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University Imaging Centers - Where the University sees the future

Journal Articles

FreeHi-C simulates high-fidelity Hi-C data for benchmarking and data augmentation

Nature Methods - 11 November 2019 - 12:00am

Nature Methods, Published online: 11 November 2019; doi:10.1038/s41592-019-0624-3

FreeHi-C takes Hi-C sequencing data as input and simulates reads with random mutations and indels from the interacting fragment pairs. FreeHi-C-simulated replicates are used for benchmarking Hi-C analysis methods and enable data augmentation for differential chromatin interaction analysis.
Categories: Journal Articles

Non-reversible tissue fixation retains extracellular vesicles for in situ imaging

Nature Methods - 11 November 2019 - 12:00am

Nature Methods, Published online: 11 November 2019; doi:10.1038/s41592-019-0623-4

Tissue fixation with formaldehyde and a water-soluble carbodiimide crosslinker (EDC) leads to retention of extracellular vesicles within tissues and allows for reliable extracellular vesicle imaging for semiquantitative imaging applications.
Categories: Journal Articles

Three-dimensional virtual refocusing of fluorescence microscopy images using deep learning

Nature Methods - 4 November 2019 - 12:00am

Nature Methods, Published online: 04 November 2019; doi:10.1038/s41592-019-0622-5

Deep-Z uses deep learning to go from a two-dimensional snapshot to three-dimensional fluorescence images. The method improves imaging speed while reducing light dose, and was shown to be useful for accurate structural and functional imaging of neurons in Caenorhabditis elegans.
Categories: Journal Articles

Simultaneous mesoscopic and two-photon imaging of neuronal activity in cortical circuits

Nature Methods - 4 November 2019 - 12:00am

Nature Methods, Published online: 04 November 2019; doi:10.1038/s41592-019-0625-2

Simultaneous two-photon microscopic and one-photon mesoscopic imaging of calcium signals enables correlation of local cellular and brain-wide network activity.
Categories: Journal Articles

Learning representations of microbe–metabolite interactions

Nature Methods - 4 November 2019 - 12:00am

Nature Methods, Published online: 04 November 2019; doi:10.1038/s41592-019-0616-3

mmvec, a neural-network-based algorithm, uses paired multiomics data (microbial sequence counts and metabolite abundances) to compute the conditional probability of observing a metabolite in the presence of a specific microorganism.
Categories: Journal Articles

MIET with graphene

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0645-y

MIET with graphene
Categories: Journal Articles

The <i>C. elegans</i> embryonic transcriptome

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0643-0

The C. elegans embryonic transcriptome
Categories: Journal Articles

Multi-input programming of cellular response

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0649-7

Multi-input programming of cellular response
Categories: Journal Articles

A picture is worth…

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0656-8

This month, we celebrate the visual beauty of scientific images and drawings.
Categories: Journal Articles

Light-sheet microscopy of cleared tissues with isotropic, subcellular resolution

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0615-4

Cleared-tissue axially swept light-sheet microscopy (ctASLM) enables high-speed, refraction index-independent imaging of live, cleared and expanded samples with isotropic, submicron resolution.
Categories: Journal Articles

Culturing uncultivated bacteria

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0634-1

Researchers develop a genome-informed approach to isolate and grow targeted cells into pure cultures from microbial communities.
Categories: Journal Articles

Spectroscopy goes nano

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0647-9

Spectroscopy goes nano
Categories: Journal Articles

Anti-anti-CRISPR

Nature Methods - 31 October 2019 - 12:00am

Nature Methods, Published online: 31 October 2019; doi:10.1038/s41592-019-0646-x

Anti-anti-CRISPR
Categories: Journal Articles

Author Correction: A genetically encodable cell-type-specific protein synthesis inhibitor

Nature Methods - 25 October 2019 - 12:00am

Nature Methods, Published online: 25 October 2019; doi:10.1038/s41592-019-0662-x

Author Correction: A genetically encodable cell-type-specific protein synthesis inhibitor
Categories: Journal Articles

Publisher Correction: Nuclear pores as versatile reference standards for quantitative superresolution microscopy

Nature Methods - 25 October 2019 - 12:00am

Nature Methods, Published online: 25 October 2019; doi:10.1038/s41592-019-0659-5

Publisher Correction: Nuclear pores as versatile reference standards for quantitative superresolution microscopy
Categories: Journal Articles

Author Correction: Molecular resolution imaging by repetitive optical selective exposure

Nature Methods - 22 October 2019 - 12:00am

Nature Methods, Published online: 22 October 2019; doi:10.1038/s41592-019-0655-9

Author Correction: Molecular resolution imaging by repetitive optical selective exposure
Categories: Journal Articles

Author Correction: An efficient auxin-inducible degron system with low basal degradation in human cells

Nature Methods - 21 October 2019 - 12:00am

Nature Methods, Published online: 21 October 2019; doi:10.1038/s41592-019-0652-z

Author Correction: An efficient auxin-inducible degron system with low basal degradation in human cells
Categories: Journal Articles

Nucleus segmentation across imaging experiments: the 2018 Data Science Bowl

Nature Methods - 21 October 2019 - 12:00am

Nature Methods, Published online: 21 October 2019; doi:10.1038/s41592-019-0612-7

The 2018 Data Science Bowl challenged competitors to develop an accurate tool for segmenting stained nuclei from diverse light microscopy images. The winners deployed innovative deep-learning strategies to realize configuration-free segmentation.
Categories: Journal Articles

Unified rational protein engineering with sequence-based deep representation learning

Nature Methods - 21 October 2019 - 12:00am

Nature Methods, Published online: 21 October 2019; doi:10.1038/s41592-019-0598-1

UniRep learns fundamental protein features from millions of amino-acid sequences using a recurrent neural network. This summary of features can then be used for protein engineering.
Categories: Journal Articles

Genome-wide quantification of ADAR adenosine-to-inosine RNA editing activity

Nature Methods - 21 October 2019 - 12:00am

Nature Methods, Published online: 21 October 2019; doi:10.1038/s41592-019-0610-9

The Alu editing index (AEI) quantifies genome-wide editing in Alu repeats and allows comparison across samples.
Categories: Journal Articles

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