# report timestamp metadata on the version of interest
1507)['time_stamp'] client.materialize.get_version_metadata(
datetime.datetime(2025, 7, 31, 8, 10, 1, 117494, tzinfo=datetime.timezone.utc)
Data Release v1507 (July 31, 2025) is the third quarterly release of 2025.
This version ADDS the following tables
digital_twin_properties_bcm_coreg_v4
: Functional properties computed from the digital twin model (Wang et al. 2025) (Ding et al. 2025) merged with coregistration_manual_v4
digital_twin_properties_bcm_coreg_auto_phase3_fwd_v2
: Functional properties computed from the digital twin model (Wang et al. 2025) (Ding et al. 2025) merged with coregistration_auto_phase3_fwd_v2
digital_twin_properties_bcm_coreg_apl_vess_fwd
: Functional properties computed from the digital twin model (Wang et al. 2025) (Ding et al. 2025) merged with apl_functional_coreg_vess_fwd
vortex_peptidergic_proofreading_status
: selected proofreading of putative neuromodulatory axons, distinguished by boutons with large secretory vesicles. Labeled as part of the VORTEX effort
The following tables have updated status or entries, from VORTEX proofreading and annotations
proofreading_status_and_strategy
(newly proofread cells and upgraded cell status)
vortex_thalamic_proofreading_status
(newly proofread cells and upgraded cell status)
The following tables from previous versions are included:
synapses_pni_2
( v117 )nucleus_detection_v0
( v117 )allen_v1_column_types_slanted_ref
( v661 )aibs_column_nonneuronal_ref
( v661 )baylor_log_reg_cell_type_coarse_v1
( v661 )nucleus_alternative_points
( v661 )allen_column_mtypes_v2
( v795 )aibs_metamodel_celltypes_v661
( v795 )aibs_metamodel_mtypes_v661_v2
( v795 )l5et_column
, bodor_pt_cells
, bodor_pt_target_proofread
, and pt_synapse_targets
( v795 )functional_properties_v3_bcm
( v943 )coregistration_manual_v4
( v943 )apl_functional_coreg_vess_fwd
( v943 )proofreading_status_and_strategy
( v1078 )vortex_astrocyte_proofreading_status
( v1078 )vortex_compartment_targets
( v1078 )vortex_manual_myelination_v0
, vortex_manual_nodes_of_ranvier
( v1078 )nucleus_functional_area_assignment
( v1078 )synapse_target_structure
( v1078 )synapse_target_predictions_ssa
( v1300 )coregistration_auto_phase3_fwd_apl_vess_combined_v2
( v1300 )coregistration_auto_phase3_fwd_v2
( v1300 )cg_cell_type_calls
, gamlin_2023_mcs
, gamlin_2023_mcs_met_types
( v1300 )vortex_thalamic_proofreading_status
( v1412 )multi_input_spine_predictions_ssa
( v1412 )The following tables have been REMOVED (removed tables still available in version 1412):
functional_properties_v3_bcm
: removed and superseded by digital_twin_properties_bcm_coreg_v4
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)
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:
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 |
This is a reference table on nucleus_detection_v0
, and can be indexed by the same nucleus id.
This table includes duplicate entries for the same ‘pt_root_id’ and nucleus id if the coregistered cell has multiple unit recordings
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
.
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:
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):
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
.
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 |
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