An unbiased template of the<i>Drosophila</i>brain and ventral nerve cord

Bogovic, John A.; Otsuna, Hideo; Heinrich, Larissa; Ito, Masayoshi; Jeter, Jennifer; Meissner, Geoffrey W.; Nern, Aljoscha; Colonell, Jennifer; Malkesman, Oz; Ito, Kei; Saalfeld, Stephan

doi:10.1101/376384

Cited by 26 publications

(47 citation statements)

References 55 publications

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“…To quantify this symmetry, we first registered the EM dataset to a standard VNC atlas to place the EMreconstructed neurons into a reference coordinate system and to correct for asymmetries introduced by EM specimen preparation. The VNC atlas is a map of synapse density across the VNC (Bogovic et al, 2018). To register the EM dataset to the atlas, we first estimated the density of synapses across the EM dataset using an artificial neural network trained to identify synapses based on their ultrastructural features ( Fig.…”

Section: Vnc Atlas Registration Reveals Uniqueness and Symmetry Of Lementioning

confidence: 99%

“…This allowed us to align the complete VNC EM volume to the adult female VNC atlas ( Fig. S4D-E and Video S4) (Bogovic et al, 2018).…”

Section: Vnc Atlas Registration Reveals Uniqueness and Symmetry Of Lementioning

confidence: 99%

“…We chose a standard VNC atlas (Bogovic et al, 2018) as our reference coordinate space. We used the presynaptic specializations predicted in the EM volume to register the EM dataset to the atlas.…”

Section: Automated Synapse Prediction and Vnc Atlas Alignmentmentioning

confidence: 99%

“…The synapse-density map of the EM dataset (Ai; seeFig. S4for generation of this map) was registered to a standard VNC synapse-density map (Aii;Bogovic et al 2018). Then, fluorescently labeled motor neurons (Aiiiiv) were also registered to the standard VNC for quantitative comparison with EM reconstructions using NBLAST(Costa et al 2016).…”

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confidence: 99%

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Reconstruction of motor control circuits in adultDrosophilausing automated transmission electron microscopy

Maniates-Selvin

Hildebrand

Graham

et al. 2020

Preprint

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Many animals use coordinated limb movements to interact with and navigate through the environment. To investigate circuit mechanisms underlying locomotor behavior, we used serial-section electron microscopy (EM) to map synaptic connectivity within a neuronal network that controls limb movements. We present a synapse-resolution EM dataset containing the ventral nerve cord (VNC) of an adult female Drosophila melanogaster. To generate this dataset, we developed GridTape, a technology that combines automated serial-section collection with automated high-throughput transmission EM. Using this dataset, we reconstructed 507 motor neurons, including all those that control the legs and wings. We show that a specific class of leg sensory neurons directly synapse onto the largest-caliber motor neuron axons on both sides of the body, representing a unique feedback pathway for fast limb control. We provide open access to the dataset and reconstructions registered to a standard atlas to permit matching of cells between EM and light microscopy data. We also provide GridTape instrumentation designs and software to make large-scale EM data acquisition more accessible and affordable to the scientific community.

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Section: Vnc Atlas Registration Reveals Uniqueness and Symmetry Of Lementioning

confidence: 99%

“…This allowed us to align the complete VNC EM volume to the adult female VNC atlas ( Fig. S4D-E and Video S4) (Bogovic et al, 2018).…”

Section: Vnc Atlas Registration Reveals Uniqueness and Symmetry Of Lementioning

confidence: 99%

Section: Automated Synapse Prediction and Vnc Atlas Alignmentmentioning

confidence: 99%

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confidence: 99%

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Reconstruction of motor control circuits in adultDrosophilausing automated transmission electron microscopy

Maniates-Selvin

Hildebrand

Graham

et al. 2020

Preprint

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“…We registered the hemibrain EM data to the JRC2018 Drosophila template brain( Bogovic et al, 2018 ) using an automatic registration algorithm followed by manual correction. We began by using the automated T-bar predictions (described in section 2.3) to generate a T-bar density volume rendered at a resolution comparable to those from light microscopic images.…”

Section: Introductionmentioning

confidence: 99%

A Connectome and Analysis of the AdultDrosophilaCentral Brain

Scheffer

Januszewski

et al. 2020

Preprint

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162

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The neural circuits responsible for animal behavior remain largely unknown. We 31 summarize new methods and present the circuitry of a large fraction of the brain of the fruit fly 32 Drosophila melanogaster. Improved methods include new procedures to prepare, image, align, 33 segment, find synapses in, and proofread such large data sets. We define cell types, refine 34 computational compartments, and provide an exhaustive atlas of cell examples and types, many of 35 them novel. We provide detailed circuits consisting of neurons and their chemical synapses for 36 most of the central brain. We make the data public and simplify access, reducing the effort needed 37 to answer circuit questions, and provide procedures linking the neurons defined by our analysis 38 with genetic reagents. Biologically, we examine distributions of connection strengths, neural motifs 39 on different scales, electrical consequences of compartmentalization, and evidence that 40 maximizing packing density is an important criterion in the evolution of the fly's brain. 41 1 of 57 53 Producing this data set required advances in sample preparation, imaging, image alignment, ma-54 chine segmentation of cells, synapse detection, data storage, proofreading software, and protocols 55 to arbitrate each decision. A number of new tests for estimating the completeness and accuracy 56 were required and therefore developed, in order to verify the correctness of the connectome. 57 These data describe whole-brain properties and circuits, as well as contain new methods to 58 classify cell types based on connectivity. Computational compartments are now more carefully 59 defined, we identify actual synaptic circuits, and each neuron is annotated by name and putative 60 cell type, making this the first complete census of neuropils, tracts, cells, and connections in this 61 2 of 57 Manuscript submitted to eLife Figure 2. Brain regions contained and defined in the hemibrain, following the naming conventions of (Ito et al., 2014) with the addition of (R) and (L) to specify the side of the soma for that region. Gray italics indicate master regions not explicitly defined in the hemibrain. Region LA is not included in the volume. The regions are hierarchical, with the more indented regions forming subsets of the less indented. The only exceptions are dACA, lACA, and vACA which are considered part of the mushroom body but are not contained in the master region MB.portion of the brain. We compare the statistics and structure of different brain regions, and for 62 the brain as a whole, without the confounds introduced by studying different circuitry in different 63 animals. 64 All data are publicly available through web interfaces. This includes a browser interface, Ne-65 uPrint (Clements et al., 2020), designed so that any interested user can query the hemibrain con-66 nectome even without specific training. NeuPrint can query the connectivity, partners, connection 67 strengths and morphologies of all specified neurons, thus making identifica...

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