Functional connectomics spanning multiple areas of mouse visual cortex

Nature, Journal Year: 2025, Volume and Issue: 640(8058), P. 435 - 447

Published: April 9, 2025

Abstract Understanding the brain requires understanding neurons’ functional responses to circuit architecture shaping them. Here we introduce MICrONS connectomics dataset with dense calcium imaging of around 75,000 neurons in primary visual cortex (VISp) and higher areas (VISrl, VISal VISlm) an awake mouse that is viewing natural synthetic stimuli. These data are co-registered electron microscopy reconstruction containing more than 200,000 cells 0.5 billion synapses. Proofreading a subset yielded reconstructions include complete dendritic trees as well local inter-areal axonal projections map up thousands cell-to-cell connections per neuron. Released open-access resource, this includes tools for retrieval analysis 1,2 . Accompanying studies describe its use comprehensive characterization cell types 3–6 , synaptic level connectivity diagram cortical column 4 uncovering cell-type-specific inhibitory can be linked gene expression 4,7 Functionally, identify new computational principles how information integrated across space 8 characterize novel neuronal invariances 9 bring structure function together uncover general principle between excitatory within 10,11

Language: Английский

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Perisomatic ultrastructure efficiently classifies cells in mouse cortex

Nature, Journal Year: 2025, Volume and Issue: 640(8058), P. 478 - 486

Published: April 9, 2025

Abstract Mammalian neocortex contains a highly diverse set of cell types. These types have been mapped systematically using variety molecular, electrophysiological and morphological approaches 1–4 . Each modality offers new perspectives on the variation biological processes underlying cell-type specialization. Cellular-scale electron microscopy provides dense ultrastructural examination an unbiased perspective subcellular organization brain cells, including their synaptic connectivity nanometre-scale morphology. In data that contain tens thousands neurons, most which incomplete reconstructions, identifying becomes clear challenge for analysis 5 Here, to address this challenge, we present systematic survey somatic region all cells in cubic millimetre cortex quantitative features obtained from microscopy. This demonstrates perisomatic is sufficient identify types, defined primarily basis patterns. We then describe how classification facilitates cell-type-specific characterization locating with rare patterns dataset.

Language: Английский

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NEURD offers automated proofreading and feature extraction for connectomics

Nature, Journal Year: 2025, Volume and Issue: 640(8058), P. 487 - 496

Published: April 9, 2025

We are in the era of millimetre-scale electron microscopy volumes collected at nanometre resolution1,2. Dense reconstruction cellular compartments these has been enabled by recent advances machine learning3-6. Automated segmentation methods produce exceptionally accurate reconstructions cells, but post hoc proofreading is still required to generate large connectomes that free merge and split errors. The elaborate 3D meshes neurons contain detailed morphological information multiple scales, from diameter, shape branching patterns axons dendrites, down fine-scale structure dendritic spines. However, extracting features can require substantial effort piece together existing tools into custom workflows. Here, building on open source software for mesh manipulation, we present Neural Decomposition (NEURD), a package decomposes meshed compact extensively annotated graph representations. With feature-rich graphs, automate variety tasks such as state-of-the-art automated errors, cell classification, spine detection, axonal-dendritic proximities other annotations. These enable many downstream analyses neural morphology connectivity, making massive complex datasets more accessible neuroscience researchers.

Language: Английский

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A petascale automated imaging pipeline for mapping neuronal circuits with high-throughput transmission electron microscopy

Nature Communications, Journal Year: 2020, Volume and Issue: 11(1)

Published: Oct. 2, 2020

Abstract Electron microscopy (EM) is widely used for studying cellular structure and network connectivity in the brain. We have built a parallel imaging pipeline using transmission electron microscopes that scales this technology, implements 24/7 continuous autonomous imaging, enables acquisition of petascale datasets. The suitability architecture large-scale was demonstrated by acquiring volume more than 1 mm 3 mouse neocortex, spanning four different visual areas at synaptic resolution, less 6 months. Over 26,500 ultrathin tissue sections from same block were imaged, yielding dataset 2 petabytes. combined burst rate Gpixel per sec net 600 Mpixel with six running parallel. This work demonstrates feasibility EM datasets scale cortical microcircuits multiple brain regions species.

Language: Английский

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Structure and function of axo-axonic inhibition

eLife, Journal Year: 2021, Volume and Issue: 10

Published: Dec. 1, 2021

Inhibitory neurons in mammalian cortex exhibit diverse physiological, morphological, molecular, and connectivity signatures. While considerable work has measured the average of several interneuron classes, there remains a fundamental lack understanding distribution distinct inhibitory cell types with synaptic resolution, how it relates to properties target cells, affects function. Here, we used large-scale electron microscopy functional imaging address these questions for chandelier cells layer 2/3 mouse visual cortex. With dense reconstructions from microscopy, mapped complete input onto 153 pyramidal neurons. We found that synapse number is highly variable across population correlated structural features neuron. This variability axo-axonic ChC synapses higher than seen perisomatic inhibition. Biophysical simulations show observed pattern inhibition particularly effective controlling excitatory output when excitation are co-active. Finally, activity awake animals using cell-type-specific calcium approach saw cells. In same experiments, vivo pupil dilation, proxy arousal. Together, results suggest provide circuit-wide signal whose strength adjusted relative

Language: Английский

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Functional connectomics reveals general wiring rule in mouse visual cortex

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 14, 2023

Understanding the relationship between circuit connectivity and function is crucial for uncovering how brain implements computation. In mouse primary visual cortex (V1), excitatory neurons with similar response properties are more likely to be synaptically connected, but previous studies have been limited within V1, leaving much unknown about broader rules. this study, we leverage millimeter-scale MICrONS dataset analyze synaptic functional of individual across cortical layers areas. Our results reveal that responses preferentially connected both areas — including feedback connections suggesting universality ‘like-to-like’ hierarchy. Using a validated digital twin model, separated neuronal tuning into feature (what respond to) spatial (receptive field location) components. We found only component predicts fine-scale connections, beyond what could explained by physical proximity axons dendrites. also higher-order rule where postsynaptic neuron cohorts downstream presynaptic cells show greater similarity than predicted pairwise like-to-like rule. Notably, recurrent neural networks (RNNs) trained on simple classification task develop patterns mirroring rules, magnitude those in data. Lesion these RNNs disrupting has significantly impact performance compared lesions random connections. These findings suggest principles may play role sensory processing learning, highlighting shared biological artificial systems.

Language: Английский

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Ultrastructural differences impact cilia shape and external exposure across cell classes in the visual cortex

Current Biology, Journal Year: 2024, Volume and Issue: 34(11), P. 2418 - 2433.e4

Published: May 14, 2024

A primary cilium is a membrane-bound extension from the cell surface that contains receptors for perceiving and transmitting signals modulate state activity. Primary cilia in brain are less accessible than on cultured cells or epithelial tissues because they protrude 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 bodies nearly all excitatory inhibitory neurons, astrocytes, oligodendrocyte precursor (OPCs) but were absent oligodendrocytes microglia. Ultrastructural comparisons revealed base microtubule organization differed between neurons glia. Investigating cilia-proximal features many directly adjacent to synapses, suggesting poised encounter locally released signaling molecules. Our analysis indicated synapse proximity likely due random encounters neuropil, with no evidence activity as would be expected tetrapartite synapses. The observed class differences synapses largely external length. Many key structural influenced both placement shape and, thus, exposure processes outside cilium. Together, ultrastructure within around suggest formation function across types brain.

Language: Английский

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Implications of variable synaptic weights for rate and temporal coding of cerebellar outputs

eLife, Journal Year: 2024, Volume and Issue: 13

Published: Jan. 19, 2024

Purkinje cell (PC) synapses onto cerebellar nuclei (CbN) neurons allow signals from the cortex to influence rest of brain. PCs are inhibitory that spontaneously fire at high rates, and many PC inputs thought converge each CbN neuron suppress its firing. It has been proposed convey information using a rate code, synchrony timing or both. The on firing was primarily examined for combined effects with comparable strengths, individual not extensively studied. Here, we find single highly variable in size, dynamic clamp modeling reveal this important implications PC-CbN transmission. Individual regulate both Large strongly rates transiently eliminate several milliseconds. Remarkably, refractory period leads brief elevation prior suppression. Thus, suited concurrently codes generate precisely timed responses neurons. Either synchronous pauses promote rapid time scales nonuniform inputs, but less effectively than uniform inputs. This is secondary consequence input sizes elevating baseline by increasing variability conductance. These findings may generalize other brain regions synapse sizes.

Language: Английский

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Connectomic reconstruction of a cortical column

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: March 25, 2024

ABSTRACT The cerebral cortex of mammals has long been proposed to comprise unit-modules, so-called cortical columns. detailed synaptic-level circuitry such a neuronal network about 10 4 neurons is still unknown. Here, using 3-dimensional electron microscopy, AI-based image processing and automated proofreading, we report the connectomic reconstruction defined column in mouse barrel cortex. appears as structural feature connectome, without need for geometrical or morphological landmarks. We then used connectome definition cell types column, determine intracolumnar circuit modules, analyze logic inhibitory circuits, investigate circuits combination bottom-up top-down signals specificity input, search higher-order structure within homogeneous populations, estimate degree symmetry Hebbian learning various connection types. With this, provide first column-level description cortex, likely substrate mechanistic understanding sensory-conceptual integration learning.

Language: Английский

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Ultrastructural analysis of dendritic spine necks reveals a continuum of spine morphologies

Developmental Neurobiology, Journal Year: 2021, Volume and Issue: 81(5), P. 746 - 757

Published: May 12, 2021

Dendritic spines are membranous protrusions that receive essentially all excitatory inputs in most mammalian neurons. Spines, with a bulbous head connected to the dendrite by thin neck, have variety of morphologies likely impact their functional properties. Nevertheless, question whether belong distinct morphological subtypes is still open. Addressing this quantitatively requires clear identification and measurements spine necks. Recent advances electron microscopy enable large-scale systematic reconstructions nanometer precision 3D. Analyzing ultrastructural from mouse neocortical neurons computer vision algorithms, we demonstrate vast majority structures can be rigorously separated into heads necks, enabling We then used database parameters explore potential existence different classes. Without exception, our analysis revealed unimodal distributions individual without evidence for spines. The postsynaptic density size was strongly correlated volume. neck diameter, but not length, also Spines larger volumes often had apparatus pairs post-synaptic cell contacted same axon similar volumes. Our data reveal lack indicate length volume must independently regulated. These results repercussions understanding function dendritic neuronal circuits.

Language: Английский

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