# report timestamp metadata on the version of interest
343)['time_stamp'] client.materialize.get_version_metadata(
datetime.datetime(2022, 2, 24, 8, 10, 0, 184668, tzinfo=datetime.timezone.utc)
Data Release v343 (February 24, 2022) is the first update to the public datastack.
This version ADDS the following tables
allen_v1_column_types_slanted
: manual annotations of neuron class and subclass in the V1 column
aibs_column_nonneuronal
: manual annotations of non-neuron cell types in the V1 column
aibs_soma_nuc_metamodel_preds_v117
: cell type predictions from an automated classifer on cells in the V1 column
func_unit_em_match_release
: a table of 200 EM centroids manually matched to Baylor unit_ids
in the functional scans
functional_coreg
: a table of 9608 EM centroids manually matched to Baylor unit_ids
in the functional scans
proofreading_status_public_release
: the proofreading status of cells in the dataset, including all neurons in the V1 column
A flat segmentation of the meshes is also available
The following tables from previous versions are included:
The following tables have been REMOVED (removed tables still available in version 117):
allen_soma_coarse_cell_class_model_v1
: removed and superseded by aibs_soma_nuc_metamodel_preds_v117
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)
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
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
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
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
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:
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 |
This table remains available from materialization versions: 343, 661, 795
This table is deprecated, use aibs_metamodel_celltypes_v661
instead.
Table name: func_unit_em_match_release
A table of 200 EM centroids manually matched to Baylor unit_ids
in the functional scans.
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.
This table remains available from materialization versions: 343
This table is deprecated, use coregistration_manual_v4
instead.
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:
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.
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.