Inferring single-trial neural population dynamics using sequential auto-encoders

Latest Research

  • Article |

    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 these dynamics.

    • Chethan Pandarinath
    • , Daniel J. O’Shea
    • , Jasmine Collins
    • , Rafal Jozefowicz
    • , Sergey D. Stavisky
    • , Jonathan C. Kao
    • , Eric M. Trautmann
    • , Matthew T. Kaufman
    • , Stephen I. Ryu
    • , Leigh R. Hochberg
    • , Jaimie M. Henderson
    • , Krishna V. Shenoy
    • , L. F. Abbott
    •  & David Sussillo
  • Brief Communication |

    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.

    • Chawin Ounkomol
    • , Sharmishtaa Seshamani
    • , Mary M. Maleckar
    • , Forrest Collman
    •  & Gregory R. Johnson
  • Brief Communication |

    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.

    • Hamidreza Heydarian
    • , Florian Schueder
    • , Maximilian T. Strauss
    • , Ben van Werkhoven
    • , Mohamadreza Fazel
    • , Keith A. Lidke
    • , Ralf Jungmann
    • , Sjoerd Stallinga
    •  & Bernd Rieger
  • Brief Communication |

    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 structural and functional imaging of the brain through an intact skull.

    • Tianyu Wang
    • , Dimitre G. Ouzounov
    • , Chunyan Wu
    • , Nicholas G. Horton
    • , Bin Zhang
    • , Cheng-Hsun Wu
    • , Yanping Zhang
    • , Mark J. Schnitzer
    •  & Chris Xu
  • Brief Communication |

    In vivo probing of RNA structures with COMRADES yields insight into RNA folding of the ZIKA virus genome and its interaction with host RNAs.

    • Omer Ziv
    • , Marta M. Gabryelska
    • , Aaron T. L. Lun
    • , Luca F. R. Gebert
    • , Jessica Sheu-Gruttadauria
    • , Luke W. Meredith
    • , Zhong-Yu Liu
    • , Chun Kit Kwok
    • , Cheng-Feng Qin
    • , Ian J. MacRae
    • , Ian Goodfellow
    • , John C. Marioni
    • , Grzegorz Kudla
    •  & Eric A. Miska

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