Concepts

Details of concepts or terms used in Virtual Fly Brain

1: Transgene Expression
2: Split Expression
3: Templates
4: Bridging Registrations
5: Confidence Values
6: FlyLight Adult CNS Imaging Tiles

1 - Transgene Expression

These techniques work by driving the expression of a target transgenes.

Here we present details of how single transgenes are curated

Transgene expression into FlyBase and Virtual Fly Brain (VFB)

Expression of single transgenes are curated from the published literature into FlyBase as expression statements. Virtual Fly Brain (VFB) combines hosted images with neuroanatomical, expression and genetic data from FlyBase in Neo4j and maps them onto Central Nervious System (CNS) templates where they can be queried using Web Ontology Language (OWL) and Solr.

2 - Split Expression

This techniques works by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes.

Thousands of hemi-driver transgenes are now available, meaning that millions of combinations/splits are possible, each targeting some precise subset of the 10s-100s of thousands of neurons in a fly Central Nervous System (CNS). Finding the right combination for an experiment is a serious bottleneck for researchers.

FlyBase & Virtual Fly Brain (VFB) solve this problem by curating information and images recording where expression is driven by combinations of hemi-drivers. Each combination gets a standard name on VFB reflecting the names of the component hemidrivers (see figure below) and is also associated with any short names for the combination used in the literature (e.g. “P{VT017411-GAL4.DBD} ∩ P{VT019018-p65.AD} expression pattern” has_exact_synonym: SS02256")

This techniques work by driving the expression of target transgenes at the intersection between the expression patterns of two hemi-driver transgenes.

We use programmatic methods to generate expression statements for hemi-driver combinations with FlyLight image data hosted by VFB. Combinations are validated against a local copy of the FlyLight dataset and a structured user readable comment is generated as part of the expression statement. These hyperlink to the partner hemi-driver in FlyBase, contain the strain designation (where available) and can be automatically parsed by Virtual Fly Brain to attach expression and genetic data to a node representing the intersection.

split expression shown in Virtual Fly Brain (VFB)

3 - Templates

Canonical templates not only allow for spatial alignment of image data but also are often painted to make a reference atlas of anatomical regions.

Many central nervious system (CNS) templates exist for Drosophila, below we provide a summary of those used in VFB.

Central Nervious System from Janelia Research Campus JRC2018

VFB displays data aligned to either the JRC 2018 unisex brain template for cephalic or JRC 2018 unisex Ventral Nerve Cord (VNC) for non-cephalic data.

Bogovic et al., “An unbiased template of the Drosophila brain and ventral nerve cord”

We recomend downloading templates from the VFB browser or the links below however the original files are available from Janelia: JRC 2018 Brain templates

Adult Brain from Janelia Research Campus/VFB (JFRC2010/JFRC2)

Superceeded by JRC2018

Template brain created by Arnim Jenett (Janelia Research Campus), Kazunori Shinomiya and Kei Ito (Tokyo University) from a staining with the neuropil marker nc82.

The voxel size is 0.62x0.62x0.62 micron.

The files are available here.

Painted domains/regions in the available templates

Template	Painted Domains
adult brain template JFRC2	saddle, epaulette, superior posterior slope, prow, inferior posterior slope, lateral accessory lobe, bulb, lobula, superior lateral protocerebrum, adult antennal lobe, wedge, anterior optic tubercle, medulla, SIP, accessory medulla, crepine, gall, anterior ventrolateral protocerebrum, nodulus, gorget, ellipsoid body, lobula plate, antennal mechanosensory and motor center, inferior bridge, posterior lateral protocerebrum, fan-shaped body, posterior ventrolateral protocerebrum, superior medial protocerebrum, vest, antler, superior clamp, inferior clamp, flange, PB, cantle, posterior slope, clamp, lobula complex, adult central complex, adult mushroom body, adult cerebral ganglion, adult subesophageal zone, optic lobe, lateral horn, ventral complex, medial lobe of adult mushroom body, central body, lobe system of adult mushroom body, ventrolateral neuropils, ventromedial neuropils, ventrolateral protocerebrum, inferior neuropils, superior neuropils, adult gnathal ganglion, lateral complex, calyx of adult mushroom body, pedunculus of adult mushroom body, vertical lobe of adult mushroom body
adult brain template Ito2014	nodulus, lobula, accessory medulla, lobula plate, inferior clamp, antennal mechanosensory and motor center, cantle, bulb, superior lateral protocerebrum, superior intermediate protocerebrum, superior medial protocerebrum, inferior bridge, ellipsoid body, adult antennal lobe, medulla, fan-shaped body, lateral horn, lateral accessory lobe, vest, protocerebral bridge, saddle, wedge commissure, superior fiber system, superior posterior lateral protocerebrum commissure, superior antennal lobe commissure, superior ellipsoid commissure, labro_frontal_nerve - painted domain, BrainName pu, lateral cerebro-cervical fascicle, lateral equatorial fascicle, lateral accessory lobe commissure, lateral antennal lobe tract, inferior antennal lobe commissure, inferior fiber system, pyriform fascicle, horizontal ventrolateral protocerebral fascicle, posterior lateral fascicle, superior AMMC commissure, mediolateral antennal lobe tract, posterior posteriolateral protocerebral commissure, medial equatorial fascicle, posterior cerebro-cervical fascicle, vertical ventrolateral protocerebral fascicle, median bundle, wedge, gorget, anterior ventrolateral protocerebrum, posterior lateral protocerebrum, calyx of adult mushroom body, horizontal ventrolateral protocerebral fascicle, anterior optic tubercle, superior posterior slope, anterior cerebro-cervical fascicle, antenno-subesophageal tract, anterior superior lateral protocerebrum fascicle, anterior dorsal commissure, giant fiber neuron, medial cerebro-cervical fascicle, prow, adult gnathal ganglion, vertical lobe of adult mushroom body, pedunculus of adult mushroom body, crepine, antler, superior clamp, mushroom body accessory calyx, flange, medial lobe of adult mushroom body, posterior optic commissure, epaulette, medial antennal lobe tract, inferior posterior slope, posterior ventrolateral protocerebrum, great commissure, adult maxillary nerve, anterior optic tract
adult VNS template - Court2018	tectulum, prothoracic leg nerve, accessory prothoracic nerve, cervical connective, abdominal segment 3 nerve, abdominal segment 4 nerve, posterior dorsal mesothoracic nerve, accessory metathoracic nerve, adult accessory mesothoracic neuromere, metathoracic leg nerve, adult metathoracic neuromere, adult mesothoracic neuromere, dorsal prothoracic nerve, adult prothoracic neuromere, anterior dorsal mesothoracic nerve, abdominal nerve trunk, adult brain cell body rind, abdominal segment 2 nerve, ventral prothoracic nerve, adult abdominal neuromere, accessory mesothoracic nerve, dorsal metathoracic nerve, mesothoracic leg nerve
L3 CNS template - Wood2018	right dorsomedial neuropil of maxillary segment, left central subdivision of ventral nerve cord, right centromedial subdivision of ventral nerve cord, left ventromedial neuropil of tritocerebrum, right central neuropil of A9, right ventral neuropil of A9, right dorsomedial neuropil of A4, lower toe, right centromedial neuropil of A8, right centromedial neuropil of A2, right central neuropil of labial segment, left ventral neuropil of A9, right dorsomedial neuropil of A7, left ventromedial neuropil of maxillary segment, ventrolateral protocerebrum, left ventromedial neuropil of A8, left dorsomedial neuropil of T3, right central neuropil of T3, right central neuropil of mandibular segment, left central neuropil of A3, right T2 leg neuropil, right central neuropil of tritocerebrum, right central neuropil of A3, right central subdivision of ventral nerve cord, left dorsomedial neuropil of A2, left central neuropil of T1, right central neuropil of A4, left central neuropil of A5, left dorsomedial neuropil of T2, right centromedial neuropil of labial segment, right centromedial neuropil of mandibular segment, right centromedial neuropil of A3, right centromedial neuropil of T2, left central neuropil of A8, right dorsomedial neuropil of A1, right dorsomedial neuropil of labial segment, left dorsomedial neuropil of A7, right central neuropil of A6, right central neuropil of maxillary segment, protocerebral bridge - primordial, left central neuropil of mandibular segment, left dorsomedial neuropil of A4, left dorsolateral neuropil of A8, left central neuropil of A4, left ventrolateral neuropil of T3, right central neuropil of A7, right central neuropil of A8, right central neuropil of A2, left dorsomedial neuropil of A3, left ventrolateral neuropil of A4, left ventrolateral neuropil of A8, left dorsomedial neuropil of A5, left central neuropil of T2, left central neuropil of A1, left central neuropil of T3, spur of mushroom body, left dorsomedial neuropil of A6, right T1 leg neuropil, left dorsomedial neuropil of maxillary segment, right dorsolateral neuropil of maxillary segment, left dorsomedial neuropil of T1, left dorsomedial neuropil of labial segment, right dorsolateral neuropil of T3, left central neuropil of labial segment, right dorsolateral neuropil of labial segment, left T3 leg neuropil, crepine, right ventrolateral neuropil of A6, right ventrolateral neuropil of maxillary segment, right dorsolateral neuropil of A2, left dorsolateral neuropil of A5, left T1 leg neuropil, left dorsolateral subdivision of ventral nerve cord, left ventrolateral neuropil of maxillary segment, left dorsolateral neuropil of A1, right central neuropil of T1, posterior ventromedial cerebrum, left ventrolateral neuropil of mandibular segment, left dorsomedial neuropil of A1, left dorsomedial neuropil of A8, left ventrolateral neuropil of A2, left ventrolateral neuropil of T1, left centromedial neuropil of A6, medial lobe of mushroom body, left ventromedial neuropil of labial segment, right dorsal neuropil of A9, right dorsolateral neuropil of A8, left ventrolateral neuropil of T2, left ventrolateral subdivision of ventral nerve cord, left dorsomedial neuropil of mandibular segment, posterior inferior protocerebrum, left ventrolateral neuropil of A3, left dorsolateral neuropil of T1, left ventrolateral neuropil of A6, left ventrolateral neuropil of labial segment, left dorsolateral neuropil of A4, right ventrolateral neuropil of mandibular segment, right ventrolateral neuropil of T3, left centrolateral neuropil of T1, left centrolateral neuropil of A8, left dorsolateral neuropil of A6, left dorsolateral neuropil of T2, left dorsolateral neuropil of maxillary segment, right ventrolateral neuropil of A3, nodulus - primordial, left centrolateral neuropil of A2, right dorsolateral neuropil of T1, right dorsolateral neuropil of A5, right dorsolateral neuropil of A3, right dorsolateral neuropil of A7, right dorsolateral subdivision of ventral nerve cord, left ventrolateral neuropil of A1, left ventrolateral neuropil of A7, left dorsomedial subdivision of ventral nerve cord, left ventrolateral neuropil of A5, left dorsolateral neuropil of T3, right ventrolateral neuropil of A7, right ventrolateral neuropil of A5, right ventrolateral neuropil of A4, right ventrolateral neuropil of A2, posterior lateral protocerebrum, left dorsolateral neuropil of labial segment, right centrolateral neuropil of labial segment, right centrolateral neuropil of A4, right centrolateral neuropil of A1, left T2 leg neuropil, left centrolateral neuropil of A3, left centrolateral neuropil of A4, right centrolateral neuropil of A5, fan-shaped body - primordial, right ventrolateral neuropil of labial segment, right ventrolateral neuropil of T2, left centrolateral neuropil of T2, left centrolateral subdivision of ventral nerve cord, left centrolateral neuropil of labial segment, left centrolateral neuropil of A6, right dorsolateral neuropil of T2, right dorsolateral neuropil of A1, right dorsolateral neuropil of A4, left dorsal neuropil of A9, right dorsolateral neuropil of A6, left dorsolateral neuropil of A7, anterior ventromedial cerebrum](http://virtualflybrain.org/reports/VFB_00050332), ventromedial cerebrum, left centrolateral neuropil of T3, posterior superior medial protocerebrum, right centrolateral neuropil of A2, left ventromedial neuropil of A5, left centrolateral neuropil of A5, left dorsomedial neuropil of tritocerebrum, left central neuropil of A9, superior intermediate protocerebrum, mushroom body, anterior superior medial protocerebrum, right centrolateral neuropil of T1, right centrolateral neuropil of A3, right centrolateral neuropil of A6, right centrolateral neuropil of T3, left central neuropil of tritocerebrum, pedunculus of mushroom body, right centrolateral neuropil of maxillary segment, right centrolateral neuropil of A8, right centrolateral neuropil of A7, right centrolateral neuropil of T2, left centrolateral neuropil of A7, left dorsolateral neuropil of A3, right ventrolateral subdivision of ventral nerve cord, vertical lobe of mushroom body, left centromedial neuropil of A7, left ventromedial neuropil of A3, left dorsolateral neuropil of A2, lateral accessory lobe, right ventrolateral neuropil of T1, right ventrolateral neuropil of A1, right T3 leg neuropil, right ventrolateral neuropil of A8, right centromedial neuropil of A5, calyx of mushroom body, left ventromedial subdivision of ventral nerve cord, left ventromedial neuropil of mandibular segment, left centromedial neuropil of A2, left centromedial neuropil of A8, left centromedial neuropil of T1, right centromedial neuropil of tritocerebrum, right ventromedial neuropil of mandibular segment, antennal lobe, superior lateral protocerebrum, right ventromedial neuropil of A8, right ventromedial neuropil of A6, right ventromedial neuropil of A2, left ventrolateral neuropil of T1, left ventromedial neuropil of A4, left ventromedial neuropil of A6, right ventromedial neuropil of A4, right ventromedial neuropil of A5, right ventromedial neuropil of maxillary segment, right ventrolateral neuropil of T3, lateral appendix of mushroom body, left centrolateral neuropil of mandibular segment, left ventrolateral neuropil of T3, left ventrolateral neuropil of T2, right centrolateral neuropil of mandibular segment, left ventromedial neuropil of A1, left centromedial neuropil of A5, left centrolateral neuropil of A1, right dorsomedial neuropil of mandibular segment, right centromedial neuropil of T3, left central neuropil of A6, left central neuropil of A7, right dorsomedial subdivision of ventral nerve cord, left centromedial neuropil of A3, right centromedial neuropil of A4, right centromedial neuropil of A7, left centromedial subdivision of ventral nerve cord, left centromedial neuropil of A1, right ventromedial subdivision of ventral nerve cord, left centromedial neuropil of A4, left centromedial neuropil of mandibular segment, left centromedial neuropil of T3, clamp, right ventromedial neuropil of labial segment, right centromedial neuropil of maxillary segment, right ventrolateral neuropil of T2, right centromedial neuropil of A6, right ventrolateral neuropil of T1, right ventromedial neuropil of A1, left centromedial neuropil of tritocerebrum, right dorsomedial neuropil of A2, right dorsomedial neuropil of A3, right centromedial neuropil of A1, left ventromedial neuropil of A2, left ventromedial neuropil of A7, right dorsomedial neuropil of tritocerebrum, right ventromedial neuropil of A3, right centrolateral subdivision of ventral nerve cord, left centrolateral neuropil of maxillary segment, superior medial protocerebrum, left centromedial neuropil of labial segment, right ventromedial neuropil of A7, left centromedial neuropil of maxillary segment, left central neuropil of A2, left central neuropil of maxillary segment, right dorsomedial neuropil of T1, left centromedial neuropil of T2, right ventromedial neuropil of tritocerebrum, right central neuropil of T2, right central neuropil of A1, right central neuropil of A5, anterior optic tubercle primordial, right centromedial neuropil of T1, right dorsomedial neuropil of A5, right dorsomedial neuropil of A6, right dorsomedial neuropil of A8, right dorsomedial neuropil of T3, right dorsomedial neuropil of T2
JRC_FlyEM_Hemibrain	PB(R3), GOR(L), BU(L), LAL(L), ATL(L), GF(R), PB(R1), PB(R2), VES(L), NO1(R), mALT(L), CA(L), PB(L6), NO3(L), PB(L8), PB(L7), SMP(L), PB(L9), gL(L), SIP(L), b'L(L), bL(L), PB(R5), CRE(L), PB(R4), PB(R7), PB(R6), PB(R8), PB(L1), PB(R9), PB(L3), PB(L2), PB(L5), PB(L4), SCL(L), SPS(L), ICL(L), RUB(L), a'L(L), aL(L), NO2(R), NO3(R), NO1(L), NO2(L), AL(L), AOT(R), GA(R), POC, IPS(R), SAD, GC, mALT(R), AL(R), VES(R), SPS(R), ATL(R), IB, ICL(R), GOR(R), EPA(R), CAN(R), PRW, FLA(R), GNG, CA(R), LOP(R), PED(R), AMMC, b'L(R), LO(R), ME(R), AME(R), a'L(R), aL(R), bL(R), RUB(R), SCL(R), SMP(R), CRE(R), ROB(R), WED(R), SLP(R), LH(R), SIP(R), PVLP(R), AVLP(R), PLP(R), AOTU(R), PB, LAL(R), FB, BU(R), EB, gL(R), AB(R), AB(L), EPA(L)
JRC2018Unisex	ICL, ROB, GOR, SLP, RUB, CRE, SMP, SPS, CAN, SCL, SIP, IB, ATL, AL, EPA, VES, LH, LO, SAD, AME, PVLP, AVLP, WED, PRW, AMMC, aL, LOP, a'L, bL, ME, PED, CA, NO, GA, AOTU, BU, PLP, GNG, EB, LAL, PB, IPS, b'L, gL, FB, FLA

4 - Bridging Registrations

Transformations to map between different cononical Drosophila templates.

Many transforms to map between different Drosophila template brains are available.

You can see how to use the above in python using navis-flybrains or in R using nat.flybrains

5 - Confidence Values

Confidence values for predictions on VFB.

Some annotations on VFB are based on predictions, for example, predicted neurotransmitters for neurons in electron microscopy datasets (see below). Where available, we include the confidence of these predictions (as a badge next to the annotation), as well as a link to the publication - in the example below, this would be by clicking on the ‘DOI’ badge.

Neurotransmitter Prediction Confidence Values

Neurotransmitter predictions for neurons in the FlyWire FAFB and Hemibrain datasets are the ‘conf_nt’ predictions from Eckstein et al. (2024). MANC and optic-lobe predictions are from Takemura et al. (2023) and Nern et al. (2024), respectively, using the methodology of Eckstein et al. (2024). This analysis only investigated a limited set of neurotransmitters and assumed a single neurotransmitter per neuron (see publications for further detail). Neurons with fewer than 100 presynapses are excluded.

6 - FlyLight Adult CNS Imaging Tiles

Tiles used during FlyLight Split-GAL4 expression pattern imaging.

While most first-generation FlyLight expression pattern images are single 20x objective acquisitions, many Split-GAL4 lines were imaged using 63x or 40x objectives. This requires multiple image acquisitions to cover the CNS regions of interest. VFB integrates only the combined images derived from these tiles and lists the tiles used to create these combined images in the comment section for each image, for example: “tile(s): ’left_dorsal, right_dorsal, ventral”. These tiles do not necessarily cover the entire brain or VNC, which complicates the assessment of the specificity of these lines. VFB notes in the comment where the combined tiles do not provide full coverage. For further information refer to Figure 4 Supplemental File 1 from ‘A split-GAL4 driver line resource for Drosophila CNS cell types’ direct link. This is a preprint and may be updated.

Sets of tiles from FlyLight (Meissner et al., 2024):