CAVE: Connectome Annotation Versioning Engine

Nature Methods, Год журнала: 2025, Номер unknown

Опубликована: Апрель 9, 2025

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 annotations correct errors the automated by proofreading. In large every proofreading edit relabels cell identities of millions voxels thousands like synapses. For analysis, require immediate reproducible access this changing expanding data landscape. Here we present Connectome Annotation Versioning Engine (CAVE), a that provides scalable solutions for flexible annotation support fast analysis queries at arbitrary time points. Deployed as suite web services, CAVE empowers distributed communities perform connectome up petascale datasets (~1 mm 3 ) while annotating is ongoing.

Язык: Английский

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Diffusion-based deep learning method for augmenting ultrastructural imaging and volume electron microscopy

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 1, 2024

Abstract Electron microscopy (EM) revolutionized the way to visualize cellular ultrastructure. Volume EM (vEM) has further broadened its three-dimensional nanoscale imaging capacity. However, intrinsic trade-offs between speed and quality of restrict attainable area volume. Isotropic with vEM for large biological volumes remains unachievable. Here, we developed EMDiffuse, a suite algorithms designed enhance capabilities, leveraging cutting-edge image generation diffusion model. EMDiffuse generates realistic predictions high resolution ultrastructural details exhibits robust transferability by taking only one pair images 3 megapixels fine-tune in denoising super-resolution tasks. also demonstrated proficiency isotropic reconstruction task, generating volume even absence training data. We robustness from seven public datasets obtained different techniques instruments. The generated enables accurate ultrastructure analysis. features self-assessment functionalities on predictions’ reliability. envision pave investigations intricate subcellular within systems.

Язык: Английский

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Multi-scale spiking network model of human cerebral cortex

Cerebral Cortex, Год журнала: 2024, Номер 34(10)

Опубликована: Окт. 1, 2024

Abstract Although the structure of cortical networks provides necessary substrate for their neuronal activity, alone does not suffice to understand activity. Leveraging increasing availability human data, we developed a multi-scale, spiking network model cortex investigate relationship between and dynamics. In this model, each area in one hemisphere Desikan–Killiany parcellation is represented by $1\,\mathrm{mm^{2}}$ column with layered structure. The aggregates data across multiple modalities, including electron microscopy, electrophysiology, morphological reconstructions, diffusion tensor imaging, into coherent framework. It predicts activity on all scales from single-neuron area-level functional connectivity. We compared electrophysiological resting-state magnetic resonance imaging (fMRI) data. This comparison reveals that can reproduce aspects both statistics fMRI correlations if inter-areal connections are sufficiently strong. Furthermore, study propagation single-spike perturbation macroscopic fluctuations through network. open-source serves as an integrative platform further refinements future silico studies structure, dynamics, function.

Язык: Английский

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THE R. GLENN NORTHCUTT COLLECTION OF COMPARATIVE VERTEBRATE NEUROANATOMY AND EMBRYOLOGY: A NOVEL MUSEUM-BASED RESOURCE FOR NEUROSCIENCE AND EVOLUTIONARY BIOLOGY

Bulletin of the Museum of Comparative Zoology, Год журнала: 2025, Номер 163(10)

Опубликована: Янв. 17, 2025

In 2019, the Harvard Museum of Comparative Zoology acquired The R. Glenn Northcutt Collection Vertebrate Neuroanatomy and Embryology, which comprises an estimated 500,000 histologic sections whole mounts prepared mounted on glass slides. Assembled by Professor between 1963 2014 to reveal microscopic anatomy nervous system related tissues, collection additionally includes valuable slide series other neuroanatomists, including John Black Johnston, Othmar Solnitzky, David Senn. Most included specimens are serially sectioned or partial brains for comparative cytoarchitectonic studies. There also entire heads hundreds embryos representing 22 genera studies development sensory systems cranial nerves. is scientifically unique in its taxonomic breadth: more than 240 270 species represent all major groups living vertebrates as well two key out-groups, acorn worms cephalochordates. Particular strengths include hagfishes, lampreys, chondrichthyans, basal actinopterygians, sarcopterygians (including lungfishes coelacanth, Latimeria), amphibians, tuatara (Sphenodon), many families squamates, turtles, crocodilians, marsupials, primates. Ongoing curatorial activities generating digital whole-slide images most collection, accessible via Internet. Here we briefly describe history scientific importance, methods used prepare slides, ancillary materials, doctoral postdoctoral students visiting scientists who utilized it their studies, a list publications based slides and, finally, inventory information that will facilitate use research education.

Язык: Английский

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Oligodendrocyte precursor cells facilitate neuronal lysosome release

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 30, 2025

Abstract Oligodendrocyte precursor cells (OPCs) shape brain function through many non-canonical regulatory mechanisms beyond myelination. Here we show that OPCs form contacts with their processes on neuronal somata in a activity-dependent manner. These facilitate exocytosis of lysosomes. A reduction the number or branching reduces these contacts, which is associated lysosome accumulation and altered metabolism neurons more senescent age. similar OPC seen an early-stage mouse model Alzheimer’s disease. Our findings have implications for prevention age-related pathologies treatment neurodegenerative diseases.

Язык: Английский

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Imaging the structural connectome with hybrid MRI-microscopy tractography

Medical Image Analysis, Год журнала: 2025, Номер 102, С. 103498 - 103498

Опубликована: Фев. 7, 2025

Язык: Английский

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Synaptic architecture of a memory engram in the mouse hippocampus

Science, Год журнала: 2025, Номер 387(6740)

Опубликована: Март 20, 2025

Memory engrams are formed through experience-dependent plasticity of neural circuits, but their detailed architectures remain unresolved. Using three-dimensional electron microscopy, we performed nanoscale reconstructions the hippocampal CA3-CA1 pathway after chemogenetic labeling cellular ensembles recruited during associative learning. Neurons with a remote history activity coinciding memory acquisition showed no strong preference for wiring each other. Instead, connectomes expanded multisynaptic boutons independently coactivation state postsynaptic partners. The rewiring representing an initial engram was accompanied by input-specific, spatially restricted upscaling individual synapses, as well remodeling mitochondria, smooth endoplasmic reticulum, and interactions astrocytes. Our findings elucidate physical hallmarks long-term offer structural basis flexibility information coding.

Язык: Английский

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A scalable and modular automated pipeline for stitching of large electron microscopy datasets

eLife, Год журнала: 2022, Номер 11

Опубликована: Июль 26, 2022

Serial-section electron microscopy (ssEM) is the method of choice for studying macroscopic biological samples at extremely high resolution in three dimensions. In nervous system, nanometer-scale images are necessary to reconstruct dense neural wiring diagrams brain, so -called connectomes . The data that can comprise up 10 8 individual EM must be assembled into a volume, requiring seamless 2D registration from physical section followed by 3D alignment stitched sections. throughput ssEM necessitates stitching done pace imaging, which currently produces tens terabytes per day. To achieve this, we present modular volume assembly software pipeline ASAP (Assembly Stitching and Alignment Pipeline) scalable datasets containing petabytes parallelized work distributed computational environment. built on top Render Trautman Saalfeld (2019) services used brain adult Drosophila melanogaster (Zheng et al. 2018). It achieves operating only image meta-data transformations. modular, allowing easy incorporation new algorithms without significant changes workflow. entire includes complete set tools stitching, automated quality control, alignment, final rendering disk. has been deployed continuous several large-scale mouse visual cortex human including one cubic millimeter (Yin 2020); Microns Consortium (2021) speeds exceed imaging. also multi-channel processing capabilities applied fluorescence multi-modal like array tomography.

Язык: Английский

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Differential cortical layer engagement during seizure initiation and spread in humans

Nature Communications, Год журнала: 2024, Номер 15(1)

Опубликована: Июнь 17, 2024

Abstract Despite decades of research, we still do not understand how spontaneous human seizures start and spread – especially at the level neuronal microcircuits. In this study, used laminar arrays micro-electrodes to simultaneously record local field potentials multi-unit neural activities across six layers neocortex during focal in humans. We found that, within ictal onset zone, discharges generated a seizure consisted current sinks sources only infra-granular granular layers. Outside reflected flow supra-granular Interestingly, these patterns evolved course outside zone where superficial extended into deeper Based on observations, framework describing cortical-cortical dynamics is proposed with implications for localization, surgical targeting, neuromodulation techniques block generation propagation seizures.

Язык: Английский

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Towards generative digital twins in biomedical research

Computational and Structural Biotechnology Journal, Год журнала: 2024, Номер 23, С. 3481 - 3488

Опубликована: Окт. 3, 2024

Digital twins in biomedical research, i.e. virtual replicas of biological entities such as cells, organs, or entire organisms, hold great potential to advance personalized healthcare. As all processes happen space, there is a growing interest modeling within their native context. Leveraging generative artificial intelligence (AI) and high-volume data profiled with spatial technologies, researchers can recreate spatially-resolved digital representations physical entity high fidelity. In application fields computational pathology, oncology, cardiology, these (GDT) thus enable compelling

Язык: Английский

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