_table('cell_type_multifeature_combo')

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

HKS Feature Spine Classification

Synapse Target Predictions

Table name: synapse_target_predictions_ssa_v2

This table contains synapse target structure predictions (‘soma’, ‘shaft’, ‘spine’) for synapses in synapses_pni_2. Predictions are currently available for the majority of cells predicted to be neurons by aibs_metamodel_mtypes_v661_v2. The predictions come from a model trained on synapse target annotations from ‘vortex_compartment_targets’ as well as some additional manual annotations where the model was failing.

The model is a random forest trained on spectral shape analysis features from the mesh. This model was trained to catch missing large spines and stubby spines relative to ‘synapse_target_predictions_ssa’. This is a straight replacement and update to ‘synapse_target_predictions_ssa’

Citation: https://www.biorxiv.org/content/10.64898/2026.02.19.706834

It contains the following columns:

Synapse target predictions column definitions
Column Description
pre_pt_position / pre_pt_supervoxel_id / pre_pt_root_id The bound spatial point data for the presynaptic side of the synapse.
post_pt_position / post_pt_supervoxel_id / post_pt_root_id The bound spatial point data for the postsynaptic side of the synapse.
size The size of the synapse in voxels. This correlates well, but not perfectly, with the surface area of synapse.
ctr_pt_position A position in the center of the detected synaptic junction. Of all points in the synapse table, this is usually the closest point to the surface (and thus mesh) of both neurons. Because it is at the edge of cells, it is not associated with a root id.
tag label of the post-synaptic structure, one of: spine, shaft, soma
Tip

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

# Standard query
client.materialize.query_table('synapse_target_predictions_ssa_v2', limit=10)

# Content-aware query
client.materialize.tables.synapse_target_predictions_ssa_v2(post_pt_root_id=example_root_id).query()

Synapse Spine Mapping

Table name: synapse_spine_mapping_v2

This table contains a mapping between synapses and the ID of the spine that they target. The spine predictions came from the model used to generate the table synapse_target_predictions_ssa_v2. The model is a random forest trained on spectral shape analysis features from the mesh. More information about the targeted spines will be added in a future release.

From this table you can query spine-predicted objects with more than one input synapse prediction. This makes it a full replacement for `multi_input_spine_predictions_ssa’.

Citation: https://www.biorxiv.org/content/10.64898/2026.02.19.706834

It contains the following columns:

Synapse target predictions column definitions
Column Description
pre_pt_position / pre_pt_supervoxel_id / pre_pt_root_id The bound spatial point data for the presynaptic side of the synapse.
post_pt_position / post_pt_supervoxel_id / post_pt_root_id The bound spatial point data for the postsynaptic side of the synapse.
size The size of the synapse in voxels. This correlates well, but not perfectly, with the surface area of synapse.
ctr_pt_position A position in the center of the detected synaptic junction. Of all points in the synapse table, this is usually the closest point to the surface (and thus mesh) of both neurons. Because it is at the edge of cells, it is not associated with a root id.
tag label of the post-synaptic structure, one of: spine, shaft, soma
Tip

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

# Standard query
client.materialize.query_table('synapse_spine_mapping_v2', limit=10)

# Content-aware query
client.materialize.tables.synapse_spine_mapping_v2(post_pt_root_id=example_root_id).query().value_counts('group_id')

Corrections tables

Table name: aibs_metamodel_celltypes_v661_corrections

This is a living table that contains cell_type label changes to cells in the table aibs_metamodel_celltypes_v661. The labels contain a “corrected” label using the anatomical cell-typing scheme outlined in (Elabbady et al. 2025). New cells will be added as more changes arise from continued manual efforts and evolving automated methods. This is a reference table on nucleus_detection_v0. Classification_system refers to the coarse class predictions and cell_type denotes nonneuronal class and neuronal subclass predictions. Errors and soma-soma mergers have been filtered out.

Table name: aibs_metamodel_mtypes_v661_v2_corrections

This is a living table that contains cell_type label changes to cells in the table aibs_metamodel_mtypes_v661_v2. The labels contain a “corrected” label using the anatomical cell-typing scheme outlined in (Schneider-Mizell et al. 2025). New cells will be added as more changes arise from continued manual efforts and evolving automated methods. This is a reference table on nucleus_detection_v0. Classification_system refers to the coarse class predictions and cell_type denotes nonneuronal class and neuronal subclass predictions. Errors and soma-soma mergers have been filtered out.

Both corrections tables are hierarchically incorporated in the super view of cell type: aibs_cell_info

# Standard query
client.materialize.query_view('aibs_cell_info')

# Content-aware query
client.materialize.views.aibs_cell_info(id=example_nucleus_id).query()

VORTEX Efforts

Proofreading Status and Strategy

Table name: proofreading_status_and_strategy

The table proofreading_status_and_strategy describes the status of cells that have undergone manual proofreading.

Because of the inherent difference in the difficulty and time required for different kinds of proofreading, we describe the status of axons and dendrites separately.

Each compartment status may be either:

  • FALSE: indicates no comprehensive proofreading has been performed, or is not applicable.
  • TRUE: indicates that false merges have been comprehensively removed, and the compartment is at least ‘clean’. Consult the strategy column if completeness of the compartment is relevant to your research.

An axon or dendrite labeled as status=TRUE can be trusted to be correct, but may not be complete. The degree of completion can be read from the strategy column. For more information, please see Proofreading and Data Quality; or also the microns-explorer page on proofreading strategies.

The key columns are:

Proofreading Status 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
valid_id The root id of the neuron when it the proofreading assessment was made. NOTE: if this does not match the pt_root_id then the cell has undergone further changes. This is usually and improvement in proofreading, but proceed with caution.
status_dendrite The status of the dendrite proofreading. May be TRUE or FALSE
status_axon The status of the axon proofreading. May be TRUE or FALSE
strategy_dendrite The strategy employed to proofread the dendrite. See strategy table below for details
strategy_axon The strategy employed to proofread the axon. See strategy table below for details

The specific strategies are as follows (and will update over time):

Proofreading Strategies

Proofreading Strategy Table
Strategy Description
none No cleaning, and no extension. Indicates an entry in proofreading_status that is FALSE for that compartment
dendrite_clean The dendrite had incorrectly-merged axon and dendritic segments comprehensively removed, meaning the input synapses are accurate. The dendrite may be incorrectly truncated by segmentation error. Not all dendrite tips have been checked for extension. No comprehensive attempt was made to re-attach spine heads.
dendrite_extended The dendrite had incorrectly-merged axon and dendritic segments comprehensively removed, meaning the input synapses are accurate. Every tip was identified, manually inspected, and extended if possible. No comprehensive attempt was made to re-attach spine heads.
axon_column_truncated AThe axon was extended within the V1 cortical column, with a preference for local connections. In some cases the axon was cut at the column boundary and/or the layer boundary, especially the boundary between layers 2/3 and layer 4. Output synapses represent a sampling of potential partners
axon_interareal The axon was extended with a preference for branches that projected to other brain areas. Some axon branches were fully extended, but local connections may be incomplete. Output synapses represent a sampling of potential partners.
axon_partially_extended The axon was extended outward from the soma, following each branch to its termination. Output synapses represent a sampling of potential partners.
axon_fully_extended Axon was extended outward from the soma, following each branch to its termination. After initial extension, every endpoint was identified, manually inspected, and extended again if possible. Output synapses represent a largely complete sampling of partners.

This table, proofreading_status_and_strategy, supercedes proofreading_status_public_release.

# Standard query
client.materialize.query_table('proofreading_status_and_strategy')

# Content-aware query
client.materialize.tables.proofreading_status_and_strategy(status_axon='t').query()
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References

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.
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.