Dr. Quirin's laboratory develops minimally invasive methods to explore the causal role individual neurons play in the emergence of behavior. To this end, the lab's strength is the development of techniques which manipulate light to both detect and restoratively modulate brain activity down to the single-neuron scale. His lab continues to innovate with new tools which map these functional relationships onto the molecular and anatomical architecture of the brain. Utilizing these techniques, the lab aims to characterize how ensembles of neurons coordinate to encode and communicate information throughout the brain for sensing and behavior.

Academic Appointments

  • Assistant Professor (Research), Psychiatry and Behavioral Sciences
  • Member, Bio-X

Professional Education

  • B.A., University of Colorado, Boulder, Astronomy/Astrophysics (2004)
  • PhD, University of Colorado, Boulder, Electrical Engineering (2012)

2023-24 Courses

All Publications

  • All-optical physiology resolves a synaptic basis for behavioral timescale plasticity. Cell Fan, L. Z., Kim, D. K., Jennings, J. H., Tian, H., Wang, P. Y., Ramakrishnan, C., Randles, S., Sun, Y., Thadhani, E., Kim, Y. S., Quirin, S., Giocomo, L., Cohen, A. E., Deisseroth, K. 2023


    Learning has been associated with modifications of synaptic and circuit properties, but the precise changes storing information in mammals have remained largely unclear. We combined genetically targeted voltage imaging with targeted optogenetic activation and silencing of pre- and post-synaptic neurons to study the mechanisms underlying hippocampal behavioral timescale plasticity. In mice navigating a virtual-reality environment, targeted optogenetic activation of individual CA1 cells at specific places induced stable representations of these places in the targeted cells. Optical elicitation, recording, and modulation of synaptic transmission in behaving mice revealed that activity in presynaptic CA2/3 cells was required for the induction of plasticity in CA1 and, furthermore, that during induction of these place fields in single CA1 cells, synaptic input from CA2/3 onto these same cells was potentiated. These results reveal synaptic implementation of hippocampal behavioral timescale plasticity and define a methodology to resolve synaptic plasticity during learning and memory in behaving mammals.

    View details for DOI 10.1016/j.cell.2022.12.035

    View details for PubMedID 36669484

  • Structural basis for channel conduction in the pump-like channelrhodopsin ChRmine. Cell Kishi, K. E., Kim, Y. S., Fukuda, M., Inoue, M., Kusakizako, T., Wang, P. Y., Ramakrishnan, C., Byrne, E. F., Thadhani, E., Paggi, J. M., Matsui, T. E., Yamashita, K., Nagata, T., Konno, M., Quirin, S., Lo, M., Benster, T., Uemura, T., Liu, K., Shibata, M., Nomura, N., Iwata, S., Nureki, O., Dror, R. O., Inoue, K., Deisseroth, K., Kato, H. E. 1800


    ChRmine, a recently discovered pump-like cation-conducting channelrhodopsin, exhibits puzzling properties (large photocurrents, red-shifted spectrum, and extreme light sensitivity) that have created new opportunities in optogenetics. ChRmine and its homologs function as ion channels but, by primary sequence, more closely resemble ion pump rhodopsins; mechanisms for passive channel conduction in this family have remained mysterious. Here, we present the 2.0A resolution cryo-EM structure of ChRmine, revealing architectural features atypical for channelrhodopsins: trimeric assembly, a short transmembrane-helix 3, a twisting extracellular-loop 1, large vestibules within the monomer, and an opening at the trimer interface. We applied this structure to design three proteins (rsChRmine and hsChRmine, conferring further red-shifted and high-speed properties, respectively, and frChRmine, combining faster and more red-shifted performance) suitable for fundamental neuroscience opportunities. These results illuminate the conduction and gating of pump-like channelrhodopsins and point the way toward further structure-guided creation of channelrhodopsins for applications across biology.

    View details for DOI 10.1016/j.cell.2022.01.007

    View details for PubMedID 35114111

  • Dendritic calcium signals in rhesus macaque motor cortex drive an optical brain-computer interface. Nature communications Trautmann, E. M., O'Shea, D. J., Sun, X., Marshel, J. H., Crow, A., Hsueh, B., Vesuna, S., Cofer, L., Bohner, G., Allen, W., Kauvar, I., Quirin, S., MacDougall, M., Chen, Y., Whitmire, M. P., Ramakrishnan, C., Sahani, M., Seidemann, E., Ryu, S. I., Deisseroth, K., Shenoy, K. V. 2021; 12 (1): 3689


    Calcium imaging is a powerful tool for recording from large populations of neurons in vivo. Imaging in rhesus macaque motor cortex can enable the discovery of fundamental principles of motor cortical function and can inform the design of next generation brain-computer interfaces (BCIs). Surface two-photon imaging, however, cannot presently access somatic calcium signals of neurons from all layers of macaque motor cortex due to photon scattering. Here, we demonstrate an implant and imaging system capable of chronic, motion-stabilized two-photon imaging of neuronal calcium signals from macaques engaged in a motor task. By imaging apical dendrites, we achieved optical access to large populations of deep and superficial cortical neurons across dorsal premotor (PMd) and gyral primary motor (M1) cortices. Dendritic signals from individual neurons displayed tuning for different directions of arm movement. Combining several technical advances, we developed an optical BCI (oBCI) driven by these dendritic signalswhich successfully decoded movement direction online. By fusing two-photon functional imaging with CLARITY volumetric imaging, we verified that many imaged dendrites which contributed to oBCI decoding originated from layer 5 output neurons, including a putative Betz cell. This approach establishes newopportunities for studying motor control and designing BCIsvia two photon imaging.

    View details for DOI 10.1038/s41467-021-23884-5

    View details for PubMedID 34140486

  • Optical Interrogation of Memory Related Activity Across the Rodent Default Mode Network Shilyansky, C., Young, N., Ramakrishnan, C., Quirin, S., Deisseroth, K. ELSEVIER SCIENCE INC. 2020: S207
  • Rational Engineering of XCaMPs, a Multicolor GECI Suite for In Vivo Imaging of Complex Brain Circuit Dynamics CELL Inoue, M., Takeuchi, A., Manita, S., Horigane, S., Sakamoto, M., Kawakami, R., Yamaguchi, K., Otomo, K., Yokoyama, H., Kim, R., Yokoyama, T., Takemoto-Kimura, S., Abe, M., Okamura, M., Kondo, Y., Quirin, S., Ramakrishnan, C., Imamura, T., Sakimura, K., Nemoto, T., Kano, M., Fujii, H., Deisseroth, K., Kitamura, K., Bito, H. 2019; 177 (5): 1346-+
  • Interacting neural ensembles in orbitofrontal cortex for social and feeding behaviour NATURE Jennings, J. H., Kim, C. K., Marshel, J. H., Raffiee, M., Ye, L., Quirin, S., Pak, S., Ramakrishnan, C., Deisseroth, K. 2019; 565 (7741): 645-+
  • Cortical layer-specific critical dynamics triggering perception. Science (New York, N.Y.) Marshel, J. H., Kim, Y. S., Machado, T. A., Quirin, S. n., Benson, B. n., Kadmon, J. n., Raja, C. n., Chibukhchyan, A. n., Ramakrishnan, C. n., Inoue, M. n., Shane, J. C., McKnight, D. J., Yoshizawa, S. n., Kato, H. E., Ganguli, S. n., Deisseroth, K. n. 2019


    Perceptual experiences may arise from neuronal activity patterns in mammalian neocortex. We probed mouse neocortex during visual discrimination using a red-shifted channelrhodopsin (ChRmine, discovered through structure-guided genome mining) alongside multiplexed multiphoton-holography (MultiSLM), achieving control of individually-specified neurons spanning large cortical volumes with millisecond precision. Stimulating a critical number of stimulus-orientation-selective neurons drove widespread recruitment of functionally-related neurons, a process enhanced by (but not requiring) orientation-discrimination task learning. Optogenetic targeting of orientation-selective ensembles elicited correct behavioral discrimination. Cortical layer specific-dynamics were apparent, as emergent neuronal activity asymmetrically propagated from layer-2/3 to layer-5, and smaller layer-5 ensembles were as effective as larger layer-2/3 ensembles in eliciting orientation discrimination behavior. Population dynamics emerging after optogenetic stimulation both correctly predicted behavior and resembled natural neural representations of visual stimuli.

    View details for DOI 10.1126/science.aaw5202

    View details for PubMedID 31320556

  • Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy OPTICS LETTERS Quirin, S., Vladimirov, N., Yang, C., Peterka, D. S., Yuste, R., Ahrens, M. B. 2016; 41 (5): 855-858


    Increasing the volumetric imaging speed of light-sheet microscopy will improve its ability to detect fast changes in neural activity. Here, a system is introduced for brain-wide imaging of neural activity in the larval zebrafish by coupling structured illumination with cubic phase extended depth-of-field (EDoF) pupil encoding. This microscope enables faster light-sheet imaging and facilitates arbitrary plane scanning-removing constraints on acquisition speed, alignment tolerances, and physical motion near the sample. The usefulness of this method is demonstrated by performing multi-plane calcium imaging in the fish brain with a 416×832×160  μm field of view at 33 Hz. The optomotor response behavior of the zebrafish is monitored at high speeds, and time-locked correlations of neuronal activity are resolved across its brain.

    View details for DOI 10.1364/OL.41.000855

    View details for Web of Science ID 000371029100003

    View details for PubMedID 26974063

    View details for PubMedCentralID PMC4894304

  • Simultaneous imaging of neural activity in three dimensions FRONTIERS IN NEURAL CIRCUITS Quirin, S., Jackson, J., Peterka, D. S., Yuste, R. 2014; 8: 29


    We introduce a scanless optical method to image neuronal activity in three dimensions simultaneously. Using a spatial light modulator and a custom-designed phase mask, we illuminate and collect light simultaneously from different focal planes and perform calcium imaging of neuronal activity in vitro and in vivo. This method, combining structured illumination with volume projection imaging, could be used as a technological platform for brain activity mapping.

    View details for DOI 10.3389/fncir.2014.00029

    View details for Web of Science ID 000333832600001

    View details for PubMedID 24772066

    View details for PubMedCentralID PMC3982072

  • Instantaneous three-dimensional sensing using spatial light modulator illumination with extended depth of field imaging OPTICS EXPRESS Quirin, S., Peterka, D. S., Yuste, R. 2013; 21 (13): 16007-16021


    Imaging three-dimensional structures represents a major challenge for conventional microscopies. Here we describe a Spatial Light Modulator (SLM) microscope that can simultaneously address and image multiple targets in three dimensions. A wavefront coding element and computational image processing enables extended depth-of-field imaging. High-resolution, multi-site three-dimensional targeting and sensing is demonstrated in both transparent and scattering media over a depth range of 300-1,000 microns.

    View details for DOI 10.1364/OE.21.016007

    View details for Web of Science ID 000321288400109

    View details for PubMedID 23842387

    View details for PubMedCentralID PMC3971059

  • Quantitative Multicolor Subdiffraction Imaging of Bacterial Protein Ultrastructures in Three Dimensions NANO LETTERS Gahlmann, A., Ptacin, J. L., Grover, G., Quirin, S., von Diezmann, A. R., Lee, M. K., Backlund, M. P., Shapiro, L., Piestun, R., Moerner, W. E. 2013; 13 (3): 987-993


    We demonstrate quantitative multicolor three-dimensional (3D) subdiffraction imaging of the structural arrangement of fluorescent protein fusions in living Caulobacter crescentus bacteria. Given single-molecule localization precisions of 20-40 nm, a flexible locally weighted image registration algorithm is critical to accurately combine the super-resolution data with <10 nm error. Surface-relief dielectric phase masks implement a double-helix response at two wavelengths to distinguish two different fluorescent labels and to quantitatively and precisely localize them relative to each other in 3D.

    View details for DOI 10.1021/nl304071h

    View details for Web of Science ID 000316243800020

    View details for PubMedID 23414562

    View details for PubMedCentralID PMC3599789

  • Depth estimation and image recovery using broadband, incoherent illumination with engineered point spread functions APPLIED OPTICS Quirin, S., Piestun, R. 2013; 52 (1): A367-A376


    The use of complementary engineered point spread functions is proposed for the joint tasks of depth estimation and image recovery over an extended depth of field. A digital imaging system with a dynamically adjustable pupil is demonstrated experimentally. The implementation of a broadband, passive camera is demonstrated with a fractional ranging error of 4/10(4) at a working distance of 1 m. Once the depth and brightness information of a scene are obtained, a synthetic camera is defined and images rendered computationally to emphasize particular features such as image focusing at different depths.

    View details for DOI 10.1364/AO.52.00A367

    View details for Web of Science ID 000313745800041

    View details for PubMedID 23292415

  • Limits of 3D dipole localization and orientation estimation for single-molecule imaging: towards Green's tensor engineering OPTICS EXPRESS Agrawal, A., Quirin, S., Grover, G., Piestun, R. 2012; 20 (24): 26667-26680


    The 3D orientation and location of individual molecules is an important marker for the local environment and the state of a molecule. Therefore dipole localization and orientation estimation is important for biological sensing and imaging. Precise dipole localization is also critical for superresolution imaging. We propose and analyze wide field microscope configurations to simultaneously measure these parameters for multiple fixed dipole emitters. Examination of the images of radiating dipoles reveals how information transfer and precise detection can be improved. We use an information theoretic analysis to quantify the performance limits of position and orientation estimation through comparison of the Cramer-Rao lower bounds in a photon limited environment. We show that bi-focal and double-helix polarization-sensitive systems are attractive candidates for simultaneously estimating the 3D dipole location and orientation.

    View details for DOI 10.1364/OE.20.026667

    View details for Web of Science ID 000312452800055

    View details for PubMedID 23187520

  • Super-resolution photon-efficient imaging by nanometric double-helix point spread function localization of emitters (SPINDLE) OPTICS EXPRESS Grover, G., DeLuca, K., Quirin, S., DeLuca, J., Piestun, R. 2012; 20 (24): 26681-26695


    Super-resolution imaging with photo-activatable or photo-switchable probes is a promising tool in biological applications to reveal previously unresolved intra-cellular details with visible light. This field benefits from developments in the areas of molecular probes, optical systems, and computational post-processing of the data. The joint design of optics and reconstruction processes using double-helix point spread functions (DH-PSF) provides high resolution three-dimensional (3D) imaging over a long depth-of-field. We demonstrate for the first time a method integrating a Fisher information efficient DH-PSF design, a surface relief optical phase mask, and an optimal 3D localization estimator. 3D super-resolution imaging using photo-switchable dyes reveals the 3D microtubule network in mammalian cells with localization precision approaching the information theoretical limit over a depth of 1.2 µm.

    View details for DOI 10.1364/OE.20.026681

    View details for Web of Science ID 000312452800056

    View details for PubMedID 23187521

    View details for PubMedCentralID PMC3971058

  • Optimal 3D single-molecule localization for superresolution microscopy with aberrations and engineered point spread functions PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA Quirin, S., Pavani, S., Piestun, R. 2012; 109 (3): 675-679


    Photo-activation localization microscopy is a far-field superresolution imaging technique based on the localization of single molecules with subdiffraction limit precision. Known under acronyms such as PALM (photo-activated localization microscopy) or STORM (stochastic optical reconstruction microscopy), these techniques achieve superresolution by allowing only a sparse, random set of molecules to emit light at any given time and subsequently localizing each molecule with great precision. Recently, such techniques have been extended to three dimensions, opening up unprecedented possibilities to explore the structure and function of cells. Interestingly, proper engineering of the three-dimensional (3D) point spread function (PSF) through additional optics has been demonstrated to theoretically improve 3D position estimation and ultimately resolution. In this paper, an optimal 3D single-molecule localization estimator is presented in a general framework for noisy, aberrated and/or engineered PSF imaging. To find the position of each molecule, a phase-retrieval enabled maximum-likelihood estimator is implemented. This estimator is shown to be efficient, meaning it reaches the fundamental Cramer-Rao lower bound of x, y, and z localization precision. Experimental application of the phase-retrieval enabled maximum-likelihood estimator using a particular engineered PSF microscope demonstrates unmatched low-photon-count 3D wide-field single-molecule localization performance.

    View details for DOI 10.1073/pnas.1109011108

    View details for Web of Science ID 000299154000013

    View details for PubMedID 22210112

    View details for PubMedCentralID PMC3271897

  • Photon efficient double-helix PSF microscopy with application to 3D photo-activation localization imaging BIOMEDICAL OPTICS EXPRESS Grover, G., Quirin, S., Fiedler, C., Piestun, R. 2011; 2 (11): 3010-3020


    We present a double-helix point spread function (DH-PSF) based three-dimensional (3D) microscope with efficient photon collection using a phase mask fabricated by gray-level lithography. The system using the phase mask more than doubles the efficiency of current liquid crystal spatial light modulator implementations. We demonstrate the phase mask DH-PSF microscope for 3D photo-activation localization microscopy (PM-DH-PALM) over an extended axial range.

    View details for DOI 10.1364/BOE.2.003010

    View details for Web of Science ID 000299883500008

    View details for PubMedID 22076263

    View details for PubMedCentralID PMC3207371