Functional connectomics spanning multiple areas of mouse visual cortex

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2021, Номер unknown

Опубликована: Июль 29, 2021

Abstract To understand the brain we must relate neurons’ functional responses to circuit architecture that shapes them. Here, present a large connectomics dataset with dense calcium imaging of millimeter scale volume. We recorded activity from approximately 75,000 neurons in primary visual cortex (VISp) and three higher areas (VISrl, VISal VISlm) an awake mouse viewing natural movies synthetic stimuli. The data were co-registered volumetric electron microscopy (EM) reconstruction containing more than 200,000 cells 0.5 billion synapses. Subsequent proofreading subset this volume yielded reconstructions include complete dendritic trees as well local inter-areal axonal projections map up thousands cell-to-cell connections per neuron. release open-access resource scientific community including set tools facilitate retrieval downstream analysis. In accompanying papers describe our findings using provide comprehensive structural characterization cortical cell types 1–3 most detailed synaptic level connectivity diagram column date 2 , uncovering unique cell-type specific inhibitory motifs can be linked gene expression 4 . Functionally, identify new computational principles how information is integrated across space 5 characterize novel neuronal invariances 6 bring structure function together decipher general principle wires excitatory within 7, 8

Язык: Английский

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The Brain Observatory Storage Service and Database (BossDB): A Cloud-Native Approach for Petascale Neuroscience Discovery

Frontiers in Neuroinformatics, Год журнала: 2022, Номер 16

Опубликована: Фев. 15, 2022

Technological advances in imaging and data acquisition are leading to the development of petabyte-scale neuroscience image datasets. These large-scale volumetric datasets pose unique challenges since analyses often span entire volume, requiring a unified platform access it. In this paper, we describe Brain Observatory Storage Service Database (BossDB), cloud-based solution for storing accessing petascale BossDB provides support ingest, storage, visualization, sharing through RESTful Application Programming Interface (API). A key feature is scalable indexing spatial automatic manual annotations facilitate discovery. Our project open source can be easily cost effectively used variety modalities applications, has worked with over petabyte size.

Язык: Английский

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Public Volume Electron Microscopy Data: An Essential Resource to Study the Brain Microvasculature

Frontiers in Cell and Developmental Biology, Год журнала: 2022, Номер 10

Опубликована: Апрель 5, 2022

Electron microscopy is the primary approach to study ultrastructural features of cerebrovasculature. However, 2D snapshots a vascular bed capture only small fraction its complexity. Recent efforts synaptically map neuronal circuitry using volume electron have also sampled brain microvasculature in 3D. Here, we perform meta-analysis 7 data sets spanning different species and regions, including two from MICrONS consortium that made segment vasculature addition all parenchymal cell types mouse visual cortex. Exploration these revealed rich information for detailed investigation Neurovascular unit (including, but not limited to, endothelial cells, mural perivascular fibroblasts, microglia, astrocytes) could be discerned across broad microvascular zones. Image contrast was sufficient identify subcellular details, junctions, caveolae, peg-and-socket interactions, mitochondria, Golgi cisternae, microvilli other cellular protrusions potential significance signaling. Additionally, non-cellular structures basement membrane spaces were visible traced between arterio-venous zones along wall. These explorations structural may important functions, such as blood-brain barrier integrity, blood flow control, clearance, bioenergetics. They identified limitations where accuracy consistency segmentation further honed by future efforts. The purpose this article introduce valuable community resources within framework cerebrovascular research. We do so providing an assessment their contents, identifying study, discussing next step ideas refining analysis.

Язык: Английский

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Nanometer-scale views of visual cortex reveal anatomical features of primary cilia poised to detect synaptic spillover

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Ноя. 1, 2023

A primary cilium is a thin membrane-bound extension off cell surface that contains receptors for perceiving and transmitting signals modulate state activity. While many types have cilium, little known about cilia in the brain, where they are less accessible than on cultured cells or epithelial tissues protrude from bodies into deep, dense network of glial neuronal processes. Here, we investigated frequency, internal structure, shape, position large, high-resolution transmission electron microscopy volumes mouse visual cortex. Cilia extended nearly all excitatory inhibitory neurons, astrocytes, oligodendrocyte precursor (OPCs), but were absent oligodendrocytes microglia. Structural comparisons revealed membrane structure at base microtubule organization differed between neurons glia. OPC distinct shortest contained pervasive vesicles only occasionally observed neuron astrocyte cilia. Investigating cilia-proximal features directly adjacent to synapses, suggesting well poised encounter locally released signaling molecules. proximity synapses was random, not enriched, synapse-rich neuropil. The anatomy, including changes centriole location, defined key structural placement shape. Together, anatomical insights both within around glia provide new formation function across brain.

Язык: Английский

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CAVE: Connectome Annotation Versioning Engine

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2023, Номер unknown

Опубликована: Июль 28, 2023

Abstract Advances in Electron Microscopy, image segmentation and computational infrastructure have given rise to large-scale richly annotated connectomic datasets which are increasingly shared across communities. To enable collaboration, users need be able concurrently create new annotations correct errors the automated by proofreading. In large datasets, every proofreading edit relabels cell identities of millions voxels thousands like synapses. For analysis, require immediate reproducible access this constantly changing expanding data landscape. Here, we present Connectome Annotation Versioning Engine (CAVE), a for connectome analysis up-to petascale (∼1mm 3 ) while annotating is ongoing. segmentation, CAVE provides distributed continuous versioning reconstructions. Annotations defined locations such that they can quickly assigned underlying segment enables fast queries CAVE’s arbitrary time points. supports schematized, extensible annotations, so researchers readily design novel annotation types. already used many connectomics including largest available date.

Язык: Английский

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