<?xml version="1.0" encoding="utf-8" standalone="yes"?>
<TEI xmlns="http://www.tei-c.org/ns/1.0">
  <teiHeader>
    <fileDesc>
      <titleStmt>
        <title type="main">Development of optical methods for real-time whole-brain functional imaging of zebrafish neuronal activity</title>
        <author>
          <persName n="1" ref="https://orcid.org/0000-0003-2519-7893" type="ORCID">
            <forename>Lapo</forename>
            <surname>Turrini</surname>
            <placeName type="affiliation">University of Florence, Italy</placeName>
          </persName>
        </author>
      </titleStmt>
      <publicationStmt>
        <publisher>Firenze University Press</publisher>
        <pubPlace>Florence</pubPlace>
        <date when="2020">2020</date>
        <idno type="DOI">https://doi.org/10.36253/978-88-5518-070-2</idno>
        <availability>
          <p>Available for academic research purposes</p>
          <p>Open Access</p>
          <p>Copyright Author(s)</p>
          <licence source="text" target="https://creativecommons.org/licenses/by/4.0/legalcode">
            <p>Content licence CC BY 4.0</p>
          </licence>
          <licence source="metadata" target="https://creativecommons.org/publicdomain/zero/1.0/legalcode">
            <p>Metadata licence CC0 1.0</p>
          </licence>
        </availability>
      </publicationStmt>
      <seriesStmt>
        <title>Premio Tesi di Dottorato</title>
        <idno type="ISSN" subtype="print">2612-8039</idno>
        <idno type="ISSN" subtype="electronic">2612-8020</idno>
      </seriesStmt>
      <sourceDesc>
        <bibl type="monograph">
          <edition n="1">Digital edition PDF</edition>
          <date>2020</date>
          <idno type="ISBN" subtype="electronic">978-88-5518-070-2</idno>
          <biblScope unit="page">200 pages</biblScope>
          <extent>0,00 MB</extent>
          <availability status="free">
            <p>This is original content, published in Open Access. It is also available to read for free online at <ref target="https://media.fupress.com/files/pdf/24/4374/14446">https://media.fupress.com/files/pdf/24/4374/14446</ref></p>
          </availability>
        </bibl>
        <bibl type="monograph">
          <edition n="2">Digital edition XML</edition>
          <date>2020</date>
          <idno type="ISBN" subtype="electronic">978-88-5518-071-9</idno>
          <availability status="free">
            <p>It is available to read for free online</p>
          </availability>
        </bibl>
        <bibl type="monograph">
          <edition n="3">Print edition</edition>
          <date>2020</date>
          <idno type="ISBN" subtype="print">978-88-5518-069-6</idno>
          <biblScope unit="page">200 pages</biblScope>
          <availability status="restricted">
            <p>It is available for online purchase at <ref target="https://books.fupress.com/isbn/9788855180702">https://books.fupress.com/isbn/9788855180702</ref></p>
          </availability>
        </bibl>
      </sourceDesc>
    </fileDesc>
    <encodingDesc>
      <appInfo>
        <application version="2.2" ident="Booksflow">
          <desc>Digital edition XML powered by Booksflow</desc>
        </application>
      </appInfo>
    </encodingDesc>
    <profileDesc>
      <creation>
        <tag>peer-reviewed</tag>
        <rs type="FUP_policy" source="https://doi.org/10.36253/fup_best_practice">Firenze University Press Best Practice in Scholarly Publishing</rs>
        <rs type="scientific_cloud" source="https://doi.org/10.36253/fup_best_practice.2">FUP Scientific Cloud for Books</rs>
        <rs type="peer_review" resp="scientific_board" source="https://books.fupress.com/scientific-board/c/104">Premio Tesi di Dottorato 2019</rs>
      </creation>
      <abstract xml:lang="it">
        <p>Each one of us in his life has, at least once, smelled the scent of roses, read one canto of Dante’s Commedia or listened to the sound of the sea from a shell. All of this is possible thanks to the astonishing capabilities of an organ, such as the brain, that allows us to collect and organize perceptions coming from sensory organs and to produce behavioural responses accordingly. Studying an operating brain in a non-invasive way is extremely difficult in mammals, and particularly in humans. In the last decade, a small teleost fish, zebrafish (Danio rerio), has been making its way into the field of neurosciences. The brain of a larval zebrafish is made up of 'only' 100000 neurons and it’s completely transparent, making it possible to optically access it. Here, taking advantage of the best of currently available technology, we devised optical solutions to investigate the dynamics of neuronal activity throughout the entire brain of zebrafish larvae.</p>
      </abstract>
      <textClass>
        <keywords>
          <list>
            <item>zebrafish</item>
            <item>calcium imaging</item>
            <item>light-sheet microscopy</item>
            <item>epilepsy</item>
            <item>behaviour</item>
          </list>
        </keywords>
      </textClass>
    </profileDesc>
  </teiHeader>
  <text>
    <body>
      <p>It is available online at https://doi.org/10.36253/978-88-5518-070-2<ref target="https://doi.org/10.36253/978-88-5518-070-2" /></p>
      <div>
        <listBibl>
          <head>References</head>
          <bibl n="6861">
            <bibl>Abraham, E., Palevitch, O., Gothilf, Y., and Zohar, Y. (2009). The zebrafish as a model system for forebrain GnRH neuronal development. Gen Comp Endocrinol 164, 151-160</bibl>
            <idno type="DOI">10.1016/j.ygcen.2009.01.012</idno>
          </bibl>
          <bibl n="6862">
            <bibl>Afrikanova, T., Serruys, A.S., Buenafe, O.E., Clinckers, R., Smolders, I., De Witte, P.A., Crawford, A.D., and Esguerra, C.V. (2013). Validation of the zebrafish pentylenetetrazol seizure model: locomotor versus electrographic responses to antiepileptic drugs. PLoS One 8, e54166</bibl>
            <idno type="DOI">10.1371/journal.pone.0054166</idno>
          </bibl>
          <bibl n="6863">
            <bibl>Ahrens, M.B., Orger, M.B., Robson, D.N., Li, J.M., and Keller, P.J. (2013). Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat Methods 10, 413-420</bibl>
            <idno type="DOI">10.1038/nmeth.2434</idno>
          </bibl>
          <bibl n="6864">
            <bibl>Akerboom, J., Chen, T.W., Wardill, T.J., Tian, L., Marvin, J.S., Mutlu, S., Calderon, N.C., Esposti, F., Borghuis, B.G., Sun, X.R., Gordus, A., Orger, M.B., Portugues, R., Engert, F., Macklin, J.J., Filosa, A., Aggarwal, A., Kerr, R.A., Takagi, R., Kracun, S., Shigetomi, E., Khakh, B.S., Baier, H., Lagnado, L., Wang, S.S., Bargmann, C.I., Kimmel, B.E., Jayaraman, V., Svoboda, K., Kim, D.S., Schreiter, E.R., and Looger, L.L. (2012). Optimization of a GCaMP calcium indicator for neural activity imaging. J Neurosci 32, 13819-13840</bibl>
            <idno type="DOI">10.1523/JNEUROSCI.2601-12.2012</idno>
          </bibl>
          <bibl n="6865">
            <bibl>Akerboom, J., Rivera, J.D., Guilbe, M.M., Malave, E.C., Hernandez, H.H., Tian, L., Hires, S.A., Marvin, J.S., Looger, L.L., and Schreiter, E.R. (2009). Crystal structures of the GCaMP calcium sensor reveal the mechanism of fluorescence signal change and aid rational design. J Biol Chem 284, 6455-6464</bibl>
            <idno type="DOI">10.1074/jbc.M807657200</idno>
          </bibl>
          <bibl n="6866">
            <bibl>Allegra Mascaro, A.L., Conti, E., Lai, S., Di Giovanna, A.P., Spalletti, C., Alia, C., Panarese, A., Scaglione, A., Sacconi, L., Micera, S., Caleo, M., and Pavone, F.S. (2019). Combined Rehabilitation Promotes the Recovery of Structural and Functional Features of Healthy Neuronal Networks after Stroke. Cell Rep 28, 3474-3485 e3476</bibl>
            <idno type="DOI">10.1016/j.celrep.2019.08.062</idno>
          </bibl>
          <bibl n="6867">
            <bibl>Attili, S., and Hughes, S.M. (2014). Anaesthetic tricaine acts preferentially on neural voltage-gated sodium channels and fails to block directly evoked muscle contraction. PLoS One 9, e103751</bibl>
            <idno type="DOI">10.1371/journal.pone.0103751</idno>
          </bibl>
          <bibl n="6868">
            <bibl>Attwell, D., Buchan, A.M., Charpak, S., Lauritzen, M., Macvicar, B.A., and Newman, E.A. (2010). Glial and neuronal control of brain blood flow. Nature 468, 232-243</bibl>
            <idno type="DOI">10.1038/nature09613</idno>
          </bibl>
          <bibl n="6869">
            <bibl>Azevedo, F.A., Carvalho, L.R., Grinberg, L.T., Farfel, J.M., Ferretti, R.E., Leite, R.E., Jacob Filho, W., Lent, R., and Herculano-Houzel, S. (2009). Equal numbers of neuronal and nonneuronal cells make the human brain an isometrically scaled-up primate brain. J Comp Neurol 513, 532-541</bibl>
            <idno type="DOI">10.1002/cne.21974</idno>
          </bibl>
          <bibl n="6870">Baird, G.S., Zacharias, D.A., and Tsien, R.Y. (1999). Circular permutation and receptor insertion within green fluorescent proteins. Proc Natl Acad Sci U S A 96, 11241-11246</bibl>
          <bibl n="6871">Baker, P.F., Hodgkin, A.L., and Ridgway, E.B. (1971). Depolarization and calcium entry in squid giant axons. J Physiol 218, 709-755</bibl>
          <bibl n="6872">
            <bibl>Baraban, S.C., Dinday, M.T., and Hortopan, G.A. (2013). Drug screening in Scn1a zebrafish mutant identifies clemizole as a potential Dravet syndrome treatment. Nat Commun 4, 2410</bibl>
            <idno type="DOI">10.1038/ncomms3410</idno>
          </bibl>
          <bibl n="6873">
            <bibl>Baraban, S.C., Taylor, M.R., Castro, P.A., and Baier, H. (2005). Pentylenetetrazole induced changes in zebrafish behavior, neural activity and c-fos expression. Neuroscience 131, 759-768</bibl>
            <idno type="DOI">10.1016/j.neuroscience.2004.11.031</idno>
          </bibl>
          <bibl n="6874">Barbazuk, W.B., Korf, I., Kadavi, C., Heyen, J., Tate, S., Wun, E., Bedell, J.A., Mcpherson, J.D., and Johnson, S.L. (2000). The syntenic relationship of the zebrafish and human genomes. Genome Res 10, 1351-1358</bibl>
          <bibl n="6875">Bargmann, C.I. (1998). Neurobiology of the Caenorhabditis elegans genome. Science 282, 2028-2033</bibl>
          <bibl n="6876">
            <bibl>Baumgart, E., and Kubitscheck, U. (2012). Scanned light sheet microscopy with confocal slit detection. Opt Express 20, 21805-21814</bibl>
            <idno type="DOI">10.1364/OE.20.021805</idno>
          </bibl>
          <bibl n="6877">
            <bibl>Baxendale, S., Holdsworth, C.J., Meza Santoscoy, P.L., Harrison, M.R., Fox, J., Parkin, C.A., Ingham, P.W., and Cunliffe, V.T. (2012). Identification of compounds with anti-convulsant properties in a zebrafish model of epileptic seizures. Dis Model Mech 5, 773-784</bibl>
            <idno type="DOI">10.1242/dmm.010090</idno>
          </bibl>
          <bibl n="6878">Blader, P., and Strahle, U. (2000). Zebrafish developmental genetics and central nervous system development. Hum Mol Genet 9, 945-951</bibl>
          <bibl n="6879">Burgess, N., and O&amp;#39;keefe, J. (2003). Neural representations in human spatial memory. Trends Cogn Sci 7, 517-519</bibl>
          <bibl n="6880">
            <bibl>Candelier, R., Murmu, M.S., Romano, S.A., Jouary, A., Debregeas, G., and Sumbre, G. (2015). A microfluidic device to study neuronal and motor responses to acute chemical stimuli in zebrafish. Sci Rep 5, 12196</bibl>
            <idno type="DOI">10.1038/srep12196</idno>
          </bibl>
          <bibl n="6881">
            <bibl>Chaigneau, E., Ronzitti, E., Gajowa, M.A., Soler-Llavina, G.J., Tanese, D., Brureau, A.Y., Papagiakoumou, E., Zeng, H., and Emiliani, V. (2016). Two-Photon Holographic Stimulation of ReaChR. Front Cell Neurosci 10, 234</bibl>
            <idno type="DOI">10.3389/fncel.2016.00234</idno>
          </bibl>
          <bibl n="6882">Chalfie, M., Tu, Y., Euskirchen, G., Ward, W.W., and Prasher, D.C. (1994). Green fluorescent protein as a marker for gene expression. Science 263, 802-805</bibl>
          <bibl n="6883">Chattoraj, M., King, B.A., Bublitz, G.U., and Boxer, S.G. (1996). Ultra-fast excited state dynamics in green fluorescent protein: multiple states and proton transfer. Proc Natl Acad Sci U S A 93, 8362-8367</bibl>
          <bibl n="6884">
            <bibl>Chen, B.R., Kozberg, M.G., Bouchard, M.B., Shaik, M.A., and Hillman, E.M. (2014). A critical role for the vascular endothelium in functional neurovascular coupling in the brain. J Am Heart Assoc 3, e000787</bibl>
            <idno type="DOI">10.1161/JAHA.114.000787</idno>
          </bibl>
          <bibl n="6885">
            <bibl>Chen, T.W., Wardill, T.J., Sun, Y., Pulver, S.R., Renninger, S.L., Baohan, A., Schreiter, E.R., Kerr, R.A., Orger, M.B., Jayaraman, V., Looger, L.L., Svoboda, K., and Kim, D.S. (2013). Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature 499, 295-300</bibl>
            <idno type="DOI">10.1038/nature12354</idno>
          </bibl>
          <bibl n="6886">
            <bibl>Chen, Y., Glaser, A., and Liu, J.T. (2017). Bessel-beam illumination in dual-axis confocal microscopy mitigates resolution degradation caused by refractive heterogeneities. J Biophotonics 10, 68-74</bibl>
            <idno type="DOI">10.1002/jbio.201600196</idno>
          </bibl>
          <bibl n="6887">Chhabria, K., Plant, K., Bandmann, O., Wilkinson, R., Martin, C., Kugler, E., Armitage, P., Santoscoy, P., Cunliffe, V.T., Huisken, J., Mcgown, A., Ramesh, R., Chico, T., and Howarth, C. (2018). The effect of Hyperglycemia on neurovascular coupling and cerebrovascular patterning in zebrafish. Journal of Cerebral Blood Flow and Metabolism</bibl>
          <bibl n="6888">
            <bibl>Chitalia, R., Mueller, J., Fu, H.L., Whitley, M.J., Kirsch, D.G., Brown, J.Q., Willett, R., and Ramanujam, N. (2016). Algorithms for differentiating between images of heterogeneous tissue across fluorescence microscopes. Biomed Opt Express 7, 3412-3424</bibl>
            <idno type="DOI">10.1364/BOE.7.003412</idno>
          </bibl>
          <bibl n="6889">
            <bibl>Cho, S.J., Byun, D., Nam, T.S., Choi, S.Y., Lee, B.G., Kim, M.K., and Kim, S. (2017). Zebrafish as an animal model in epilepsy studies with multichannel EEG recordings. Sci Rep 7, 3099</bibl>
            <idno type="DOI">10.1038/s41598-017-03482-6</idno>
          </bibl>
          <bibl n="6890">
            <bibl>Cong, L., Wang, Z., Chai, Y., Hang, W., Shang, C., Yang, W., Bai, L., Du, J., Wang, K., and Wen, Q. (2017). Rapid whole brain imaging of neural activity in freely behaving larval zebrafish (Danio rerio). Elife 6,</bibl>
            <idno type="DOI">10.7554/eLife.28158</idno>
          </bibl>
          <bibl n="6891">
            <bibl>Conti, E., Allegra Mascaro, A.L., and Pavone, F.S. (2019). Large Scale Double-Path Illumination System with Split Field of View for the All-Optical Study of Inter-and Intra-Hemispheric Functional Connectivity on Mice. Methods Protoc 2,</bibl>
            <idno type="DOI">10.3390/mps2010011</idno>
          </bibl>
          <bibl n="6892">
            <bibl>Craggs, T.D. (2009). Green fluorescent protein: structure, folding and chromophore maturation. Chem Soc Rev 38, 2865-2875</bibl>
            <idno type="DOI">10.1039/b903641p</idno>
          </bibl>
          <bibl n="6893">Creaser C.W. (1934). The technique of handling the zebrafish (Brachydanio rerio) for the production of eggs which are favourable for embryological research and are available at any specified time throughout the year. Copeia 159-161</bibl>
          <bibl n="6894">
            <bibl>Crocini, C., Ferrantini, C., Coppini, R., Scardigli, M., Yan, P., Loew, L.M., Smith, G., Cerbai, E., Poggesi, C., Pavone, F.S., and Sacconi, L. (2016). Optogenetics design of mechanistically-based stimulation patterns for cardiac defibrillation. Sci Rep 6, 35628</bibl>
            <idno type="DOI">10.1038/srep35628</idno>
          </bibl>
          <bibl n="6895">Cubitt, A.B., Heim, R., Adams, S.R., Boyd, A.E., Gross, L.A., and Tsien, R.Y. (1995). Understanding, improving and using green fluorescent proteins. Trends Biochem Sci 20, 448-455</bibl>
          <bibl n="6896">
            <bibl>Dekens, M.P., Foulkes, N.S., and Tessmar-Raible, K. (2017). Instrument design and protocol for the study of light controlled processes in aquatic organisms, and its application to examine the effect of infrared light on zebrafish. PLoS One 12, e0172038</bibl>
            <idno type="DOI">10.1371/journal.pone.0172038</idno>
          </bibl>
          <bibl n="6897">Denk, W., Strickler, J.H., and Webb, W.W. (1990). Two-photon laser scanning fluorescence microscopy. Science 248, 73-76</bibl>
          <bibl n="6898">
            <bibl>Dinday, M.T., and Baraban, S.C. (2015). Large-Scale Phenotype-Based Antiepileptic Drug Screening in a Zebrafish Model of Dravet Syndrome. eNeuro 2,</bibl>
            <idno type="DOI">10.1523/ENEURO.0068-15.2015</idno>
          </bibl>
          <bibl n="6899">
            <bibl>Dombeck, D.A., Harvey, C.D., Tian, L., Looger, L.L., and Tank, D.W. (2010). Functional imaging of hippocampal place cells at cellular resolution during virtual navigation. Nat Neurosci 13, 1433-1440</bibl>
            <idno type="DOI">10.1038/nn.2648</idno>
          </bibl>
          <bibl n="6900">Duchen, M.R. (1999). Contributions of mitochondria to animal physiology: from homeostatic sensor to calcium signalling and cell death. J Physiol 516 ( Pt 1), 1-17</bibl>
          <bibl n="6901">
            <bibl>Dunn, T.W., Gebhardt, C., Naumann, E.A., Riegler, C., Ahrens, M.B., Engert, F., and Del Bene, F. (2016). Neural Circuits Underlying Visually Evoked Escapes in Larval Zebrafish. Neuron 89, 613-628</bibl>
            <idno type="DOI">10.1016/j.neuron.2015.12.021</idno>
          </bibl>
          <bibl n="6902">
            <bibl>Dunn, T.W., Mu, Y., Narayan, S., Randlett, O., Naumann, E.A., Yang, C.T., Schier, A.F., Freeman, J., Engert, F., and Ahrens, M.B. (2016). Brain-wide mapping of neural activity controlling zebrafish exploratory locomotion. Elife 5, e12741</bibl>
            <idno type="DOI">10.7554/eLife.12741</idno>
          </bibl>
          <bibl n="6903">Dunsby, C. (2008). Optically sectioned imaging by oblique plane microscopy. Opt Express 16, 20306-20316</bibl>
          <bibl n="6904">Durnin, J. (1987). Exact solution for nondiffracting beams. Journal of the Optical Society of America A 4, 651-654</bibl>
          <bibl n="6905">
            <bibl>Durnin, J., Miceli, J., Jr., and Eberly, J.H. (1987). Diffraction-free beams. Phys Rev Lett 58, 1499-1501</bibl>
            <idno type="DOI">10.1103/PhysRevLett.58.1499</idno>
          </bibl>
          <bibl n="6906">
            <bibl>Eimon, P.M., Ghannad-Rezaie, M., De Rienzo, G., Allalou, A., Wu, Y., Gao, M., Roy, A., Skolnick, J., and Yanik, M.F. (2018). Brain activity patterns in high-throughput electrophysiology screen predict both drug efficacies and side effects. Nat Commun 9, 219</bibl>
            <idno type="DOI">10.1038/s41467-017-02404-4</idno>
          </bibl>
          <bibl n="6907">
            <bibl>Emran, F., Rihel, J., Adolph, A.R., and Dowling, J.E. (2010). Zebrafish larvae lose vision at night. Proc Natl Acad Sci U S A 107, 6034-6039</bibl>
            <idno type="DOI">10.1073/pnas.0914718107</idno>
          </bibl>
          <bibl n="6908">
            <bibl>Ernst, L.D., and Boudreau, E.A. (2016). Recent advances in epilepsy management. Curr Opin Anaesthesiol 29, 558-562</bibl>
            <idno type="DOI">10.1097/ACO.0000000000000376</idno>
          </bibl>
          <bibl n="6909">Ester, M., Kriegel, H., Sander, J., and Xu, X. (1996). A density-based algorithm for discovering clusters in large spatial databases with noise. Proceeding of the Second International Conference on Knowledge Discovery and Data Mining KDD-96, 226-231</bibl>
          <bibl n="6910">Ferrer, I., Soriano, E., Del Rio, J.A., Alcantara, S., and Auladell, C. (1992). Cell death and removal in the cerebral cortex during development. Prog Neurobiol 39, 1-43</bibl>
          <bibl n="6911">Finlay, B.L., and Slattery, M. (1983). Local differences in the amount of early cell death in neocortex predict adult local specializations. Science 219, 1349-1351</bibl>
          <bibl n="6912">
            <bibl>Fosque, B.F., Sun, Y., Dana, H., Yang, C.T., Ohyama, T., Tadross, M.R., Patel, R., Zlatic, M., Kim, D.S., Ahrens, M.B., Jayaraman, V., Looger, L.L., and Schreiter, E.R. (2015). Neural circuits. Labeling of active neural circuits in vivo with designed calcium integrators. Science 347, 755-760</bibl>
            <idno type="DOI">10.1126/science.1260922</idno>
          </bibl>
          <bibl n="6913">
            <bibl>Freeman, J., Vladimirov, N., Kawashima, T., Mu, Y., Sofroniew, N.J., Bennett, D.V., Rosen, J., Yang, C.T., Looger, L.L., and Ahrens, M.B. (2014). Mapping brain activity at scale with cluster computing. Nat Methods 11, 941-950</bibl>
            <idno type="DOI">10.1038/nmeth.3041</idno>
          </bibl>
          <bibl n="6914">
            <bibl>Friedrich, J., Zhou, P., and Paninski, L. (2017). Fast online deconvolution of calcium imaging data. PLoS Comput Biol 13, e1005423</bibl>
            <idno type="DOI">10.1371/journal.pcbi.1005423</idno>
          </bibl>
          <bibl n="6915">
            <bibl>Galland, R., Grenci, G., Aravind, A., Viasnoff, V., Studer, V., and Sibarita, J.B. (2015). 3D high- and super-resolution imaging using single-objective SPIM. Nat Methods 12, 641-644</bibl>
            <idno type="DOI">10.1038/nmeth.3402</idno>
          </bibl>
          <bibl n="6916">
            <bibl>Garcia-Campmany, L., Stam, F.J., and Goulding, M. (2010). From circuits to behaviour: motor networks in vertebrates. Curr Opin Neurobiol 20, 116-125</bibl>
            <idno type="DOI">10.1016/j.conb.2010.01.002</idno>
          </bibl>
          <bibl n="6917">
            <bibl>Gebhardt, J.C., Suter, D.M., Roy, R., Zhao, Z.W., Chapman, A.R., Basu, S., Maniatis, T., and Xie, X.S. (2013). Single-molecule imaging of transcription factor binding to DNA in live mammalian cells. Nat Methods 10, 421-426</bibl>
            <idno type="DOI">10.1038/nmeth.2411</idno>
          </bibl>
          <bibl n="6918">
            <bibl>Gee, K.R., Brown, K.A., Chen, W.N., Bishop-Stewart, J., Gray, D., and Johnson, I. (2000). Chemical and physiological characterization of fluo-4 Ca(2+)-indicator dyes. Cell Calcium 27, 97-106</bibl>
            <idno type="DOI">10.1054/ceca.1999.0095</idno>
          </bibl>
          <bibl n="6919">
            <bibl>Go, C., and Snead, O.C., 3rd (2008). Pharmacologically intractable epilepsy in children: diagnosis and preoperative evaluation. Neurosurg Focus 25, E2</bibl>
            <idno type="DOI">10.3171/FOC/2008/25/9/E2</idno>
          </bibl>
          <bibl n="6920">Goldman D.E. (1943). Potential, Impedance, and Rectification in Membranes. J Gen Physiol 27, 37-60</bibl>
          <bibl n="6921">Golgi, C. (1885). Sulla fina anatomia degli organi centrali del sistema nervoso.</bibl>
          <bibl n="6922">G&amp;#246;ppert-Mayer, M. (1931). Uber elementarakte mit zwei quantenspr&amp;#252;ngen. Ann Phys 9, 273-294</bibl>
          <bibl n="6923">Granato, M., and Nusslein-Volhard, C. (1996). Fishing for genes controlling development. Curr Opin Genet Dev 6, 461-468</bibl>
          <bibl n="6924">
            <bibl>Greenberg, D.S., Houweling, A.R., and Kerr, J.N. (2008). Population imaging of ongoing neuronal activity in the visual cortex of awake rats. Nat Neurosci 11, 749-751</bibl>
            <idno type="DOI">10.1038/nn.2140</idno>
          </bibl>
          <bibl n="6925">Grynkiewicz, G., Poenie, M., and Tsien, R.Y. (1985). A new generation of Ca2+ indicators with greatly improved fluorescence properties. J Biol Chem 260, 3440-3450</bibl>
          <bibl n="6926">
            <bibl>Guggiana-Nilo, D.A., and Engert, F. (2016). Properties of the Visible Light Phototaxis and UV Avoidance Behaviors in the Larval Zebrafish. Front Behav Neurosci 10, 160</bibl>
            <idno type="DOI">10.3389/fnbeh.2016.00160</idno>
          </bibl>
          <bibl n="6927">
            <bibl>Ha, T., and Tinnefeld, P. (2012). Photophysics of fluorescent probes for single-molecule biophysics and super-resolution imaging. Annu Rev Phys Chem 63, 595-617</bibl>
            <idno type="DOI">10.1146/annurev-physchem-032210-103340</idno>
          </bibl>
          <bibl n="6928">
            <bibl>Haesemeyer, M., Robson, D.N., Li, J.M., Schier, A.F., and Engert, F. (2018). A Brain-wide Circuit Model of Heat-Evoked Swimming Behavior in Larval Zebrafish. Neuron 98, 817-831 e816</bibl>
            <idno type="DOI">10.1016/j.neuron.2018.04.013</idno>
          </bibl>
          <bibl n="6929">
            <bibl>Hallett, M., and Carbone, E. (1972). Studies of calcium influx into squid giant axons with aequorin. J Cell Physiol 80, 219-226</bibl>
            <idno type="DOI">10.1002/jcp.1040800208</idno>
          </bibl>
          <bibl n="6930">Hastings J.W., and Morin J.G. (1969). Comparative biochemestry of calcium-activated photoproteins from the ctenophore, Mnemiopsis and the coelenterates Aequorea, Obelia, Pelagia and Renilla. Biology Bulletin 137, 402</bibl>
          <bibl n="6931">Hatta, K., and Kimmel, C.B. (1993). Midline structures and central nervous system coordinates in zebrafish. Perspect Dev Neurobiol 1, 257-268</bibl>
          <bibl n="6932">
            <bibl>Hayashi, Y., Yawata, S., Funabiki, K., and Hikida, T. (2017). In vivo calcium imaging from dentate granule cells with wide-field fluorescence microscopy. PLoS One 12, e0180452</bibl>
            <idno type="DOI">10.1371/journal.pone.0180452</idno>
          </bibl>
          <bibl n="6933">Heim, R., Cubitt, A.B., and Tsien, R.Y. (1995). Improved green fluorescent. Nature 373, 663-664</bibl>
          <bibl n="6934">Heim, R., Prasher, D.C., and Tsien, R.Y. (1994). Wavelength mutations and posttranslational autoxidation of green fluorescent protein. Proc Natl Acad Sci U S A 91, 12501-12504</bibl>
          <bibl n="6935">Heim, R., and Tsien, R.Y. (1996). Engineering green fluorescent protein for improved brightness, longer wavelengths and fluorescence resonance energy transfer. Curr Biol 6, 178-182</bibl>
          <bibl n="6936">
            <bibl>Hewapathirane, D.S., Dunfield, D., Yen, W., Chen, S., and Haas, K. (2008). In vivo imaging of seizure activity in a novel developmental seizure model. Exp Neurol 211, 480-488</bibl>
            <idno type="DOI">10.1016/j.expneurol.2008.02.012</idno>
          </bibl>
          <bibl n="6937">
            <bibl>Higashijima, S., Mandel, G., and Fetcho, J.R. (2004). Distribution of prospective glutamatergic, glycinergic, and GABAergic neurons in embryonic and larval zebrafish. J Comp Neurol 480, 1-18</bibl>
            <idno type="DOI">10.1002/cne.20278</idno>
          </bibl>
          <bibl n="6938">Hodgkin, A.L., and Huxley, A.F. (1952). A quantitative description of membrane current and its application to conduction and excitation in nerve. J Physiol 117, 500-544</bibl>
          <bibl n="6939">Hodgkin, A.L., and Katz, B. (1949). The effect of sodium ions on the electrical activity of the giant axon of the squid. Journal of Physiology 108, 37-77</bibl>
          <bibl n="6940">
            <bibl>Holtmaat, A., Bonhoeffer, T., Chow, D.K., Chuckowree, J., De Paola, V., Hofer, S.B., Hubener, M., Keck, T., Knott, G., Lee, W.C., Mostany, R., Mrsic-Flogel, T.D., Nedivi, E., Portera-Cailliau, C., Svoboda, K., Trachtenberg, J.T., and Wilbrecht, L. (2009). Long-term, high-resolution imaging in the mouse neocortex through a chronic cranial window. Nat Protoc 4, 1128-1144</bibl>
            <idno type="DOI">10.1038/nprot.2009.89</idno>
          </bibl>
          <bibl n="6941">
            <bibl>Hong, S., Lee, P., Baraban, S.C., and Lee, L.P. (2016). A Novel Long-term, Multi-Channel and Non-invasive Electrophysiology Platform for Zebrafish. Sci Rep 6, 28248</bibl>
            <idno type="DOI">10.1038/srep28248</idno>
          </bibl>
          <bibl n="6942">
            <bibl>Hortopan, G.A., Dinday, M.T., and Baraban, S.C. (2010). Zebrafish as a model for studying genetic aspects of epilepsy. Dis Model Mech 3, 144-148</bibl>
            <idno type="DOI">10.1242/dmm.002139</idno>
          </bibl>
          <bibl n="6943">
            <bibl>Howe, K., Clark, M.D., Torroja, C.F., Torrance, J., Berthelot, C., Muffato, M., Collins, J.E., Humphray, S., Mclaren, K., Matthews, L., Mclaren, S., Sealy, I., Caccamo, M., Churcher, C., Scott, C., Barrett, J.C., Koch, R., Rauch, G.J., White, S., Chow, W., Kilian, B., Quintais, L.T., Guerra-Assuncao, J.A., Zhou, Y., Gu, Y., Yen, J., Vogel, J.H., Eyre, T., Redmond, S., Banerjee, R., Chi, J., Fu, B., Langley, E., Maguire, S.F., Laird, G.K., Lloyd, D., Kenyon, E., Donaldson, S., Sehra, H., Almeida-King, J., Loveland, J., Trevanion, S., Jones, M., Quail, M., Willey, D., Hunt, A., Burton, J., Sims, S., Mclay, K., Plumb, B., Davis, J., Clee, C., Oliver, K., Clark, R., Riddle, C., Elliot, D., Threadgold, G., Harden, G., Ware, D., Begum, S., Mortimore, B., Kerry, G., Heath, P., Phillimore, B., Tracey, A., Corby, N., Dunn, M., Johnson, C., Wood, J., Clark, S., Pelan, S., Griffiths, G., Smith, M., Glithero, R., Howden, P., Barker, N., Lloyd, C., Stevens, C., Harley, J., Holt, K., Panagiotidis, G., Lovell, J., Beasley, H., Henderson, C., Gordon, D., Auger, K., Wright, D., Collins, J., Raisen, C., Dyer, L., Leung, K., Robertson, L., Ambridge, K., Leongamornlert, D., Mcguire, S., Gilderthorp, R., Griffiths, C., Manthravadi, D., Nichol, S., Barker, G., et al. (2013). The zebrafish reference genome sequence and its relationship to the human genome. Nature 496, 498-503</bibl>
            <idno type="DOI">10.1038/nature12111</idno>
          </bibl>
          <bibl n="6944">Huang, R.Q., Bell-Horner, C.L., Dibas, M.I., Covey, D.F., Drewe, J.A., and Dillon, G.H. (2001). Pentylenetetrazole-induced inhibition of recombinant gamma-aminobutyric acid type A (GABA(A)) receptors: mechanism and site of action. J Pharmacol Exp Ther 298, 986-995</bibl>
          <bibl n="6945">Huisken, J., and Stainier, D.Y. (2007). Even fluorescence excitation by multidirectional selective plane illumination microscopy (mSPIM). Opt Lett 32, 2608-2610</bibl>
          <bibl n="6946">
            <bibl>Huisken, J., and Stainier, D.Y. (2009). Selective plane illumination microscopy techniques in developmental biology. Development 136, 1963-1975</bibl>
            <idno type="DOI">10.1242/dev.022426</idno>
          </bibl>
          <bibl n="6947">
            <bibl>Huisken, J., Swoger, J., Del Bene, F., Wittbrodt, J., and Stelzer, E.H. (2004). Optical sectioning deep inside live embryos by selective plane illumination microscopy. Science 305, 1007-1009</bibl>
            <idno type="DOI">10.1126/science.1100035</idno>
          </bibl>
          <bibl n="6948">Inouye S., and Sasaki S. (2006). Blue fluorescent protein from the calcium-sensitive photoprotein aequorin: catalytic properties for the oxidation of coelenterazine as an oxygenase. FEBS Letters 580, 1977-1982</bibl>
          <bibl n="6949">Itoh, M., Kim, C.H., Palardy, G., Oda, T., Jiang, Y.J., Maust, D., Yeo, S.Y., Lorick, K., Wright, G.J., Ariza-Mcnaughton, L., Weissman, A.M., Lewis, J., Chandrasekharappa, S.C., and Chitnis, A.B. (2003). Mind bomb is a ubiquitin ligase that is essential for efficient activation of Notch signaling by Delta. Dev Cell 4, 67-82</bibl>
          <bibl n="6950">
            <bibl>Jia, H., Rochefort, N.L., Chen, X., and Konnerth, A. (2011). In vivo two-photon imaging of sensory-evoked dendritic calcium signals in cortical neurons. Nat Protoc 6, 28-35</bibl>
            <idno type="DOI">10.1038/nprot.2010.169</idno>
          </bibl>
          <bibl n="6951">Johnson F.H., Shimomura O., and Saiga Y. (1962). Action of cyanide on Cypridina luciferin. J Cell Comp Physiol 59, 265-272</bibl>
          <bibl n="6952">Johnson F.H., Shimomura O., Saiga Y., Gershman L.C., Reynolds G.T., and Waters J.R. (1962). Quantum efficiency of Cypridina luminescence, with a note on that of Aequorea. Journal of Cellular and Comparative Physiology 60, 85-103</bibl>
          <bibl n="6953">
            <bibl>Jones, J.M., and Gellert, M. (2004). The taming of a transposon: V(D)J recombination and the immune system. Immunol Rev 200, 233-248</bibl>
            <idno type="DOI">10.1111/j.0105-2896.2004.00168.x</idno>
          </bibl>
          <bibl n="6954">
            <bibl>Jorgensen P.L., Hakansson K.O., and Karlish S.J. (2003). Structure and mechanism of Na,K-ATPase: functional sites and their interactions. Annu Rev Physiol 65, 817-849</bibl>
            <idno type="DOI">10.1146/annurev.physiol.65.092101.142558</idno>
          </bibl>
          <bibl n="6955">
            <bibl>Kalueff, A.V., Gebhardt, M., Stewart, A.M., Cachat, J.M., Brimmer, M., Chawla, J.S., Craddock, C., Kyzar, E.J., Roth, A., Landsman, S., Gaikwad, S., Robinson, K., Baatrup, E., Tierney, K., Shamchuk, A., Norton, W., Miller, N., Nicolson, T., Braubach, O., Gilman, C.P., Pittman, J., Rosemberg, D.B., Gerlai, R., Echevarria, D., Lamb, E., Neuhauss, S.C., Weng, W., Bally-Cuif, L., Schneider, H., and Consortium, Z.N.R. (2013). Towards a comprehensive catalog of zebrafish behavior 1.0 and beyond. Zebrafish 10, 70-86</bibl>
            <idno type="DOI">10.1089/zeb.2012.0861</idno>
          </bibl>
          <bibl n="6956">Kandel, E.R. (2013). Principles of neural science. New York: McGraw-Hill.</bibl>
          <bibl n="6957">Kasha, M. (1950). Characterization of electronic transitions in complex molecules. Discussion of the Faraday Society 9, 14-19</bibl>
          <bibl n="6958">
            <bibl>Kawakami, K. (2007). Tol2: a versatile gene transfer vector in vertebrates. Genome Biol 8 Suppl 1, S7</bibl>
            <idno type="DOI">10.1186/gb-2007-8-s1-s7</idno>
          </bibl>
          <bibl n="6959">
            <bibl>Kawashima, T., Zwart, M.F., Yang, C.T., Mensh, B.D., and Ahrens, M.B. (2016). The Serotonergic System Tracks the Outcomes of Actions to Mediate Short-Term Motor Learning. Cell 167, 933-946 e920</bibl>
            <idno type="DOI">10.1016/j.cell.2016.09.055</idno>
          </bibl>
          <bibl n="6960">
            <bibl>Keller, P.J., Schmidt, A.D., Wittbrodt, J., and Stelzer, E.H. (2008). Reconstruction of zebrafish early embryonic development by scanned light sheet microscopy. Science 322, 1065-1069</bibl>
            <idno type="DOI">10.1126/science.1162493</idno>
          </bibl>
          <bibl n="6961">
            <bibl>Kim, D.H., Kim, J., Marques, J.C., Grama, A., Hildebrand, D.G.C., Gu, W., Li, J.M., and Robson, D.N. (2017). Pan-neuronal calcium imaging with cellular resolution in freely swimming zebrafish. Nat Methods 14, 1107-1114</bibl>
            <idno type="DOI">10.1038/nmeth.4429</idno>
          </bibl>
          <bibl n="6962">Kimmel, C.B. (1989). Genetics and early development of zebrafish. Trends Genet 5, 283-288</bibl>
          <bibl n="6963">
            <bibl>Kimmel, C.B. (1993). Patterning the brain of the zebrafish embryo. Annu Rev Neurosci 16, 707-732</bibl>
            <idno type="DOI">10.1146/annurev.ne.16.030193.003423</idno>
          </bibl>
          <bibl n="6964">
            <bibl>Kimmel, C.B., Ballard, W.W., Kimmel, S.R., Ullmann, B., and Schilling, T.F. (1995). Stages of embryonic development of the zebrafish. Dev Dyn 203, 253-310</bibl>
            <idno type="DOI">10.1002/aja.1002030302</idno>
          </bibl>
          <bibl n="6965">
            <bibl>Krzic, U., Gunther, S., Saunders, T.E., Streichan, S.J., and Hufnagel, L. (2012). Multiview light-sheet microscope for rapid in toto imaging. Nat Methods 9, 730-733</bibl>
            <idno type="DOI">10.1038/nmeth.2064</idno>
          </bibl>
          <bibl n="6966">Lakowicz, J.R. (2006). Principles of Fluorescence Spectroscopy. Springer.</bibl>
          <bibl n="6967">
            <bibl>Leung, L.C., Wang, G.X., and Mourrain, P. (2013). Imaging zebrafish neural circuitry from whole brain to synapse. Front Neural Circuits 7, 76</bibl>
            <idno type="DOI">10.3389/fncir.2013.00076</idno>
          </bibl>
          <bibl n="6968">Li B., Shahid R., Peshkepija P., and Zimmer M. (2012). Water diffusion in and out of the β-barrel of GFP and the fast maturing fluorescent protein, TurboGFP. Chemical Physiology 392, 143-148</bibl>
          <bibl n="6969">
            <bibl>Li, Y., Van Hooser, S.D., Mazurek, M., White, L.E., and Fitzpatrick, D. (2008). Experience with moving visual stimuli drives the early development of cortical direction selectivity. Nature 456, 952-956</bibl>
            <idno type="DOI">10.1038/nature07417</idno>
          </bibl>
          <bibl n="6970">
            <bibl>Lin, J.Y., Knutsen, P.M., Muller, A., Kleinfeld, D., and Tsien, R.Y. (2013). ReaChR: a red-shifted variant of channelrhodopsin enables deep transcranial optogenetic excitation. Nat Neurosci 16, 1499-1508</bibl>
            <idno type="DOI">10.1038/nn.3502</idno>
          </bibl>
          <bibl n="6971">
            <bibl>Lin, X., Wang, S., Yu, X., Liu, Z., Wang, F., Li, W.T., Cheng, S.H., Dai, Q., and Shi, P. (2015). High-throughput mapping of brain-wide activity in awake and drug-responsive vertebrates. Lab Chip 15, 680-689</bibl>
            <idno type="DOI">10.1039/c4lc01186d</idno>
          </bibl>
          <bibl n="6972">
            <bibl>Liu, S., Zhang, D., Liu, S., Feng, D., Peng, H., and Cai, W. (2016). Rivulet: 3D Neuron Morphology Tracing with Iterative Back-Tracking. Neuroinformatics 14, 387-401</bibl>
            <idno type="DOI">10.1007/s12021-016-9302-0</idno>
          </bibl>
          <bibl n="6973">Llinas, R., and Nicholson, C. (1975). Calcium role in depolarization-secretion coupling: an aequorin study in squid giant synapse. Proc Natl Acad Sci U S A 72, 187-190</bibl>
          <bibl n="6974">
            <bibl>Looger, L.L., and Griesbeck, O. (2012). Genetically encoded neural activity indicators. Curr Opin Neurobiol 22, 18-23</bibl>
            <idno type="DOI">10.1016/j.conb.2011.10.024</idno>
          </bibl>
          <bibl n="6975">
            <bibl>Ma, H., Harris, S., Rahmani, R., Lacefield, C.O., Zhao, M., Daniel, A.G., Zhou, Z., Bruno, R.M., Berwick, J., and Schwartz, T.H. (2014). Wide-field in vivo neocortical calcium dye imaging using a convection-enhanced loading technique combined with simultaneous multiwavelength imaging of voltage-sensitive dyes and hemodynamic signals. Neurophotonics 1, 015003</bibl>
            <idno type="DOI">10.1117/1.NPh.1.1.015003</idno>
          </bibl>
          <bibl n="6976">
            <bibl>Ma, Y., Shaik, M.A., Kim, S.H., Kozberg, M.G., Thibodeaux, D.N., Zhao, H.T., Yu, H., and Hillman, E.M. (2016). Wide-field optical mapping of neural activity and brain haemodynamics: considerations and novel approaches. Philos Trans R Soc Lond B Biol Sci 371,</bibl>
            <idno type="DOI">10.1098/rstb.2015.0360</idno>
          </bibl>
          <bibl n="6977">Magiorkinis, E., Sidiropoulou, K., and Diamantis, A. (2010). Hallmarks in the history of epilepsy: epilepsy in antiquity. Epilepsy and Behavior 17, 103-108</bibl>
          <bibl n="6978">
            <bibl>Makino, H., Ren, C., Liu, H., Kim, A.N., Kondapaneni, N., Liu, X., Kuzum, D., and Komiyama, T. (2017). Transformation of Cortex-wide Emergent Properties during Motor Learning. Neuron 94, 880-890 e888</bibl>
            <idno type="DOI">10.1016/j.neuron.2017.04.015</idno>
          </bibl>
          <bibl n="6979">
            <bibl>Meyer, M., Dhamne, S.C., Lacoursiere, C.M., Tambunan, D., Poduri, A., and Rotenberg, A. (2016). Microarray Noninvasive Neuronal Seizure Recordings from Intact Larval Zebrafish. PLoS One 11, e0156498</bibl>
            <idno type="DOI">10.1371/journal.pone.0156498</idno>
          </bibl>
          <bibl n="6980">Minta, A., Kao, J.P., and Tsien, R.Y. (1989). Fluorescent indicators for cytosolic calcium based on rhodamine and fluorescein chromophores. J Biol Chem 264, 8171-8178</bibl>
          <bibl n="6981">Mione, M., Baldessari, D., Deflorian, G., Nappo, G., and Santoriello, C. (2008). How neuronal migration contributes to the morphogenesis of the CNS: insights from the zebrafish. Dev Neurosci 30, 66-81</bibl>
          <bibl n="6982">
            <bibl>Miyawaki, A., Llopis, J., Heim, R., Mccaffery, J.M., Adams, J.A., Ikura, M., and Tsien, R.Y. (1997). Fluorescent indicators for Ca2+ based on green fluorescent proteins and calmodulin. Nature 388, 882-887</bibl>
            <idno type="DOI">10.1038/42264</idno>
          </bibl>
          <bibl n="6983">Morin J.G., and Hastings J.W. (1971). Energy transfer in a bioluminescent system. Journal of Cellular Physiology 77, 313-318</bibl>
          <bibl n="6984">Morise, H., Shimomura, O., Johnson, F.H., and Winant, J. (1974). Intermolecular energy transfer in the bioluminescent system of Aequorea. Biochemistry 13, 2656-2662</bibl>
          <bibl n="6985">
            <bibl>Mueller, T. (2012). What is the Thalamus in Zebrafish? Front Neurosci 6, 64</bibl>
            <idno type="DOI">10.3389/fnins.2012.00064</idno>
          </bibl>
          <bibl n="6986">
            <bibl>Muotri, A.R., and Gage, F.H. (2006). Generation of neuronal variability and complexity. Nature 441, 1087-1093</bibl>
            <idno type="DOI">10.1038/nature04959</idno>
          </bibl>
          <bibl n="6987">Nagai, T., Sawano, A., Park, E.S., and Miyawaki, A. (2001). Circularly permuted green fluorescent proteins engineered to sense Ca2+. Proc Natl Acad Sci U S A 98, 3197-3202</bibl>
          <bibl n="6988">
            <bibl>Nakai, J., Ohkura, M., and Imoto, K. (2001). A high signal-to-noise Ca(2+) probe composed of a single green fluorescent protein. Nat Biotechnol 19, 137-141</bibl>
            <idno type="DOI">10.1038/84397</idno>
          </bibl>
          <bibl n="6989">
            <bibl>Naumann, E.A., Fitzgerald, J.E., Dunn, T.W., Rihel, J., Sompolinsky, H., and Engert, F. (2016). From Whole-Brain Data to Functional Circuit Models: The Zebrafish Optomotor Response. Cell 167, 947-960 e920</bibl>
            <idno type="DOI">10.1016/j.cell.2016.10.019</idno>
          </bibl>
          <bibl n="6990">
            <bibl>Naumann, E.A., Kampff, A.R., Prober, D.A., Schier, A.F., and Engert, F. (2010). Monitoring neural activity with bioluminescence during natural behavior. Nat Neurosci 13, 513-520</bibl>
            <idno type="DOI">10.1038/nn.2518</idno>
          </bibl>
          <bibl n="6991">Nernst, W. (1888). On the kinetics of substances in solution. Zeitschrift f&amp;#252;r Physikalische Chemie 2, 613-622, 634-637</bibl>
          <bibl n="6992">
            <bibl>Ngugi, A.K., Bottomley, C., Kleinschmidt, I., Sander, J.W., and Newton, C.R. (2010). Estimation of the burden of active and life-time epilepsy: a meta-analytic approach. Epilepsia 51, 883-890</bibl>
            <idno type="DOI">10.1111/j.1528-1167.2009.02481.x</idno>
          </bibl>
          <bibl n="6993">
            <bibl>Nobrega, M.A., and Pennacchio, L.A. (2004). Comparative genomic analysis as a tool for biological discovery. J Physiol 554, 31-39</bibl>
            <idno type="DOI">10.1113/jphysiol.2003.050948</idno>
          </bibl>
          <bibl n="6994">
            <bibl>Noebels, J.L. (2003). The biology of epilepsy genes. Annu Rev Neurosci 26, 599-625</bibl>
            <idno type="DOI">10.1146/annurev.neuro.26.010302.081210</idno>
          </bibl>
          <bibl n="6995">
            <bibl>Ohki, K., Chung, S., Ch&amp;#39;ng, Y.H., Kara, P., and Reid, R.C. (2005). Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. Nature 433, 597-603</bibl>
            <idno type="DOI">10.1038/nature03274</idno>
          </bibl>
          <bibl n="6996">
            <bibl>Ohkura, M., Matsuzaki, M., Kasai, H., Imoto, K., and Nakai, J. (2005). Genetically encoded bright Ca2+ probe applicable for dynamic Ca2+ imaging of dendritic spines. Anal Chem 77, 5861-5869</bibl>
            <idno type="DOI">10.1021/ac0506837</idno>
          </bibl>
          <bibl n="6997">Olson, H.E., Poduri, A., and Pearl, P.L. (2014). Genetic forms of epilepsies and other paroxysmal disorders. Seminars in neurology 34, 266-279</bibl>
          <bibl n="6998">
            <bibl>Oppenheim, R.W. (1991). Cell death during development of the nervous system. Annu Rev Neurosci 14, 453-501</bibl>
            <idno type="DOI">10.1146/annurev.ne.14.030191.002321</idno>
          </bibl>
          <bibl n="6999">Ormo, M., Cubitt, A.B., Kallio, K., Gross, L.A., Tsien, R.Y., and Remington, S.J. (1996). Crystal structure of the Aequorea victoria green fluorescent protein. Science 273, 1392-1395</bibl>
          <bibl n="7000">Pakkenberg, B., Pelvig, D., Marner, L., Bundgaard, M.J., Gundersen, H.J., Nyengaard, J.R., and Regeur, L. (2003). Aging and the human neocortex. Exp Gerontol 38, 95-99</bibl>
          <bibl n="7001">
            <bibl>Panier, T., Romano, S.A., Olive, R., Pietri, T., Sumbre, G., Candelier, R., and Debregeas, G. (2013). Fast functional imaging of multiple brain regions in intact zebrafish larvae using selective plane illumination microscopy. Front Neural Circuits 7, 65</bibl>
            <idno type="DOI">10.3389/fncir.2013.00065</idno>
          </bibl>
          <bibl n="7002">Pedersen, P.L., and Carofoli, E. (1987). Ion motive ATPases. Ubiquity, properties, and significance to cell function. Trends in Biochemical Science 12, 146-150</bibl>
          <bibl n="7003">
            <bibl>Pisanello, F., Mandelbaum, G., Pisanello, M., Oldenburg, I.A., Sileo, L., Markowitz, J.E., Peterson, R.E., Della Patria, A., Haynes, T.M., Emara, M.S., Spagnolo, B., Datta, S.R., De Vittorio, M., and Sabatini, B.L. (2017). Dynamic illumination of spatially restricted or large brain volumes via a single tapered optical fiber. Nat Neurosci 20, 1180-1188</bibl>
            <idno type="DOI">10.1038/nn.4591</idno>
          </bibl>
          <bibl n="7004">
            <bibl>Portugues, R., Feierstein, C.E., Engert, F., and Orger, M.B. (2014). Whole-brain activity maps reveal stereotyped, distributed networks for visuomotor behavior. Neuron 81, 1328-1343</bibl>
            <idno type="DOI">10.1016/j.neuron.2014.01.019</idno>
          </bibl>
          <bibl n="7005">Porumb, T., Yau, P., Harvey, T.S., and Ikura, M. (1996). A calmodulin-target peptide hybrid molecule with unique calcium-binding properties. Protein Engineering 7, 109-115</bibl>
          <bibl n="7006">
            <bibl>Power, R.M., and Huisken, J. (2017). A guide to light-sheet fluorescence microscopy for multiscale imaging. Nat Methods 14, 360-373</bibl>
            <idno type="DOI">10.1038/nmeth.4224</idno>
          </bibl>
          <bibl n="7007">Pozzan, T., Arslan, P., Tsien, R.Y., and Rink, T.J. (1982). Anti-immunoglobulin, cytoplasmic free calcium, and capping in B lymphocytes. J Cell Biol 94, 335-340</bibl>
          <bibl n="7008">Prasher, D.C., Eckenrode, V.K., Ward, W.W., Prendergast, F.G., and Cormier, M.J. (1992). Primary structure of the Aequorea victoria green-fluorescent protein. Gene 111, 229-233</bibl>
          <bibl n="7009">Ram&amp;#242;n Y Cajal, S. (1917). Recuerdos de mi vida. Imprenta y libreria de Nicolas Moya</bibl>
          <bibl n="7010">
            <bibl>Randlett, O., Wee, C.L., Naumann, E.A., Nnaemeka, O., Schoppik, D., Fitzgerald, J.E., Portugues, R., Lacoste, A.M., Riegler, C., Engert, F., and Schier, A.F. (2015). Whole-brain activity mapping onto a zebrafish brain atlas. Nat Methods 12, 1039-1046</bibl>
            <idno type="DOI">10.1038/nmeth.3581</idno>
          </bibl>
          <bibl n="7011">Ridgway, E.B., and Ashley, C.C. (1967). Calcium transients in single muscle fibers. Biochem Biophys Res Commun 29, 229-234</bibl>
          <bibl n="7012">Ringer, S. (1883). A further contribution regarding the influence of the different constituents of the blood on the contraction of the heart. Journal of Physiology 29-43</bibl>
          <bibl n="7013">
            <bibl>Robles, E., Smith, S.J., and Baier, H. (2011). Characterization of genetically targeted neuron types in the zebrafish optic tectum. Front Neural Circuits 5, 1</bibl>
            <idno type="DOI">10.3389/fncir.2011.00001</idno>
          </bibl>
          <bibl n="7014">
            <bibl>Romano, S.A., Pietri, T., Perez-Schuster, V., Jouary, A., Haudrechy, M., and Sumbre, G. (2015). Spontaneous neuronal network dynamics reveal circuit&amp;#39;s functional adaptations for behavior. Neuron 85, 1070-1085</bibl>
            <idno type="DOI">10.1016/j.neuron.2015.01.027</idno>
          </bibl>
          <bibl n="7015">
            <bibl>Rosch, R.E., Hunter, P.R., Baldeweg, T., Friston, K.J., and Meyer, M.P. (2018). Calcium imaging and dynamic causal modelling reveal brain-wide changes in effective connectivity and synaptic dynamics during epileptic seizures. PLoS Comput Biol 14, e1006375</bibl>
            <idno type="DOI">10.1371/journal.pcbi.1006375</idno>
          </bibl>
          <bibl n="7016">Rose, A. (1946). A unified approach to the performance of photographic film, television pickup tubes and the human eye. J Soc Motion Pict Eng 47, 273-294</bibl>
          <bibl n="7017">Sabatini, B., Oertner, T.G., and Svoboda, K. (2002). The life cycle of Ca2+ ions in dendritic spines. Neuron 33, 439-452</bibl>
          <bibl n="7018">Safford, W.E. (1915). Annual Report of the Board of Reagents of the Smithsonin Institution. 271-298</bibl>
          <bibl n="7019">
            <bibl>Shimomura, O. (2005). The discovery of aequorin and green fluorescent protein. J Microsc 217, 1-15</bibl>
            <idno type="DOI">10.1111/j.0022-2720.2005.01441.x</idno>
          </bibl>
          <bibl n="7020">Shimomura O. (1979). Structure of the chromophore of Aequorea green fluorescent protein. FEBS Letters 104, 220-222</bibl>
          <bibl n="7021">Shimomura O., and Johnson F.H. (1970). Calcium binding, quantum yield, and emitting molecule in aequorin biolumnescence. Nature 227, 1356-1357</bibl>
          <bibl n="7022">Shimomura O., Johnson F.H., and Saiga Y. (1962). Extraction, purification and properties of aequorin, a bioluminescent protein from the luminous hydromedusan, Aequorea. J Cell Comp Physiol 59, 223-239</bibl>
          <bibl n="7023">Siedentopf, H., and Zsigmondy, R. (1902). &amp;#220;ber sichtbarmachung und gr&amp;#246;&amp;#223;enbestimmung ultramikoskopischer teilchen, mit besonderer anwendung auf goldrubingl&amp;#228;ser. Annualen der Physik 315, 1-39</bibl>
          <bibl n="7024">
            <bibl>Silasi, G., Xiao, D., Vanni, M.P., Chen, A.C., and Murphy, T.H. (2016). Intact skull chronic windows for mesoscopic wide-field imaging in awake mice. J Neurosci Methods 267, 141-149</bibl>
            <idno type="DOI">10.1016/j.jneumeth.2016.04.012</idno>
          </bibl>
          <bibl n="7025">Silvestri, L. (2012). Confocal ultramicroscopy: micron-scale neuroanatomy of the entire mouse brain. Doctoral dissertation, Universit&amp;#224; degli Studi di Firenze.</bibl>
          <bibl n="7026">
            <bibl>Silvestri, L., Bria, A., Sacconi, L., Iannello, G., and Pavone, F.S. (2012). Confocal light sheet microscopy: micron-scale neuroanatomy of the entire mouse brain. Opt Express 20, 20582-20598</bibl>
            <idno type="DOI">10.1364/OE.20.020582</idno>
          </bibl>
          <bibl n="7027">Stafstorm, C.E. (2010). Mechanisms of action of antiepileptic drugs: the search for synergy. Curr Opin Neurol 23, 157-163</bibl>
          <bibl n="7028">
            <bibl>Stewart, A.M., Desmond, D., Kyzar, E., Gaikwad, S., Roth, A., Riehl, R., Collins, C., Monnig, L., Green, J., and Kalueff, A.V. (2012). Perspectives of zebrafish models of epilepsy: what, how and where next? Brain Res Bull 87, 135-143</bibl>
            <idno type="DOI">10.1016/j.brainresbull.2011.11.020</idno>
          </bibl>
          <bibl n="7029">Stinnakre, J., and Tauc, L. (1973). Calcium influx in active Aplysia neurons detected by injected aequorin. Nature New Biology 242,</bibl>
          <bibl n="7030">Streisinger, G., Walker, C., Dower, N., Knauber, D., and Singer, F. (1981). Production of clones of homozygous diploid zebra fish (Brachydanio rerio). Nature 291, 293-296</bibl>
          <bibl n="7031">
            <bibl>Sullivan, M.R., Nimmerjahn, A., Sarkisov, D.V., Helmchen, F., and Wang, S.S. (2005). In vivo calcium imaging of circuit activity in cerebellar cortex. J Neurophysiol 94, 1636-1644</bibl>
            <idno type="DOI">10.1152/jn.01013.2004</idno>
          </bibl>
          <bibl n="7032">
            <bibl>Sumbre, G., Muto, A., Baier, H., and Poo, M.M. (2008). Entrained rhythmic activities of neuronal ensembles as perceptual memory of time interval. Nature 456, 102-106</bibl>
            <idno type="DOI">10.1038/nature07351</idno>
          </bibl>
          <bibl n="7033">
            <bibl>Tallini, Y.N., Ohkura, M., Choi, B.R., Ji, G., Imoto, K., Doran, R., Lee, J., Plan, P., Wilson, J., Xin, H.B., Sanbe, A., Gulick, J., Mathai, J., Robbins, J., Salama, G., Nakai, J., and Kotlikoff, M.I. (2006). Imaging cellular signals in the heart in vivo: Cardiac expression of the high-signal Ca2+ indicator GCaMP2. Proc Natl Acad Sci U S A 103, 4753-4758</bibl>
            <idno type="DOI">10.1073/pnas.0509378103</idno>
          </bibl>
          <bibl n="7034">
            <bibl>Tao, L., Lauderdale, J.D., and Sornborger, A.T. (2011). Mapping Functional Connectivity between Neuronal Ensembles with Larval Zebrafish Transgenic for a Ratiometric Calcium Indicator. Front Neural Circuits 5, 2</bibl>
            <idno type="DOI">10.3389/fncir.2011.00002</idno>
          </bibl>
          <bibl n="7035">
            <bibl>Tian, L., Hires, S.A., Mao, T., Huber, D., Chiappe, M.E., Chalasani, S.H., Petreanu, L., Akerboom, J., Mckinney, S.A., Schreiter, E.R., Bargmann, C.I., Jayaraman, V., Svoboda, K., and Looger, L.L. (2009). Imaging neural activity in worms, flies and mice with improved GCaMP calcium indicators. Nat Methods 6, 875-881</bibl>
            <idno type="DOI">10.1038/nmeth.1398</idno>
          </bibl>
          <bibl n="7036">Tokunaga, M., Imamoto, N., and Sakata-Sogawa, K. (2008). Highly inclined thin illumination enables clear single-molecule imaging in cells. Nature Methods 5, 159-161</bibl>
          <bibl n="7037">
            <bibl>Tomer, R., Khairy, K., Amat, F., and Keller, P.J. (2012). Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nat Methods 9, 755-763</bibl>
            <idno type="DOI">10.1038/nmeth.2062</idno>
          </bibl>
          <bibl n="7038">
            <bibl>Tomer, R., Lovett-Barron, M., Kauvar, I., Andalman, A., Burns, V.M., Sankaran, S., Grosenick, L., Broxton, M., Yang, S., and Deisseroth, K. (2015). SPED Light Sheet Microscopy: Fast Mapping of Biological System Structure and Function. Cell 163, 1796-1806</bibl>
            <idno type="DOI">10.1016/j.cell.2015.11.061</idno>
          </bibl>
          <bibl n="7039">Tsien, R.Y. (1980). New calcium indicators and buffers with high selectivity against magnesium and protons: design, synthesis, and properties of prototype structures. Biochemistry 19, 2396-2404</bibl>
          <bibl n="7040">Tsien, R.Y. (1981). A non-disruptive technique for loading calcium buffers and indicators into cells. Nature 290, 527-528</bibl>
          <bibl n="7041">Tsien, R.Y., Pozzan, T., and Rink, T.J. (1982). Calcium homeostasis in intact lymphocytes: cytoplasmic free calcium monitored with a new, intracellularly trapped fluorescent indicator. J Cell Biol 94, 325-334</bibl>
          <bibl n="7042">
            <bibl>Turrini, L., Fornetto, C., Marchetto, G., Mullenbroich, M.C., Tiso, N., Vettori, A., Resta, F., Masi, A., Mannaioni, G., Pavone, F.S., and Vanzi, F. (2017). Optical mapping of neuronal activity during seizures in zebrafish. Sci Rep 7, 3025</bibl>
            <idno type="DOI">10.1038/s41598-017-03087-z</idno>
          </bibl>
          <bibl n="7043">
            <bibl>Valeur, B., and Berberan-Santos M.N. (2011). A Brief History of Fluorescence and Phosphorescence before the Emergence of Quantum Theory. Journal of Chemical Education 88, 731-738</bibl>
            <idno type="DOI">10.1021/ed100182h</idno>
          </bibl>
          <bibl n="7044">
            <bibl>Vanni, M.P., and Murphy, T.H. (2014). Mesoscale transcranial spontaneous activity mapping in GCaMP3 transgenic mice reveals extensive reciprocal connections between areas of somatomotor cortex. J Neurosci 34, 15931-15946</bibl>
            <idno type="DOI">10.1523/JNEUROSCI.1818-14.2014</idno>
          </bibl>
          <bibl n="7045">
            <bibl>Verveer, P.J., Swoger, J., Pampaloni, F., Greger, K., Marcello, M., and Stelzer, E.H. (2007). High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy. Nat Methods 4, 311-313</bibl>
            <idno type="DOI">10.1038/nmeth1017</idno>
          </bibl>
          <bibl n="7046">
            <bibl>Vladimirov, N., Mu, Y., Kawashima, T., Bennett, D.V., Yang, C.T., Looger, L.L., Keller, P.J., Freeman, J., and Ahrens, M.B. (2014). Light-sheet functional imaging in fictively behaving zebrafish. Nat Methods 11, 883-884</bibl>
            <idno type="DOI">10.1038/nmeth.3040</idno>
          </bibl>
          <bibl n="7047">Voie, A.H., Burns, D.H., and Spelman, F.A. (1993). Orthogonal-plane fluorescence optical sectioning: three-dimensional imaging of macroscopic biological specimens. J Microsc 170, 229-236</bibl>
          <bibl n="7048">
            <bibl>Wang, Q., Shui, B., Kotlikoff, M.I., and Sondermann, H. (2008). Structural basis for calcium sensing by GCaMP2. Structure 16, 1817-1827</bibl>
            <idno type="DOI">10.1016/j.str.2008.10.008</idno>
          </bibl>
          <bibl n="7049">Ward, W.W., Prentice, H.J., Roth, A.F., Cody, C.W., and Reeves, C.S. (1982). Spectral perturbations of the aequorea green-fluorescent protein. Photochem Photobiol 35, 803-808</bibl>
          <bibl n="7050">
            <bibl>Weisenburger, S., and Vaziri, A. (2018). A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity. Annu Rev Neurosci 41, 431-452</bibl>
            <idno type="DOI">10.1146/annurev-neuro-072116-031458</idno>
          </bibl>
          <bibl n="7051">
            <bibl>Werley, C.A., Chien, M.P., and Cohen, A.E. (2017). Ultrawidefield microscope for high-speed fluorescence imaging and targeted optogenetic stimulation. Biomed Opt Express 8, 5794-5813</bibl>
            <idno type="DOI">10.1364/BOE.8.005794</idno>
          </bibl>
          <bibl n="7052">Westerfield, M. (1993). The zebrafish book : a guide for the laboratory use of zebrafish (Brachydanio rerio). Eugene, OR: M. Westerfield.</bibl>
          <bibl n="7053">Williams, D.A., Fogarty, K.E., Tsien, R.Y., and Fay, F.S. (1985). Calcium gradients in single smooth muscle cells revealed by the digital imaging microscope using Fura-2. Nature 318, 558-561</bibl>
          <bibl n="7054">Williams, R.P.J. (1999). Calcium: the developing role of its chemestry in biological evolution. In Calcium as a Cellular Regulator (Carofoli E. &amp;amp; Klee C., eds). 3-27</bibl>
          <bibl n="7055">
            <bibl>Winter, M.J., Redfern, W.S., Hayfield, A.J., Owen, S.F., Valentin, J.P., and Hutchinson, T.H. (2008). Validation of a larval zebrafish locomotor assay for assessing the seizure liability of early-stage development drugs. J Pharmacol Toxicol Methods 57, 176-187</bibl>
            <idno type="DOI">10.1016/j.vascn.2008.01.004</idno>
          </bibl>
          <bibl n="7056">
            <bibl>Winter, M.J., Windell, D., Metz, J., Matthews, P., Pinion, J., Brown, J.T., Hetheridge, M.J., Ball, J.S., Owen, S.F., Redfern, W.S., Moger, J., Randall, A.D., and Tyler, C.R. (2017). 4-dimensional functional profiling in the convulsant-treated larval zebrafish brain. Sci Rep 7, 6581</bibl>
            <idno type="DOI">10.1038/s41598-017-06646-6</idno>
          </bibl>
          <bibl n="7057">
            <bibl>Wolf, S., Dubreuil, A.M., Bertoni, T., Bohm, U.L., Bormuth, V., Candelier, R., Karpenko, S., Hildebrand, D.G.C., Bianco, I.H., Monasson, R., and Debregeas, G. (2017). Sensorimotor computation underlying phototaxis in zebrafish. Nat Commun 8, 651</bibl>
            <idno type="DOI">10.1038/s41467-017-00310-3</idno>
          </bibl>
          <bibl n="7058">Wu, P., Sui, C., and Huang, W. (2014). Theoretical analysis of a quasi-Bessel beam for laser ablation. Photonics Research 2, 82-86</bibl>
          <bibl n="7059">
            <bibl>Xiao, D., Vanni, M.P., Mitelut, C.C., Chan, A.W., Ledue, J.M., Xie, Y., Chen, A.C., Swindale, N.V., and Murphy, T.H. (2017). Mapping cortical mesoscopic networks of single spiking cortical or sub-cortical neurons. Elife 6,</bibl>
            <idno type="DOI">10.7554/eLife.19976</idno>
          </bibl>
          <bibl n="7060">
            <bibl>Yokoe, H., and Meyer, T. (1996). Spatial dynamics of GFP-tagged proteins investigated by local fluorescence enhancement. Nat Biotechnol 14, 1252-1256</bibl>
            <idno type="DOI">10.1038/nbt1096-1252</idno>
          </bibl>
          <bibl n="7061">
            <bibl>Zdebik, A.A., Mahmood, F., Stanescu, H.C., Kleta, R., Bockenhauer, D., and Russell, C. (2013). Epilepsy in kcnj10 morphant zebrafish assessed with a novel method for long-term EEG recordings. PLoS One 8, e79765</bibl>
            <idno type="DOI">10.1371/journal.pone.0079765</idno>
          </bibl>
          <bibl n="7062">
            <bibl>Zheng, Q., Jockusch, S., Zhou, Z., and Blanchard, S.C. (2014). The contribution of reactive oxygen species to the photobleaching of organic fluorophores. Photochem Photobiol 90, 448-454</bibl>
            <idno type="DOI">10.1111/php.12204</idno>
          </bibl>
        </listBibl>
      </div>
    </body>
  </text>
</TEI>