The natverse, a versatile toolbox for combining and analysing neuroanatomical data

Bates, Alexander Shakeel; Manton, James D.; Jagannathan, Sridhar R.; Costa, Marta; Schlegel, Philipp; Rohlfing, Torsten; Jefferis, Gregory

doi:10.7554/elife.53350

Cited by 175 publications

(175 citation statements)

References 143 publications

(271 reference statements)

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“…We also grouped vTel y321 neurons using NBLAST hierarchical clustering methods applied to zebrafish forebrain neurons in a previous study, which yielded similar results (data not shown). 44,45 Complex arbors remain over-represented in 14 dpf XGF larvae relative to their CVZ siblings ( Figure 4c, d: aqua, purple). Therefore, it appears that the majority of vTel y321 neurons analyzed in GF or XGF fish are morphologically similar to those from CVZ siblings, but that the microbiota normally restrains arborization of a subset of vTel y321 neurons that become dramatically more complex in GF or XGF conditions.…”

Section: Resultsmentioning

confidence: 97%

“…This generated transformed images and image rotation, translation, scaling, shearing, and centering coordinates used to achieve that transformation. These transformation coordinates were then applied to SWC-formatted neurons using Natverse package functions in R. 45 Formatting neurons as SWC files converts them into a matrix of (x,y,z) coordinates so that they can be read across platforms. For each condition, transformed neurons were exported from R in SWC format and imported into the average vTel y321 GFP forebrain for 3D visualization in Imaris software (Oxford Instruments, Concord MA).…”

Section: Image Analysis Neuronal Morphology Was Extracted From Confomentioning

confidence: 99%

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The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons

Bruckner

Stednitz

Grice

et al. 2020

Preprint

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Host-associated microbiotas normally guide the trajectory of intrinsically encoded developmental programs, and dysbiosis is linked to neurodevelopmental disorders such as autism spectrum disorder.Recent work suggests that microbiotas modulate social phenotypes associated with these disorders, though developmental mechanisms linking microbiotas to social behavior are not well understood. We discovered that the zebrafish microbiota is required for normal social behavior. Using this model to examine neuronal features modulated by the microbiota during early development, we found that the microbiota restrains neurite complexity and targeting of specific forebrain neurons required for normal social behavior. The microbiota is also required for normal forebrain infiltration of microglia, the brain's resident phagocytes that remodel neuronal arbors, suggesting the microbiota modulates arborization via a neuro-immune route. Our work establishes a foundation for study of microbial and host mechanisms that link the microbiota and social behavior in an experimentally tractable model vertebrate.

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Section: Resultsmentioning

confidence: 97%

Section: Image Analysis Neuronal Morphology Was Extracted From Confomentioning

confidence: 99%

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons

Bruckner

Stednitz

Grice

et al. 2020

Preprint

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“…Similar tools have been developed for other model organisms, such as the Allen Mouse Brain Connectivity Atlas [43], the WormAtlas for C. elegans [3] and the Z Brain for zebra fish [44]. A number of projects, e.g., [5], offer a more specialized capability for visualizing and analyzing neuroanatomy data.…”

Section: Discussionmentioning

confidence: 99%

FlyBrainLab: Accelerating the Discovery of the Functional Logic of theDrosophilaBrain in the Connectomic/Synaptomic Era

Lazar¹,

Liu²,

Türkcan³

et al. 2020

Preprint

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In recent years, a wealth of Drosophila neuroscience data have become available. These include cell type, connectome and synaptome datasets for both the larva and adult fly. To facilitate integration across data modalities and to accelerate the understanding of the functional logic of the fly brain, we developed an interactive computing environment called FlyBrainLab.FlyBrainLab is uniquely positioned towards accelerating the discovery of the functional logic of the Drosophila brain. Its interactive open source architecture seamlessly integrates and brings together computational models with neuroanatomical, neurogenetic and electrophysiological data, changing the organization of neuroscientific fly brain data from a group of unconnected databases, arrays and tables, to a well structured data and executable circuit repository. The FlyBrainLab User Interface supports a highly intuitive and automated workflow that streamlines the 3D exploration and visualization of fly brain circuits, and the interactive exploration of the functional logic of executable circuits created directly from the explored and visualized fly brain data.FlyBrainLab methodologically supports the efficient comparison of fly brain circuit models, across model instances developed by different researchers, across different developmental stages of the fruit fly and across different datasets. The FlyBrainLab Utility and Circuit Libraries accelerate the creation of models of executable circuits. The Utility Libraries help untangle the graph structure of neural circuits from raw connectome and synaptome data. The Circuit Libraries facilitate the exploration of neural circuits of the neuropils of the central complex and, the development and implementation of models of the adult and larva fruit fly early olfactory systems.To elevate its executable circuit construction capability beyond the connectome, FlyBrainLab provides additional libraries for molecular transduction arising in sensory coding in vision and olfaction. Together with sensory neuron activity data, these libraries serve as entry points for discovering circuit function in the sensory systems of the fruit fly brain. They also enable the biological validation of developed executable circuits within the same platform.

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“…To classify the reconstructed cells into neuronal and other cell types, we used various approaches. For a morphological classification of neurons based on the similarity of their skeleton arbots, we used Sholl analysis (Sholl, 1953) and NBLAST as implemented in CATMAID and the natverse (Bates et al, 2020;Costa et al, 2016), respectively. Hierarchical clustering of distance matrices obtained from NBLAST and Sholl analysis often delineated neurons with similar arbors that we consider cell types (shown for the motoneurons in Figure 3 -figure supplement 1).…”

Section: Classification Of Cell Typesmentioning

confidence: 99%

“…NBLAST was carried out in the natverse (Bates et al, 2020;Costa et al, 2016) by a custom R script. We compared 1,772 neurons in the connectome (annotated: "connectome_neuron").…”

Section: Network Analysis Nblast and Sholl Analysismentioning

confidence: 99%

Whole-animal connectome and cell-type complement of the three-segmentedPlatynereis dumeriliilarva

Verasztó

Jasek

Gühmann

et al. 2020

Preprint

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Nervous systems coordinate effectors across the body during movements. We know little about the cellular-level structure of synaptic circuits for such body-wide control. Here we describe the whole-body synaptic connectome and cell-type complement of a three-segmented larva of the marine annelid Platynereis dumerilii. We reconstructed and annotated over 1,500 neurons and 6,500 non-neuronal cells in a whole-body serial electron microscopy dataset. The differentiated cells fall into 180 neuronal and 90 non-neuronal cell types. We analyse the modular network architecture of the entire nervous system and describe polysynaptic pathways from 428 sensory neurons to four effector systems - ciliated cells, glands, pigment cells and muscles. The complete somatic musculature and its innervation will be described in a companion paper. We also investigated intersegmental differences in cell-type complement, descending and ascending pathways, and mechanosensory and peptidergic circuits. Our work provides the basis for understanding whole-body coordination in annelids.

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The natverse, a versatile toolbox for combining and analysing neuroanatomical data

Cited by 175 publications

References 143 publications

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons

The microbiota promotes social behavior by modulating microglial remodeling of forebrain neurons

FlyBrainLab: Accelerating the Discovery of the Functional Logic of theDrosophilaBrain in the Connectomic/Synaptomic Era

Whole-animal connectome and cell-type complement of the three-segmentedPlatynereis dumeriliilarva

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