Connecto-informatics at the mesoscale: current advances in image processing and analysis for mapping the brain connectivity

Brain Informatics, Journal Year: 2024, Volume and Issue: 11(1)

Published: June 4, 2024

Abstract Mapping neural connections within the brain has been a fundamental goal in neuroscience to understand better its functions and changes that follow aging diseases. Developments imaging technology, such as microscopy labeling tools, have allowed researchers visualize this connectivity through high-resolution brain-wide imaging. With this, image processing analysis become more crucial. However, despite wealth of images generated, access an integrated pipeline process these data is challenging due scattered information on available tools methods. To map connections, registration atlases feature extraction segmentation signal detection are necessary. In review, our provide updated overview recent advances image-processing methods, with particular focus fluorescent mouse brain. Our outline pathway toward tailored for connecto-informatics. An workflow will facilitate researchers’ approach mapping complex networks their underlying functions. By highlighting fluroscent brain, review contribute deeper grasp connecto-informatics, paving way comprehension implications.

Language: Английский

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Neuronal diversity and stereotypy at multiple scales through whole brain morphometry

Nature Communications, Journal Year: 2024, Volume and Issue: 15(1)

Published: Nov. 26, 2024

We conducted a large-scale whole-brain morphometry study by analyzing 3.7 peta-voxels of mouse brain images at the single-cell resolution, producing one largest multi-morphometry databases mammalian brains to date. registered 204 three major imaging modalities Allen Common Coordinate Framework (CCF) atlas, annotated 182,497 neuronal cell bodies, modeled 15,441 dendritic microenvironments, characterized full morphology 1876 neurons along with their axonal motifs, and detected 2.63 million varicosities that indicate potential synaptic sites. Our analyzed six levels information related populations, morphology, arborization, varicosities, sub-neuronal structural quantification diversity stereotypy patterns each level. This integrative provides key anatomical descriptions types across multiple scales features, contributing substantial resource for understanding in brains.

Language: Английский

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Correlative light and electron microscopy reveals the fine circuit structure underlying evidence accumulation in larval zebrafish

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 15, 2025

Accumulating information is a critical component of most circuit computations in the brain across species, yet its precise implementation at synaptic level remains poorly understood. Dissecting such neural circuits vertebrates requires knowledge functional properties and ability to directly correlate dynamics with underlying wiring diagram same animal. Here we combine calcium imaging ultrastructural reconstruction, using visual motion accumulation paradigm larval zebrafish. Using connectomic analyses functionally identified cells computational modeling, show that bilateral inhibition, disinhibition, recurrent connectivity are prominent motifs for sensory within anterior hindbrain. We also demonstrate similar insights about structure-function relationship this can be obtained through complementary methods involving cell-specific morphological labeling via photo-conversion neuronal response types. used our unique ground truth datasets train test novel classifier algorithm, allowing us assign labels neurons from libraries where lacking. The resulting feature-rich library identities connectomes enabled constrain biophysically realistic network model hindbrain reproduce observed make testable predictions future experiments. Our work exemplifies power hypothesis-driven electron microscopy paired recordings gain mechanistic into signal processing provides framework dissecting vertebrates.

Language: Английский

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Connectivity of single neurons classifies cell subtypes in mouse brains

Nature Methods, Journal Year: 2025, Volume and Issue: unknown

Published: March 21, 2025

Classification of single neurons at a brain-wide scale is way to characterize the structural and functional organization brains. Here we acquired standardized large morphology database 20,158 mouse generated potential connectivity map based on their dendritic axonal arbors. With such an anatomy–morphology–connectivity mapping, defined neuron subtypes for in 31 brain regions. We found that cell types by show distinct separation from each other. Within this context, were able diversity secondary motor cortical neurons, subtype patterns thalamocortical pathways. Our findings underscore importance characterizing modularity anatomy single-cell level. These results highlight supplement conventionally recognized transcriptomic types, electrophysiological morphological as factors classify classes identities. This Resource presents method define spatially registered containing more than 20,000 neuronal reconstructions. A also using features.

Language: Английский

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Clustering the cortical laminae: in vivo parcellation

Brain Structure and Function, Journal Year: 2024, Volume and Issue: 229(2), P. 443 - 458

Published: Jan. 9, 2024

Abstract The laminar microstructure of the cerebral cortex has distinct anatomical characteristics development, function, connectivity, and even various pathologies brain. In recent years, multiple neuroimaging studies have utilized magnetic resonance imaging (MRI) relaxometry to visualize explore this intricate microstructure, successfully delineating cortical components. Despite progress, T1 is still primarily considered a direct measure myeloarchitecture (myelin content), rather than probe tissue cytoarchitecture (cellular composition). This study aims offer robust, whole-brain validation as practical effective tool for exploring composition cortex. To do so, we cluster complex microstructural datasets both human ( N = 30) macaque 1) brains using an adaptation algorithm clustering cell omics profiles. resulting patterns are then compared established atlases cytoarchitectonic features, exhibiting significant correspondence in species. Lastly, demonstrate expanded applicability by some features behind unique skillsets, such musicality athleticism.

Language: Английский

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Full-Spectrum Neuronal Diversity and Stereotypy through Whole Brain Morphometry

Research Square (Research Square), Journal Year: 2023, Volume and Issue: unknown

Published: July 25, 2023

We conducted a large-scale study of whole-brain morphometry, analyzing 3.7 peta-voxels mouse brain images at the single-cell resolution, producing one largest multi-morphometry databases mammalian brains to date. spatially registered 205 and associated data from six Brain Initiative Cell Census Network (BICCN) sources covering three major imaging modalities five collaborative projects Allen Common Coordinate Framework (CCF) atlas, annotated 3D locations cell bodies 227,581 neurons, modeled 15,441 dendritic microenvironments, characterized full morphology 1,891 neurons along with their axonal motifs, detected 2.58 million putative synaptic boutons. Our analysis covers levels information related neuronal populations, morphology, sub-neuronal arborization, boutons, structural quantitative characterization diversity stereotypy patterns each level. identified 16 modules consisting highly intercorrelated regions in 13 functional areas corresponding 314 anatomical CCF. revealed microenvironment as powerful method for delineating types potential subtypes. also found that morphologies can be categorized into four distinct classes based on tuned morphological features, substantial cross-areal apical dendrites, basal arbors, quantified within cortical, thalamic striatal regions. The lamination somas was more effective differentiating neuron arbors cortex. Further diverging converging projections individual 25 throughout reveals branching preferences brain-wide local distributions Overall, our provides comprehensive description key structures types, wide range scales contributes understanding its function brain.

Language: Английский

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Genomic, molecular, and cellular divergence of the human brain

Trends in Neurosciences, Journal Year: 2024, Volume and Issue: 47(7), P. 491 - 505

Published: June 18, 2024

While many core biological processes are conserved across species, the human brain has evolved with unique capacities. Current understanding of neurobiological mechanisms that endow traits as well associated vulnerabilities remains limited. However, emerging data have illuminated species divergence in DNA elements and genome organization, molecular, morphological, functional features neural cell types, temporal differences development. Here, we summarize recent on their complex implications for study treatment diseases. We also consider key outstanding questions field discuss technologies foundational knowledge will be required to accelerate neurobiology.

Language: Английский

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Collaborative augmented reconstruction of 3D neuron morphology in mouse and human brains

Nature Methods, Journal Year: 2024, Volume and Issue: unknown

Published: Sept. 4, 2024

Language: Английский

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Distinctive biophysical features of human cell-types: insights from studies of neurosurgically resected brain tissue

Frontiers in Synaptic Neuroscience, Journal Year: 2023, Volume and Issue: 15

Published: Oct. 4, 2023

Electrophysiological characterization of live human tissue from epilepsy patients has been performed for many decades. Although initially these studies sought to understand the biophysical and synaptic changes associated with epilepsy, recently, it become mainstay exploring distinctive features cell-types. Both epochs cellular electrophysiological explorations have faced criticism. Early revealed that cortical pyramidal neurons obtained individuals appeared function “normally” in comparison non-epilepsy controls or other species thus there was little gain study patients. On hand, contemporary are often questioned “normalcy” recorded since they derived In this review, we discuss our current understanding distinct glia removed tumors. We then explore concept within cell-type diversity its loss (i.e., “neural homogenization”). introduce neural homogenization help reconcile epileptogenicity seemingly “normal” cells circuits. propose should be continued efforts quest what makes cell-types “human”.

Language: Английский

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The neuroscience of mental illness: Building toward the future

Cell, Journal Year: 2024, Volume and Issue: 187(21), P. 5858 - 5870

Published: Oct. 1, 2024

Language: Английский

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