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Abstract

To elicit voluntary movements and integrative reflexes underlying behavior, the brain sends command signals to the spinal cord via specialized long-range descending neurons, known as spinal-projecting neurons (SPNs). The vast and widespread distribution of SPNs, combined with their complex long-distance connectivity, poses a significant challenge for mapping their anatomical organization and associating specific populations with distinct functions. Here we took advantage of the transparency and genetic accessibility of larval zebrafish to uncover the fundamental principles of SPN anatomical organization in a Teleost. Using an optical backfilling method relying on photoactivable GFP, we generate a whole-brain map of all neurons sending axons towards the spinal cord. This approach reveals far more SPNs than previously described through conventional strategies, offering an unparalleled opportunity to revisit distinct spinal-projecting nuclei distributed across hindbrain, midbrain, and diencephalic structures. Combining information on cell location, morphology, and projection patterns, we propose tentative homological designations for zebrafish of SPN nuclei based on established descriptions in mammals and other vertebrates.

In-depth summary

Claude Opus 5.5 · xhigh effort · 7 Nov 2026 · from the full text of version 2 (1 Sept 2026) · CC BY 4.0

Two-photon optical backfills of pan-neuronal photoactivatable GFP in larval zebrafish yield an estimated 1,300 spinal-projecting neurons per larva across hindbrain, midbrain and diencephalon, with tentative homologies to mammalian nuclei.

Earlier retrograde tracing in larval zebrafish labelled fewer than 200 mostly large reticulospinal neurons, and Kaede-based optical backfills covered only genetically defined subsets, so the descending system appeared simpler than in other vertebrates. Activating pan-neuronal photoactivatable GFP in the spinal cord gives a whole-brain census of spinal-projecting neurons and a basis for proposing homologies with mammalian nuclei.

Key results

  1. ShownPan-neuronal PAGFP backfills reveal many more spinal-projecting neurons than earlier dye tracing in larvae. The cells span hindbrain, midbrain and diencephalon, with the largest population in the hindbrain and an overall ipsilateral bias.

    Unilateral photoactivation labelled 654.5 ± 53 (mean ± SD) neurons per larva (n = 8 larvae), from which the whole population is estimated at 1,309 ± 106; earlier larval tracing labelled fewer than 200. Region counts against Zbrain masks put the largest population in the hindbrain, most of it in the medulla oblongata. · Brainwide distribution of spinal descending…; Introduction; Discussion; Figure legends

  2. SuggestedHindbrain spinal-projecting neurons are assigned to putative homologs of mammalian reticulospinal (e.g. gigantocellular), vestibulospinal and raphe-spinal groups. Across six vertebrates, reticulospinal neurons share a Y-shaped layout in dorsal view, and zebrafish fits it.

    Assignments follow Watson et al. 2019 brainstem subdivisions and use soma size, laterality and Tg(pet1:GFP) atlas expression (two medullary columns flank the inferior raphe). Figure 9 plots published maps for lamprey larvae, ray, lizard, snake and mouse with zebrafish, binned into Hoevell's (1911) superior, middle and inferior reticular nuclei; the comparison is qualitative, with no statistics. · Rhombencephalic projections; Reticulospinal neurons: conserved core of motor…; Figure legends

  3. SuggestedA GnRH2-expressing cluster in the interstitial tegmental region is proposed to be the Edinger-Westphal (EW) nucleus. This recasts the classical nucleus of the medial longitudinal fasciculus (nMLF) as the interstitial nucleus of Cajal and the nucleus of Darkschewitsch, both lying lateral to it.

    In Tg(GnRH2:EGFP) larvae, biocytin Alexa Fluor 594 spinal backfills labelled the nMLF but not the GFP+ cluster, which lies medial to it. cart2 and uts1 mRNA from mapZbrain (homologs of the mammalian EW peptides CART and Ucn) overlap the GnRH2+ cluster. The support is atlas overlap, not co-labelling in the same larvae. · Diencephalic projections; Diencephalic descending projections; Figure legends

  4. SuggestedDiencephalic spinal-projecting neurons include the rostral oxytocinergic preoptic cluster, which projects only ipsilaterally, and two posterior tuberculum clusters at the positions of dopaminergic groups DC2 and DC4. Hypothalamic, thalamic, accessory optic system and pretectal groups also project to the cord.

    Preoptic backfilled cells coincide with Tg(oxt:GAL4;UAS:mCherry) neurons whose axons descend only ipsilaterally; the tuberculum clusters sit anterior and posterior to the caudal oxytocin cluster. A per-region laterality index (n = 8 larvae) shows the accessory optic system projecting bilaterally with a strong contralateral bias and the rostral hypothalamus only ipsilaterally. · Diencephalic projections; Diencephalic descending projections; Figure legends

  5. SuggestedA few olfactory bulb neurons project to the spinal cord, and atlas tracings add ipsilaterally projecting subpallial neurons. The authors take this as evidence that telencephalospinal projections are not unique to mammals.

    Olfactory bulb neurons were backfilled in 4 of 8 larvae and matched single-neuron tracings in the ZExplorer atlas. The atlas also showed subpallial spinal-projecting neurons that were not detected optically; their atlas morphologies extend only to the rostral-most spinal cord. · Telencephalic projections to spinal cord; Telencephalic descending projections

Methods, data and reproducibility

Larvae expressing photoactivatable GFP (PAGFP) and FusionRed pan-neuronally received unilateral two-photon PAGFP activation in the rostral spinal cord at 5 days post fertilization (dpf), were imaged confocally at 6 dpf and registered with ANTs to a FusionRed template bridged to Zbrain and mapZbrain; backfilled somata were hand-segmented and assigned to nuclei by position, soma size, laterality and atlas markers.

  • Tg(Cau.Tuba1:PAGFP; elavl3:FusionRed) mitfa(-/-) larvae with unilateral optical spinal backfills (photoactivation at 5 dpf, imaging at 6 dpf) · zebrafish (Danio rerio) · n = 8 larvae
  • 6-dpf Tg(elavl3:stGtACR1-FusionRed) larvae registered and averaged into the reference brain template · zebrafish (Danio rerio) · n = 6 larvae
  • Tg(GnRH2:EGFP) larvae with unilateral biocytin Alexa Fluor 594 retrograde spinal labelling · zebrafish (Danio rerio)
  • Tg(oxt:GAL4;UAS:mCherry) larvae used for anatomical comparison of preoptic oxytocin neurons · zebrafish (Danio rerio)
  • Zbrain atlas (Anti-Zrf2 signal, anatomical region masks) · zebrafish
  • mapZbrain atlas (Tg(elavl3:lynTagRFP), cart2 and uts1 mRNA, Tg(pet1:GFP), single-cell projection data) · zebrafish
  • ZExplorer larval brain and spinal cord single-neuron tracing atlas · zebrafish · n = thousands of single neuron tracings
  • Published reticulospinal neuron distributions compiled for cross-species comparison (Figure 9) · multiple species (lamprey larvae, ray, lizard, snake, mouse, plus zebrafish) · n = six vertebrate species
Methods & tools
PAGFP optical backfilling (two-photon photoactivation), 3i 2p-vivo two-photon microscope with Slidebook, Olympus FV1200 confocal microscope, Biocytin Alexa Fluor 594 retrograde tracing, Fiji stitching plugin, ANTs (SlicerANTs extension, 3D Slicer 5.8.1), napari, R 4.5.3 (RStudio) and Python 3.7, Inkscape 1.4.3, Zbrain atlas, mapZbrain atlas, ZExplorer atlas
Reagents & environment
R 4.5.3 in RStudio 2025.9.0.387; Python 3.7; 3D Slicer 5.8.1 with the SlicerANTs extension (revision 4e622b5); Inkscape 1.4.3 for figures. No requirement files or containers stated.
Reproducibility gaps
No code or data deposit is given for the soma coordinates, reference brain or image stacks; the data links are third-party atlases that were queried. The ANTs parameters are attributed to a citation that is missing from the text.
Limitations (6)
  • Optical backfilling labels somata reliably but not dendrites or axons, so identification rests mainly on somatic features; for example, red nucleus axons could not be traced to confirm their projections. · stated by the authors
  • Somatic brightness depends on the ratio of activated PAGFP to soma volume, so large neurons (Mauthner cells, some pontine reticular cells) are faint and thin-axon rostral diencephalic and telencephalic neurons are probably undercounted; subpallial neurons were not detected. · stated by the authors
  • Imaging from the dorsal side, with diffuse PAGFP signal and 488 nm autofluorescence, degrades image quality in ventral brain regions. Automatic segmentation failed, so all neurons were segmented manually. · stated by the authors
  • The authors call the homologies working hypotheses: the developing 6-dpf brain is compact, nucleus boundaries are unclear, and the anatomical masks still use uncorrected boundaries around the nMLF region. · stated by the authors
  • The whole-population figure of about 1,300 is an estimate built on unilateral backfills, not a count from bilateral photoactivation. · noted in this summary
  • Many identities (Edinger-Westphal, dopaminergic tuberculum groups, medullary nuclei) rest on overlap with registered atlas expression from other animals, not on co-labelling of backfilled cells in the same larvae. · noted in this summary

Read this if you need a whole-brain anatomical reference for spinal-projecting neurons in larval zebrafish, for instance to target reticulospinal, vestibulospinal or neuromodulatory populations, or to compare brainstem organization with mammals.

Citations
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