1507 (Jul 2025)

Data Release v1507 (July 31, 2025) is the third 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:

The following tables have been REMOVED (removed tables still available in version 1412):

Information about the version 1507 release can be queried with the following:

# report timestamp metadata on the version of interest
client.materialize.get_version_metadata(1507)['time_stamp']
datetime.datetime(2025, 7, 31, 8, 10, 1, 117494, tzinfo=datetime.timezone.utc)

Functional digital twin properties

Merged to manual coregistration

Table name: digital_twin_properties_bcm_coreg_v4

A summary of the functional properties for each of the coregistered neurons using the coregistration information from: coregistration_manual_v4. For details, see (Wang et al. 2025) and (Ding et al. 2025).

The key columns are:

Fuctional properties of coregistered neurons
Column Description
cc_abs Test set performance of the digital twin model unit, higher is better
cc_max Neuron variability score used to normalize digital twin model unit performance
cc_norm Normalized model unit performance, higher is better
OSI orientation selectivity index
DSI direction selectivity index
gOSI global orientation selectivity index
gDSI global direction selectivity index
pref_ori Preferred orientation in degrees (0 - 180), vertical bar moving right is 0 and orientation increases counter-clockwise
pref_dir Preferred direction in degrees (0 - 360), vertical bar moving right is 0 and orientation increases counter-clockwise
readout_loc_x X coordinate of the readout location, an approximation of receptive field center in stimulus space; (-1, -1) bottom-left, (1, 1) top-right
readout_loc_y Y coordinate of the readout location, an approximation of receptive field center in stimulus space; (-1, -1) bottom-left, (1, 1) top-right
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('digital_twin_properties_bcm_coreg_v4')

# Content-aware query
client.materialize.tables.digital_twin_properties_bcm_coreg_v4(id=example_nucleus_id).query()

Merged to Automatic Coregistration

Table name: digital_twin_properties_bcm_coreg_auto_phase3_fwd_v2

Follows the same scheme as digital_twin_properties_bcm_coreg_v4, but uses the coregistration information from: coregistration_auto_phase3_fwd_v2.

# Standard query
client.materialize.query_table('digital_twin_properties_bcm_coreg_auto_phase3_fwd_v2')

# Content-aware query
client.materialize.tables.digital_twin_properties_bcm_coreg_auto_phase3_fwd_v2(id=example_nucleus_id).query()

Table name: digital_twin_properties_bcm_coreg_apl_vess_fwd

Follows the same scheme as digital_twin_properties_bcm_coreg_v4, but uses the coregistration information from: apl_functional_coreg_vess_fwd.

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

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

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 neuromodulatory axons

Table name: vortex_peptidergic_proofreading_status

This table reports the status of a manually selected subset of putative neuromodulatory axons, distinguished by boutons with large secretory vesicles. Labeled 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 a representative point of axon
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

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_peptidergic_proofreading_status')

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

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

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References

Ding, Zhuokun, Paul G. Fahey, Stelios Papadopoulos, Eric Y. Wang, Brendan Celii, Christos Papadopoulos, Andersen Chang, et al. 2025. “Functional Connectomics Reveals General Wiring Rule in Mouse Visual Cortex.” Nature 640 (8058): 459–69. https://doi.org/10.1038/s41586-025-08840-3.
Wang, Eric Y., Paul G. Fahey, Zhuokun Ding, Stelios Papadopoulos, Kayla Ponder, Marissa A. Weis, Andersen Chang, et al. 2025. “Foundation Model of Neural Activity Predicts Response to New Stimulus Types.” Nature 640 (8058): 470–77. https://doi.org/10.1038/s41586-025-08829-y.