Tools for recording high-speed brain dynamics
The brain is a three-dimensional, densely-wired circuit that computes via large sets of widely distributed neurons interacting at fast timescales. In order to understand the brain, ideally it would be possible to observe the activity of many neurons with as great a degree of precision as possible, so as to understand the neural codes and dynamics that are produced by the circuits of the brain. And, ideally, it would be possible to understand how those neural codes and dynamics emerge from subcellular computational events within individual cells. Our lab and our collaborators are developing a number of innovations to enable such analyses of neural circuit dynamics. These tools will hopefully enable pictures of how neurons work together to implement brain computations, and how these computations go awry in brain disorder states. Such neural observation strategies may also serve as detailed biomarkers of brain disorders or indicators of potential drug side effects. These technologies may, in conjunction with optogenetics, enable closed-loop neural control technologies, which can introduce information into the brain as a function of brain state ("brain co-processors"), enabling new kinds of circuit characterization tool as well as new kinds of advanced brain-repair prosthetic.
Hochbaum, D.R.*, Zhao, Y.*, Farhi, S.L., Klapoetke, N.C., Werley, C.A., Kapoor, V., Zou, P., Kralj, J.M., Maclaurin, D., Smedemark-Margulies, N., Saulnier, J., Boulting, G.L., Straub, C., Cho, Y., Melkonian, M., Wong, G.K.-S., Harrison, D. J., Murthy, V.N., Sabatini, B., Boyden, E.S.**, Campbell, R.E.**, Cohen, A.E. (2014) All-optical electrophysiology in mammalian neurons using engineered microbial rhodopsins, Nature Methods, advance online publication, doi:10.1038/nmeth.3000. (*, equal contribution, **, jointly directed work)
Prevedel, R.**, Yoon, Y.-G.**, Hoffman, M., Pak, N., Wetzstein, G., Kato, S., Schrodel, T., Raskar, R., Zimmer, M., Boyden, E. S.*, Vaziri, A. * (2014) Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy, Nature Methods 11:727-730. (** equal contribution, * co-corresponding authors)
Marblestone, A. H.**+, Zamft, B. M.+, Maguire, Y. G., Shapiro, M. G., Cybulski, T. R., Glaser, J. I., Amodei, D., Stranges, P. B., Kalhor, R., Dalrymple, D. A., Seo, D., Alon, E., Maharbiz, M. M., Carmena, J. M., Rabaey, J. M., Boyden, E. S.*, Church, G. M. *, Kording, K. P. * (2013) Physical Principles for Scalable Neural Recording, Frontiers in Computational Neuroscience, 7:137. (** corresponding author, + equal contribution, * equal contribution)
Glaser J.I.**, Zamft B.M.*, Marblestone A.H.*, Moffitt J.R., Tyo K., Boyden E.S., Church G., Kording K.P. (2013) Statistical analysis of molecular signal recording, PLoS Computational Biology 9(7):e1003145. (** corresponding author, * equal contribution)
J. Go, A. Fan, C. Lu, S.B. Kodandaramaiah, G.L. Holst, W. Stoy, I. Kolb, E.S. Boyden, C.R. Forest (2013) Fully-automated, in-vivo, single cell electrophysiology, Proceedings of the 28th Annual Meeting of the American Society for Precision Engineering, Saint Paul, MN, Oct 20-25, 2013.
Kodandaramaiah, S. B., Boyden, E. S.*, Forest, C. F.* (2013) In vivo robotics: the automation of neuroscience and other intact-system biological fields, Annals of the New York Academy of Sciences, 1305(1):63-71. (* co-corresponding authors)
I. Kolb, G. Holst, B. Goldstein, S.B. Kodandaramaiah, E.S. Boyden, E. Culurciello, C.R. Forest (2013) Automated, in-vivo, whole-cell electrophysiology using an integrated patch-clamp amplifier, Proceedings of the 22nd Annual Computational Neuroscience Meeting (CNS 2013), Paris, France, July 13-18, 2013.
Alivisatos, A., Andrews, A., Boyden, E. S., Chun, M., Church, G., Deisseroth, K., Donoghue, J., Fraser, S., Lippincott-Schwartz, J., Looger, L., Masmanidis, S., McEuen, P., Nurmikko, A., Park, H., Peterka, D., Reid, C., Roukes, M., Scherer, A., Schnitzer, M., Sejnowski, T., Shepard, K., Tsao, D., Turrigiano, G., Weiss, P., Xu, C., Yuste, R., Zhuang, X. (2013) Nanotools for Neuroscience and Brain Activity Mapping, ACS Nano, 7(3):1850-66.
Zamft, B. M.*, Marblestone, A. H.*, Kording, K., Schmidt, D., Martin-Alarcon, D., Tyo, K., Boyden, E. S., Church, G. (2012) Measuring Cation Dependent DNA Polymerase Fidelity Landscapes by Deep Sequencing, PLoS ONE 7(8): e43876. (* co-first authors)
Kodandaramaiah, S., Talei Franzesi, G., Chow, B., Boyden, E. S.*, Forest, C.* (2012) Automated whole-cell patch clamp electrophysiology of neurons in vivo, Nature Methods 9:585–587. (* co-corresponding authors)
Kodandaramaiah, S., Krijnen, M., Go, J., Malik, S., Sondej, N., Khatait, J. P., Boyden, E. S., Aarts, R. G. K. M., Brouwer, D. M., Forest, C. F. (2011) Characterization of translation of fused silica micropipettes in non-rectilinear trajectories, Proceedings of the 26th Annual Meeting of the American Society for Precision Engineering, Denver, CO.
Desai M., Kahn I., Knoblich U., Bernstein J., Atallah H., Yang A., Kopell, N., Buckner R.L., Graybiel A. M., Moore C. I.*, and Boyden E. S.* (2011) Mapping Brain Networks in Awake Mice Using Combined Optical Neural Control and fMRI, Journal of Neurophysiology 105(3):1393-405. (* co-corresponding authors)
Boyden, E. S., Han, X., Talei Franzesi, G., Chan, S., Bernstein, J., Qian, X., Li, M. (2009) "New Techniques for Investigating Brain Rhythms: Optical Neural Control and Multielectrode Recording," In: Rhythms of the Neocortex: Where Do They Come From and What Are They Good For? (Kopell N., ed.) pp. 65-75. Washington, DC: Society for Neuroscience.
Han, X.*, Qian, X., Bernstein, J.G., Zhou, H.-H., Talei Franzesi, G., Stern, P., Bronson, R.T., Graybiel, A.M., Desimone, R., and Boyden, E.S.* (2009) Millisecond-Timescale Optical Control of Neural Dynamics in the Nonhuman Primate Brain, Neuron 62(2):191-198. (* co-corresponding authors)