Browse Articles

  • Brief Communication |

    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.

    • Bo Li
    • , Chunyan Wu
    • , Mengran Wang
    • , Kriti Charan
    •  & Chris Xu
  • Perspective |

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

    • Robert A. Amezquita
    • , Aaron T. L. Lun
    • , Etienne Becht
    • , Vince J. Carey
    • , Lindsay N. Carpp
    • , Ludwig Geistlinger
    • , Federico Martini
    • , Kevin Rue-Albrecht
    • , Davide Risso
    • , Charlotte Soneson
    • , Levi Waldron
    • , Hervé Pagès
    • , Mike L. Smith
    • , Wolfgang Huber
    • , Martin Morgan
    • , Raphael Gottardo
    •  & Stephanie C. Hicks
  • Research Highlight |

    Stereochemically defined chemical probes aid discovery of ligandable proteins.

    • Arunima Singh
  • Editorial |

    Deep learning has made a resounding impact on microscopy; we highlight the state-of-the-art and potential future directions in this focus issue.

  • Analysis |

    The 2018 Human Protein Atlas Image Classification competition sought to improve automated classification of protein subcellular localizations from fluorescence images. The winning strategies involved innovative deep learning approaches for multi-label classification.

    • Wei Ouyang
    • , Casper F. Winsnes
    • , Martin Hjelmare
    • , Anthony J. Cesnik
    • , Lovisa Åkesson
    • , Hao Xu
    • , Devin P. Sullivan
    • , Shubin Dai
    • , Jun Lan
    • , Park Jinmo
    • , Shaikat M. Galib
    • , Christof Henkel
    • , Kevin Hwang
    • , Dmytro Poplavskiy
    • , Bojan Tunguz
    • , Russel D. Wolfinger
    • , Yinzheng Gu
    • , Chuanpeng Li
    • , Jinbin Xie
    • , Dmitry Buslov
    • , Sergei Fironov
    • , Alexander Kiselev
    • , Dmytro Panchenko
    • , Xuan Cao
    • , Runmin Wei
    • , Yuanhao Wu
    • , Xun Zhu
    • , Kuan-Lun Tseng
    • , Zhifeng Gao
    • , Cheng Ju
    • , Xiaohan Yi
    • , Hongdong Zheng
    • , Constantin Kappel
    •  & Emma Lundberg
  • Research Highlight |

    Higher-order processes can be harnessed for super-resolution CARS vibrational microscopy.

    • Nina Vogt
  • Article |

    The unique advantages of single-particle cryo-electron microscopy and cryo-electron tomography are combined in a method called TYGRESS, here applied to determine the structure of the intact ciliary axoneme at a resolution of 12 Å.

    • Kangkang Song
    • , Zhiguo Shang
    • , Xiaofeng Fu
    • , Xiaochu Lou
    • , Nikolaus Grigorieff
    •  & Daniela Nicastro
  • Article |

    An approach combining cryo-electron microscopy and mass spectrometry analysis of protein complexes enriched directly from cells enables structure determination of unknown complexes at atomic resolution.

    • Chi-Min Ho
    • , Xiaorun Li
    • , Mason Lai
    • , Thomas C. Terwilliger
    • , Josh R. Beck
    • , James Wohlschlegel
    • , Daniel E. Goldberg
    • , Anthony W. P. Fitzpatrick
    •  & Z. Hong Zhou
  • Article |

    Single-cell isolation following time-lapse imaging (SIFT) enables high-throughput screening of complex and dynamic phenotypes from pooled bacterial libraries. SIFT was used to generate ultraprecise synthetic gene oscillators.

    • Scott Luro
    • , Laurent Potvin-Trottier
    • , Burak Okumus
    •  & Johan Paulsson
  • Article |

    A new method of autophagy measurement is based on the detection of phospho-ATG16L1, a conserved early marker of autophagy. Sensitive detection can be achieved in multiple biological systems and assays with advantages over standard methods.

    • Wensheng Tian
    • , Reham Alsaadi
    • , Zhihao Guo
    • , Alena Kalinina
    • , Micaël Carrier
    • , Marie-Eve Tremblay
    • , Baptiste Lacoste
    • , Diane Lagace
    •  & Ryan C. Russell
  • Brief Communication |

    A miniaturized NMR-on-a-chip needle can be implanted into rodent brains and can measure blood flow and oxygenation changes in vivo in a small volume at an unprecedentedly high temporal resolution of a few milliseconds.

    • Jonas Handwerker
    • , Marlon Pérez-Rodas
    • , Michael Beyerlein
    • , Franck Vincent
    • , Armin Beck
    • , Nicolas Freytag
    • , Xin Yu
    • , Rolf Pohmann
    • , Jens Anders
    •  & Klaus Scheffler
  • This Month |

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

    • Vivien Marx
  • Article |

    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.

    • Rachael E. Workman
    • , Alison D. Tang
    • , Paul S. Tang
    • , Miten Jain
    • , John R. Tyson
    • , Roham Razaghi
    • , Philip C. Zuzarte
    • , Timothy Gilpatrick
    • , Alexander Payne
    • , Joshua Quick
    • , Norah Sadowski
    • , Nadine Holmes
    • , Jaqueline Goes de Jesus
    • , Karen L. Jones
    • , Cameron M. Soulette
    • , Terrance P. Snutch
    • , Nicholas Loman
    • , Benedict Paten
    • , Matthew Loose
    • , Jared T. Simpson
    • , Hugh E. Olsen
    • , Angela N. Brooks
    • , Mark Akeson
    •  & Winston Timp
  • Article |

    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.

    • Daniel Camsund
    • , Michael J. Lawson
    • , Jimmy Larsson
    • , Daniel Jones
    • , Spartak Zikrin
    • , David Fange
    •  & Johan Elf
  • Article |

    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.

    • Xiaoyan Qian
    • , Kenneth D. Harris
    • , Thomas Hauling
    • , Dimitris Nicoloutsopoulos
    • , Ana B. Muñoz-Manchado
    • , Nathan Skene
    • , Jens Hjerling-Leffler
    •  & Mats Nilsson
  • Correspondence |

    • Robert Haase
    • , Loic A. Royer
    • , Peter Steinbach
    • , Deborah Schmidt
    • , Alexandr Dibrov
    • , Uwe Schmidt
    • , Martin Weigert
    • , Nicola Maghelli
    • , Pavel Tomancak
    • , Florian Jug
    •  & Eugene W. Myers
  • Brief Communication |

    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.

    • Dominic Grün
  • Article |

    European XFEL allows investigation of the picosecond time range in the photocycle of photoactive yellow protein.

    • Suraj Pandey
    • , Richard Bean
    • , Tokushi Sato
    • , Ishwor Poudyal
    • , Johan Bielecki
    • , Jorvani Cruz Villarreal
    • , Oleksandr Yefanov
    • , Valerio Mariani
    • , Thomas A. White
    • , Christopher Kupitz
    • , Mark Hunter
    • , Mohamed H. Abdellatif
    • , Saša Bajt
    • , Valerii Bondar
    • , Austin Echelmeier
    • , Diandra Doppler
    • , Moritz Emons
    • , Matthias Frank
    • , Raimund Fromme
    • , Yaroslav Gevorkov
    • , Gabriele Giovanetti
    • , Man Jiang
    • , Daihyun Kim
    • , Yoonhee Kim
    • , Henry Kirkwood
    • , Anna Klimovskaia
    • , Juraj Knoska
    • , Faisal H. M. Koua
    • , Romain Letrun
    • , Stella Lisova
    • , Luis Maia
    • , Victoria Mazalova
    • , Domingo Meza
    • , Thomas Michelat
    • , Abbas Ourmazd
    • , Guido Palmer
    • , Marco Ramilli
    • , Robin Schubert
    • , Peter Schwander
    • , Alessandro Silenzi
    • , Jolanta Sztuk-Dambietz
    • , Alexandra Tolstikova
    • , Henry N. Chapman
    • , Alexandra Ros
    • , Anton Barty
    • , Petra Fromme
    • , Adrian P. Mancuso
    •  & Marius Schmidt
  • Article |

    Harmony, for the integration of single-cell transcriptomic data, identifies broad and fine-grained populations, scales to large datasets, and can integrate sequencing- and imaging-based data.

    • Ilya Korsunsky
    • , Nghia Millard
    • , Jean Fan
    • , Kamil Slowikowski
    • , Fan Zhang
    • , Kevin Wei
    • , Yuriy Baglaenko
    • , Michael Brenner
    • , Po-ru Loh
    •  & Soumya Raychaudhuri
  • Brief Communication |

    Micropatterning of cryo-EM grids enables controlled adhesion of mammalian cells for cryo-ET-based structural studies. This approach leads to reproducible cellular morphology and improves focused ion beam thinning of cells for in-cell structural analyses.

    • Mauricio Toro-Nahuelpan
    • , Ievgeniia Zagoriy
    • , Fabrice Senger
    • , Laurent Blanchoin
    • , Manuel Théry
    •  & Julia Mahamid
  • Brief Communication |

    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.

    • Ye Zheng
    •  & Sündüz Keleş
  • Brief Communication |

    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.

    • Mrinali P. Gupta
    • , Sangeetha Tandalam
    • , Shariss Ostrager
    • , Alexander S. Lever
    • , Angus R. Fung
    • , David D. Hurley
    • , Gemstonn B. Alegre
    • , Jasmin E. Espinal
    • , H. Lawrence Remmel
    • , Sushmita Mukherjee
    • , Benjamin M. Levine
    • , Russell P. Robins
    • , Henrik Molina
    • , Brian D. Dill
    • , Candia M. Kenific
    • , Thomas Tuschl
    • , David Lyden
    • , Donald J. D’Amico
    •  & John T. G. Pena
  • Article |

    Deep-Z uses deep learning to go from a two-dimensional snapshot to three-dimensional fluorescence images. The method improves imaging speed while reducing light dose, and was shown to be useful for accurate structural and functional imaging of neurons in Caenorhabditis elegans.

    • Yichen Wu
    • , Yair Rivenson
    • , Hongda Wang
    • , Yilin Luo
    • , Eyal Ben-David
    • , Laurent A. Bentolila
    • , Christian Pritz
    •  & Aydogan Ozcan
  • Article |

    mmvec, a neural-network-based algorithm, uses paired multiomics data (microbial sequence counts and metabolite abundances) to compute the conditional probability of observing a metabolite in the presence of a specific microorganism.

    • James T. Morton
    • , Alexander A. Aksenov
    • , Louis Felix Nothias
    • , James R. Foulds
    • , Robert A. Quinn
    • , Michelle H. Badri
    • , Tami L. Swenson
    • , Marc W. Van Goethem
    • , Trent R. Northen
    • , Yoshiki Vazquez-Baeza
    • , Mingxun Wang
    • , Nicholas A. Bokulich
    • , Aaron Watters
    • , Se Jin Song
    • , Richard Bonneau
    • , Pieter C. Dorrestein
    •  & Rob Knight
  • Editorial |

    This month, we celebrate the visual beauty of scientific images and drawings.

  • Brief Communication |

    Cleared-tissue axially swept light-sheet microscopy (ctASLM) enables high-speed, refraction index-independent imaging of live, cleared and expanded samples with isotropic, submicron resolution.

    • Tonmoy Chakraborty
    • , Meghan K. Driscoll
    • , Elise Jeffery
    • , Malea M. Murphy
    • , Philippe Roudot
    • , Bo-Jui Chang
    • , Saumya Vora
    • , Wen Mai Wong
    • , Cara D. Nielson
    • , Hua Zhang
    • , Vladimir Zhemkov
    • , Chitkale Hiremath
    • , Estanislao Daniel De La Cruz
    • , Yating Yi
    • , Ilya Bezprozvanny
    • , Hu Zhao
    • , Raju Tomer
    • , Rainer Heintzmann
    • , Julian P. Meeks
    • , Denise K. Marciano
    • , Sean J. Morrison
    • , Gaudenz Danuser
    • , Kevin M. Dean
    •  & Reto Fiolka
  • Research Highlight |

    Researchers develop a genome-informed approach to isolate and grow targeted cells into pure cultures from microbial communities.

    • Lei Tang
  • Research Highlight |

    The hybrid voltage-indicator Voltron combines the voltage sensitivity of microbial rhodopsins with the brightness and photostability of chemical dyes.

    • Nina Vogt