title: Pan-neuronal imaging in roaming Caenorhabditis elegans.
abstract: We present an imaging system for pan-neuronal recording in crawling Caenorhabditis elegans. A spinning disk confocal microscope, modified for automated tracking of the C. elegans head ganglia, simultaneously records the activity and position of ∼80 neurons that coexpress cytoplasmic calcium indicator GCaMP6s and nuclear localized red fluorescent protein at 10 volumes per second. We developed a behavioral analysis algorithm that maps the movements of the head ganglia to the animal's posture and locomotion. Image registration and analysis software automatically assigns an index to each nucleus and calculates the corresponding calcium signal. Neurons with highly stereotyped positions can be associated with unique indexes and subsequently identified using an atlas of the worm nervous system. To test our system, we analyzed the brainwide activity patterns of moving worms subjected to thermosensory inputs. We demonstrate that our setup is able to uncover representations of sensory input and motor output of individual neurons from brainwide dynamics. Our imaging setup and analysis pipeline should facilitate mapping circuits for sensory to motor transformation in transparent behaving animals such as C. elegans and Drosophila larva.
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138; vivek@physics.harvard.edu samuel@physics.harvard.edu.
authors.forename: Vivek
authors.initials: V
authors.lastname: Venkatachalam
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138;
authors.forename: Ni
authors.initials: N
authors.lastname: Ji
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138;
authors.forename: Xian
authors.initials: X
authors.lastname: Wang
authors.affiliation: Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605;
authors.forename: Christopher
authors.initials: C
authors.lastname: Clark
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138;
authors.forename: James Kameron
authors.initials: JK
authors.lastname: Mitchell
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138;
authors.forename: Mason
authors.initials: M
authors.lastname: Klein
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138;
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Tabone
authors.affiliation: Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605;
authors.forename: Jeremy
authors.initials: J
authors.lastname: Florman
authors.affiliation: Department of Physics, Nanjing University, 210093 Nanjing, China;
authors.forename: Hongfei
authors.initials: H
authors.lastname: Ji
authors.affiliation: Center for Brain Science, Harvard University, Cambridge, MA 02138;
authors.forename: Joel
authors.initials: J
authors.lastname: Greenwood
authors.affiliation: Division of Biological Sciences, Section of Neurobiology, University of California, San Diego, La Jolla, CA 92093;
authors.forename: Andrew D
authors.initials: AD
authors.lastname: Chisholm
authors.affiliation: Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01609;
authors.forename: Jagan
authors.initials: J
authors.lastname: Srinivasan
authors.affiliation: Department of Neurobiology, University of Massachusetts Medical School, Worcester, MA 01605;
authors.forename: Mark
authors.initials: M
authors.lastname: Alkema
authors.affiliation: Samuel Lunenfeld Research Institute, Mount Sinai Hospital, Toronto, ON, Canada M5G 1X5; Departments of Molecular Genetics and Physiology, University of Toronto, Toronto, ON, Canada M5S 1A8.
authors.forename: Mei
authors.initials: M
authors.lastname: Zhen
authors.affiliation: Department of Physics, Harvard University, Cambridge, MA 02138; Center for Brain Science, Harvard University, Cambridge, MA 02138; vivek@physics.harvard.edu samuel@physics.harvard.edu.
authors.forename: Aravinthan D T
authors.initials: AD
authors.lastname: Samuel
mesh_terms: D000818:Animals; D001522:Behavior, Animal; D017173:Caenorhabditis elegans / Q000166:cytology / Q000378:metabolism; D002467:Cell Nucleus / Q000378:metabolism*; D017952:Ganglia, Invertebrate / Q000166:cytology / Q000378:metabolism; D008124:Locomotion; D008164:Luminescent Proteins / Q000235:genetics / Q000378:metabolism; D009474:Neurons / Q000166:cytology / Q000378:metabolism; D061848:Optical Imaging / Q000379:methods*; D000097573:Red Fluorescent Protein
chemical_list: D008164:Luminescent Proteins; D000097573:Red Fluorescent Protein
keywords: C. elegans; Drosophila; calcium imaging; thermotaxis