Annotation Tables

The minnie65_public data release includes a number of annotation tables that help label the dataset. This section describes the content of each of these tables — see here for instructions for how to query and filter tables.

Unless otherwise specificied (i.e. via desired_resolution), all positions are in units of 4,4,40 nm/voxel resolution.

Common Fields

Several fields (or column names) are common to many tables. These fall into two main classes: the spatial point columns that are how we assign annotations to cells via points in the 3d space and book-keeping columns, that are used internally to track the state of the data.

Spatial Point Columns

Most tables have one or more Bound Spatial Points, which is a location in the 3d space that tells the annotation to remain associated with the root id at that location.

Bound spatial points have will have one prefix, usually pt (i.e. “point”) and three associated columns with different suffixes: _position, _supervoxel_id, and _root_id.

For a given prefix {pt}, the three columns are as follows:

  • The {pt}_position indicates the location of the point in 3d space.
  • The {pt}_supervoxel_id indicates a unique identifier in the segmentation, and is mostly internal bookkeeping.
  • The {pt}_root_id indicates the root id of the annotation at that location.

Book-keeping Columns

Several columns are common to many or all tables, and mostly used as internal book-keeping. Rather than describe these for every table, they will just be mentioned briefly here:

Common columns
Column Description
id A unique ID specific to the annotation within that table
created Internal bookkeeping column, should always be t for data you can download
valid A unique ID specific to the annotation within that table
target_id Some tables reference other tables, particularly the nucleus table. If present, this column will be the same as id
created_ref / valid_ref / id_ref (optional) For reference tables, the data shows both the created/valid/id of the reference annotation and the target annotation. The values with the _ref suffix are those of the reference table (usually something like proofreading state or cell type) and the values without a suffix ar ethose of the target table (usually a nucleus)

Synapse Table

Table name: synapses_pni_v2

The only synapse table is synapses_pni_v2. This is by far the largest table in the dataset with 337 million entries, one for each synapse. It contains the following columns (in addition to the bookkeeping columns):

Synapse table column definitions
Column Description
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 IThe bound spatial point data for the postsynaptic side of the synapse.
size The size of the synapse in voxels. This correlates well, but not perfectly, with the surface area of synapse.
ctr_pt_position A position in the center of the detected synaptic junction. Of all points in the synapse table, this is usually the closest point to the surface (and thus mesh) of both neurons. Because it is at the edge of cells, it is not associated with a root id.

Nucleus tables

The ‘nucleus centroid’ of a cell is unlikely to change with proofreading, and so is a useful static identifier for a given cell. The results of automatic nucleus segmentation and neuron-detection are avialable in the following tables. These tables are often the ‘reference’ table for other annotations.

Nucleus Detection Table

Table name: nucleus_detection_v0

Nucleus detection has been used to define unique cells in the dataset. Distinct from the neuronal segmentation, a convolutional neural network was trained to segment nuclei. Each nucleus detection was given a unique ID, and the centroid of the nucleus was recorded as well as its volume. Many other tables in the dataset are reference tables on nucleus_detection_v0, meaning they are linked by the same annotation id. The id of the segmented nucelus, a 6-digit integer, is static across data versions and for this reason is the preferred method to identify the same ‘cell’ across time.

The key columns of nucleus_detection_v0 are:

Nucleus table column definitions
Column Description
id 6-digit number of the segmentation for that nucleus; ‘nucleus ID’
pt_position  pt_supervoxel_id  pt_root_id Bound spatial point columns associated with the centroid of the nucleus

Note that the id column is the nucleus ID, also called the ‘soma ID’ or the ‘cell ID’.

Neuron-Nucleus Table

Table name: nucleus_ref_neuron_svm

While the table of centroids for all nuclei is nucleus_detection_v0, this includes neuronal nuclei, non-neuronal nuclei, and some erroneous detections. The table nucleus_ref_neuron_svm shows the results of a classifier that was trained to distinguish neuronal nuclei from non-neuronal nuclei and errors. For the purposes of analysis, we recommend using the nucleus_ref_neuron_svm table to get the most broad collection of neurons in the dataset.

The key columns of nucleus_ref_neuron_svm are:

Nucleus table column definitions
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 nucleus
classification-system Describes how the classification was done. All values will be is_neuron for this table
cell_type The output of the classifier. All values will be either neuron or not-neuron (glia or error) for this table

Note that the id column is the same as the nucleus id.

Nucleus brain area assignment

Given the nucleus detection table nucleus_detection_v0 and the transformation of 2-photon in vivo imaging to the EM structural space (see functional-coregistration-tables ), each cell in the volume has been assigned to one of four visual cortical areas.

The inferred functional brain area based on the position of the nucleus in the EM volume. Area boundaries estimated from the area-membership assignments of the 2P recorded cells, after transformation to EM space.

The table nucleus_functional_area_assignment is a reference table on nucleus_detection_v0 and adds the following columns:

Functional area assignment
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
tag the brain area label (one of V1, AL, RL, LM)
value the distance to the area boundary (in um), calculated as the mean-distance of the 10 nearest neighbors in a non-matching brain area. A larger value is further from the area boundaries, and can be interpretted as higher confidence in area assignment.

Cell Type Tables

There are several tables that contain information about the cell type of neurons in the dataset, with each table representing a different method of doing the classificaiton. Because each method requires a different kind of information, not all cells are present in all tables. Each of the cell types tables has the same format and in all cases the id column references the nucleus id of the cell in question.

Manual Cell Types (V1 Column)

Table name: allen_v1_column_types_slanted_ref and aibs_column_nonneuronal_ref

A subset of nucleus detections in a 100 um column (n=2204) in VISp were manually classified by anatomists at the Allen Institute into categories of cell subclasses, first distinguishing cells into classes of non-neuronal, excitatory and inhibitory.

The key columns are:

AIBS Manual Cell Types, V1 COlumn
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
classification-system One of aibs_coarse_excitatory or aibs_coarse_inhibitory for detected neurons, or aibs_coarse_nonneuronal for non-neurons (glia/pericytes).
cell_type One of several cell types, detailed below

This is a reference table on nucleus_detection_v0. The cell types in the table are:

AIBS Manual Cell Type definitions (neurons)
Cell Type Subclass Description
23P Excitatory Layer 2/3 cells
4P Excitatory Layer 4 cells
5P-IT Excitatory Layer 5 intratelencephalic cells
5P-ET Excitatory Layer 5 extratelencephalic cells
5P-NP Excitatory Layer 5 near-projecting cells
6P-IT Excitatory Layer 6 intratelencephalic cells
6P-CT Excitatory Layer 6 corticothalamic cells
BC Inhibitory Basket cell
BPC Inhibitory Bipolar cell. In practice, this was used for all cells thought to be VIP cell, not only those with a bipolar dendrite
MC Inhibitory Martinotti cell. In practice, this label was used for all inhibitory neurons that appeared to be Somatostatin cell, not only those with a Martinotti cell morphology
Unsure Inhibitory Unsure. In practice, this label also is used for all likely-inhibitory neurons that did not match other types
AIBS Manual Cell Type definitions (non-neurons)
Cell Type Subclass Description
OPC Non-neuronal Oligodendrocyte precursor cell
astrocyte Non-neuronal Astrocyte
microglia Non-neuronal Microglia
pericyte Non-neuronal Pericyte
oligo Non-neuronal Oligodendrocyte

Predictions from soma/nucleus features

Table name: aibs_metamodel_celltypes_v661

This table contains the results of a hierarchical classifier trained on features of the cell body and nucleus of cells. This was applied to most cells in the dataset that had complete cell bodies (e.g. not cut off by the edge of the data). For more details, see Elabbady et al. 2022. In general, this does a good job, but sometimes confuses layer 5 inhibitory neurons as being excitatory:

The key columns are:

AIBS Soma Nuc Metamodel 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
classification-system One of excitatory_neuron or inhibitory_neuron for detected neurons, or nonneuron for non-neurons (glia/pericytes).
cell_type One of several cell types, detailed below

This is a reference table on nucleus_detection_v0, with small-objects and multi-soma errors removed. The model was run with cell-based features as of version 661 of the dataset. The cell types in the table are:

AIBS Soma Nuc Metamodel: Cell Type definitions
Cell Type Subclass Description
23P Excitatory Layer 2/3 cells
4P Excitatory Layer 4 cells
5P-IT Excitatory Layer 5 intratelencephalic cells
5P-ET Excitatory Layer 5 extratelencephalic cells
5P-NP Excitatory Layer 5 near-projecting cells
6P-IT Excitatory Layer 6 intratelencephalic cells
6P-CT Excitatory Layer 6 corticothalamic cells
BC Inhibitory Basket cell
BPC Inhibitory Bipolar cell. In practice, this was used for all cells thought to be VIP cell, not only those with a bipolar dendrite
MC Inhibitory Martinotti cell. In practice, this label was used for all inhibitory neurons that appeared to be Somatostatin cell, not only those with a Martinotti cell morphology
NGC Inhibitory Neurogliaform cell. In practice, this label also is used for all inhibitory neurons in layer 1, many of which may not be neurogliaform cells although they might be in the same molecular family
OPC Non-neuronal Oligodendrocyte precursor cell
astrocyte Non-neuronal Astrocyte
microglia Non-neuronal Microglia
pericyte Non-neuronal Pericyte
oligo Non-neuronal Oligodendrocyte

Previous versions of this table include: aibs_soma_nuc_metamodel_preds_v117 (run on a subset of data, the V1 column) and aibs_soma_nuc_exc_mtype_preds_v117 (using training data labeled by another classifier: see mtypes below).

Coarse prediction from spine detection

Table name: baylor_log_reg_cell_type_coarse_v1

This table contains the results of a logistic regression classifier trained on properties of neuronal dendrites. This was applied to many cells in the dataset, but required more data than soma and nucleus features alone and thus more cells did not complete the pipeline. It has very good performance on excitatory vs inhibitory neurons because it focuses on dendritic spines, a characteristic property of excitatory neurons. It is a good table to double check E/I classifications if in doubt.

The key columns are:

Baylor Dendrite Feature 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
classification-system baylor_log_reg_cell_type_coarse for all entries
cell_type excitatory or inhibitory

Fine prediction from dendritic features

Table name: aibs_metamodel_mtypes_v661_v2

This table contains all detected neurons across the dataset,

Excitatory neurons and inhibitory neurons were distinguished with the soma_nucleus model above, and subclasses were assigned based on a data-driven clustering of the neuronal features. Inhibitory neurons were classified based on how they distributed they synaptic outputs onto target cells, while exictatory neurons were classified based on a collection of dendritic features.

For more details, see the section on the minnie column or read the preprint (Schneider-Mizell et al. 2023).

Note that all cell-type labels in this table come from a clustering specific to this paper, and while they are intended to align with the broader literature they are not a direct mapping or a well-established convention.

For a more conventional set of labels on the same set of cells, look at the manual table allen_v1_column_types_slanted_ref. Cell types in that table align with those in the aibs_metamodel_celltypes_v661 classifier above.

The key columns are:

Column M-type 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
classification-system excitatory or inhibitory
cell_type One of several cell types, detailed below

This is a reference table on nucleus_detection_v0, with non-neuronal objects removed. The model was run with cell-based features as of version 661 of the dataset. The cell types in the table are:

The cell types in the table are:

Cell Type Subclass Description
L2a Excitatory A cluster of layer 2 (upper layer 2/3) excitatory neurons
L2b Excitatory A cluster of layer 2 (upper layer 2/3) excitatory neurons
L3a Excitatory A cluster of excitatory neurons transitioning between upper and lower layer 2/3
L3b Excitatory A cluster of layer 3 (upper layer 2/3) excitatory neurons
L3c Excitatory A cluster of layer 3 (upper layer 2/3) excitatory neurons
L4a Excitatory The largest cluster of layer 4 excitatory neurons
L4b Excitatory Another cluster of layer 4 excitatory neurons
L4c Excitatory A cluster of layer 4 excitatory neurons along the border with layer 5
L5a Excitatory A cluster of layer 5 IT neurons at the top of layer 5
L5b Excitatory A cluster of layer 5 IT neurons throughout layer 5
L5ET Excitatory The cluster of layer 5 ET neurons
L5NP Excitatory The cluster of layer 5 NP neurons
L6a Excitatory A cluster of layer 6 IT neurons at the top of layer 6
L6b Excitatory A cluster of layer 6 IT neurons throughout layer 6. Note that this is different than the label “Layer 6b” which refers to a narrow band at the border between layer 6 and white matter
L6c Excitatory A cluster of tall layer 6 cells (unsure if IT or CT)
L6CT Excitatory A cluster of tall layer 6 cells matching manual CT labels
L6wm Excitatory A cluster of layer 6 cells along the border with white matter
PTC Inhibitory Perisomatic targeting cells, a cluster of inhibitory neurons that target the soma and proximal dendrites of excitatory neurons. Approximately corresponds to basket cell
DTC Inhibitory Dendrite targeting cells, a cluster of inhibitory neurons that target the distal dendrites of excitatory neurons. Most SST cells would be DTC
STC Inhibitory Sparsely targeting cells, a cluster of inhibitory neurons that don’t concentrate multiple synapses onto the same target neurons. Many neurogliaform cells and layer 1 interneurons fall into this category
ITC Inhibitory Inhibitory targeting cells, a cluster of inhibitory neurons that preferntially target other inhibitory neurons. Most VIP cells would be ITCs

Previous versions of this table include: allen_column_mtypes_v1 (run on a subset of data, the V1 column)

Proofreading Tables

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
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.

Important

This table is out-of-date, and remains here for convenient reference

Table name: proofreading_status_public_release

The table proofreading_status_public_release describes the status of cells selected for manual proofreading.

Because of the inherent difference in the challenge and time required for different kinds of proofreading, we describe the status of axons and dendrites separately. Further, we distinguish three different categories of proofreading:

  • non: No proofreading has been comprehensively performed.
  • clean: Proofreading has comprehensively removed false merges, but not necessarily added missing parts.
  • extended: Proofreading has comprehensively removed false merges and attempted to add all or most missing parts.

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
status_dendrite The status of the dendrite proofreading. One of the three categories described above
status_axon The status of the axon proofreading. One of the three categories described above

Functional Coregistration Tables

To relate the structural data to functional data, cell bodies must be coregistered between the functional imaging and EM volumes. The results of this coregistration are stored in two tables with the same columns:

  • coregistration_manual_v4 : The results of manually verified coregistration. This table is well-verified, but contains fewer {term}ROIs (N=15,352 root ids, 19,181 ROIs).
  • coregistration_auto_phase3_fwd_apl_vess_combined : The results of automated functional matching between the EM and 2-p functional data. This table is not manually verified, but contains more {term}ROIs (N=84,233 ROIs). 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.
Important

Please see the Functional Data section for more information about using this data.

fix broken link

The column descriptions 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.

Previous versions of this analysis include the following tables:

  • coregistration_manual_v3 : The results of manually verified coregistration. This table is well-verified, but contains fewer {term}ROIs (N=12,052 root ids, 13,925 ROIs).
  • apl_functional_coreg_forward_v5 : The results of automated functional matching between the EM and 2-p functional data. This table is not manually verified, but contains more {term}ROIs (N=36,078 root ids, 68,873 ROIs).

Functional properties

A summary of the functional properties for each of the coregistered neurons (as of coregistration_manual_v3) are available for convenience.

The table functional_properties_v3_bcm is a reference table on the nucleus_detection_v0, and adds the following columns

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

Overview of relevant tables

heard you like tables–here’s a table for your tables
Table Name Number of Annotations Description
synapses_pni_v2 337,312,429 The locations of synapses and the segment ids of the pre and post-synaptic automated synapse detection
nucleus_detection_v0 144,120 The locations of nuclei detected via a fully automated method
nucleus_alternative_points 8,388 A reference annotation table marking alternative segment_id lookup locations for a subset of nuclei in nucleus_detection_v0 that is more accurate than the centroid location listed there
nucleus_ref_neuron_svm 144,120 reference annotation indicating the output of a model detecting which nucleus detections are neurons versus which are not 1
coregistration_manual_v4 19,181 A table indicating the association between individual units in the functional imaging data and nuclei in the structural data, derived from human powered matching. Includes residual and separation scores to help assess confidence
coregistration_auto_phase3_fwd_apl_vess_combined 84,233 A table indicating the association between individual units in the functional imaging data and nuclei in the structural data, derived from the automated procedure. Includes residuals and separation scores to help assess confidence
proofreading_status_and_strategy 1421 A table indicating which neurons have been proofread on their axons or dendrites
aibs_column_nonneuronal_ref 542 Cell type reference annotations from a human expert of non-neuronal cells located amongst the Minnie Column
allen_v1_column_types_slanted_ref 1,357 Neuron cell type reference annotations from human experts of neuronal cells located amongst the Minnie Column
allen_column_mtypes_v1 1,357 Neuron cell type reference annotations from data driven unsupervised clustering of neuronal cells
aibs_metamodel_mtypes_v661_v2 72,158 Reference annotations indicating the output of a model predicting cell types across the dataset based on the labels from allen_column_mtypes_v1.1
aibs_metamodel_celltypes_v661 94,014 Reference annotations indicating the output of a model predicting cell classes based on the labels from allen_v1_column_types_slanted_ref and aibs_column_nonneuronal_ref
baylor_log_reg_cell_type_coarse_v1 55,063 Reference annotations indicated the output of a logistic regression model predicting whether the nucleus is part of an excitatory or inhibitory cell
baylor_gnn_cell_type_fine_model_v2 49,051 Reference annotations indicated the output of a graph neural network model predicting the cell type based on the human labels in allen_v1_column_types_slanted_ref
proofreading_edits 121,271 A table containing the number of edits on every segment_id associated with a nucleus in the volume
vortex_astrocyte_proofreading_status 12 This table reports the status of a manually selected subset of astrocytes within the VISP column. Astrocyte seelection and proofreading performed as part of VORTEX.
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References

Schneider-Mizell, Casey M., Agnes Bodor, Derrick Brittain, JoAnn Buchanan, Daniel J. Bumbarger, Leila Elabbady, Daniel Kapner, et al. 2023. “Cell-Type-Specific Inhibitory Circuitry from a Connectomic Census of Mouse Visual Cortex.” bioRxiv. https://doi.org/10.1101/2023.01.23.525290.