Self-supervised image restoration in coherent X-ray neuronal microscopy
bioRxiv (Cold Spring Harbor Laboratory)
Abstract
ABSTRACT Coherent X-ray microscopy is emerging as a transformative technology for neuronal imaging, with the potential to offer a scalable solution for reconstruction of neural circuits in millimeter sized tissue volumes. Specifically, X-ray holographic nanoto-mography (XNH) brings together outstanding capabilities in terms of contrast, spatial resolution and data acquisition speed. While recent XNH developments already enabled generating valuable datasets for neuro-sciences, a major challenge for reconstruction of neural circuits remained overcoming resolving power limits to distinguish smaller neurites and synapses in the reconstructed volumes. Here we present a self-supervised image restoration approach that simultaneously improves spatial resolution, contrast, and data acquisition speed. This enables revealing synapses with XNH, marking a major milestone in the quest for generating connectomes of full mammalian brains. We demonstrate that this method is effective for various types of neuronal tissues and acquisition schemes. We propose a scalable implementation compatible with multi-terabyte image volumes. Altogether, this work brings large-scale X-ray nanotomography to a new precision level.
Authors 18
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF, The European Synchrotron, Grenoble, France
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF, The European Synchrotron, Grenoble, France
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Affiliation as printed
Sensory Circuits and Neurotechnology Lab, The Francis Crick Institute, London, UK
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Centrum Wiskunde & Informatica
Affiliation as printed
Department of Computational Imaging, Centrum Wiskunde en Informatica (CWI), Amsterdam, The Netherlands
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF, The European Synchrotron, Grenoble, France
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Harvard University · Yale University
Affiliation as printed
Harvard Medical School, Boston, USA
Yale School of Medicine, New Haven, USA
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European Synchrotron Radiation Facility
Affiliation as printed
ESRF, The European Synchrotron, Grenoble, France
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Affiliation as printed
Sensory Circuits and Neurotechnology Lab, The Francis Crick Institute, London, UK
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Centrum Wiskunde & Informatica
Affiliation as printed
Department of Computational Imaging, Centrum Wiskunde en Informatica (CWI), Amsterdam, The Netherlands
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Affiliation as printed
Paul Scherrer Institute, Villigen, Switzerland
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Affiliation as printed
Paul Scherrer Institute, Villigen, Switzerland
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Affiliation as printed
Department of Neurobiology and Biophysics, University of Washington, Seattle, USA
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Affiliation as printed
Leiden Institute of Advanced Computer Science, Leiden University, The Netherlands
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Affiliation as printed
Department of Neurobiology and Biophysics, University of Washington, Seattle, USA
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Boston Children's Hospital · Harvard University
Affiliation as printed
Boston Children’s Hospital, Boston, USA
Harvard Medical School, Boston, USA
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The Francis Crick Institute · University College London
Affiliation as printed
Department of Neuroscience, Physiology and Pharmacology, University College, London, UK
Sensory Circuits and Neurotechnology Lab, The Francis Crick Institute, London, UK
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Commissariat à l'Énergie Atomique et aux Énergies Alternatives · European Synchrotron Radiation Facility · CEA Grenoble · Institut de Recherche Interdisciplinaire de Grenoble
Affiliation as printed
ESRF, The European Synchrotron, Grenoble, France
University Grenoble Alpes, CEA, IRIG-MEM, Grenoble, France
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Alexandra Pacureanu corresponding
European Synchrotron Radiation Facility
Affiliation as printed
ESRF, The European Synchrotron, Grenoble, France
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