Data Release v1078 (June 6 2024) includes all tables from the previous public release (v943), as well as the following new tables.

Proofreading status (v1078)

CAVE table name: proofreading_status_and_strategy

This table describes the status of cells selected for manual proofreading.

Column	Description
`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
`status_dendrite`	`True` or `False`, indicates whether the dendrite is at least clean of false-marges. For extenstion status, see `strategy_axon`
`status_axon`	`True` or `False`, indicates whether the axon is at least clean of false-marges. For extenstion status, see `strategy_axon`
`strategy_dendrite`	Text codifying of most comprehensive proofreading strategy used on the dendrite. For details see Proofreading Strategies
`strategy_axon`	Text codifying of most comprehensive proofreading strategy used on the axon. For details see Proofreading Strategies

VORTEX astrocytes v1: select and clean astrocytes in the column

CAVE table name: vortex_astrocyte_proofreading_status

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

  
    Column
    Description
  
    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 astrocyte when it the proofreading assessment was made
  
    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

VORTEX synapse compartments v1: labeling the targets of basket cell axons

CAVE table name: vortex_compartment_targets

Manual labeling of synaptic targets of putative parvalbumin basket cells, as part of the VORTEX project. This is a reference table on the synapses table synapses_pni_2, and shares reference ids with the automatic synapse labeling table synapse_target_structure.

  
    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

VORTEX myelin labels v0: the myelination status of axons

CAVE 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, listed below as vortex_manual_nodes_of_ranvier.

  
    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
  
    tag
    Myelination status, either True or False
  
    valid_id 
    The segmentation root_id associated with this assessment is the valid_id, NOT necessarily the pt_root_id associated with the point
  
    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.

VORTEX node or Ranvier: the identifying putative nodes of Ranvier on myelinated axons

CAVE 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.

  
    Column
    Description
  
    pt_position
    The position along the axon that was evaluated for myelin and likely node of Ranvier. Note that this position is not always on the segmentation of the axon
  
    tag
    presence of a node of Ranvier, labeled as 'node'
  
    valid_id 
    The segmentation root_id associated with this assessment is the valid_id, NOT necessarily the pt_root_id associated with the point
  
    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.

Functional brain area cell look-up

CAVE table name: nucleus_functional_area_assignment

This table infers the brain area for all detected cell nuclei in the dataset, using area borders derived from the functional imaging data. This is a reference table on nucleus_detection_v0 and can be indexed by root id or nucleus id. Visual brain area labels are one of: V1, AL, RL, LM. Area boundaries estimated from the area-membership assignments of the 2P recorded cells, after transformation to EM space (2P > EM coregistration spline tranformation (transform_id=5, in cajal/microns_phase3_nda github)). Area boundaries drawn using a SVC (scikitlearn) on the 2P->EM positions in XZ plane.

  
    Column
    Description
  
    pt_position, pt_supervoxel_id, pt_root_id 
    Bound spatial point columns associated with the centroid of the cell nucleus
  
    tag
    the inferred functional brain area, one of: V1, AL, RL, LM 
  
    valid_id 
    The segmentation root_id associated with this assessment is the valid_id, NOT necessarily the pt_root_id associated with the point