Datasets by developmental stage
Every VFB dataset grouped by developmental stage — embryo, larva (L1 and L3 instars), pupa and adult — with the number of datasets at each stage.
Drosophila melanogaster is holometabolous: it passes from egg through three larval instars, pupates, and emerges as an adult – the whole cycle takes about 10 days at 25°C. Image: Allocca, Zola & Bellosta, 2018, CC BY 3.0, via Wikimedia Commons.
VFB’s datasets are documented by technique and by source elsewhere on this site; this page groups them by the developmental stage of the animal they came from, so a question like “how many larval datasets does VFB hold, and which is newest?” has one place to look. Stage labels are now being added to dataset entities in the knowledge base itself, so the grouping below will also become queryable through the API and the VFB chat as that release propagates.
The page 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.
At a glance. Of the 210 dataset entities, 2 are embryonic, 36 are larval
(27 first-instar, 5 third-instar, and 4 larval with no instar stated), 2 are pupal and
170 are adult (134 brain, 9 ventral nerve cord, 6 leg, head and thorax, and 21 full CNS or
whole body). None are stage-agnostic. The newest larval datasets by publication year are
the split-GAL4 lines of Meissner et al. (SplitMeissner2024, L3, 2024) and, for
connectomics, the L1 CNS reconstruction of Winding, Pedigo et al. (WindingPedigo2023,
2023).
| Stage | Datasets |
|---|---|
| Embryo | 2 |
| Larva — L1 (first instar) | 27 |
| Larva — L3 (third instar) | 5 |
| Larva — instar not stated | 4 |
| Pupa | 2 |
| Adult | 170 |
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.
| Dataset | Short form |
|---|---|
| Single-cell RNA-seq study of gastrulating embryos | FBlc0006191 |
| The continuum of Drosophila embryonic development at single-cell resolution | FBlc0007797 |
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. VFB holds 36 larval datasets in all: 27 at L1, 5 at L3 and 4 with no instar stated. 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.
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) and the split-GAL4 lines of Meissner et al.
(SplitMeissner2024, published 2024) — currently the newest of VFB’s larval datasets by
publication year.
| Dataset | Short form |
|---|---|
| L3 Larval CNS Template (Truman2016) | Truman2016 |
| L3 neuropils (WoodHartenstein2018) | WoodHartenstein2018 |
| Split-GAL4 lines from Meissner et al., 2024 | SplitMeissner2024 |
| Truman Larval Flip-Out Collection | TrumanWood2018 |
| Truman Larval Flip-Out Collection | TrumanWood2018public |
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.
| Dataset | Short form |
|---|---|
| MCFO images of GMR-GAL4 lines from Jovanic et al., 2019 | Gen1MCFOJovanic2019 |
| Single-cell RNA-seq study of larval optic lobes | FBlc0006404 |
| Split-GAL4 lines from Jovanic et al., 2019 | SplitJovanic2019 |
| Split-GAL4 lines from Takagi et al., 2017 | SplitTakagi2017 |
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.
| Dataset | Short form |
|---|---|
| Single-cell RNA-seq study of pupal and adult optic lobes | FBlc0005659 |
| Single-cell RNA-seq study of the pupal optic lobe | FBlc0006237 |
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.
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).
| Dataset | Short 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 cords | FBlc0005603 |
| Split-GAL4 lines from Bidaye et al., 2014 | SplitBidaye2014 |
| Split-GAL4 lines from Bidaye et al., 2020 | SplitBidaye2020 |
| Split-GAL4 lines from Gorko et al., 2024 | SplitGorko2024 |
| Split-GAL4 lines from Lillvis et al., 2024 | SplitLillvis2024 |
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.
| Dataset | Short form |
|---|---|
| Biomechanical origins of proprioceptive maps in the Drosophila leg | Mamiya2022 |
| GAL4 lines from McKellar et al., 2020 | McKellar2020 |
| Images of proboscis muscles from McKellar et al., 2020 | HeadMusclesMcKellar2020 |
| Millimeter-scale imaging of a Drosophila leg at single-neuron resolution | Kuan2020 |
| Single-cell RNA-seq study of the adult thorax | FBlc0006361 |
| Split-GAL4 lines from Tuthill et al., 2013 | SplitTuthill2013 |
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.
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.