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      Simultaneous whole-animal 3D-imaging of neuronal activity using light-field microscopy

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          Abstract

          High-speed large-scale 3D imaging of neuronal activity poses a major challenge in neuroscience. Here, we demonstrate intrinsically simultaneous functional imaging of neuronal activity at single neuron resolution for an entire Caenorhabditis elegans as well as for the whole-brain of larval zebrafish. Our technique captures dynamics of spiking neurons in volumes of ~700 μm x 700 μm x 200 μm at 20 Hz and its simplicity makes it an attractive tool for high-speed volumetric calcium imaging.

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          Going deeper than microscopy: the optical imaging frontier in biology.

          Vasilis Ntziachristos (2010)
          Optical microscopy has been a fundamental tool of biological discovery for more than three centuries, but its in vivo tissue imaging ability has been restricted by light scattering to superficial investigations, even when confocal or multiphoton methods are used. Recent advances in optical and optoacoustic (photoacoustic) imaging now allow imaging at depths and resolutions unprecedented for optical methods. These abilities are increasingly important to understand the dynamic interactions of cellular processes at different systems levels, a major challenge of postgenome biology. This Review discusses promising photonic methods that have the ability to visualize cellular and subcellular components in tissues across different penetration scales. The methods are classified into microscopic, mesoscopic and macroscopic approaches, according to the tissue depth at which they operate. Key characteristics associated with different imaging implementations are described and the potential of these technologies in biological applications is discussed.
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            Automated analysis of cellular signals from large-scale calcium imaging data.

            Eran Mukamel, Axel Nimmerjahn, Mark J. Schnitzer (2009)
            Recent advances in fluorescence imaging permit studies of Ca(2+) dynamics in large numbers of cells, in anesthetized and awake behaving animals. However, unlike for electrophysiological signals, standardized algorithms for assigning optically recorded signals to individual cells have not yet emerged. Here, we describe an automated sorting procedure that combines independent component analysis and image segmentation for extracting cells' locations and their dynamics with minimal human supervision. In validation studies using simulated data, automated sorting significantly improved estimation of cellular signals compared to conventional analysis based on image regions of interest. We used automated procedures to analyze data recorded by two-photon Ca(2+) imaging in the cerebellar vermis of awake behaving mice. Our analysis yielded simultaneous Ca(2+) activity traces for up to >100 Purkinje cells and Bergmann glia from single recordings. Using this approach, we found microzones of Purkinje cells that were stable across behavioral states and in which synchronous Ca(2+) spiking rose significantly during locomotion.
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              The brain activity map project and the challenge of functional connectomics.

              A. Paul Alivisatos, Miyoung Chun, George M. Church … (2012)
              The function of neural circuits is an emergent property that arises from the coordinated activity of large numbers of neurons. To capture this, we propose launching a large-scale, international public effort, the Brain Activity Map Project, aimed at reconstructing the full record of neural activity across complete neural circuits. This technological challenge could prove to be an invaluable step toward understanding fundamental and pathological brain processes. Copyright © 2012 Elsevier Inc. All rights reserved.
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                Author and article information

                Journal
                Journal ID (nlm-journal-id): 101215604
                Journal ID (pubmed-jr-id): 32338
                Journal ID (nlm-ta): Nat Methods
                Journal ID (iso-abbrev): Nat. Methods
                Title: Nature methods
                ISSN (Print): 1548-7091
                ISSN (Electronic): 1548-7105
                Publication date Nihms-submitted: 23 May 2014
                Publication date (Electronic): 18 May 2014
                Publication date (Print): July 2014
                Publication date PMC-release: 01 January 2015
                Volume: 11
                Issue: 7
                Pages: 727-730
                Affiliations
                [1 ]Research Institute of Molecular Pathology, Vienna, Austria
                [2 ]Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
                [3 ]Research Platform Quantum Phenomena & Nanoscale Biological Systems (QuNaBioS), University of Vienna, Austria
                [4 ]Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
                [5 ]MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
                [6 ]Department of Mechanical Engineering, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
                [7 ]Department of Biological Engineering, Massachusetts Institute of Technology(MIT), Cambridge, MA, USA
                [8 ]Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
                [9 ]McGovern Institute, Massachusetts Institute of Technology (MIT), Cambridge, MA, USA
                Author notes
                Correspondence should be addressed to E.S.B. ( esb@ 123456media.mit.edu ) or A.V. ( vaziri@ 123456imp.ac.at ).
                Article
                Manuscript ID: NIHMS589552
                DOI: 10.1038/nmeth.2964
                PMC ID: 4100252
                PubMed ID: 24836920
                SO-VID: e9df071c-89fc-4dc2-9ec9-d4d6eb00325b
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                ScienceOpen disciplines: Life sciences

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