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Whole-brain annotation and multi-connectome cell typing of Drosophila

Affiliations
  • 1Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK.
  • 2Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
  • 3Department of Neurobiology and Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA.
  • 4Centre for Neural Circuits and Behaviour, University of Oxford, Oxford, UK.
  • 5Computer Science Department, Princeton University, Princeton, NJ, USA.
  • 6Princeton Neuroscience Institute, Princeton University, Princeton, NJ, USA.
  • 7School of Mathematics and Statistics, University of New South Wales, Sydney, New South Wales, Australia.
  • 8Yikes, Baltimore, MD, USA.
  • 9kazmos, Dresden, Germany.
  • 10Eyewire, Boston, MA, USA.
  • 11Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, CA, USA.
  • 12Department of Neurological Sciences, Larner College of Medicine, University of Vermont, Burlington, VT, USA. dbock@uvm.edu.
  • 13Neurobiology Division, MRC Laboratory of Molecular Biology, Cambridge, UK. jefferis@mrc-lmb.cam.ac.uk.
  • 14Drosophila Connectomics Group, Department of Zoology, University of Cambridge, Cambridge, UK. jefferis@mrc-lmb.cam.ac.uk.

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October 2, 2024

Abstract

The fruit fly Drosophila melanogaster has emerged as a key model organism in neuroscience, in large part due to the concentration of collaboratively generated molecular, genetic and digital resources available for it. Here we complement the approximately 140,000 neuron FlyWire whole-brain connectome with a systematic and hierarchical annotation of neuronal classes, cell types and developmental units (hemilineages). Of 8,453 annotated cell types, 3,643 were previously proposed in the partial hemibrain connectome, and 4,581 are new types, mostly from brain regions outside the hemibrain subvolume. Although nearly all hemibrain neurons could be matched morphologically in FlyWire, about one-third of cell types proposed for the hemibrain could not be reliably reidentified. We therefore propose a new definition of cell type as groups of cells that are each quantitatively more similar to cells in a different brain than to any other cell in the same brain, and we validate this definition through joint analysis of FlyWire and hemibrain connectomes. Further analysis defined simple heuristics for the reliability of connections between brains, revealed broad stereotypy and occasional variability in neuron count and connectivity, and provided evidence for functional homeostasis in the mushroom body through adjustments of the absolute amount of excitatory input while maintaining the excitation/inhibition ratio. Our work defines a consensus cell type atlas for the fly brain and provides both an intellectual framework and open-source toolchain for brain-scale comparative connectomics.