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University Imaging Center
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University Imaging Centers - Where the University sees the future

Journal Articles

An adaptive excitation source for high-speed multiphoton microscopy

Nature Methods - 2 December 2019 - 12:00am

Nature Methods, Published online: 02 December 2019; doi:10.1038/s41592-019-0663-9

An adaptive excitation source enables two- and three-photon imaging of the awake mouse brain with high spatial and temporal resolution at 30-fold-reduced laser power relative to conventional approaches.
Categories: Journal Articles

Orchestrating single-cell analysis with Bioconductor

Nature Methods - 2 December 2019 - 12:00am

Nature Methods, Published online: 02 December 2019; doi:10.1038/s41592-019-0654-x

This Perspective highlights open-source software for single-cell analysis released as part of the Bioconductor project, providing an overview for users and developers.
Categories: Journal Articles

Culturing HSPCs

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0684-4

Culturing HSPCs
Categories: Journal Articles

Studying human lung infection in mice

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0672-8

Mice implanted with human lung tissue model pathogen infection and immune responses.
Categories: Journal Articles

ImJoy: an open-source computational platform for the deep learning era

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0627-0

ImJoy: an open-source computational platform for the deep learning era
Categories: Journal Articles

Polarized structured illumination microscopy

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0682-6

Polarized structured illumination microscopy
Categories: Journal Articles

Pose estimation with deep learning

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0678-2

Pose estimation with deep learning
Categories: Journal Articles

Inducing protein degradation using light

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0685-3

Inducing protein degradation using light
Categories: Journal Articles

Ligandable proteome mapping

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0673-7

Stereochemically defined chemical probes aid discovery of ligandable proteins.
Categories: Journal Articles

Modeling neurulation

Nature Methods - 28 November 2019 - 12:00am

Nature Methods, Published online: 28 November 2019; doi:10.1038/s41592-019-0680-8

Modeling neurulation
Categories: Journal Articles

It’s free imaging — label-free, that is

Nature Methods - 21 November 2019 - 12:00am

Nature Methods, Published online: 21 November 2019; doi:10.1038/s41592-019-0664-8

Label-free imaging lets labs ‘see’ their samples less invasively than other techniques.
Categories: Journal Articles

Juan C. Caicedo

Nature Methods - 19 November 2019 - 12:00am

Nature Methods, Published online: 19 November 2019; doi:10.1038/s41592-019-0668-4

A machine-learning competition in microscopy and the fun of gazing into the night sky.
Categories: Journal Articles

Nanopore native RNA sequencing of a human poly(A) transcriptome

Nature Methods - 18 November 2019 - 12:00am

Nature Methods, Published online: 18 November 2019; doi:10.1038/s41592-019-0617-2

Directly sequencing RNA strands through a nanopore retains the full length of the transcript and allows for analysis of polyA tail length, transcript haplotypes and base modifications.
Categories: Journal Articles

Time-resolved imaging-based CRISPRi screening

Nature Methods - 18 November 2019 - 12:00am

Nature Methods, Published online: 18 November 2019; doi:10.1038/s41592-019-0629-y

DuMPLING (dynamic μ-fluidic microscopy phenotyping of a library before in situ genotyping) enables screening of dynamic phenotypes in strain libraries and was used here to study genes that coordinate replication and cell division in Escherichia coli.
Categories: Journal Articles

Probabilistic cell typing enables fine mapping of closely related cell types in situ

Nature Methods - 18 November 2019 - 12:00am

Nature Methods, Published online: 18 November 2019; doi:10.1038/s41592-019-0631-4

Probabilistic cell typing by in situ sequencing (pciSeq), leverages previous single-cell RNA sequencing classification and multiplexed in situ RNA detection to spatially map cell types accurately in the mouse hippocampus and isocortex.
Categories: Journal Articles

CLIJ: GPU-accelerated image processing for everyone

Nature Methods - 18 November 2019 - 12:00am

Nature Methods, Published online: 18 November 2019; doi:10.1038/s41592-019-0650-1

CLIJ: GPU-accelerated image processing for everyone
Categories: Journal Articles

Gas cluster ion beam SEM for imaging of large tissue samples with 10 nm isotropic resolution

Nature Methods - 18 November 2019 - 12:00am

Nature Methods, Published online: 18 November 2019; doi:10.1038/s41592-019-0641-2

An alternative to focused ion beam scanning electron microscopy (FIB-SEM), gas cluster ion beam scanning electron microscopy (GCIB-SEM) is compatible with large tissue samples while achieving similar isotropic resolution.
Categories: Journal Articles

Revealing dynamics of gene expression variability in cell state space

Nature Methods - 18 November 2019 - 12:00am

Nature Methods, Published online: 18 November 2019; doi:10.1038/s41592-019-0632-3

VarID is a computational method that quantifies the dynamics of transcriptional variability with the goal of identifying the role of highly variable genes, such as weakly expressed transcription factors, in cell differentiation or state transitions.
Categories: 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

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