343 (Feb 2022)

Data Release v343 (February 24, 2022) is the first update to the public datastack.

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 117):

Information about the version 343 release can be queried with the following:

# report timestamp metadata on the version of interest
client.materialize.get_version_metadata(343)['time_stamp']
datetime.datetime(2022, 2, 24, 8, 10, 0, 184668, tzinfo=datetime.timezone.utc)

Manual Cell Types (V1 Column)

Neurons

Table name: allen_v1_column_types_slanted

A subset of nucleus detections in a 100 um column (n=2204) in VISp were manually classified by anatomists at the Allen Institute into categories of cell subclasses, first distinguishing cells into classes of non-neuronal, excitatory and inhibitory; then into subclasses.

For the non-neuronal subclasses, see aibs_column_nonneuronal_ref

Deprecated table

This table remains available from materialization versions: 343

It is recommended to use allen_v1_column_types_slanted_ref instead, which indexes on a consistent nucleus_id

Non-neurons

Table name: aibs_column_nonneuronal

A subset of nucleus detections in a 100 um column (n=2204) in VISp were manually classified by anatomists at the Allen Institute into categories of cell subclasses, first distinguishing cells into classes of non-neuronal, excitatory and inhibitory; then into subclasses.

For the neuronal subclasses, see allen_v1_column_types_slanted_ref

Deprecated table

This table remains available from materialization versions: 343

It is recommended to use aibs_column_nonneuronal_ref instead, which indexes on a consistent nucleus_id

Automated cell-type classifier

Table name: aibs_soma_nuc_metamodel_preds_v117

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 117 of the dataset. For more details, see (Elabbady et al. 2025).

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
Deprecated table

This table remains available from materialization versions: 343, 661, 795

This table is deprecated, use aibs_metamodel_celltypes_v661 instead.

Coregistration

Table name: func_unit_em_match_release

A table of 200 EM centroids manually matched to Baylor unit_ids in the functional scans.

Deprecated table

This table remains available from materialization versions: 343

This table is deprecated, use coregistration_manual_v4 instead.

Table name: functional_coreg

A table of 9608 EM centroids manually matched to Baylor unit_ids in the functional scans.

Deprecated table

This table remains available from materialization versions: 343

This table is deprecated, use coregistration_manual_v4 instead.

Proofreading Status

Table name: proofreading_status_public_release

The table proofreading_status_public_release describes the status of cells selected for manual proofreading.

Because of the inherent difference in the challenge and time required for different kinds of proofreading, we describe the status of axons and dendrites separately. Further, we distinguish three different categories of proofreading:

  • non: No proofreading has been comprehensively performed.
  • clean: Proofreading has comprehensively removed false merges, but not necessarily added missing parts.
  • extended: Proofreading has comprehensively removed false merges and attempted to add all or most missing parts.

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
status_dendrite The status of the dendrite proofreading. One of the three categories described above
status_axon The status of the axon proofreading. One of the three categories described above

This table is deprecated and superseded by proofreading_status_and_strategy.

# Set version to 1078 or before
client.version = 1078

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

# Content-aware query
client.materialize.tables.proofreading_status_public_release(status_axon='extended').query()

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

Flat Segmentation

minnie65 flat segmentation v343
Name Volume Cloudpath Short Description Type (size)
Proofread Segmentation (v343) minnie65 https://storage.googleapis.com/iarpa_microns/minnie/minnie65/seg_m343 Mulit-resolution flat / static cellular segmentation voxels and meshes from 8,8,40 nm and above Precomputed Shareded Compressed Segmentation (12 TB)

This contains the fixed state of the cellular segmentation at each version, where each voxel has been assigned an ID which is unique to each cellular object at 8,8,40, along with downsampled versions. Not all objects have been proofread, but a summary of the most focused efforts on cells can be found in the proofreading status metadata. In addition the mesh folder contains meshes of each object available at 3 different levels of downsampling. Folder contains many files, for download use cloud-volume, tensor-store, for bulk download use igneous, AWS CLI or gsutil CLI.

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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.