Microscopy articles within Nature Communications

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  • Article
    | Open Access

    Building synthetic protocells and prototissues hinges on the formation of biomimetic skeletal frameworks. Here, the authors harness simplicity to create complexity by assembling DNA subunits into structural frameworks which support membrane-based protocells and prototissues.

    • Nishkantha Arulkumaran
    • , Mervyn Singer
    •  & Jonathan R. Burns

  • Article
    | Open Access

    Endosomal escape and subsequent cytosolic delivery of siRNA therapeutics is inefficient, and quantification is difficult. Here the authors report a confocal microscopy-based method to quantify cytosolic delivery of fluorescently labelled siRNA during lipid-mediated delivery.

    • Hampus Hedlund
    • , Hampus Du Rietz
    •  & Anders Wittrup

  • Article
    | Open Access

    The antigen-B-cell-receptor interaction is the driving force of terminal B cell development that spans from B cell activation to antibody secreting plasma cells. Here authors determine, using DNA-PAINT super-resolution microscopy, how antigen affinity and valency define antigen binding to BCR in an in vitro system allowing precision control of these parameters.

    • Alexey Ferapontov
    • , Marjan Omer
    •  & Søren Egedal Degn

  • Article
    | Open Access

    Neutral helium microscopy is a completely nondestructive, surface-sensitive imaging technique. Here, the authors demonstrate sub-resolution contrast using an advanced facet scattering model to reconstruct the topography of technological thin films in the ångström range.

    • Sabrina D. Eder
    • , Adam Fahy
    •  & Paul C. Dastoor

  • Article
    | Open Access

    Living snakes replace their teeth without external resorption. Here, the authors use histology to show that odontoclasts resorb dentine internally and investigate this mechanism in fossil snakes.

    • A. R. H. LeBlanc
    • , A. Palci
    •  & M. W. Caldwell

  • Article
    | Open Access

    Weak interlayer van der Waals (vdW) bonding has significant impact on the structure and properties of vdW layered materials. Here authors use in-situ aberration-corrected ADF-STEM for an atomistic insight into the cation diffusion in the vdW gaps and the etching of vdW surfaces at high temperatures.

    • Wenjun Cui
    • , Weixiao Lin
    •  & Xiahan Sang

  • Article
    | Open Access

    Studying chemosensory processing desires precise chemical cue presentation, behavioral response monitoring, and large-scale neuronal activity recording. Here, the authors report a fluidics-based toolkit for studying chemosensation in larval zebrafish, and used it to reveal the brainwide neural representations of cadaverine sensing and its binasal input-dependent behavioral avoidance.

    • Samuel K. H. Sy
    • , Danny C. W. Chan
    •  & Ho Ko

  • Article
    | Open Access

    Mica is a naturally occurring 2D mineral that has been heavily studied in many diverse areas. Here authors present atomic force microscopy images to study the mica surface in ultra-high vacuum conditions; they unveil the distribution of its surface K+ ions and give insights into the distribution of subsurface Al3+ ions.

    • Giada Franceschi
    • , Pavel Kocán
    •  & Ulrike Diebold

  • Article
    | Open Access

    GABAB receptors mediate the effects of the main inhibitory neurotransmitter in the brain. Here, authors identify the cytoskeletal protein filamin A as a key player that controls the exact location and function of GABAB receptors at the cell surface.

    • Marie-Lise Jobin
    • , Sana Siddig
    •  & Davide Calebiro

  • Article
    | Open Access

    Structured Illumination Microscopy allows for the visualization of biological structures at resolutions below the diffraction limit, but this imaging modality is still hampered by high experimental complexity. Here, the authors present a combination of interferometry and machine learning to construct a structured illumination microscope for super resolution imaging of dynamic sub-cellular biological structures in multiple colors.

    • Edward N. Ward
    • , Lisa Hecker
    •  & Clemens F. Kaminski

  • Article
    | Open Access

    Signals about head orientation and movement in the vestibular periphery are fundamental to the sense of balance and motion, but difficult to measure systematically during head motion. Here, the authors build a microscope that visualizes neural activity in hair cells and vestibular ganglion cells during 360° head tilt and vibration in zebrafish larvae, and reveal a topographic organization of direction- and static/dynamic stimulus-selective responses.

    • Masashi Tanimoto
    • , Ikuko Watakabe
    •  & Shin-ichi Higashijima

  • Article
    | Open Access

    It is currently debated how to reliably distinguish liquid–liquid phase separation (LLPS) from other mechanisms. Here the authors report model-free calibrated half-FRAP (MOCHA-FRAP) to probe the barrier at the condensate interface that is responsible for preferential internal mixing in LLPS.

    • Fernando Muzzopappa
    • , Johan Hummert
    •  & Fabian Erdel

  • Article
    | Open Access

    The authors introduce Bond-selective Intensity Diffraction Tomography, a computational mid-infrared photothermal microscopy technique based on a standard bright-field microscope and an add-on pulsed light source. It recovers both mid-infrared spectra and bond-selective 3D refractive index maps based on intensity-only measurements.

    • Jian Zhao
    • , Alex Matlock
    •  & Ji-Xin Cheng

  • Article
    | Open Access

    Super-resolution microscopy techniques can be challenging for live cells and thick samples. Here, the authors propose a method to reduce beam intensity and remove out-of-focus fluorescence background in image-scanning microscopy (ISM) and its combination with stimulated emission depletion (STED).

    • Giorgio Tortarolo
    • , Alessandro Zunino
    •  & Giuseppe Vicidomini

  • Article
    | Open Access

    The neurophysiological mechanisms of deep brain stimulation remain poorly understood. Through fluorescence voltage imaging of individual hippocampal neurons in awake mice, the authors show that deep brain stimulation causes membrane depolarization that impairs a neuron’s ability to respond to intrinsic network activity patterns and optogenetic somatic depolarization, thereby creating an informational lesion.

    • Eric Lowet
    • , Krishnakanth Kondabolu
    •  & Xue Han

  • Article
    | Open Access

    Object detection using machine learning universally requires vast amounts of training datasets. Midtvedt et al. proposes a deep-learning method that enables detecting microscopic objects with sub-pixel accuracy from a single unlabeled image by exploiting the roto-translational symmetries of the problem.

    • Benjamin Midtvedt
    • , Jesús Pineda
    •  & Giovanni Volpe

  • Article
    | Open Access

    The presented Mean-Shift Super Resolution (MSSR) algorithm can extend spatial resolution within a single microscopy image. Its applicability extends across a wide range of experimental and instrumental configurations and it is compatible with other super-resolution microscopy approaches.

    • Esley Torres-García
    • , Raúl Pinto-Cámara
    •  & Adán Guerrero

  • Article
    | Open Access

    The translational states of eukaryotic ribosomes have so far been only investigated in vitro. Here, authors obtained the 3.8 Å in situ 80S ribosome structure, the distribution of translational states and unique arrangement of rRNA expansion segments.

    • Patrick C. Hoffmann
    • , Jan Philipp Kreysing
    •  & Martin Beck

  • Article
    | Open Access

    Spatially resolved proteomics is an emerging approach for mapping proteome heterogeneity. Here, the authors report a method based on the combination of hydrogel-based tissue transformation with mass spectrometry-based proteomics, that enables proteome profiling with a lateral resolution of 160 µm.

    • Lu Li
    • , Cuiji Sun
    •  & Kiryl D. Piatkevich

  • Article
    | Open Access

    Traditional methods for cell stiffness measurements are limited by long processing times and unsuitability for multiple cell analysis. Here, the authors demonstrate a fast technique based on acoustic stimulation and holographic imaging to reconstruct whole-cell stiffness maps of individual and multiple cells.

    • Rahmetullah Varol
    • , Zeynep Karavelioglu
    •  & Huseyin Uvet

  • Article
    | Open Access

    Single-molecule localization microscopy relies on stochastic blinking events, treated as independent events without assignment to a particular emitter. Here, BaGoL takes low precision localizations generated from multiple emitter blinkings during DNAPAINT and dSTORM and finds the underlying emitter positions with high precision.

    • Mohamadreza Fazel
    • , Michael J. Wester
    •  & Keith A. Lidke

  • Article
    | Open Access

    Air-water interface and preferential orientation problems are crucial challenges in cryo-EM specimen preparation. Here, the authors utilize graphene-coated EM grids functionalized by salts with various electrostatic properties, successfully overcoming preferred orientation.

    • Ye Lu
    • , Nan Liu
    •  & Hong-Wei Wang

  • Article
    | Open Access

    Chromatin compaction affects many nuclear processes yet compaction levels at individual genomic loci have been notoriously difficult to assess. Here, Ana Mota and co-authors from the Bienko-Crosetto Lab present FRET-FISH for probing chromatin compaction at selected loci in single cells.

    • Ana Mota
    • , Szymon Berezicki
    •  & Magda Bienko

  • Article
    | Open Access

    The authors demonstrate a label-free superresolution imaging method by using a hyperbolic material as a substrate for tailored light-matter interactions. The hyperbolic material enhanced scattering, combined with dark-field detection, result in 5.5-fold resolution improvement beyond the diffraction limit.

    • Yeon Ui Lee
    • , Shilong Li
    •  & Zhaowei Liu

  • Article
    | Open Access

    The authors report high-efficiency emission depletion through a surface migration emission depletion mechanism, which takes advantage of the effects of surface quenching and energy migration in nanocrystals. They demonstrate super-resolution microscopy with very low depletion saturation intensities.

    • Rui Pu
    • , Qiuqiang Zhan
    •  & Xiaogang Liu

  • Article
    | Open Access

    Non-random chemical mixings that are intrinsic to medium- and high-entropy alloys are difficult to detect and quantify. Here the authors perform a diffraction data-mining analysis, revealing nanoclusters of short-range orders in a CrCoNi alloy, and their impacts on chemical homogeneity and dislocations slip.

    • Haw-Wen Hsiao
    • , Rui Feng
    •  & Jian-Min Zuo

  • Article
    | Open Access

    The authors developed a pristine hyperspectral SPR microscopy that enables monochromatic and polychromatic SPR imaging with flexible field-of-view option, single-pixel spectral SPR sensing and 2D quantification of thin films with resonant wavelength images.

    • Ziwei Liu
    • , Jingning Wu
    •  & Zhi-mei Qi

  • Comment
    | Open Access

    Advances in atomic force microscopy (AFM) techniques and methodologies for microbiology contribute to our understanding of the microbial cell surface. Recent studies show that AFM imaging of cells and membranes at (near) molecular resolution allows detailed visualization of membranes interacting with drugs.

    • Telmo O. Paiva
    • , Albertus Viljoen
    •  & Yves F. Dufrêne

  • Article
    | Open Access

    Measuring sub-cellular pH with high accuracy and spatiotemporal resolution remains challenging. Here, Johnston and co-workers develop a pH biosensor that combines the pH dependant fluorescent lifetime of mApple with deep learning to accurately determine sub-cellular pH in individual vesicles.

    • Joshua J. Rennick
    • , Cameron J. Nowell
    •  & Angus P. R. Johnston

  • Article
    | Open Access

    The effect of aliovalent doping on grain boundary is not yet fully understood at the atomic level. Here, the authors report grain boundary structural transformation in α-Al2O3 is induced by co-segregation of multiple dopants using atomic-resolution electron microscopy and theoretical calculations.

    • Toshihiro Futazuka
    • , Ryo Ishikawa
    •  & Yuichi Ikuhara

  • Article
    | Open Access

    A major challenge of enzyme-linked immunosorbent assays is discriminating true signal from non-specific binding. Here the authors present a Single-Molecule Colocalization Assay (SiMCA) which eliminates such effects, enabling reproducible detection of picomolar protein concentrations.

    • Amani A. Hariri
    • , Sharon S. Newman
    •  & H. Tom Soh

  • Article
    | Open Access

    Optical binding enables light-induced assembly of many particles within a focus area. Here, the authors demonstrate that optical binding can occur outside the irradiated area by scattered light interacting with the particles outside the focus, generating arc-shape potential wells for particle trapping.

    • Chih-Hao Huang
    • , Boris Louis
    •  & Hiroshi Masuhara

  • Article
    | Open Access

    Particulate methane monooxygenase (pMMO) is the main enzyme used by methanotrophs. Here, the authors determined the native structure of pMMO by cryo-electron tomography, revealing lipid-stabilized features and a higher-order hexagonal array arrangement in intact cells.

    • Yanan Zhu
    • , Christopher W. Koo
    •  & Peijun Zhang

  • Article
    | Open Access

    Obtaining information about the structure of metal-organic layers (MOLs) using standard electron microscopy methods is challenging due to damage under electron beam irradiation. Here, the authors reveal a multistep formation process of MOLs and identify missing clusters, dislocations, loop and flat surface terminations and ligand connector of MOLs via complementary electron microscopy techniques.

    • Xinxing Peng
    • , Philipp M. Pelz
    •  & Mary C. Scott

  • Article
    | Open Access

    DNA-PAINT image acquisition is limited by speed. Here the authors use the neural network DeepSTORM to predict fluorophore positions from high emitter density DNA-PAINT data in order to achieve image acquisition in one minute; they demonstrate multi-colour and large-area imaging of semi-thin neuronal tissue.

    • Kaarjel K. Narayanasamy
    • , Johanna V. Rahm
    •  & Mike Heilemann

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