943 (Jan 2024)

Data Release v943 (January 22, 2024) is the first quarterly release of 2024.

This version ADDS the following tables

The following tables from previous versions are included:

The following tables have been REMOVED (removed tables still available in version 795):

Information about the version 943 release can be queried with the following:

# report timestamp metadata on the version of interest
client.materialize.get_version_metadata(943)['time_stamp']
datetime.datetime(2024, 1, 22, 8, 10, 1, 497934, tzinfo=datetime.timezone.utc)

Functional properties of coregistered cells

Table name: functional_properties_v3_bcm

A summary of the functional properties for each of the coregistered neurons (as of coregistration_manual_v3). For details, see (Ding et al. 2025)

The key columns are:

Fuctional properties of coregistered neurons
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
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
pref_ori preferred orientation in radians (0 - pi), horizontal bar moving upward is 0 and orientation increases clockwise, extracted from model responses to oriented noise stimuli
pref_dir preferred direction in radians (0 - 2pi), horizontal bar moving upward is 0 and orientation increases clockwise, extracted from model responses to oriented noise stimuli
gOSI global orientation selectivity index
gDSI global direction selectivity index
cc_abs prediction performance of the model, higher is better
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('functional_properties_v3_bcm')

# Content-aware query
client.materialize.tables.functional_properties_v3_bcm(id=example_nucleus_id).query()

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

Manual Coregistration

Table name: coregistration_manual_v4

A table of EM nucleus centroids manually matched to Baylor functional units. 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_manual_v4')

# Content-aware query
client.materialize.tables.coregistration_manual_v4(id=example_nucleus_id).query()

This table coregistration_manual_v4 supercedes previous iterations of this table:

  • coregistration_manual_v3
  • coregistration_manual

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

Automated Coregistration

Table name: coregistration_auto_phase3_fwd_apl_vess_combined

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 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.
Deprecated table

This table remains available from materialization versions: 943, 1078, 1181

Use coregistration_auto_phase3_fwd_apl_vess_combined_v2 instead.

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

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

Flat Segmentation

minnie65 flat segmentation v943
Name Volume Cloudpath Short Description Type (size)
Proofread Segmentation (v943) minnie65 https://storage.googleapis.com/iarpa_microns/minnie/minnie65/seg_m943 Mulit-resolution flat / static cellular segmentation voxels and meshes from 8,8,40 nm and above Precomputed Shareded Compressed Segmentation (12 TB)

This contains the fixed state of the cellular segmentation at each version, where each voxel has been assigned an ID which is unique to each cellular object at 8,8,40, along with downsampled versions. Not all objects have been proofread, but a summary of the most focused efforts on cells can be found in the proofreading status metadata. In addition the mesh folder contains meshes of each object available at 3 different levels of downsampling. Folder contains many files, for download use cloud-volume, tensor-store, for bulk download use igneous, AWS CLI or gsutil CLI.

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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.