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Preview: Nature Methods - Issue - science feeds

Nature Methods - Issue - science feeds

Nature Methods is a science methodology journal publishing laboratory techniques and methods papers in the life sciences and areas of chemistry relevant to the life sciences.


The Author File: Chris Xu
Deep brain imaging with three-photon microscopy and a swim from the US to China.

Points of Significance: Tabular data


Tabulating the number of objects in categories of interest dates back to the earliest records of commerce and population censuses.

MotionCor2: anisotropic correction of beam-induced motion for improved cryo-electron microscopy


MotionCor2 software corrects for beam-induced sample motion, improving the resolution of cryo-EM reconstructions.

Automatic tracing of ultra-volumes of neuronal images


Automated tracing algorithms can extract neuronal morphology from fluorescent or brightfield images. UltraTracer scales up the capability of existing tracing algorithms to handle datasets of ever-increasing size.

Neuroscience: Connectomics at the single-cell level


Trans-synaptic tracing that starts from a single neuron provides a detailed view of that neuron's inputs.

Sensors and probes: A magnetic alternative to FRET


A new approach measures nanoscale distances based on magnetic resonance tuning.

Genomics: SLICE-ing a genome's architecture


Thin slices through nuclei provide an unbiased view of the complex 3D organization of mammalian genomes.

Imaging: Volumetric functional imaging two ways


Bessel focus scanning and stereoscopy speed up volumetric brain imaging.

Genetics: DNA variants or DNA damage?


Cryptic, widespread DNA damage is commonly interpreted as sequence variation.

Choosing CRISPR-based screens in cancer


Many possibilities for parsing cancer emerge when labs combine gene editing and screens. And RNAi retains its spot in the menu of options.

Nanopore sequencing meets epigenetics


Advanced signal processing techniques enable the genome-wide analysis of methylation in native DNA using nanopore sequencing.

A guide to light-sheet fluorescence microscopy for multiscale imaging


This Review introduces the fundamental considerations for building a light sheet microscope, describes the pros and cons associated with available implementations, and offers practical advice for users.

Power analysis of single-cell RNA-sequencing experiments


A comparison framework applied to 15 single-cell RNA-seq protocols reveals differences in accuracy and sensitivity and discusses the utility of RNA spike-in standards.

In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain


Ouzounov et al. report calcium imaging with three-photon microscopy in the mouse brain. The approach enabled noninvasive recording of activity with high spatial and temporal resolution from GCaMP6-labeled neurons located as deep as the hippocampus.

Optogenetic control with a photocleavable protein, PhoCl


A photocleavable protein (PhoCl) that spontaneously dissociates into two fragments after illumination with violet light expands the toolkit for cellular optogenetics.

Seq-Well: portable, low-cost RNA sequencing of single cells at high throughput


Seq-Well provides similar scale and data quality to massively parallel, droplet-based single-cell RNA-seq methods in an easy to use, inexpensive and portable microwell format compatible with low-input samples.

Atomic-resolution structures from fragmented protein crystals with the cryoEM method MicroED


Fragmentation of large, imperfect crystals into nanocrystals by sonication, vortexing, or vigorous pipetting facilitates atomic-resolution analysis by the cryo-EM method MicroED.

Prospective identification of hematopoietic lineage choice by deep learning


A deep learning approach enables fast and robust prediction of hematopoietic stem cell lineage choice in time-lapse imaging three generations before conventional marker onset.

Detecting DNA cytosine methylation using nanopore sequencing


A hidden Markov model (HMM)-based tool enables detection of 5-methylcytosine (5-mC) from single-molecule nanopore-sequencing data generated directly from human genomic DNA without chemical treatment.

Mapping DNA methylation with high-throughput nanopore sequencing


A tool based on hidden Markov model and hierarchical Dirichlet process (HMM-HDP) can call two methylated cytosine variants and a methylated adenine variant directly from genomic DNA using nanopore sequencing data.

Visualization and analysis of single-cell RNA-seq data by kernel-based similarity learning


The SIMLR software identifies similarities between cells across a range of single-cell RNA-seq data, enabling effective dimension reduction, clustering and visualization.

Salmon provides fast and bias-aware quantification of transcript expression


Salmon is a computational tool that uses sample-specific models and a dual-phase inference procedure to correct biases in RNA-seq data and rapidly quantify transcript abundances.

Volumetric two-photon imaging of neurons using stereoscopy (vTwINS)


vTwINS enables high-speed volumetric calcium imaging via a V-shaped point spread function and a dedicated data-processing algorithm. Song et al. apply this strategy to image population activity in the mouse visual cortex and hippocampus.

Genetically encoded biosensors for visualizing live-cell biochemical activity at super-resolution


New fluorescent biosensors enable the first super-resolution imaging of enzyme activity in live cells via fluorescence fluctuation increase by contact (FLINC).

Automated synaptic connectivity inference for volume electron microscopy


SyConn is a computational framework that infers the synaptic wiring of neurons in volume electron microscopy data sets with machine learning. It has been applied to zebra finch, mouse and zebrafish neuronal tissue samples.

Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers


A robust acoustic droplet ejection–drop-on-tape method delivers samples to an X-ray free-electron laser source for combined serial femtosecond crystallography and X-ray emission spectroscopy analysis, providing detailed insights into macromolecular reaction dynamics.

A genetic system to study Plasmodium falciparum protein function


Selection-linked integration in the Plasmodium genome allows for rapid selection of genes inserted at a genomic locus or induction of the inactivation of gene products.