1078 (Jun 2024)

Data Release v1078 (June 5, 2024) is the second quarterly release of 2024.

This version ADDS the following tables

The following tables from previous versions are included:

Information about the version 1078 release can be queried with the following:

# report timestamp metadata on the version of interest
client.materialize.get_version_metadata(1078)['time_stamp']
datetime.datetime(2024, 6, 5, 10, 10, 1, 203215, tzinfo=datetime.timezone.utc)

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 proofread astrocytes

Table name: vortex_astrocyte_proofreading_status

Manual screening and proofreading of astrocytes as part of the as part of the VORTEX project.

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
status One of ‘non’ indicating no cleaning or extension; ‘clean’ indicating neurite and non-astrocytic elements have been manually removed; ‘extended’ meaning astrocytic processes within the volume of the astrocyte have been comprehensively reviewed and assigned to the most likely cell
valid_id The root id of the astrocyte when it the proofreading assessment was made 
# Standard query
client.materialize.query_table('vortex_astrocyte_proofreading_status')

# Content-aware query
client.materialize.tables.vortex_astrocyte_proofreading_status(status='clean').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()

VORTEX nodes of Ranvier

Table name: vortex_manual_nodes_of_ranvier

This table annotates manually identified nodes of Ranvier on the axon of a subset of cells. Each point listed was inspected and manually labeled for the presence of myelin; nodes were suggested where myelination disappeared and reappeared within 5 um. Labeling performed as part of the VORTEX project, and created in parallel to the myelin labeling, listed below as vortex_manual_myelination_v0.

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 presence of a node of Ranvier, labeled as node
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_nodes_of_ranvier')

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

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

Functional area nucleus look-up

Table name: nucleus_functional_area_assignment

Given the nucleus detection table nucleus_detection_v0 and the transformation of 2-photon in vivo imaging to the EM structural space (see functional-coregistration-tables ), each cell in the volume has been assigned to one of four visual cortical areas.

The inferred functional brain area based on the position of the nucleus in the EM volume. Area boundaries estimated from the area-membership assignments of the 2P recorded cells, after transformation to EM space.

The table nucleus_functional_area_assignment is a reference table on nucleus_detection_v0 and adds the following columns:

Functional area assignment
Column Description
target_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
tag the brain area label (one of V1, AL, RL, LM)
value the distance to the area boundary (in um), calculated as the mean-distance of the 10 nearest neighbors in a non-matching brain area. A larger value is further from the area boundaries, and can be interpretted as higher confidence in area assignment.
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('nucleus_functional_area_assignment')

# Content-aware query
client.materialize.tables.nucleus_functional_area_assignment(tag='V1').query()

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

Synapse target structure

Table name: synapse_target_structure

Postsynaptic structure classification for individual synapses by Brendan Celii and Jacob Reimer at Baylor College of Medicine based on mesh structure and initial synapse detection and classification.

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.
value Each synapse has a value from 0-6 indicating spine, shaft, or other target compartments. 0 : Synapse onto spine head 1 : Synapse onto spine neck 2 : Synapse onto dendritic shaft 3 : Synapse onto spine but no clear head/neck separation for spine. 4 : Synapse onto axonal bouton. 5 : Synapse onto axonal structure other than a bouton. 6 : Synapse onto 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_structure', limit=10)

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

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

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