Methods

Fast, in vivo voltage imaging using a red fluorescent indicator Fast, in vivo voltage imaging using a red fluorescent indicator, Published online: 12 November 2018; doi:10.1038/s41592-018-0188-7 VARNAM is a red-shifted genetically encoded voltage sensor based on the Ace opsin. It is applied in Drosophila, mouse brain slices and behaving mice. It can be readily combined
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Closed-loop all-optical interrogation of neural circuits in vivo Closed-loop all-optical interrogation of neural circuits in vivo, Published online: 12 November 2018; doi:10.1038/s41592-018-0183-z A closed-loop all-optical strategy allows manipulation of neurons on the basis of their ongoing activity and can be used to clamp neuronal activity to a preset level, boost sensory-evoked activity or yoke together
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Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure Nanobody immunostaining for correlated light and electron microscopy with preservation of ultrastructure, Published online: 05 November 2018; doi:10.1038/s41592-018-0177-x NATIVE is a correlative light and electron microscopy approach that is based on nanobody-mediated immunohistochemistry. The approach does not require harsh permeabilization and preserves ultrastructure
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Publisher Correction: Transparent Danionella translucida as a genetically tractable vertebrate brain model Publisher Correction: Transparent <i>Danionella translucida</i> as a genetically tractable vertebrate brain model, Published online: 05 November 2018; doi:10.1038/s41592-018-0217-6 Publisher Correction: Transparent Danionella translucida as a genetically tractable vertebrate brain model
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Diploid genome in 3D Diploid genome in 3D, Published online: 30 October 2018; doi:10.1038/s41592-018-0208-7 Dip-C, a descendent of the 3C method, reveals 3D genome structures of single diploid human cells.
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A call for public archives for biological image data A call for public archives for biological image data, Published online: 30 October 2018; doi:10.1038/s41592-018-0195-8 Public data archives are the backbone of modern biological research. Biomolecular archives are well established, but bioimaging resources lag behind them. The technology required for imaging archives is now available, thus
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Spatial organization of the somatosensory cortex revealed by osmFISH Spatial organization of the somatosensory cortex revealed by osmFISH, Published online: 30 October 2018; doi:10.1038/s41592-018-0175-z osmFISH applies automated cycles of single-molecule fluorescence in situ hybridization without barcoding to provide spatial gene expression in tissue sections at high sensitivity, accuracy and throughput.
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FLIRT: fast local infrared thermogenetics for subcellular control of protein function FLIRT: fast local infrared thermogenetics for subcellular control of protein function, Published online: 30 October 2018; doi:10.1038/s41592-018-0168-y FLIRT enables spatiotemporally precise control of protein function in C. elegans by harnessing existing temperature-sensitive mutations. Proteins can be inactivated at desired sites by infrared laser light
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emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging emClarity: software for high-resolution cryo-electron tomography and subtomogram averaging, Published online: 22 October 2018; doi:10.1038/s41592-018-0167-z A software tool, emClarity, implements several improvements in cryo-electron tomography image-processing algorithms to achieve sub-nanometer resolution for diverse macromolecular structures.
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Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study, Published online: 16 October 2018; doi:10.1038/s41592-018-0193-x Publisher Correction: Precision and accuracy of single-molecule FRET measurements—a multi-laboratory benchmark study
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Transparent Danionella translucida as a genetically tractable vertebrate brain model Transparent <i>Danionella translucida</i> as a genetically tractable vertebrate brain model, Published online: 15 October 2018; doi:10.1038/s41592-018-0144-6 The combination of transparency, small brain size and genetic access positions Danionella translucida as a promising model organism for functional imaging of neuronal circuits, especially during complex behaviors in
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Guide Swap enables genome-scale pooled CRISPR–Cas9 screening in human primary cells Guide Swap enables genome-scale pooled CRISPR–Cas9 screening in human primary cells, Published online: 08 October 2018; doi:10.1038/s41592-018-0149-1 Guide Swap challenges the hypothesis that Cas9–sgRNA binding is irreversible. The authors find that instead, nontargeting sgRNAs are swapped for targeting sgRNAs in the Cas9 complex. The
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Publisher Correction: Image Data Resource: a bioimage data integration and publication platform Publisher Correction: Image Data Resource: a bioimage data integration and publication platform, Published online: 04 October 2018; doi:10.1038/s41592-018-0169-x Publisher Correction: Image Data Resource: a bioimage data integration and publication platform
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Coloring electron microscopy connectomes Coloring electron microscopy connectomes, Published online: 01 October 2018; doi:10.1038/s41592-018-0166-0 FluoEM aligns axon reconstructions from fluorescence and 3D electron microscopy on the same tissue to allow multicolor labeling of distant inputs.
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Phototoxicity revisited Phototoxicity revisited, Published online: 01 October 2018; doi:10.1038/s41592-018-0170-4 As microscopy methods for studying biology in living samples advance and demand for them grows, assessment of light damage caused by imaging becomes increasingly important.
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A tissue-to-organelle view of cellular proteins A tissue-to-organelle view of cellular proteins, Published online: 01 October 2018; doi:10.1038/s41592-018-0163-3 By coupling multiplex iterative indirect immunofluorescence imaging with computer vision methods, researchers can detect at least 40 different proteins with subcellular resolution.
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Deep generative models of genetic variation capture the effects of mutations Deep generative models of genetic variation capture the effects of mutations, Published online: 24 September 2018; doi:10.1038/s41592-018-0138-4 DeepSequence is an unsupervised deep latent-variable model that predicts the effects of mutations on the basis of evolutionary sequence information.
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Reducing effects of particle adsorption to the air–water interface in cryo-EM Reducing effects of particle adsorption to the air–water interface in cryo-EM, Published online: 24 September 2018; doi:10.1038/s41592-018-0139-3 Reducing the length of time that protein particles spend on a sample grid prior to freezing mitigates deleterious effects caused by particle adsorption to the air–water interface
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Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy Label-free prediction of three-dimensional fluorescence images from transmitted-light microscopy, Published online: 17 September 2018; doi:10.1038/s41592-018-0111-2 Convolutional neural networks enable prediction of fluorescently labeled structures from three-dimensional time-lapse transmitted-light images. Applications include multiplexed long time-lapse imaging and prediction of fluorescence in electron micrographs.
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Template-free 2D particle fusion in localization microscopy Template-free 2D particle fusion in localization microscopy, Published online: 17 September 2018; doi:10.1038/s41592-018-0136-6 An all-to-all registration approach allows for improved, high-resolution, template-free single-particle reconstruction from localization microscopy data under realistic experimental conditions such as low labeling density.
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Inferring single-trial neural population dynamics using sequential auto-encoders Inferring single-trial neural population dynamics using sequential auto-encoders, Published online: 17 September 2018; doi:10.1038/s41592-018-0109-9 LFADS, a deep learning method for analyzing neural population activity, can extract neural dynamics from single-trial recordings, stitch separate datasets into a single model, and infer perturbations, for example, from behavioral choices to
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Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms Terminal exon characterization with TECtool reveals an abundance of cell-specific isoforms, Published online: 10 September 2018; doi:10.1038/s41592-018-0114-z TECtool identifies terminal exons from RNA-seq data, uncovering novel isoforms, many of which are translated.
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Three-photon imaging of mouse brain structure and function through the intact skull Three-photon imaging of mouse brain structure and function through the intact skull, Published online: 10 September 2018; doi:10.1038/s41592-018-0115-y Wang et al. demonstrate that the effects of aberrations and scattering caused by the mouse skull can be reduced with three-photon microscopy. Their approach allows
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Detecting acetylcholine Detecting acetylcholine, Published online: 31 August 2018; doi:10.1038/s41592-018-0131-y A genetically encoded sensor based on G-protein-coupled receptors can detect the neurotransmitter acetylcholine in vitro and in vivo.
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Easing the burden of code review Easing the burden of code review, Published online: 31 August 2018; doi:10.1038/s41592-018-0137-5 Nature Methods is one of several Nature journals undertaking a trial with Code Ocean, a cloud-based reproducibility platform, to make it easier to peer review computational code.
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Detecting repeated cancer evolution from multi-region tumor sequencing data Detecting repeated cancer evolution from multi-region tumor sequencing data, Published online: 31 August 2018; doi:10.1038/s41592-018-0108-x REVOLVER uses transfer learning on multi-region tumor sequencing data to jointly infer tumor evolution models in multiple individuals and to detect repeated evolutionary trajectories. Repeated evolution can be used to stratify
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CDeep3M—Plug-and-Play cloud-based deep learning for image segmentation CDeep3M—Plug-and-Play cloud-based deep learning for image segmentation, Published online: 31 August 2018; doi:10.1038/s41592-018-0106-z CDeep3M provides a user-friendly tool for deep-learning-based image segmentation via a cloud-based deep convolutional neural network. Demonstrations include challenging light, X-ray, and electron microscopy segmentation tasks.
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XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules XCMS-MRM and METLIN-MRM: a cloud library and public resource for targeted analysis of small molecules, Published online: 27 August 2018; doi:10.1038/s41592-018-0110-3 A resource of multiple reaction monitoring–mass spectrometry transitions for quantitative analysis of biological small molecules is provided in METLIN-MRM,
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Rapid and efficient induction of functional astrocytes from human pluripotent stem cells Rapid and efficient induction of functional astrocytes from human pluripotent stem cells, Published online: 20 August 2018; doi:10.1038/s41592-018-0103-2 A simple transcription-factor-based protocol generates functional astrocytes rapidly and efficiently from human pluripotent stem cells.
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