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

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 connectome1 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 connectome2, 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

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

Acknowledgements: We thank A. Champion and the members of the MRC LMB Scientific Computing group for assistance with compute and web infrastructure; A. McLachlan, R. Court, C. Pilgrim, D. Goutte-Gattat and D. Osumi-Sutherland from the Virtual Fly Brain for helping mapping annotations into their ontology; F. Collman and C. Schneider-Mizell for developing and maintaining the CAVE engine and associated tools; B. Pedigo for discussions as well as help with matching and typing of some FlyWire neurons; we thank the members of R. Wilson’s laboratory (A.S.B. with Q. Vanderbeck, A. Li, I. Haber and P. Gibb), who reconstructed the asymmetric body neurons; P. Kandimalla, S. Noselli and the members of R. Wilson’s laboratory for pointing out the left/right inversion of FAFB; and P. Kandimalla and S. Noselli for sharing their observations that situs inversus is extremely rare in wild-type Drosophila; L. Luo and J. Macke for comments on an early version of this manuscript; reviewers for suggestions and criticisms on the submitted version; and I. Tastekin and the members of the Ribeiro laboratory for their input on gustatory sensory neuron typing. A.S.B. thanks R. I. Wilson for her support and interest as he finished this project after having moved to the Wilson laboratory. D.S.H. thanks A. Cardona for support and mentoring while in his group. This work was supported by an NIH BRAIN Initiative grant 1RF1MH120679-01 to D.D.B. with G.S.X.E.J.; a Neuronex2 award to G.S.X.E.J. and D.D.B. (NSF 2014862, MRC MC_EX_MR/T046279/1); Wellcome Trust Collaborative Awards (203261/Z/16/Z, 220343/Z/20/Z and 221300/Z/20/Z) and core support from the MRC (MC-U105188491) to G.S.X.E.J.; DFG Walter-Benjamin-Fellowship (STU 793/2-1) to T.S.; EMBO fellowship (ALTF 1258-2020) and a Sir Henry Wellcome Postdoctoral Fellowship (222782/Z/21/Z) to A.S.B.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 connectome1 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 connectome2, 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

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

Acknowledgements: We thank A. Champion and the members of the MRC LMB Scientific Computing group for assistance with compute and web infrastructure; A. McLachlan, R. Court, C. Pilgrim, D. Goutte-Gattat and D. Osumi-Sutherland from the Virtual Fly Brain for helping mapping annotations into their ontology; F. Collman and C. Schneider-Mizell for developing and maintaining the CAVE engine and associated tools; B. Pedigo for discussions as well as help with matching and typing of some FlyWire neurons; we thank the members of R. Wilson’s laboratory (A.S.B. with Q. Vanderbeck, A. Li, I. Haber and P. Gibb), who reconstructed the asymmetric body neurons; P. Kandimalla, S. Noselli and the members of R. Wilson’s laboratory for pointing out the left/right inversion of FAFB; and P. Kandimalla and S. Noselli for sharing their observations that situs inversus is extremely rare in wild-type Drosophila; L. Luo and J. Macke for comments on an early version of this manuscript; reviewers for suggestions and criticisms on the submitted version; and I. Tastekin and the members of the Ribeiro laboratory for their input on gustatory sensory neuron typing. A.S.B. thanks R. I. Wilson for her support and interest as he finished this project after having moved to the Wilson laboratory. D.S.H. thanks A. Cardona for support and mentoring while in his group. This work was supported by an NIH BRAIN Initiative grant 1RF1MH120679-01 to D.D.B. with G.S.X.E.J.; a Neuronex2 award to G.S.X.E.J. and D.D.B. (NSF 2014862, MRC MC_EX_MR/T046279/1); Wellcome Trust Collaborative Awards (203261/Z/16/Z, 220343/Z/20/Z and 221300/Z/20/Z) and core support from the MRC (MC-U105188491) to G.S.X.E.J.; DFG Walter-Benjamin-Fellowship (STU 793/2-1) to T.S.; EMBO fellowship (ALTF 1258-2020) and a Sir Henry Wellcome Postdoctoral Fellowship (222782/Z/21/Z) to A.S.B.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 connectome1 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 connectome2, 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

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

Acknowledgements: We thank A. Champion and the members of the MRC LMB Scientific Computing group for assistance with compute and web infrastructure; A. McLachlan, R. Court, C. Pilgrim, D. Goutte-Gattat and D. Osumi-Sutherland from the Virtual Fly Brain for helping mapping annotations into their ontology; F. Collman and C. Schneider-Mizell for developing and maintaining the CAVE engine and associated tools; B. Pedigo for discussions as well as help with matching and typing of some FlyWire neurons; we thank the members of R. Wilson’s laboratory (A.S.B. with Q. Vanderbeck, A. Li, I. Haber and P. Gibb), who reconstructed the asymmetric body neurons; P. Kandimalla, S. Noselli and the members of R. Wilson’s laboratory for pointing out the left/right inversion of FAFB; and P. Kandimalla and S. Noselli for sharing their observations that situs inversus is extremely rare in wild-type Drosophila; L. Luo and J. Macke for comments on an early version of this manuscript; reviewers for suggestions and criticisms on the submitted version; and I. Tastekin and the members of the Ribeiro laboratory for their input on gustatory sensory neuron typing. A.S.B. thanks R. I. Wilson for her support and interest as he finished this project after having moved to the Wilson laboratory. D.S.H. thanks A. Cardona for support and mentoring while in his group. This work was supported by an NIH BRAIN Initiative grant 1RF1MH120679-01 to D.D.B. with G.S.X.E.J.; a Neuronex2 award to G.S.X.E.J. and D.D.B. (NSF 2014862, MRC MC_EX_MR/T046279/1); Wellcome Trust Collaborative Awards (203261/Z/16/Z, 220343/Z/20/Z and 221300/Z/20/Z) and core support from the MRC (MC-U105188491) to G.S.X.E.J.; DFG Walter-Benjamin-Fellowship (STU 793/2-1) to T.S.; EMBO fellowship (ALTF 1258-2020) and a Sir Henry Wellcome Postdoctoral Fellowship (222782/Z/21/Z) to A.S.B.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 connectome1 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 connectome2, 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