Squidpy: a scalable framework for spatial omics analysis

Nature Methods, Journal Year: 2022, Volume and Issue: 19(2), P. 171 - 178

Published: Jan. 31, 2022

Spatial omics data are advancing the study of tissue organization and cellular communication at an unprecedented scale. Flexible tools required to store, integrate visualize large diversity spatial data. Here, we present Squidpy, a Python framework that brings together from image analysis enable scalable description molecular data, such as transcriptome or multivariate proteins. Squidpy provides efficient infrastructure numerous methods allow efficiently manipulate interactively is extensible can be interfaced with variety already existing libraries for

Language: Английский

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CAT – A Computational Anatomy Toolbox for the Analysis of Structural MRI Data

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2022, Volume and Issue: unknown

Published: June 13, 2022

Abstract A large range of sophisticated brain image analysis tools have been developed by the neuroscience community, greatly advancing field human mapping. Here we introduce Computational Anatomy Toolbox (CAT) – a powerful suite for morphometric analyses with an intuitive graphical user interface, but also usable as shell script. CAT is suitable beginners, casual users, experts, and developers alike providing comprehensive set options, workflows, integrated pipelines. The available streams illustrated on example dataset allow voxel-based, surface-based, well region-based analyses. Notably, incorporates multiple quality control options covers entire workflow, including preprocessing cross-sectional longitudinal data, statistical analysis, visualization results. overarching aim this article to provide complete description evaluation CAT, while offering citable standard community.

Language: Английский

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Quantitative magnetic resonance imaging of brain anatomy and in vivo histology

Nature Reviews Physics, Journal Year: 2021, Volume and Issue: 3(8), P. 570 - 588

Published: June 28, 2021

Language: Английский

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Advances in human intracranial electroencephalography research, guidelines and good practices

NeuroImage, Journal Year: 2022, Volume and Issue: 260, P. 119438 - 119438

Published: July 2, 2022

Since the second half of twentieth century, intracranial electroencephalography (iEEG), including both electrocorticography (ECoG) and stereo-electroencephalography (sEEG), has provided an intimate view into human brain. At interface between fundamental research clinic, iEEG provides high temporal resolution spatial specificity but comes with constraints, such as individual's tailored sparsity electrode sampling. Over years, researchers in neuroscience developed their practices to make most approach. Here we offer a critical review didactic framework for newcomers, well addressing issues encountered by proficient researchers. The scope is threefold: (i) common research, (ii) suggest potential guidelines working data answer frequently asked questions based on widespread practices, (iii) current neurophysiological knowledge methodologies, pave way good practice standards research. organization this paper follows steps processing. first section contextualizes collection. focuses localization electrodes. third highlights main pre-processing steps. fourth presents signal analysis methods. fifth discusses statistical approaches. sixth draws some unique perspectives Finally, ensure consistent nomenclature throughout manuscript align other guidelines, e.g., Brain Imaging Data Structure (BIDS) OHBM Committee Best Practices Analysis Sharing (COBIDAS), provide glossary disambiguate terms related

Language: Английский

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A petavoxel fragment of human cerebral cortex reconstructed at nanoscale resolution

Science, Journal Year: 2024, Volume and Issue: 384(6696)

Published: May 9, 2024

To fully understand how the human brain works, knowledge of its structure at high resolution is needed. Presented here a computationally intensive reconstruction ultrastructure cubic millimeter temporal cortex that was surgically removed to gain access an underlying epileptic focus. It contains about 57,000 cells, 230 millimeters blood vessels, and 150 million synapses comprises 1.4 petabytes. Our analysis showed glia outnumber neurons 2:1, oligodendrocytes were most common cell, deep layer excitatory could be classified on basis dendritic orientation, among thousands weak connections each neuron, there exist rare powerful axonal inputs up 50 synapses. Further studies using this resource may bring valuable insights into mysteries brain.

Language: Английский

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Early Alzheimer’s disease pathology in human cortex involves transient cell states

Cell, Journal Year: 2023, Volume and Issue: 186(20), P. 4438 - 4453.e23

Published: Sept. 1, 2023

Language: Английский

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Transcriptomic cytoarchitecture reveals principles of human neocortex organization

Science, Journal Year: 2023, Volume and Issue: 382(6667)

Published: Oct. 12, 2023

Variation in cytoarchitecture is the basis for histological definition of cortical areas. We used single cell transcriptomics and performed cellular characterization human cortex to better understand areal specialization. Single-nucleus RNA-sequencing 8 areas spanning structural variation showed a highly consistent makeup 24 subclasses. However, proportions excitatory neuron subclasses varied substantially, likely reflecting differences connectivity across primary sensorimotor association cortices. Laminar organization astrocytes oligodendrocytes also differed Primary visual characteristic with major changes inhibitory ratio, expansion layer 4 neurons, specialized neurons. These results lay groundwork refined molecular

Language: Английский

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Gradients in brain organization

NeuroImage, Journal Year: 2022, Volume and Issue: 251, P. 118987 - 118987

Published: Feb. 10, 2022

Language: Английский

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Post mortem mapping of connectional anatomy for the validation of diffusion MRI

NeuroImage, Journal Year: 2022, Volume and Issue: 256, P. 119146 - 119146

Published: March 26, 2022

Diffusion MRI (dMRI) is a unique tool for the study of brain circuitry, as it allows us to image both macroscopic trajectories and microstructural properties axon bundles in vivo. The Human Connectome Project ushered an era impressive advances dMRI acquisition analysis. As result these efforts, quality data that could be acquired vivo improved substantially, large collections such became widely available. Despite this progress, main limitation remains: does not axons directly, but only provides indirect measurements based on diffusion water molecules. Thus, must validated by methods allow direct visualization can performed post mortem tissue. In review, we discuss validating various features connectional anatomy are extracted from dMRI, at macro-scale (trajectories bundles), micro-scale (axonal orientations other properties). We present range validation tools, including anatomic tracer studies, Klingler's dissection, myelin stains, label-free optical imaging techniques, others. provide overview basic principles each technique, its limitations, what has taught so far about accuracy different analysis approaches.

Language: Английский

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A tripartite view of the posterior cingulate cortex

Nature reviews. Neuroscience, Journal Year: 2022, Volume and Issue: 24(3), P. 173 - 189

Published: Dec. 1, 2022

Language: Английский

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