1300 (Jan 2025)

Data Release v1300 (January 13, 2025) is the first quarterly release of 2025.

This version ADDS the following tables

It includes all other tables as of v1181, with the following exceptions (removed tables still available in version 1181):

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

Synapse-target classifier

Table name: synapse_target_predictions_ssa

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. Current failure modes include some stubby spines being predicted as shafts, and some very thin dendrites being classified as spines.

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 IThe 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', limit=10)

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

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

Automated Coregistration

Table name: coregistration_auto_phase3_fwd_apl_vess_combined_v2

A table of EM nucleus centroids automatically matched to Baylor functional units. This table reconciles the following two tables that both make a best match of the of registration using different techniques: coregistration_auto_phase3_fwd_v2 and apl_functional_coreg_vess_fwd. A unique functional unit is identified by its session, scan_idx and unit_id. An EM nucleus centroid may have matched to more than one functional unit if it was scanned on more than one imaging field.

The key columns are:

Coregistration 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
session The session index from functional imaging
scan_idx The scan index from functional imaging
unit_id The functional unit index from imaging. Only unique within scan and session
field The field index from functional imaging
residual The residual distance between the functional and the assigned structural points after transformation, in microns
score A separation score, measuring the difference between the residual distance to the assigned neuron and the distance to the nearest non-assigned neuron, in microns. This can be negative if the non-assigned neuron is closer than the assigned neuron. Larger values indicate fewer nearby neurons that could be confused with the assigned neuron.
Tip

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

Warning

This table includes duplicate entries for the same pt_root_id and nucleus id if the coregistered cell has multiple unit recordings

# Standard query
client.materialize.query_table('coregistration_auto_phase3_fwd_apl_vess_combined_v2')

# Content-aware query
client.materialize.tables.coregistration_auto_phase3_fwd_apl_vess_combined_v2(id=example_nucleus_id).query()

This table coregistration_auto_phase3_fwd_apl_vess_combined_v2 supercedes previous iterations of this table:

  • coregistration_auto_phase3_fwd_apl_vess_combined_v2
  • apl_functional_coreg_forward_v5

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

Publication: Gamlin et al.

Martinotti cells

Table name: gamlin_2023_mcs

A table containing the manually selected Martinotti cells (MC) included in Gamlin et al., 2023 paper.

The key columns are:

Gamlin et al. Martinotti cells
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 allen_cortex_inhibitory.
cell_type Martinotti
Tip

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

# Standard query
client.materialize.query_table('gamlin_2023_mcs')

# Content-aware query
client.materialize.tables.gamlin_2023_mcs(id=example_nucleus_id).query()

Martinotti cell synaptic targets

Table name: cg_cell_type_calls

Manual cell type calls on the targets of L5 Martinotti cells (MC) in gamlin_2023_mcs, annotated for Gamlin et al., 2023 paper.

It contains the following columns:

Gamlin et al. Martinotti targets
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 IThe 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.
classification_system cg_calls
cell_type The excitatory subtype or inhibitory type of the target. One of: ‘1P’, ‘23P’, ‘4P’, ‘5P_IT’, ‘5P_PT’, ‘5P_NP’, ‘6P’, ‘INH’
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('cg_cell_type_calls')

# Content-aware query
client.materialize.tables.cg_cell_type_calls(pre_pt_root_id=example_root_id).query()

Martinotti cell MET-types

Table name: gamlin_2023_mcs_met_types

A table matching Martinotti cells (MC) included in Gamlin et al., 2023 paper to link the EM and MET-types (morphology, electrophysiology, transcriptomic cell types).

The key columns are:

Gamlin et al. Martinotti MET types
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
tag predicted MET-type label
value prediction reliability from the MET-type classifier, specifically the fraction of times that the cell was classified under that MET-type label in all the folds of the cross-validation
Tip

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

# Standard query
client.materialize.query_table('gamlin_2023_mcs_met_types')

# Content-aware query
client.materialize.tables.gamlin_2023_mcs_met_types(id=example_nucleus_id).query()

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

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()

VORTEX synapse compartments

Table name: vortex_compartment_targets

Manual labeling of synaptic targets of putative parvalbumin basket cells, and inputs to pyramidal cells as part of the VORTEX project. This is a reference table on the synapses table synapses_pni_2, and provided ground truth for the automatic classifier behind synapse_target_predictions_ssa.

Proofreading Status Table
Column Description
target_id reference id of the synapse in synapses_pni_2
tag Manual label of synapse type. One of: ‘spine’, ‘shaft’, ‘soma’, ‘soma_spine’, ‘orphan’, ‘other’. Orphan refers to orphan neurites; other is a catch-all for synapses that do not match other labels
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
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('vortex_compartment_targets', limit=10)

# Content-aware query
client.materialize.tables.vortex_compartment_targets(pre_pt_root_id=example_root_id).query()

VORTEX manual myelin

Table name: vortex_manual_myelination_v0

Manual labeling of myelin at 1 um resolution along axons, as part of the VORTEX project. This table was created in parallel to the node of Ranvier labeling, vortex_manual_nodes_of_ranvier, and used for ground truth of the myelin_auto_tags myelination classifier.

Manual Myelination
Column Description
pt_position The position along the axon that was evaluated for myelin. Note that this position is not always on the segmentation of the axon
valid_id The segmentation root_id associated with this assessment is the valid_id, NOT necessarily the pt_root_id associated with the point
tag Myelination status, either True or False
pt_supervoxel_id  pt_root_id The bound spatial point data for the evaluated point. This may not match the valid_id due to proofreading, or spatial downsampling when evaluating the points.
Warning

The myelination was evaluated for the valid_id and not necessarily the pt_root_id.

# Standard query
client.materialize.query_table('vortex_manual_myelination_v0', limit=10)

# Content-aware query
client.materialize.tables.vortex_manual_myelination_v0(valid_id=example_root_id).query()

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

Back to top