Project Outcomes - Year 2

Year 2: Period 1

Projects completed in the first period of Year 2. Addressing requests recieved during the second half of Year 1. See: Proposals Received

Includes data releases: Y2: 1181 and Y2: 1300

VORTEX Proofreading Plans | Year 2 Period 1
SSG Rank Task Outcome
1.3 Forward-tracing of pyramidal cell axons Added 546 cells
1.7 Annotation of basket cell spine targets Added 31502 spine annotations
on 5 cells
2 Annotation of pyramidal spine input Added 35938 spine annotations
on 8 cells
3.7 Annotation of basket cell myelin 53517 spine annotations
73237 myelin annotations
5 Annotation of spine input within microglia Released automated spine-detection resource
5 OPC proofreading and annotation Incomplete in Y2
5.7 Annotation of myelin (any cell type) Added 26393 myelin annotations

Axon extension of functionally recorded cells

Proofreading and extending functionally coregistered pyramidal cells, which were a set of excitatory cell types in different layers.This effort includes proofreading done to excitatory cells in the V1 column that are not coregistered, but are interconnected with the coregistered cells.

Synaptic connectivity added from version 1078 to 1300:

Queried from CAVE table: proofreading_status_and_strategy:

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

# Content-aware query
client.materialize.tables.proofreading_status_and_strategy(status_axon='t').query()

Convergence of inputs from functionally coregistered cells

With the combined effort across Year 1 (1078) and Year 2 (1300), VORTEX proofreading has doubled the number of synapses between excitatory cells, and tripled the number of coregistered-coregistered connections.

Improvement in connectivity between functionally-coregistered pyramidal cells

This connectivity, combined with the derived visual functional properties, means we can evaluate the convergence of inputs such as preferred orientation of visual stimuli:

Interactive: Preferred orientation of functionally-characterized cell inputs





For a coding example of how to render this cell with its inputs, see: Analysis Gallery: Functional properties as synaptic input

Annotation of spine synapses

Manual annotation of spine and shaft synaptic targets of 1) basket cells, and 2) inputs onto pyramidal cells: 67440 annotations

Dense manual annotations on the inputs to a pyramidal cell

Queried from CAVE table: vortex_compartment_targets

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

# Content-aware query
client.materialize.tables.vortex_compartment_targets(pre_pt_root_id=example_root_id).query()

Provided ground truth for a new automatic classifier:

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

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

Annotation of myelin

Manual annotation of myelination and nodes of Ranvier 1) along basket cell axons, and 2) dense annotations within a subvolume: 26393 annotations

For a coding example of how to a cell with its myelin, see: Analysis Gallery: Myelin Labels

CAVE table: vortex_manual_myelination_v0

# Standard query
client.materialize.query_table('vortex_manual_myelination_v0', limit=10)

# Content-aware query
client.materialize.tables.vortex_manual_myelination_v0(valid_id=example_root_id).query()

CAVE table: vortex_manual_nodes_of_ranvier

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

# Content-aware query
client.materialize.tables.vortex_manual_nodes_of_ranvier(valid_id=example_root_id).query()

Year 2 Period 2

Projects completed in Year 2. Addressing requests recieved during the first half of Year 2 See: Proposals Received

Includes data releases: Y2: 1412 and Y2: 1507

SSG Rank Task Outcome
2 Axon proofreading of excitatory cells Added 248 cells in the V1 column
3 Axon proofreading of inhibitory cells Added 100 putative PV basket cells around the V1 column; 28 peptidergic targets (putative CCK basket) in superficial layers
3.5 Astrocyte proofreading: remove neurites Cleaned 110 astrocytes in the V1 column
3.75 Axon proofreading of thalamocortical axons Added 21 axons, improved 12 axons
4.5 Annotate dense core vesicles Incomplete pending resources
4.75 Annotate microglia lysosomes Incomplete; proofreading into Y3
5 Characterize neuromodulatory synapses Ongoing into Y3
7 Axon proofreading of neuromodulatory synapses Labeled and cleaned 20 axons
Synaptic connectivity added from version 1300 to 1507:

Axon extension of functionally recorded cells

Proofreading and extending functionally coregistered pyramidal cells, which were a set of excitatory cell types in different layers. This effort includes proofreading done to 248 excitatory cells in the V1 column that are not coregistered, but are interconnected with the coregistered cells.

Queried from CAVE table: proofreading_status_and_strategy:

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

# Content-aware query
client.materialize.tables.proofreading_status_and_strategy(status_axon='t').query()

Axon extension of inhibitory cells

Proofreading basket cells in all layers in the expanded column, a 50 um radius around the V1 column. Added 100 putative PV basket cells around the V1 column. Seperately added 28 peptidergic targets (putative CCK basket) in superficial layers

Y3: v1621 further added 56 Martinotti cells across all layers, 10 neurogliaform cells, and 55 bipolar cells.

Queried from CAVE table: proofreading_status_and_strategy:

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

# Content-aware query
client.materialize.tables.proofreading_status_and_strategy(status_axon='t').query()

Astrocyte proofreading: remove neurites

This task selected all single-soma astrocytes in the V1 column for proofreading, where the criteria was to ‘clean’ the astrocyte of all neurites, but not yet to ‘extend’ the astrocyte to fill internal holes in the astrocytic volume.

CAVE table: vortex_astrocyte_proofreading_status

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

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

Three apposed, cleaned astrocytes. Shown with a branch of the capillary (red) wrapped by the endfeet of two astrocytes

Axon proofreading: thalamocortical axons

Added 21 newly proofread thalamic axons, improved 12 previously proofread axons, and identified 50 additional thalamic axons for future work.

CAVE table: vortex_thalamic_proofreading_status

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

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

Axon proofreading: neuromodulatory axons

We began to identify and extend putative neuromodulatory axons, distinguished branching in cortical layer 1 and by boutons with large secretory vesicles. A total of 20 manually identified and partially extended putative neuromodulatory axons are available. Further characterization of the synaptic connectivity, morphology, and identity of these axons continues outside of VORTEX.

CAVE table: vortex_peptidergic_proofreading_status

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

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

Annotate: dense core vesicles

This annotation task terminated after a feasibility pilot, due to the difficulty in finding very sparse dense core vesicles in the dendrites of cells of interest. Identifying dense core vesicles would be benefited by an automated segmentation of organelles, which is the subject of a Year 3 request and project.

Annotate: microglia lysosomes

Terminated in favor of proofreading microglia instead, a project completed in Y3: 1621.

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