Templates
Reference templates used on Virtual Fly Brain and the painted domains/regions available in each.
Canonical templates allow image data to be spatially aligned, and are often painted to make a reference atlas of anatomical regions. Many central nervous system (CNS) templates exist for Drosophila; below is a summary of those used on VFB, grouped by the part of the nervous system and life stage they cover. Each template and its painted domains can be viewed and downloaded from their Term Info pages.
Adult brain templates
JRC2018 unisex adult brain
The current standard adult brain template on VFB. An unbiased, averaged template built from many individual brains by Bogovic et al., 2020; most adult brain image data on VFB is aligned to it. Original files: JRC 2018 Brain templates. View on VFB.
Painted domains (46)
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
Adult brain — BrainName standard (Ito2014)
The reference template for the BrainName unified adult brain nomenclature (Ito et al., 2014). A tricolor brain (presynaptic n-syb-GFP, postsynaptic Rdl-HA, and nc82) carrying the canonical BrainName neuropil domains. View on VFB.
Painted domains (75)
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 brain — JFRC2 (Jenett/JFRC2010)
An earlier adult brain template created by Arnim Jenett (Jenett et al., 2012) and painted to the BrainName standard by Jenett, Shinomiya and Ito from an nc82 (neuropil marker) staining; voxel size 0.62 µm isotropic. Superseded by the JRC2018 unisex brain above, but retained because some older data is aligned to it. Painted-domain source files: DrosAdultBRAINdomains. View on VFB.
Painted domains (58)
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 ventral nerve cord templates
JRC2018 unisex VNC
The current standard adult ventral nerve cord (VNC) template — the VNC counterpart to the JRC2018 unisex brain, built by combining male and female confocal images (Bogovic et al., 2020). Adult VNC connectome data (e.g. MANC) is aligned to it; its neuropil regions are available from the template’s Term Info page. View on VFB.
Adult VNS — Court2018
An adult VNC atlas (Court et al., 2020): annotated confocal images registered to a common coordinate space, providing a standard adult VNC neuropil and tract nomenclature. View on VFB.
Painted domains (23)
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
Larval CNS templates
L3 CNS template (Wood2018)
A third-instar (L3) larval CNS confocal template (Wood et al., 2018) imaging neuroglian (BP-104) staining of the central brain and ventral nerve cord, carrying the L3 neuropil domains. View on VFB.
Painted domains (255)
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, 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
Adult EM connectome templates
JRC_FlyEM_Hemibrain
The JRC_FlyEM_Hemibrain EM volume — a dense reconstruction of a portion of an adult female brain (Scheffer et al., 2020). Its painted domains are the neuprint ROI parcellation used by the hemibrain connectome. View on VFB.
Painted domains (97)
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)
Other templates
VFB also hosts non-CNS adult templates: the adult head (McKellar et al., 2020) and the adult T1 leg (Kuan et al., 2020).