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

Journal Articles

Putting advanced microscopy in the hands of biologists

Nature Methods - 16 October 2019 - 12:00am

Nature Methods, Published online: 16 October 2019; doi:10.1038/s41592-019-0618-1

The growth of advanced, custom microscopy has outpaced commercialization, with biologists unable to benefit from these developments. We propose a complementary model for access based on shareable, traveling and configurable microscopes, with potential benefits for biologists, developers and the community.
Categories: Journal Articles

Won Do Heo

Nature Methods - 16 October 2019 - 12:00am

Nature Methods, Published online: 16 October 2019; doi:10.1038/s41592-019-0626-1

Growing up curious in the countryside leads to tools for manipulating endogenous proteins.
Categories: Journal Articles

Optogenetic activation of intracellular antibodies for direct modulation of endogenous proteins

Nature Methods - 14 October 2019 - 12:00am

Nature Methods, Published online: 14 October 2019; doi:10.1038/s41592-019-0592-7

Optobodies combine split intracellular antibodies (intrabodies) with light-controlled dimerization tools for spatiotemporal control of intrabody activity. The developed tools demonstrate the versatility and power of this approach for probing protein function.
Categories: Journal Articles

Machine learning-guided channelrhodopsin engineering enables minimally invasive optogenetics

Nature Methods - 14 October 2019 - 12:00am

Nature Methods, Published online: 14 October 2019; doi:10.1038/s41592-019-0583-8

An engineering approach guided by machine learning results in high-performance channelrhodopsin variants that are suitable for systemic viral delivery and illumination through a thinned skull.
Categories: Journal Articles

Multiplexed and single cell tracing of lipid metabolism

Nature Methods - 14 October 2019 - 12:00am

Nature Methods, Published online: 14 October 2019; doi:10.1038/s41592-019-0593-6

Cellular lipids, labeled with a charged reporter, yield characteristic MS1 and MS2 patterns during mass spectrometry. These reporters allow sample multiplexing and sensitive detection of lipid metabolism at single cell resolution.
Categories: Journal Articles

mEosEM withstands osmium staining and Epon embedding for super-resolution CLEM

Nature Methods - 14 October 2019 - 12:00am

Nature Methods, Published online: 14 October 2019; doi:10.1038/s41592-019-0613-6

mEosEM survives 1% OsO4 treatment and Epon embedding for improved super-resolution correlative light and electron microscopy.
Categories: Journal Articles

A complete data processing workflow for cryo-ET and subtomogram averaging

Nature Methods - 14 October 2019 - 12:00am

Nature Methods, Published online: 14 October 2019; doi:10.1038/s41592-019-0591-8

An integrated pipeline for processing cryo-ET data implemented in EMAN2 streamlines data processing to minimize human bias, and improves the quality and resolution of resulting macromolecular structures, both in vitro and in cells.
Categories: Journal Articles

Exploring single-cell data with deep multitasking neural networks

Nature Methods - 7 October 2019 - 12:00am

Nature Methods, Published online: 07 October 2019; doi:10.1038/s41592-019-0576-7

SAUCIE, a deep learning platform to analyze single-cell data across samples and platforms, allows information to be obtained from the internal layers of the network, which provides additional mechanistic understanding that can be used to further tune data analysis.
Categories: Journal Articles

Engineering of human brain organoids with a functional vascular-like system

Nature Methods - 7 October 2019 - 12:00am

Nature Methods, Published online: 07 October 2019; doi:10.1038/s41592-019-0586-5

Expression of ETV2 in human cortical organoids induces the formation of vascular-like networks, which reduces cell death within organoids and increases their functional maturation.
Categories: Journal Articles

Real-time cryo-electron microscopy data preprocessing with Warp

Nature Methods - 7 October 2019 - 12:00am

Nature Methods, Published online: 07 October 2019; doi:10.1038/s41592-019-0580-y

The user-friendly software tool Warp enables automated, on-the-fly preprocessing of cryo-EM data, including motion correction, defocus estimation, particle picking and image denoising.
Categories: Journal Articles

An order of magnitude faster DNA-PAINT imaging by optimized sequence design and buffer conditions

Nature Methods - 7 October 2019 - 12:00am

Nature Methods, Published online: 07 October 2019; doi:10.1038/s41592-019-0584-7

DNA-PAINT is sped up by an order of magnitude by optimizing sequences and buffer conditions, enabling faster imaging with no compromise to image quality or resolution, improved single-molecule counting and enhanced cellular imaging.
Categories: Journal Articles

Positive-unlabeled convolutional neural networks for particle picking in cryo-electron micrographs

Nature Methods - 7 October 2019 - 12:00am

Nature Methods, Published online: 07 October 2019; doi:10.1038/s41592-019-0575-8

The challenge of accurate particle picking in cryo-EM analysis is addressed with Topaz, a neural-network-based algorithm that shows advantages over other tools, especially in picking unusually shaped particles.
Categories: Journal Articles

Depth-resolved fiber photometry with a single tapered optical fiber implant

Nature Methods - 7 October 2019 - 12:00am

Nature Methods, Published online: 07 October 2019; doi:10.1038/s41592-019-0581-x

Fiber photometry with tapered fibers allows monitoring of neural activity in larger volumes than with flat-cleaved fibers. In addition, signals from different depths can be resolved with the same tapered fiber.
Categories: Journal Articles

ilastik: interactive machine learning for (bio)image analysis

Nature Methods - 30 September 2019 - 12:00am

Nature Methods, Published online: 30 September 2019; doi:10.1038/s41592-019-0582-9

ilastik is an user-friendly interactive tool for machine-learning-based image segmentation, object classification, counting and tracking.
Categories: Journal Articles

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