1621 (Nov 2025)

Data Release v1621 (November 25, 2025) 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 1621 release can be queried with the following:

# report timestamp metadata on the version of interest
client.materialize.get_version_metadata(1621)['time_stamp']
datetime.datetime(2025, 11, 25, 8, 10, 1, 94430, tzinfo=datetime.timezone.utc)

Automated myelin annotation

Table name: myelin_auto_tags_2points

This table annotates the presence (TRUE) or absence (FALSE) of myelin along the axons of a subset of proofread cells (currently from v1300). Each point was processed using an automated myelin detection pipeline, which evaluates the proportion of the segmentation outline adjacent to segment == 0. If more than half of the outline is closely surrounded by segment == 0, the location is labeled as TRUE.

For questions and citation, contact Wan-Qing Yu.

Auto Myelination
Column Description
pt_position The position along the axon that was evaluated for myelin.
pt2_position The next point position along the axon that was evaluated for myelin, outward from the soma. For branch end points, pt_position is equal to pt2_position
tag  tag2 Myelination status, either True or False, for the respective pt_position or pt2_position
pt_supervoxel_id  pt_root_id  pt2_root_id The bound spatial point data for the evaluated point.
Warning

The myelination was evaluated for the a specific version of the segmentaion (v1300) and may not match the current segmentation of the selected neurons.

Note: the two-point annotation allows for easy rendering of myelinated stretches in neuroglancer, like in the following: Myelin precomputed annotations in neuroglancer (takes a moment to load).

# Standard query
client.materialize.query_table('myelin_auto_tags_2points', limit=10)

# Content-aware query
client.materialize.tables.myelin_auto_tags_2points(pt_root_id=example_root_id).query()

VORTEX Efforts

Backtracing axons in proximity to cortical minicolumns

This vortex effort produced two tables to densely proofread inputs to a set of apical axons: 1) a table annotating the backtracing effort, and 2) a table quantifying the number of disconnected synapses in a small area and the outcome of evaluating the synapse as a disconnected spine head.

Table name: vortex_axon_backtrace_column

This table reports the status of a subset of local axons that have been proofread within the V1 column as part of a backtracing pilot: extending the disconnected axon from a synapse of interest. The axons are CLEAN but only complete within the borders of the VISP column. Axon selection and proofreading performed as part of the VORTEX project.

The key columns are:

Column Description
id/target_id Synapse ID for the source synapse of the axon of interest. This table is reference on synapses_pni_2.
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 Status of the backtrace, one of: complete indicating the axons was evaluated to be excitatory and successfully proofread within the column; incomplete indicating the axon was evaluated to be inhibitory or shaft-targetting and abandoned; error indicating an error of synapses detection. 
# Standard query
client.materialize.query_table('vortex_axon_backtrace_column')

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

client.materialize.tables.vortex_axon_backtrace_column(tag='complete').query()

Table name: vortex_synapse_reattachment

This table reports the status of a subset of synapses in the V1 column that were not connected to a postsynaptic soma (as of v1300). All synapses in this table were evaluated for reattachment as part of a VORTEX proofreading pilot. Synapse selection and proofreading performed as part of the VORTEX project.

The key columns are:

Column Description
id/target_id Synapse ID for the previously disconnected synapse. This table is reference on synapses_pni_2.
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 The final state of synapse attachment, one of: ‘spine’ indicating the disconnected synapse was a spinehead and successfully attached to a dendrite; ‘dendrite’ indicating the synapse was part of a disconnected dendrite and successfully attached to the soma; ‘disconnected’: indicating a real spinehead that could not be connected to a dendrite; and ‘error’ indicating an error of synapse detection. 
# Standard query
client.materialize.query_table('vortex_synapse_reattachment')

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

client.materialize.tables.vortex_synapse_reattachment(tag='spine').query()

VORTEX proofread microglia

Table name: vortex_microglia_proofreading_status

Manual screening and proofreading of microglia within the V1 column, as part of the as part of the VORTEX project.

The key columns are:

Column Description
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-microglia elements have been manually removed and the substantive processes attached; ‘extended’ meaning all endpoints of the microglia evaluated and extended.
valid_id The root id of the microglia when it the proofreading assessment was made. 
# Standard query
client.materialize.query_table('vortex_microglia_proofreading_status')

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

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 thalamic axons

Table name: vortex_thalamic_proofreading_status

This table reports the status of a manually selected subset of putative thalamocortical axons 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 entry point of the axon into the EMvolume
status One of ‘non’ indicating no cleaning or extension; ‘clean’ indicating synapses can be trusted but may not be complete; ‘extended’ meaning all end points visited and extended to completion
valid_id The root id of the axon when it the proofreading assessment was made
Tip

Thalamic axons in this table that are complete and extended are also posted to proofreading_status_and_strategy with strategy: axon_fully_extended and dendrite_none.

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

# Content-aware query
client.materialize.tables.vortex_thalamic_proofreading_status(status='extended').query()

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

Back to top