Brief Communications

  • Brief Communication |

    Sorting RT-FDC combines real-time fluorescence and deformability cytometry with sorting based on standing surface acoustic waves to transfer molecular specificity to label-free, image-based cell sorting using an efficient deep neural network.

    • Ahmad Ahsan Nawaz
    • , Marta Urbanska
    • , Maik Herbig
    • , Martin Nötzel
    • , Martin Kräter
    • , Philipp Rosendahl
    • , Christoph Herold
    • , Nicole Toepfner
    • , Markéta Kubánková
    • , Ruchi Goswami
    • , Shada Abuhattum
    • , Felix Reichel
    • , Paul Müller
    • , Anna Taubenberger
    • , Salvatore Girardo
    • , Angela Jacobi
    •  & Jochen Guck
  • Brief Communication |

    Theoretical and experimental guidelines to determine laser intensity for single-photon excitation in microcrystals for ultrafast pump–probe experiments by serial femtosecond crystallography.

    • Marie Luise Grünbein
    • , Miriam Stricker
    • , Gabriela Nass Kovacs
    • , Marco Kloos
    • , R. Bruce Doak
    • , Robert L. Shoeman
    • , Jochen Reinstein
    • , Sylvain Lecler
    • , Stefan Haacke
    •  & Ilme Schlichting
  • Brief Communication |

    jYCaMP1, a yellow variant of the calcium indicator jGCaMP7, enables fast multicolor two-photon imaging at excitation wavelengths above 1,000 nm for use with popular ytterbium-doped fiber and modelocked semiconductor lasers.

    • Manuel Alexander Mohr
    • , Daniel Bushey
    • , Abhi Aggarwal
    • , Jonathan S. Marvin
    • , Jeong Jun Kim
    • , Emiliano Jimenez Marquez
    • , Yajie Liang
    • , Ronak Patel
    • , John J. Macklin
    • , Chi-Yu Lee
    • , Arthur Tsang
    • , Getahun Tsegaye
    • , Allison M. Ahrens
    • , Jerry L. Chen
    • , Douglas S. Kim
    • , Allan M. Wong
    • , Loren L. Looger
    • , Eric R. Schreiter
    •  & Kaspar Podgorski
  • Brief Communication |

    A head-mounted three-photon microscope based on a custom-designed optical fiber and dispersion compensation enables imaging of activity from neuronal populations deep in the cortex of freely moving rats.

    • Alexandr Klioutchnikov
    • , Damian J. Wallace
    • , Michael H. Frosz
    • , Richard Zeltner
    • , Juergen Sawinski
    • , Verena Pawlak
    • , Kay-Michael Voit
    • , Philip St. J. Russell
    •  & Jason N. D. Kerr
  • Brief Communication |

    ‘Nativeomics’ enables identification of ligands bound to membrane proteins through detection of intact protein–ligand assemblies followed by dissociation and identification of individual ligands within the same mass spectrometry experiment.

    • Joseph Gault
    • , Idlir Liko
    • , Michael Landreh
    • , Denis Shutin
    • , Jani Reddy Bolla
    • , Damien Jefferies
    • , Mark Agasid
    • , Hsin-Yung Yen
    • , Marcus J. G. W. Ladds
    • , David P. Lane
    • , Syma Khalid
    • , Christopher Mullen
    • , Philip M. Remes
    • , Romain Huguet
    • , Graeme McAlister
    • , Michael Goodwin
    • , Rosa Viner
    • , John E.P. Syka
    •  & Carol V. Robinson
  • Brief Communication |

    Three-photon microscopy provides access to most of the adult zebrafish brain for both structural and functional imaging, as well as to the Danionella dracula brain.

    • Dawnis M. Chow
    • , David Sinefeld
    • , Kristine E. Kolkman
    • , Dimitre G. Ouzounov
    • , Najva Akbari
    • , Rose Tatarsky
    • , Andrew Bass
    • , Chris Xu
    •  & Joseph R. Fetcho
  • Brief Communication |

    High-speed two-photon laser scanning microscopy using a passive laser scanner based on free-space angular-chirp-enhanced delay achieves frame rates suitable for voltage imaging in vivo in the mouse brain.

    • Jianglai Wu
    • , Yajie Liang
    • , Shuo Chen
    • , Ching-Lung Hsu
    • , Mariya Chavarha
    • , Stephen W. Evans
    • , Dongqing Shi
    • , Michael Z. Lin
    • , Kevin K. Tsia
    •  & Na Ji
  • Brief Communication |

    Charge assignment for individual ions unlocks complex mixtures of proteoforms and their assemblies by native mass spectrometry.

    • Jared O. Kafader
    • , Rafael D. Melani
    • , Kenneth R. Durbin
    • , Bon Ikwuagwu
    • , Bryan P. Early
    • , Ryan T. Fellers
    • , Steven C. Beu
    • , Vlad Zabrouskov
    • , Alexander A. Makarov
    • , Joshua T. Maze
    • , Deven L. Shinholt
    • , Ping F. Yip
    • , Danielle Tullman-Ercek
    • , Michael W. Senko
    • , Philip D. Compton
    •  & Neil L. Kelleher
  • Brief Communication |

    Engineered nanobody allows reversible control of activity in cells through the binding of small molecules.

    • Helen Farrants
    • , Miroslaw Tarnawski
    • , Thorsten G. Müller
    • , Shotaro Otsuka
    • , Julien Hiblot
    • , Birgit Koch
    • , Moritz Kueblbeck
    • , Hans-Georg Kräusslich
    • , Jan Ellenberg
    •  & Kai Johnsson
  • Brief Communication |

    Reverberation two-photon microscopy enables video-rate multiplane neuroimaging by performing near-instantaneous axial scanning over large depth ranges while maintaining 3D micrometer-scale resolution.

    • Devin R. Beaulieu
    • , Ian G. Davison
    • , Kıvılcım Kılıç
    • , Thomas G. Bifano
    •  & Jerome Mertz
  • Brief Communication |

    Wtdbg2 assembles genomes with comparable contiguity and accuracy to existing tools using long-read sequencing data, and is several times faster, especially for large genomes.

    • Jue Ruan
    •  & Heng Li
  • Brief Communication |

    SIMFLUX combines elements of MINFLUX with structured illumination to double localization precision and improve resolution in localization microscopy. The approach was demonstrated on DNA origami and on cellular microtubules.

    • Jelmer Cnossen
    • , Taylor Hinsdale
    • , Rasmus Ø. Thorsen
    • , Marijn Siemons
    • , Florian Schueder
    • , Ralf Jungmann
    • , Carlas S. Smith
    • , Bernd Rieger
    •  & Sjoerd Stallinga
  • 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
  • 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
  • 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
  • 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 |

    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
  • 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 |

    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
  • Brief Communication |

    A multi-beam two-photon microscope enables imaging of calcium activity or neurovascular dynamics in the brain with millisecond-scale temporal resolution.

    • Tong Zhang
    • , Oscar Hernandez
    • , Radosław Chrapkiewicz
    • , Adam Shai
    • , Mark J. Wagner
    • , Yanping Zhang
    • , Cheng-Hsun Wu
    • , Jin Zhong Li
    • , Masatoshi Inoue
    • , Yiyang Gong
    • , Biafra Ahanonu
    • , Hongkui Zeng
    • , Haruhiko Bito
    •  & Mark J. Schnitzer
  • Brief Communication |

    Seamless integration of single-molecule localization microscopy and STED allows for correlative live imaging of protein position and movement at the nanoscale in the context of fine morphological features.

    • V. V. G. Krishna Inavalli
    • , Martin O. Lenz
    • , Corey Butler
    • , Julie Angibaud
    • , Benjamin Compans
    • , Florian Levet
    • , Jan Tønnesen
    • , Olivier Rossier
    • , Gregory Giannone
    • , Olivier Thoumine
    • , Eric Hosy
    • , Daniel Choquet
    • , Jean-Baptiste Sibarita
    •  & U. Valentin Nägerl
  • Brief Communication |

    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.

    • Daseuli Yu
    • , Hansol Lee
    • , Jongryul Hong
    • , Hyunjin Jung
    • , YoungJu Jo
    • , Byung-Ha Oh
    • , Byung Ouk Park
    •  & Won Do Heo
  • Brief Communication |

    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.

    • Florian Schueder
    • , Johannes Stein
    • , Florian Stehr
    • , Alexander Auer
    • , Bianca Sperl
    • , Maximilian T. Strauss
    • , Petra Schwille
    •  & Ralf Jungmann
  • Brief Communication |

    Functional ultrasound (fUS) imaging of neural activity has been extended to volumetric imaging across the whole brain. 4D fUS is demonstrated in the rat brain in response to sensory stimuli and during seizure-like activity.

    • Claire Rabut
    • , Mafalda Correia
    • , Victor Finel
    • , Sophie Pezet
    • , Mathieu Pernot
    • , Thomas Deffieux
    •  & Mickael Tanter
  • Brief Communication |

    The mesoSPIM is an open hardware axially scanned light-sheet microscope for the rapid imaging of large cleared samples with isotropic resolution.

    • Fabian F. Voigt
    • , Daniel Kirschenbaum
    • , Evgenia Platonova
    • , Stéphane Pagès
    • , Robert A. A. Campbell
    • , Rahel Kastli
    • , Martina Schaettin
    • , Ladan Egolf
    • , Alexander van der Bourg
    • , Philipp Bethge
    • , Karen Haenraets
    • , Noémie Frézel
    • , Thomas Topilko
    • , Paola Perin
    • , Daniel Hillier
    • , Sven Hildebrand
    • , Anna Schueth
    • , Alard Roebroeck
    • , Botond Roska
    • , Esther T. Stoeckli
    • , Roberto Pizzala
    • , Nicolas Renier
    • , Hanns Ulrich Zeilhofer
    • , Theofanis Karayannis
    • , Urs Ziegler
    • , Laura Batti
    • , Anthony Holtmaat
    • , Christian Lüscher
    • , Adriano Aguzzi
    •  & Fritjof Helmchen
  • Brief Communication |

    A rapid sample mixing approach enables time-resolved structural studies of enzymatic reactions using serial synchrotron crystallography.

    • Pedram Mehrabi
    • , Eike C. Schulz
    • , Michael Agthe
    • , Sam Horrell
    • , Gleb Bourenkov
    • , David von Stetten
    • , Jan-Philipp Leimkohl
    • , Hendrik Schikora
    • , Thomas R. Schneider
    • , Arwen R. Pearson
    • , Friedjof Tellkamp
    •  & R. J. Dwayne Miller
  • Brief Communication |

    Garnett uses a hierarchical markup language and machine learning to define cell types and their marker genes and identifies these cell types in scRNA-seq datasets from tissues and whole organisms and across species.

    • Hannah A. Pliner
    • , Jay Shendure
    •  & Cole Trapnell
  • Brief Communication |

    A dense, spatially barcoded bead array captures RNA from histological tissue sections for spatially resolved gene expression analysis.

    • Sanja Vickovic
    • , Gökcen Eraslan
    • , Fredrik Salmén
    • , Johanna Klughammer
    • , Linnea Stenbeck
    • , Denis Schapiro
    • , Tarmo Äijö
    • , Richard Bonneau
    • , Ludvig Bergenstråhle
    • , José Fernandéz Navarro
    • , Joshua Gould
    • , Gabriel K. Griffin
    • , Åke Borg
    • , Mostafa Ronaghi
    • , Jonas Frisén
    • , Joakim Lundeberg
    • , Aviv Regev
    •  & Patrik L. Ståhl
  • Brief Communication |

    Repetitive optical selective exposure (ROSE) is an interferometric single-molecule localization microscopy method offering twofold improvement in lateral resolution with the same photon budget compared with conventional approaches.

    • Lusheng Gu
    • , Yuanyuan Li
    • , Shuwen Zhang
    • , Yanhong Xue
    • , Weixing Li
    • , Dong Li
    • , Tao Xu
    •  & Wei Ji
  • Brief Communication |

    Pepper, an RNA aptamer that prevents degradation of degron-tagged fluorescent proteins, enables fully genetically encoded fluorescence imaging of mRNA in living cells.

    • Jiahui Wu
    • , Sara Zaccara
    • , Deepak Khuperkar
    • , Hyaeyeong Kim
    • , Marvin E. Tanenbaum
    •  & Samie R. Jaffrey
  • Brief Communication |

    SAVER-X trains a deep neural network for transfer learning that improves the quality of scRNA-seq data using prior information learnt from existing public studies.

    • Jingshu Wang
    • , Divyansh Agarwal
    • , Mo Huang
    • , Gang Hu
    • , Zilu Zhou
    • , Chengzhong Ye
    •  & Nancy R. Zhang
  • Brief Communication |

    Single-molecule oblique-plane microscopy (obSTORM) enables deep volumetric super-resolution imaging in a light-sheet microscopy platform that is convenient for standard tissues and small intact animals.

    • Jeongmin Kim
    • , Michal Wojcik
    • , Yuan Wang
    • , Seonah Moon
    • , Emilia A. Zin
    • , Nadia Marnani
    • , Zachary L. Newman
    • , John G. Flannery
    • , Ke Xu
    •  & Xiang Zhang
  • Brief Communication |

    By embedding DNA sequences that are known to bind transcription factors in vitro together with labels for the TFs in a high-dimensional space, the machine learning approach BindSpace distinguishes between the binding preferences of even closely related TFs.

    • Han Yuan
    • , Meghana Kshirsagar
    • , Lee Zamparo
    • , Yuheng Lu
    •  & Christina S. Leslie
  • Brief Communication |

    BigStitcher enables fast and accurate alignment and reconstruction of terabyte-sized imaging datasets of cleared and expanded samples.

    • David Hörl
    • , Fabio Rojas Rusak
    • , Friedrich Preusser
    • , Paul Tillberg
    • , Nadine Randel
    • , Raghav K. Chhetri
    • , Albert Cardona
    • , Philipp J. Keller
    • , Hartmann Harz
    • , Heinrich Leonhardt
    • , Mathias Treier
    •  & Stephan Preibisch
  • Brief Communication |

    Methyl-HiC combines the elucidation of chromatin architecture with the reading of DNA methylomes in pools and single cells. Regions that are distant on the linear-genome but close in three-dimensional space show coordinated DNA methylation.

    • Guoqiang Li
    • , Yaping Liu
    • , Yanxiao Zhang
    • , Naoki Kubo
    • , Miao Yu
    • , Rongxin Fang
    • , Manolis Kellis
    •  & Bing Ren
  • Brief Communication |

    The search engine Thesaurus detects and quantifies phosphopeptide positional isomers from data-independent acquisition and parallel reaction monitoring mass spectrometry data, enabling studies of how neighboring phosphosites are regulated.

    • Brian C. Searle
    • , Robert T. Lawrence
    • , Michael J. MacCoss
    •  & Judit Villén
  • Brief Communication |

    A genetically encodable protein synthesis inhibitor (gePSI) for cell-specific inhibition of protein synthesis that is efficient and reversible enables the study of structural plasticity following single-synapse activation in neurons.

    • Maximilian Heumüller
    • , Caspar Glock
    • , Vidhya Rangaraju
    • , Anne Biever
    •  & Erin M. Schuman
  • Brief Communication |

    Conos constructs a joint graph between single cells in different samples based on multiple pairwise alignments of the samples and identifies recurrent subpopulations across all of the datasets.

    • Nikolas Barkas
    • , Viktor Petukhov
    • , Daria Nikolaeva
    • , Yaroslav Lozinsky
    • , Samuel Demharter
    • , Konstantin Khodosevich
    •  & Peter V. Kharchenko
  • Brief Communication |

    The red form of the photoconvertible fluorescent protein mEos4b has a long-lived dark state with specific chromophore conformation. Weak 488-nm light depopulates this state, improving track lengths in single-particle tracking experiments.

    • Elke De Zitter
    • , Daniel Thédié
    • , Viola Mönkemöller
    • , Siewert Hugelier
    • , Joël Beaudouin
    • , Virgile Adam
    • , Martin Byrdin
    • , Luc Van Meervelt
    • , Peter Dedecker
    •  & Dominique Bourgeois
  • Brief Communication |

    Pathway-level information extractor (PLIER) uses prior knowledge of pathways to extract biologically interpretable latent variables from large gene expression datasets.

    • Weiguang Mao
    • , Elena Zaslavsky
    • , Boris M. Hartmann
    • , Stuart C. Sealfon
    •  & Maria Chikina