Virtual Fly Brain Drosophila CNS atlas
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Datasets by developmental stage

Every VFB dataset grouped by the developmental stage of the animal it was collected from.

31 Aug 2026

VFB’s datasets are documented by technique and by source elsewhere on this site, but nothing groups them by the stage of the animal they came from. That gap has come up in practice: it is why a question like “how many larval datasets does VFB hold, and which is newest?” has no direct answer on the site today, and can only be approximated by searching dataset names for the word “larval” — a search that misses anything not named that way, and catches nothing at all for embryo or pupal material.

This page is that missing reference. It lists all 210 dataset entities currently in the VFB knowledge base (DataSet individuals — the same list search_terms returns when filtered to dataset), grouped by developmental stage, with a link to each dataset’s own page where a stage-agnostic reader would want to jump straight to the data.

How this was built. VFB does not currently record a structured “stage” field on dataset entities — this table was compiled by hand from each dataset’s name, description and publication, cross-checked against a more reliable structured signal where one exists: which template a dataset’s images are registered to. Registration is stage-specific — the L1 CNS template (Seymour, VFB_00050000) only ever receives first-instar larval images, the L3 CNS template (Wood2018, VFB_00049000) only third-instar images — so a dataset’s AlignedDatasets membership on those templates is firmer evidence than its name. That check changed three classifications from the first, label-only pass: the TrumanWood2018/TrumanWood2018public Truman Larval Flip-Out Collection and SplitMeissner2024 are all registered to the L3 template rather than an unspecified larval stage or, in Meissner’s case, no stage at all. This is a documentation convenience, not a data-model change — nothing here is queryable from the API. A dataset missing from a future data release, or one whose stage was misjudged, should be corrected here directly; if VFB’s data model gains a real structured stage field later, this page should be regenerated from it instead of maintained by hand.

Embryo

Approximately 0–22 hours after egg laying, from fertilisation to hatching. The two datasets here are single-cell/single-nucleus transcriptomic surveys of the whole embryo; VFB holds no embryonic imaging data at this time.

DatasetShort form
Single-cell RNA-seq study of gastrulating embryosFBlc0006191
The continuum of Drosophila embryonic development at single-cell resolutionFBlc0007797

Larva

The larval period runs from hatching to pupariation and is divided into three instars — L1, L2 and L3 — separated by moults. VFB’s larval holdings cluster almost entirely at the first and third instars; no dataset here is recorded as L2. Anatomy differs enough between instars that a “larval” dataset with no instar stated should not be assumed comparable to one that states it, particularly for connectomic data.

L1 (first instar)

The stage most larval EM connectomics is drawn from: the larval CNS is small enough for a first-instar animal to be reconstructed at synaptic resolution in a single study. Most entries below are single-paper EM reconstructions built on the l1em connectome (Ohyama et al. 2015 and the studies that extended it) and registered to the L1 CNS template.

DatasetShort form
Comparative Connectomics Reveals How Partner Identity, Location, and Activity Specify Synaptic Connectivity in Drosophila (Valdes-Aleman et al. 2021)Valdes_Aleman2021
EM L1 Andrade et al. 2019Andrade2019
EM L1 Barnes et al., 2022Barnes2022
EM L1 Carreira-Rosario, Arzan Zarin, Clark et al. 2018CarreiraRosario2018
EM L1 Eschbach et al 2020Eschbach2020
EM L1 Eschbach et al 2020bEschbach2020b
EM L1 Imambocus et al., 2022Imambocus2022
EM L1 Jovanic et al. 2019Jovanic2019
EM L1 Mark et al. 2019Mark2019
EM L1 Miroschnikow et al. 2018Miroschnikow2018
EM L1 Tastekin et al 2018Tastekin2018
EM L1 Winding, Pedigo et al., 2023WindingPedigo2023
EM L1 Zarin, Mark et al. 2019Zarin2019
Eve+ neurons, sensorimotor circuit - EM (Heckscher2015)Heckscher2015
Full CNS EM, sparse (manually traced) reconstruction (L1 larva)Ohyama2015
larval hugin neurons - EM (Schlegel2016)Schlegel2016
Larval MB neurons - EM (Eichler2017)Eichler2017
Larval motor circuit neurons (Zwart2016)Zwart2016
Larval olfactory system neurons - EM (Berck2016)Berck2016
Larval peristaltic locomotor system neurons - EM (Fushiki2016)Fushiki2016
larval sensorimotor decision pathways (Jovanic2016)Jovanic2016
larval visual circuit neurons (Larderet2017)Larderet2017
Larval wave neurons and circuit partners - EM (Takagi2017)Takagi2017
Nociceptive circuit neurons - EM (Gerhard2017)Gerhard2017
Nociceptive system neurons - EM (Burgos2017)Burgos2018
Single-cell RNA-seq study of first instar larval brains upon starvationFBlc0005362
Unveiling the sensory and interneuronal pathways of the neuroendocrine connectome in Drosophila (Hueckesfeld et al. 2020)Hueckesfeld2020

L3 (third instar)

The last and largest larval instar, imaged shortly before pupariation. VFB’s L3 material is registered to the Wood2018 L3 CNS template and includes the Truman Larval Flip-Out Collection (TrumanWood2018, published 2018) — currently the newest of VFB’s larval datasets by publication year.

DatasetShort form
L3 Larval CNS Template (Truman2016)Truman2016
L3 neuropils (WoodHartenstein2018)WoodHartenstein2018
Split-GAL4 lines from Meissner et al., 2024SplitMeissner2024
Truman Larval Flip-Out CollectionTrumanWood2018
Truman Larval Flip-Out CollectionTrumanWood2018public

Larva (instar not stated)

Larval by name, publication or genetic targeting, but without enough evidence in VFB to assign a specific instar — none of these are registered to either larval template, most likely because they are driver-line metadata without their own aligned images. Treat the instar as unknown rather than assuming L1 or L3.

DatasetShort form
MCFO images of GMR-GAL4 lines from Jovanic et al., 2019Gen1MCFOJovanic2019
Single-cell RNA-seq study of larval optic lobesFBlc0006404
Split-GAL4 lines from Jovanic et al., 2019SplitJovanic2019
Split-GAL4 lines from Takagi et al., 2017SplitTakagi2017

Pupa

Metamorphosis, from pupariation to eclosion. Both datasets here are transcriptomic surveys of the optic lobe spanning the pupal-to-adult transition; VFB holds no pupal-only imaging data.

DatasetShort form
Single-cell RNA-seq study of pupal and adult optic lobesFBlc0005659
Single-cell RNA-seq study of the pupal optic lobeFBlc0006237

Adult

By far VFB’s largest holding: 170 of the 210 dataset entities. Almost everything here is light-microscopy driver-line and split-GAL4 material from FlyLight, VDRC, FlyCircuit and individual labs, plus the per-paper EM connectome datasets (FAFB, hemibrain and their derivatives) and the adult-focused Fly Cell Atlas / Aging Fly Cell Atlas scRNAseq series. Sex is usually stated for the EM connectomes (FAFB and hemibrain are each a single traced female brain; MANC and Male-CNS are male) and usually unstated for driver-line collections, which typically pool both sexes.

Brain

The overwhelming majority of VFB’s adult data: everything above that targets or images central brain and optic lobe circuitry, without a more specific VNC, leg or whole-body grouping below.

DatasetShort form
Adult Brain fru clones (Cachero2010)Cachero2010
AMMC local and projection neurons (Matsuo2016)Matsuo2016
BrainName neuropils and tracts - Ito half-brainBrainName_Ito_half_brain
BrainName neuropils on adult brain JFRC2 (Jenett, Shinomya)JenettShinomya_BrainName
BrainTrap lines (Knowles-Barley2010)Knowles_Barley2010
central brain neurons by lineage, Lee2020Lee_Lineage2020
Dickson lab VT line collection - VDRC imagesDickson_VT
Dickson lab VT lines - FlyLight/Janelia images (2017)Dickson2017
EM FAFB Baltruschat et al 2021Baltruschat2021
EM FAFB Bates and Schlegel et al 2020BatesSchlegel2020
EM FAFB Coates et al 2020Coates2020
EM FAFB Dolan and Belliart-Guerin et al. 2018Dolan2018
EM FAFB Dolan et al. 2019FafbDolan2019
EM FAFB Dombrovski et al 2023Dombrovski2023
EM FAFB Engert et al. 2022Engert2022
EM FAFB Erginkaya et al 2025Erginkaya2025
EM FAFB Felsenberg et al. 2018Felsenberg2018
EM FAFB Gorko et al 2024Gorko2024
EM FAFB Hampel and Eichler et al 2020HampelEichler2020
EM FAFB Kim et al 2020Kim2020
EM FAFB Kind et al. 2021Kind2021
EM FAFB Marin et al 2020Marin2020
EM FAFB Morimoto et al 2020Morimoto2020
EM FAFB Otto et al 2020Otto2020
EM FAFB Sayin et al 2019Sayin2019
EM FAFB Shiu et al. 2022Shiu2022
EM FAFB Taisz and Galili et al., 2022TaiszGalili2022
EM FAFB Turner-Evans et al 2020Turner_Evans2020
EM FAFB Wang et al 2020aWang2020a
EM FAFB Wang et al 2020bWang2020b
EM FAFB Wang et al 2020cWang2020c
EM FAFB Zhao et al., 2023Zhao2023
EM FAFB Zheng et al 2020 (published 2022)Zheng2020
FlyCircuit 1.0 - single neurons (Chiang2010)Chiang2010
FlyLight - Gen1 GAL4/LexA collection (exported 2019)FlyLightGen1Set2019
FlyLight - GMR GAL4 collection (Jenett2012)Jenett2012
FlyLight split-GAL4 lines for Lateral HornFlyLight2019LateralHorn2019
FlyLight split-GAL4 lines for Lateral Horn (LateralHorn2019)LateralHorn2019
Full brain EM connectome, dense reconstruction (adult female)Dorkenwald2023
Full brain EM, sparse (manually traced) reconstruction (adult female)Zheng2018
GAL4 Split expression patterns from Dolan et al. 2019Dolan2019
Grooming neurons and drivers (Hampel 2015)FlyLight2019Hampel2015
Grooming neurons and drivers (Hampel 2015)Hampel2015
Images of aSP22 descending neuron from McKellar et al., 2019McKellar2019
Ito lab adult brain lineage clone image setIto2013
JRC 2018 templates & ROIsJRC2018
JRC_FlyEM_Hemibrain painted domainsXu2020roi
Lee lab adult brain lineage clone image setYu2013
LexA driver targetting mechanosensory eye bristles (Hampel2017)Hampel2017
MBONs and split-GAL4 lines that target them (Aso2014)Aso2014
MCFO images of GMR-GAL4 lines from Dionne et al., 2018Gen1MCFODionne2018
MCFO images of GMR-GAL4 lines from Jenett et al., 2012Gen1MCFOJenett2012
MCFO images of GMR-GAL4 lines from Pfeiffer et al., 2010Gen1MCFOPfeiffer2010
MCFO images of VT-GAL4 lines from Tirian et al., 2017Gen1MCFOTirian2017
Optic lobe EM connectome, dense reconstruction (adult male)Nern2024
Partial brain EM connectome, dense reconstruction (adult female)Xu2020NeuronsV1point2point1
RNAseq_2020_DavisPRJNA480794
Single-cell RNA-seq study of adult brain without alcohol exposureFBlc0005420
Single-cell RNA-seq study of adult brain without cocaine exposureFBlc0005515
Single-cell RNA-seq study of the aging brainFBlc0006090
Single-cell RNA-seq study of visual motion-sensing neuronsFBlc0006305
Single-nucleus RNA-seq on cells from 30-days old male fliesFBlc0006611
Split GAL4 lines for dopaminergic neurons, Xie2018Xie2018
split-GAL4 lines for EB neurons (Robie2017)Robie2017
split-GAL4 lines for dopaminergic neurons (AsoRubin2016)AsoRubin2016
split-GAL4 lines for dopaminergic neurons (AsoRubin2016)FlyLight2019AsoRubin2016
split-GAL4 lines for EB neurons (Robie2017)FlyLight2019Robie2017
split-GAL4 lines for LC VPNs (Wu2016)FlyLight2019Wu2016
split-GAL4 lines for LC VPNs (Wu2016)Wu2016
Split-GAL4 lines from Aso et al., 2014bSplitAso2014b
Split-GAL4 lines from Baker et al., 2022SplitBaker2022
Split-GAL4 lines from Bogovic et al., 2020SplitBogovic2020
Split-GAL4 lines from Cheong et al., 2023SplitCheong2023
Split-GAL4 lines from Cheong et al., 2024SplitCheong2024
Split-GAL4 lines from Dag et al., 2019SplitDag2019
Split-GAL4 lines from Davis et al., 2020SplitDavis2020
Split-GAL4 lines from Ehrhardt et al., 2023SplitEhrhardt2023
Split-GAL4 lines from Feng et al., 2014SplitFeng2014
Split-GAL4 lines from Gao et al., 2019SplitGao2019
Split-GAL4 lines from Garner et al., 2023SplitGarner2023
Split-GAL4 lines from Giraldo et al., 2018SplitGiraldo2018
Split-GAL4 lines from Hattori et al., 2017SplitHattori2017
Split-GAL4 lines from Hulse et al., 2021SplitHulse2021
Split-GAL4 lines from Isaacson et al., 2023SplitIsaacson2023
Split-GAL4 lines from Kind et al., 2021SplitKind2021
Split-GAL4 lines from Klapoetke et al. 2017FlyLight2019Klapoetke2017
Split-GAL4 lines from Klapoetke et al. 2017Klapoetke2017
Split-GAL4 lines from Klapoetke et al., 2022SplitKlapoetke2022
Split-GAL4 lines from Lillvis et al., 2022SplitLillvis2022
Split-GAL4 lines from Liu et al., 2019SplitLiu2019
Split-GAL4 lines from Longden et al., 2021SplitLongden2021
Split-GAL4 lines from Longden et al., 2023SplitLongden2023
Split-GAL4 lines from Mais et al., 2021SplitMais2021
Split-GAL4 lines from Masek et al., 2015SplitMasek2015
Split-GAL4 lines from Meissner et al., 2018SplitMeissner2018
Split-GAL4 lines from Minegishi et al., 2023SplitMinegishi2023
Split-GAL4 lines from Montague et al., 2019SplitMontague2019
Split-GAL4 lines from Morimoto et al., 2020SplitMorimoto2020
Split-GAL4 lines from Nallasivan et al 2025SplitNallasivan2025
Split-GAL4 lines from Nern et al., 2025SplitNern2025
Split-GAL4 lines from Nojima et al., 2021Nojima2021
Split-GAL4 lines from Ribeiro et al., 2018SplitRibeiro2018
Split-GAL4 lines from Rubin et al., 2024SplitRubin2024
Split-GAL4 lines from Schlichting et al., 2019SplitSchlichting2019
Split-GAL4 lines from Schretter et al., 2020SplitSchretter2020
Split-GAL4 lines from Schretter et al., 2024SplitSchretter2024
Split-GAL4 lines from Shao et al., 2017SplitShao2017
Split-GAL4 lines from Shuai et al., 2023SplitShuai2023
Split-GAL4 lines from Sitaraman et al., 2015SplitSitaraman2015
Split-GAL4 lines from Sterne et al., 2021SplitSterne2021
Split-GAL4 lines from Sun et al., 2017SplitSun2017
Split-GAL4 lines from Takemura et al., 2017SplitTakemura2017
Split-GAL4 lines from Tanaka et al., 2008SplitTanaka2008
Split-GAL4 lines from Triphan et al., 2016SplitTriphan2016
Split-GAL4 lines from Turner-Evans et al., 2017SplitDavis2017
Split-GAL4 lines from Turner-Evans et al., 2017SplitTurner_Evans2017
Split-GAL4 lines from Turner-Evans et al., 2020SplitTurner_Evans2020
Split-GAL4 lines from Vijayan et al., 2023SplitVijayan2023
Split-GAL4 lines from Vogt et al., 2014SplitVogt2014
Split-GAL4 lines from Vogt et al., 2016SplitVogt2016
Split-GAL4 lines from Wang et al., 2020aSplitWang2020a
Split-GAL4 lines from Wang et al., 2020bSplitWang2020b
Split-GAL4 lines from Wang et al., 2020cSplitWang2020c
Split-GAL4 lines from Wolff et al., 2025SplitWolff2025
Split-GAL4 lines from Xie et al., 2021SplitXie2021
Split-GAL4 lines from Yamagata et al., 2015SplitYamagata2015
Split-GAL4 lines from Yoo et al., 2023SplitYoo2023
Split-GAL4 lines from Zhao et al., 2023SplitZhao2023
Split-GAL4 lines from Zhao et al., 2025SplitZhao2025
Splits targetting CX neurons, Wolff2018FlyLight2019Wolff2018
Splits targetting CX neurons, Wolff2018Wolff2018
Splits targetting the visual motion pathway, Strother2017FlyLight2019Strother2017
Splits targetting the visual motion pathway, Strother2017Strother2017
Third order olfactory neurons involved in pheromone response - backfills (Kohl2013)Kohl2013

VNC (ventral nerve cord)

Datasets specific to the adult ventral nerve cord — MANC and FANC on the EM side, the Court VNC/VNS templates and neuropils, and the handful of driver-line and scRNAseq sets built around VNC circuits (walking, courtship song, neck motor control).

DatasetShort form
Adult VNC neuropils (Court2020)Court2020
Adult VNS neuropils (Court2017)Court2017
Full VNC EM connectome, dense reconstruction (adult male)Takemura2023
Full VNS EM, sparse reconstruction (adult female)Maniates_Selvin2020
Single-cell RNA-seq study of adult ventral nerve cordsFBlc0005603
Split-GAL4 lines from Bidaye et al., 2014SplitBidaye2014
Split-GAL4 lines from Bidaye et al., 2020SplitBidaye2020
Split-GAL4 lines from Gorko et al., 2024SplitGorko2024
Split-GAL4 lines from Lillvis et al., 2024SplitLillvis2024

Leg, head and thorax

Peripheral and body-wall datasets that are neither brain nor VNC proper: leg proprioception and imaging, proboscis motor neurons, and thoracic scRNAseq.

DatasetShort form
Biomechanical origins of proprioceptive maps in the Drosophila legMamiya2022
GAL4 lines from McKellar et al., 2020McKellar2020
Images of proboscis muscles from McKellar et al., 2020HeadMusclesMcKellar2020
Millimeter-scale imaging of a Drosophila leg at single-neuron resolutionKuan2020
Single-cell RNA-seq study of the adult thoraxFBlc0006361
Split-GAL4 lines from Tuthill et al., 2013SplitTuthill2013

Full CNS and whole body

Resources that deliberately span more than one region: whole-CNS connectomes (BANC, Male-CNS), descending-neuron driver-line sets that by design run from the brain into the VNC, and the Fly Cell Atlas / Aging Fly Cell Atlas scRNAseq series, which sample the whole animal rather than the nervous system alone.

DatasetShort form
Full CNS EM connectome, dense reconstruction (adult female)Bates2025
Full CNS EM connectome, dense reconstruction (adult male)Berg2025
Neurons involved in courtship and song (Lillvis2018)Lillvis2018
Single-nucleus RNA-seq on cells from 30-days old female fliesFBlc0006424
Single-nucleus RNA-seq on cells from 30-days old fliesFBlc0006423
Single-nucleus RNA-seq on cells from 5-days old female and male fliesFBlc0004785
Single-nucleus RNA-seq on cells from 5-days old female fliesFBlc0003846
Single-nucleus RNA-seq on cells from 5-days old male fliesFBlc0004307
Single-nucleus RNA-seq on cells from 50-days old female fliesFBlc0006888
Single-nucleus RNA-seq on cells from 50-days old fliesFBlc0006887
Single-nucleus RNA-seq on cells from 50-days old male fliesFBlc0007071
Single-nucleus RNA-seq on cells from 70-days old female fliesFBlc0007348
Single-nucleus RNA-seq on cells from 70-days old fliesFBlc0007347
Single-nucleus RNA-seq on cells from 70-days old male fliesFBlc0007532
split-GAL4 lines for descending neurons (Namiki2018)FlyLight2019Namiki2018
split-GAL4 lines for descending neurons (Namiki2018)Namiki2018
Split-GAL4 lines from Feng et al., 2020SplitFeng2020
Split-GAL4 lines from Liang et al., 2017SplitLiang2017
Split-GAL4 lines from Namiki et al., 2022SplitNamiki2022
Split-GAL4 lines from Reyn et al., 2017SplitReyn2017
Split-GAL4 lines from Zung et al., 2025SplitZung2025

Stage-agnostic resources

A small number of dataset entities in VFB’s knowledge base are reference resources rather than material from an animal at a particular stage — reused across stages by design. None fall in this bucket at the time of writing (VFB’s templates and neuropil domain sets are all stage-specific and appear above under their own stage), but the category is kept here for anything added later that should not be forced into a stage it does not have.