Deep learning-enhanced light-field imaging with continuous validation

Research output: Contribution to journalResearch articleContributedpeer-review

Contributors

  • Nils Wagner - , European Molecular Biology Laboratory (EMBL) Heidelberg, Technical University of Munich, Helmholtz Information & Data Science Academy (HIDA) (Author)
  • Fynn Beuttenmueller - , European Molecular Biology Laboratory (EMBL) Heidelberg, Heidelberg University  (Author)
  • Nils Norlin - , European Molecular Biology Laboratory (EMBL) Heidelberg, Lund University (Author)
  • Jakob Gierten - , Heidelberg University  (Author)
  • Juan Carlos Boffi - , European Molecular Biology Laboratory (EMBL) Heidelberg (Author)
  • Joachim Wittbrodt - , Heidelberg University  (Author)
  • Martin Weigert - , Swiss Federal Institute of Technology Lausanne (EPFL) (Author)
  • Lars Hufnagel - , European Molecular Biology Laboratory (EMBL) Heidelberg (Author)
  • Robert Prevedel - , European Molecular Biology Laboratory (EMBL) Heidelberg, European Molecular Biology Laboratory (EMBL) Monterotondo (Author)
  • Anna Kreshuk - , European Molecular Biology Laboratory (EMBL) Heidelberg (Author)

Abstract

Visualizing dynamic processes over large, three-dimensional fields of view at high speed is essential for many applications in the life sciences. Light-field microscopy (LFM) has emerged as a tool for fast volumetric image acquisition, but its effective throughput and widespread use in biology has been hampered by a computationally demanding and artifact-prone image reconstruction process. Here, we present a framework for artificial intelligence–enhanced microscopy, integrating a hybrid light-field light-sheet microscope and deep learning–based volume reconstruction. In our approach, concomitantly acquired, high-resolution two-dimensional light-sheet images continuously serve as training data and validation for the convolutional neural network reconstructing the raw LFM data during extended volumetric time-lapse imaging experiments. Our network delivers high-quality three-dimensional reconstructions at video-rate throughput, which can be further refined based on the high-resolution light-sheet images. We demonstrate the capabilities of our approach by imaging medaka heart dynamics and zebrafish neural activity with volumetric imaging rates up to 100 Hz.

Details

Original languageEnglish
Pages (from-to)557-563
Number of pages7
JournalNature methods
Volume18
Issue number5
Publication statusPublished - May 2021
Peer-reviewedYes
Externally publishedYes

External IDs

PubMed 33963344
ORCID /0000-0002-7780-9057/work/205992958