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A connectomic resource for neural cataloguing and circuit dissection of the larval zebrafish brain

under review
  • We present a correlated light and electron microscopy (CLEM) dataset from a 7-day-old larval zebrafish, integrating confocal imaging of genetically labeled excitatory (vglut2a) and inhibitory (gad1b) neurons with nanometer-resolution serial section EM. The dataset spans the brain and anterior spinal cord, capturing >180,000 segmented soma, >40,000 molecularly annotated neurons, and 30 million synapses, most of which were classified as excitatory, inhibitory, or modulatory. To characterize the directional flow of activity across the brain, we leverage the synaptic and cell body annotations to compute region-wise input and output drive indices at single cell resolution. We illustrate the dataset’s utility by dissecting and validating circuits in three distinct systems: water flow direction encoding in the lateral line, recurrent excitation and contralateral inhibition in a hindbrain motion integrator, and functionally relevant targeted long-range projections from a tegmental excitatory nucleus, demonstrating that this resource enables rigorous hypothesis testing as well as exploratory-driven circuit analysis. The dataset is integrated into an open-access platform optimized to facilitate community reconstruction and discovery efforts throughout the larval zebrafish brain.
Metadaten
Author:Mariela D. PetkovaORCiD, Michał JanuszewskiORCiD, Tim BlakelyORCiD, Kristian J. HerreraORCiD, Gregor F.P. SchuhknechtORCiD, Robert TillerORCiD, Jinhan ChoiORCiD, Richard L. SchalekORCiD, Jonathan Boulanger-WeillORCiD, Adi Peleg, Yuelong Wu, Shuohong WangORCiD, Jakob TroidlORCiD, Sumit Kumar VohraORCiD, Donglai WeiORCiD, Zudi LinORCiD, Armin BahlORCiD, Juan Carlos Tapia, Nirmala IyerORCiD, Zachary T. Miller, Kathryn B. HebertORCiD, Elisa C. PavarinoORCiD, Milo TaylorORCiD, Zixuan Deng, Moritz StinglORCiD, Dana Hockling, Alina HeblingORCiD, Ruohong C. Wang, Lauren L. Zhang, Sam Dvorak, Zainab Faik, Kareem I. King, Jr.ORCiD, Pallavi Goel, Julian Wagner-CarenaORCiD, David AleyORCiD, Selimzhan Chalyshkan, Dominick Contreas, Xiong Li, Akila V. MuthukumarORCiD, Marina S. Vernaglia, Teodoro Tapia Carrasco, Sofia MelnychuckORCiD, TingTing YanORCiD, Ananya Dalal, James DiMartinoORCiD, Sam Brown, Nana Safo-Mensa, Ethan Greenberg, Michael CookORCiD, Samantha FinleyORCiD, Miriam A. FlynnORCiD, Gary Patrick HopkinsORCiD, Julie KovalyakORCiD, Meghan LeonardORCiD, Alanna LohffORCiD, Christopher OrdishORCiD, Ashley L. ScottORCiD, Satoko TakemuraORCiD, Claire SmithORCiD, John J. WalshORCiD, Daniel R. BergerORCiD, Hanspeter PfisterORCiD, Stuart BergORCiD, Christopher KnechtORCiD, Geoffrey W. Meissner, Wyatt KorffORCiD, Misha B AhrensORCiD, Viren JainORCiD, Jeff W. LichtmanORCiD, Florian EngertORCiD
Document Type:Article
Parent Title (English):bioRxiv
Year of first publication:2025
DOI:https://doi.org/10.1101/2025.06.10.658982
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