Term Info Queries Reference

The Term Info pane offers a set of ready-made queries relevant to the currently selected entity. Each query finds related entities (neurons, images, datasets, publications, stocks…) or related data (connectivity, expression, transcriptomics) and shows them in a sortable, filterable results table.

Queries are specialised by entity type: the query menu for a brain region is not the same as the menu for an individual EM neuron, a driver line, a gene, a template or a publication. This page is the complete reference to those queries — use it to understand what a query does before running it, and what its results columns mean.

How queries work

• Queries appear as a menu in the Term Info pane, offered according to the type of the selected entity — the menu for a brain region differs from that for a neuron, driver line, gene or template. A number badge on each query shows how many results it has for the current term; this can be 0 when the term has no matching results (for example a region with no annotated subclasses or clones).

• Selecting a query runs it and opens the results in a table. Results can be filtered by typing in the top bar and sorted by clicking a column header. Clicking a term in the results — the name in the first column, or any highlighted term elsewhere in a row — opens its Term Info. Where images are available, a thumbnail is shown and can be clicked to add the image to the 3D viewer; the checkboxes next to the thumbnails let you add or remove several images to/from the viewer at once.

• The query menu shows a short label with the entity’s name filled in, e.g. “Neurons with some part in medulla”. In the sections below the entity name is written as [term]. The gold ? at the right of each query row opens that query’s section on this page; the same icon on the Graphs for and Circuit Browser rows opens the Term Context and Circuit Browser pages.
• Some individuals inherit their class’s queries — but not all. An individual image is offered its parent class’s queries only when it is one of these anatomical types: painted domain, synaptic neuropil (or its domains and subdomains), tract or nerve, split, expression pattern, or muscle. For those, it shows the queries its class shows, run on the class. Other individuals — in particular individual cells and neurons (e.g. EM reconstructions) — do not inherit their class’s queries; they get only the individual-level queries listed under Individual neurons & images.

Each query below lists the columns in its results table; for what those columns mean, see Result columns explained at the foot of this page.

Queries are powered by the open-source VFBquery engine, which is also reachable programmatically — see APIs.

Anatomy: regions, neuropils, tracts, nerves & clones

These queries appear on anatomical class pages — brain regions, synaptic neuropils, tracts and nerves, clones and other structures. They do not appear on individual cell types (neurons, glia): see Neuron types.

List all available images of [term]

All images (individuals) of an anatomical class. Shown on: anatomy classes. Columns: Name, Parent Type, Gross Types, Template, Data Source, Dataset, License, Thumbnail.

Parts of [term]

Anatomical sub-parts of the structure (part_of). Shown on: anatomy classes (not individual cells or expression patterns). Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Neurons with some part in [term]

Neuron classes with any part overlapping the region. Shown on: anatomy / synaptic-neuropil classes (not cells or expression patterns). Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Neurons with synaptic terminals in [term]

Neuron classes with synaptic terminals (of either polarity) in the region. Shown on: nervous-system anatomy classes (not cells). Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Neurons with presynaptic terminals in [term]

Neuron classes with presynaptic (output) terminals in the region. Shown on: nervous-system anatomy classes (not cells). Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Neurons with postsynaptic terminals in [term]

Neuron classes with postsynaptic (input) terminals in the region. Shown on: nervous-system anatomy classes (not cells). Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Images of neurons with some part in [term]

Individual neuron images (instances) with a part in the region — the image counterpart of Neurons with some part in. Shown on: anatomy / synaptic-neuropil classes (not cells). Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Tracts/nerves innervating [term]

Tracts and nerves that innervate the neuropil. Shown on: synaptic neuropils and their domains. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Lineage clones found in [term]

Lineage clones overlapping the neuropil. Shown on: synaptic neuropils and their domains. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Neurons fasciculating in [term]

Neuron classes that fasciculate with (run along) the tract or nerve. Shown on: tract / nerve classes. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Components of [term]

The component parts of a clone. Shown on: clone classes. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Transgene expression in [term]

Transgenes/driver lines reported to be expressed in the region or neuron type. Shown on: nervous-system anatomy classes and neuron types. Columns: Expression Pattern, Expressed_in, Publications, Tags, Template, Imaging Technique, Thumbnail.

scRNAseq data for [term]

Single-cell transcriptomics clusters and datasets for the anatomical region. Shown on: anatomy classes that have scRNAseq data. Columns: Cluster, Cell type, Cluster stage (from expression), Stages of samples, Tissues of samples, Dataset, Cells, Publications, Tags.

Neuron types (classes)

Neuron classes are also anatomical classes, so they additionally offer List all available images, Subclasses of, Transgene expression in and, where data exists, scRNAseq data for.

Downstream connectivity classes for [term]

Neuron classes that receive synapses from this neuron class, aggregated over the ontology hierarchy. Shown on: neuron classes. Columns: Upstream Class, Downstream Class, Total N, Connected N, % Connected, Pairwise Connections, Total Weight, Avg Weight.

Upstream connectivity classes for [term]

Neuron classes that send synapses to this neuron class, aggregated over the ontology hierarchy. Shown on: neuron classes. Columns: Upstream Class, Downstream Class, Total N, Connected N, % Connected, Pairwise Connections, Total Weight, Avg Weight.

Splits targeting [term]

Split-GAL4 driver lines that specifically target this neuron type. Shown on: neuron classes. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Split drivers, neuroblasts & process terms

Neurons targeted by [term]

Neuron types targeted by a split-GAL4 driver line. Shown on: split (intersectional driver) classes. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Images of neurons that develop from [term]

Individual neuron images that develop from a neuroblast. Shown on: neuroblast classes. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Neurons capable of [term]

Individual neurons capable of a process — e.g. neurons capable of secreting a particular neurotransmitter. Shown on: neurotransmitter-secretion (GO) process terms. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Subclasses of [term]

Direct subclasses of a class. Shown on: any class that has subclasses. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Individual neurons & images

These appear on individual neuron pages (e.g. EM reconstructions and registered LM images), depending on the data each neuron carries.

Neurons connected to [term]

Synaptic partners of this neuron, with per-partner input and output synapse counts. Shown on: individual neurons with connectivity data. Columns: Partner Neuron, Type, Outputs, Inputs, Template, Imaging Technique, Tags, Thumbnail.

Connectivity per region for [term]

This neuron’s synaptic terminal counts broken down by brain region. Shown on: individual neurons with regional connectivity data. Columns: Brain Region, Type, Presynaptic Terminals (T-bars), Downstream Synapses, Postsynaptic Terminals, Template, Imaging Technique, Tags, Thumbnail.

Individual neurons with connectivity data can also be added to the Circuit Browser to explore connectivity interactively.

Similarity queries

NBLAST and NeuronBridge find entities with similar morphology. Which of these is offered depends on the similarity data a neuron or expression pattern carries. All are sorted by score, best match first.

Neurons with similar morphology to [term] [NBLAST]

NBLAST matches to an individual neuron. Shown on: individual neurons with NBLAST data. Columns: Score, Name, Tags, Type, Source, Source ID, Template, Imaging Technique, Thumbnail.

Expression patterns with similar morphology to part of [term] [NBLAST]

NBLAST matches from a neuron to expression patterns. Shown on: individual neurons with expression-pattern NBLAST data. Columns: Expression Pattern, NBLAST Score, Tags, Template, Imaging Technique, Thumbnail.

Neurons with similar morphology to part of [term] [NBLAST]

The reverse: NBLAST matches from an expression pattern to neurons. Shown on: individual expression patterns / fragments with NBLAST data. Columns: Neuron, NBLAST Score, Tags, Template, Imaging Technique, Thumbnail.

Expression patterns matching [term] [NeuronBridge]

NeuronBridge matches from a neuron to driver/expression images. Shown on: individual neurons with NeuronBridge data. Columns: Match, NB Score, Tags, Template, Imaging Technique, Thumbnail.

Neurons matching [term] [NeuronBridge]

The reverse: NeuronBridge matches from an expression pattern to neurons. Shown on: individual expression patterns / fragments with NeuronBridge data. Columns: Match, NB Score, Tags, Type, Template, Imaging Technique, Thumbnail.

Neurons with similar morphology to your upload [term] [NBLAST]

NBLAST matches to a neuron you have uploaded. Shown on: user-uploaded neuron data. Columns: Match, Score.

Expression patterns & driver lines

Images of fragments of [term]

Individual expression-pattern fragment images belonging to an expression pattern. Shown on: expression-pattern classes. Columns: Name, Tags, Template, Imaging Technique, Thumbnail.

Anatomy where [term] is expressed

Anatomical classes in which an expression pattern (or fragment) is expressed. Shown on: expression-pattern and expression-pattern-fragment classes. Columns: Anatomy, Publications, Tags, Stage, Template, Imaging Technique, Thumbnail.

Expression patterns also offer the reverse similarity queries Neurons with similar morphology to part of [NBLAST] and Neurons matching [NeuronBridge].

Genes

Clusters expressing [term]

Single-cell transcriptomics clusters that express the gene. Shown on: gene classes with scRNAseq data. Columns: Cluster, Cell type, Cluster stage (from expression), Stages of samples, Tissues of samples, Expression Level, Expression Extent, Tags.

Genes (and other FlyBase features) also offer Find fly stocks.

Single-cell transcriptomics

Genes expressed in [term]

Genes expressed by a scRNAseq cluster, with expression level and extent. Shown on: scRNAseq clusters. Columns: Gene, Cell type, Expression Level, Expression Extent, Tags, Function.

Clusters in dataset [term]

All clusters in a single-cell RNA-seq dataset. Shown on: scRNAseq datasets. Columns: Cluster, Cell type, Cluster stage (from expression), Stages of samples, Tissues of samples, Tags, Publications.

See also scRNAseq data for [term] on anatomy pages.

How a scRNAseq dataset is organised

A dataset’s Samples are the dissected tissue it sequenced, each with its stage, tissue, sex and the fly stock, strain or genotype it came from. Each Sample was sequenced as one or more Assays (sequencing libraries), linked to their GEO, SRA and BioSample records. A Clustering is one of the authors’ analyses: the Clusters it found, from the Samples it used. A dataset can have several Clusterings (for example one per stage), and a Clustering can use Samples curated under another dataset. The queries below move between them. See Stage and tissue columns for what a cluster’s stage means.

Clusters in [term]

The clusters a Clustering found. Shown on: scRNAseq clusterings. Columns: Cluster, Cell type, Cluster stage (from expression), Cells, Genes, Dataset, Tags.

Samples in [term]

The Samples a Clustering’s cells came from. Shown on: scRNAseq clusterings. Columns: Sample, Tissue, Stage, Sex, Dataset, Tags.

Assays in [term]

The Assays (sequencing libraries) of a Clustering’s Samples. Shown on: scRNAseq clusterings. Columns: Assay, Method, Sample, Dataset.

Clusterings using [term]

The Clusterings that use a Sample, including those of other datasets that reuse it. Shown on: scRNAseq samples. Columns: Clustering, Clusters, Samples, Sample stages, Sample tissues, Dataset, Tags.

Clusterings in [term]

A dataset’s Clusterings. Shown on: scRNAseq datasets. Columns: Clustering, Clusters, Samples, Sample stages, Sample tissues, Dataset, Tags.

Samples in [term]

A dataset’s own Samples, and those its Clusterings use from other datasets (each row names its own dataset). Shown on: scRNAseq datasets. Columns: Sample, Tissue, Stage, Sex, Dataset, Tags.

Assays in [term]

The Assays of those Samples. Shown on: scRNAseq datasets. Columns: Assay, Method, Sample, Dataset.

Templates

Template brains are the reference spaces images are aligned to.

Painted domains for [term]

The painted anatomical domains defined in the template. Shown on: template brains. Columns: Domain, Type, Definition, Thumbnail.

All images aligned to [term]

Every image registered to the template’s coordinate space. Shown on: template brains. Columns: Image, Tags, Type, Template, Imaging Technique, Thumbnail.

Datasets aligned to [term]

Datasets with images aligned to the template. Shown on: template brains. Columns: Dataset, Reference, Tags, License, Template, Imaging Technique, Thumbnail, Image_count.

All available datasets

Every dataset available in VFB (offered from any template page). Shown on: template brains. Columns: Dataset, Reference, Tags, License, Template, Imaging Technique, Thumbnail, Image_count.

Datasets

Images in dataset [term]

All images belonging to a dataset. Shown on: datasets that contain images. Columns: Image, Tags, Type, Template, Imaging Technique, Thumbnail.

scRNAseq datasets also offer Clusters in dataset, Clusterings in, Samples in and Assays in.

Publications

Terms referencing [term]

Entities (terms and images) that cite the publication. Shown on: publications. Columns: Term, Reference type, Tags, Type, Template, Imaging Technique, Thumbnail.

FlyBase features & stocks

Available on FlyBase feature pages (genes, alleles, insertions, constructs, combinations, stocks and strains).

Find fly stocks for [term]

Available fly stocks for the feature, sourced from FlyBase. Shown on: FlyBase features (FBgn, FBal, FBti, FBtp, FBco, FBst), strains (FBsn) and expression patterns driven by them. For a strain (e.g. a DGRP line or Canton-S) it lists the stock-centre stocks FlyBase records as derived from it. Columns: Stock ID, Stock Number, Genotype, Collection (plus Match for split combinations).

For a split driver expression pattern the query runs on the FlyBase split combination (FBco) built from its two hemidrivers, and the combination is named in brackets — e.g. Find fly stocks for MB109B (FBco0000061). Only the most useful stocks are listed:

1. Exact combination — stocks carrying both hemidrivers. When any exist, only these are shown.
2. Hemidriver alone — otherwise, stocks of each hemidriver on its own.
3. Hemidriver in other combination — for a hemidriver with no stock of its own, stocks that carry it paired with a different hemidriver.

Steps 2 and 3 apply to each hemidriver separately, so one half may be listed on its own while the other is only available in another combination. If FlyBase has no combination for the pair, the pattern instead offers one query per hemidriver construct (FBtp).

scRNAseq samples from [term]

scRNAseq Samples taken from a fly stock or strain, or from animals whose genotype includes the allele, insertion, construct or split combination. Shown on: stocks, strains and genetic entities that scRNAseq Samples link. Columns: Sample, Tissue, Stage, Sex, Dataset, Tags.

scRNAseq clusters from samples of [term]

Clusters of the Clusterings that use those Samples. A Clustering can pool Samples of several genotypes (for example a panel of DGRP lines), so a cluster’s cells need not all come from this stock or strain. Shown on: stocks, strains and genetic entities that scRNAseq Samples link. Columns: Cluster, Cell type, Cluster stage (from expression), Stages of samples, Tissues of samples, Cells, Genes, Dataset, Tags.

Find publications for [term]

Publications for a split-GAL4 combination, from FlyBase. Shown on: FlyBase combination (FBco) features. Columns: FBrf, Title, Year, Reference, Type, DOI, PMID, PMCID.

Result columns explained

The header shown above each results column is a human-readable title, not the underlying data key. The same kind of data can appear under slightly different headers depending on the query — for example the classification badges are headed Tags in most tables but Gross Types in “List all available images”. As the site is progressively updated some tables may still show older header names (for example Gross Type for Tags, or Template Space for Template); the equivalences are noted below.

Columns in most tables

Similarity columns

NBLAST scores the 3D shape/branching similarity between two neurons. NeuronBridge finds cross-modality shape matches between light-microscopy (driver/expression) images and EM neurons. See Similarity queries.

Connectivity columns

Per-partner and per-region (individual neurons):

Per-class (neuron classes) — each row is a presynaptic class → postsynaptic class pair, rolled up over the ontology’s subclass hierarchy:

Because class-level rows roll up over the subclass hierarchy, a single raw connection can appear in more than one row, so per-row counts do not sum to a simple grand total.

Expression & transcriptomics columns

| Cells | Number of cells in a cluster. | | Genes | Number of genes expressed in more than 20% of a cluster’s cells (the genes VFB loads for it). | | Tissue / Stage / Sex (Samples) | What was dissected, the developmental stage and the sex of the animals a Sample came from. | | Method | The assay method of a sequencing library (e.g. 10x, Smart-seq2). | | Clusters / Samples (Clusterings) | How many clusters a Clustering found, and how many Samples it used. |

A cluster is a group of single cells with similar transcriptomes identified in a single-cell RNA-seq (scRNAseq) dataset, taken to represent one cell type.

Stage and tissue columns

Stage and tissue are recorded on Samples, so they are shown separately from anything known about the cluster itself:

The Samples’ stages describe what the Clustering was built from: a cluster need not have cells from each of them. Where a Clustering’s Samples span several stages of one period they are shown as the narrowest stage covering them, but never more broadly than embryonic, larval, prepupal, pupal, pharate adult or adult stage. For example, Samples from adults aged 0 to 50 days show as adult stage, and Samples from late pupae and pharate adults show as pupal stage and pharate adult stage.

Publication & stock columns

For developers

The queries above are defined and executed by the VFBquery engine and can be run outside the website via its HTTP API and the VFB MCP tools — see APIs. The engine decides which queries apply to a given entity from that entity’s classification (its types/tags), which is why the menu differs between entity types. Each query’s response carries a headers block giving the column titles used above.