Publications

2024

  • J. Manley, J. Demas, H. Kim, F. Martínez Traub and A. Vaziri
    Simultaneous, cortex-wide and cellular-resolution neuronal population dynamics reveal an unbounded scaling of dimensionality with neuron number

    BioRxiv (2024). (Download)

2023

  • C. Yu, Y. Yu, L. M. Adsit, J. T. Chang, J. Barchini, A. H. Moberly, H. Benisty, J. Kim, B. K. Young, K. Heng, D. M. Farinella, A. Leikvoll, R. Pavan, R. Vistein, B. R. Nanfito, D. G. C. Hildebrand, S. Otero-Coronel, A. Vaziri, J. L. Goldberg, A. J. Ricci, D. Fitzpatrick, J. A. Cardin, M. Higley, G. B. Smith, P. Kara, K. J. Nielsen, I. T. Smith and S. L. Smith
    The Cousa objective: a long working distance air objective for multiphoton imaging in vivo
    Nature Methods (2023). (Download)
  • C. Yu, Y. Yu, L. M. Adsit, J. T. Chang, J. Barchini, A. H. Moberly, H. Benisty, J. Kim, B. K. Young, K. Heng, D. M. Farinella, A. Leikvoll, R. Pavan, R. Vistein, B. R. Nanfito, D. G. C. Hildebrand, S. Otero-Coronel, A. Vaziri, J. L. Goldberg, A. J. Ricci, D. Fitzpatrick, J. A. Cardin, M. Higley, G. B. Smith, P. Kara, K. J. Nielsen, I. T. Smith and S. L. Smith
    The Cousa objective: a long working distance air objective for multiphoton imaging in vivo
    BioRxiv (2023). (Download)
  • F. Soldevila, C. Moretti, T. Nöbauer, H. Sarafraz, A. Vaziri, and S. Gigan
    Functional imaging through scattering medium via fluorescence speckle demixing and localization
    Optics Express 31 (13), 21107-21117 (2023). (Download)
  • T. Nöbauer*, Y. Zhang*, H. Kim and A. Vaziri
    Mesoscale volumetric light-field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz
    Nature Methods 20, 600-609 (2023). (Download)
  • T. Nöbauer*, Y. Zhang*, H. Kim and A. Vaziri
    Mesoscale volumetric light-field (MesoLF) imaging of neuroactivity across cortical areas at 18 Hz
    BioRxiv (2023). (Download)

2022

  • B. Tan*, T. Nöbauer*, C.J. Browne, E.J. Nestler, A. Vaziri, and J.M. Friedman
    Dynamic Processing of Hunger and Thirst by Common Mesolimbic Neural Ensembles
    PNAS 119 (43), e2211688119 (2022). (Download)   
                     
  • A. Abdelfattah, S. Ahuja, T. Akkin, S.R. Allu, D. Boas, J. Brake, E. Buckley, R. Campbell, A. Vaziri
    Neurophotonic tools for microscopic measurements and manipulation: status report
    Neurophoton. 9 (S1), 013001 (2022). (Download)

2021

  • J. Demas, J. Manley, F. Tejera, K. Barber, H. Kim, F. Martínez Traub, B. Chen, and A. Vaziri
    High-Speed, Cortex-Wide Volumetric Recording of Neuroactivity at Cellular Resolution using Light Beads Microscopy
    Nature Methods 18, 1103-1111 (2021). (Download)

     

  • R.G. Alexander, R.J. Mintz, P.J. Custodio, S.L. Macknik, A. Vaziri, A. Venkatakrishnan, S. Gindina, and S. Martinez-Conde
    Gaze mechanisms enabling the detection of faint stars in the night sky
    European Journal of Neuroscience 54, 5357-5367 (2021). (Download)

     

  • J. Demas, J. Manley, F. Tejera, H. Kim, F. Martínez Traub, B. Chen, A. Vaziri
    High-Speed, Cortex-Wide Volumetric Recording of Neuroactivity at Cellular Resolution using Light Beads Microscopy
    BioRxiv (2021). (Download

2020

  • Q. Lin, J. Manley, M. Helmreich, F. Schlumm, J. M. Li, D. N. Robson, F. Engert, A. Schier, T. Nöbauer, and A. Vaziri
    Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level.
    Cell 180, 1-16 (2020). (Download)
  • T. Nöbauer and A. Vaziri
    Light Field Microscopy for In Vivo Ca2+ Imaging
    Book chapter in: Pavone F.S., Shoham S., editors. Handbook of Neurophotonics. 1st Edition. Boca Raton, FL: CRC Press (2020). p. 81–112. (Download)

2019

  • Q. Lin, M. Helmreich, F. Schlumm, J. Li, D. Robson, F. Engert, A. Schier, T. Nöbauer, and A. Vaziri
    Cerebellar Neurodynamics during Motor Planning Predict Decision Timing and Outcome on Single-Trial Level
    BioRxiv, (Download)
  • S. Weisenburger, F. Tejera, J. Demas, B. Chen, J. Manley, F. T. Sparks, F. Martínez Traub, T. Daigle, H. Zeng, A. Losonczy, and A. Vaziri
    Volumetric Ca2+ Imaging in the Mouse Brain using Hybrid Multiplexed Sculpted Light (HyMS) Microscopy
    Cell 177, 1–17 (2019). (Download)
    Featured as a Nature Methods Research Highlight

2018

  • O. Skocek*, T. Nöbauer*, L. Weilguny, F. Martínez Traub, C. N. Xia, M. I. Molodtsov, A. Grama, M. Yamagata, D. Aharoni, D. D. Cox, P. Golshani, and A. Vaziri
    High-speed volumetric imaging of neuronal activity in freely moving rodents
    Nature Methods 15, 429–432 (2018). (Download)
  • S. Weisenburger and A. Vaziri
    A Guide to Emerging Technologies for Large-Scale and Whole-Brain Optical Imaging of Neuronal Activity
    Annual Review of Neuroscience 41, 431 – 452 (2018). (Download | arXiv preprint)
  • M. A. Taylor, T. Nöbauer, A. Pernia-Andrade, F. Schlumm, and A. Vaziri
    Brain-wide 3D light-field imaging of neuronal activity with speckle-enhanced resolution
    Optica 5, 345-353 (2018). (Download, Open Access)

2017

  • T. Nöbauer*, O. Skocek*, A. J Pernía-Andrade, L. Weilguny, F. Martínez Traub, M. I. Molodtsov, and A. Vaziri
    Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy
    Nature Methods 14, 811-818 (2017). (Download | bioRxiv preprint)
  • S. Weisenburger*, R. Prevedel* and A. Vaziri
    Quantitative evaluation of two-photon calcium imaging modalities for high-speed volumetric calcium imaging in scattering brain tissue
    Submitted (2017). (bioRxiv preprint)

2016

  • I. F. Davidson, D. Goetz, M. P. Zaczek, M. I. Molodtsov, P. J. Huis in’t Veld, F. Weissmann, G. Litos, D. A. Cisneros, M. Ocampo‐Hafalla, R. Ladurner, F. Uhlmann, A. Vaziri, and J‐M. Peters
    Rapid movement and transcriptional re‐localization of human cohesin on DNA
    The EMBO Journal 35, 2671-2685 (2016). (Download, Open Access)
  • R. Prevedel, A. J. Verhoef, A. J. Pernía-Andrade*, S. Weisenburger*, B. S. Huang, T. Nöbauer, A. Fernández, J. E. Delcour, P. Golshani, A. Baltuska, and A. Vaziri
    Fast volumetric calcium imaging across multiple cortical layers using sculpted light
    Nature Methods 13, 1021-1028 (2016). (Download | PMC Full text)
  • M. I. Molodtsov, C. Mieck, J. Dobbelaere, A. Dammermann, S. Westermann and A. Vaziri
    A force-induced directional switch of a molecular motor enables parallel microtubule bundle formation
    Cell 176:2, 539 (2016). (Download, Open Access)
  • J. N. Tinsley, M. I. Molodtsov, R. Prevedel, D. Wartmann, Jofre Espigulé-Pons, M. Lauwers, and A. Vaziri
    Direct Detection of a Single Photon by Humans
    Nature Communications 7, 12172 (2016). (Download, Open Access)

2015

  • Y. Park, H. Wang, T. Nobauer, A. Vaziri, and C. E. Priebe
    Anomaly Detection on Whole-Brain Functional Imaging of Neuronal Activity using Graph Scan Statistics
    ACM Conference on Knowledge Discovery and Data Mining (KDD), Workshop on Outlier Definition, Detection, and Description (ODDx3) (2015). (Download PDF)
  • P. Stevenson, C. Götz, C. R. Baiz, J. Akerboom, A. Tokmakoff, and A. Vaziri
    Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling
    J. Phys. Chem. B 119 (18), 5824–5831 (2015). (Download)
  • U. Sezer, L. Wörner, J. Horak, L. Felix, J. Tüxen, C. Götz, A. Vaziri, M. Mayor, and M. Arndt
    Laser-induced acoustic desorption of natural and functionalized biochromophores
    Anal. Chem., 87 (11), 5614-5619 (2015). (Download)
  • T. Nöbauer, R. Prevedel, F. Schlumm, M. Hoffmann, M. I. Molodtsov, and A. Vaziri
    Whole-brain dynamics of neuronal circuits enabled by sculpted light and light field microscopy
    IEEE/EMBS – Neural Engineering, 869-872 (2015) (Download)
  • C. Mieck, M. I. Molodtsov, K. Drzewicka, B. van der Vaart, G. Litos, G. Schmauss, A. Vaziri, and S. Westermann
    Non-catalytic motor domains enable processive movement and functional diversification of the kinesin-14 Kar3
    eLife 10.7554/eLife.04489 (2015). (Download, Open Access)
  • P. Rupprecht, R. Prevedel, F. Groessl, W. Haubensak, and A. Vaziri
    Optimizing and extending light-sculpting microscopy for fast functional imaging in neuroscience
    Biomedical Optics Express 6:2, 353-368 (2015). (Download) | arXiv preprint)

2014

  • J. Espigulé-Pons, C. Goetz, A. Vaziri, and M. Arndt
    Physical constraints for the Stoneham model for light-dependent magnetoreception
    arXiv:1412.7369 (2014). (Download)
  • P. Stevenson, C. Goetz, C. R. Baiz, A. Vaziri, and A. Tokmakoff
    2D IR as an Experimental Probe of Ion-Induced Structural Changes in KcsA
    Biophysical Journal 106:2, 539A (2014). (Download)
  • R. Prevedel*, Y. Yoon*, M. Hoffmann, N. Pak, G. Wetzstein, S.Kato, T. Schrödel, R. Raskar, M. Zimmer, E. Boyden and A. Vaziri
    Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy
    Nature Methods 11, 727–730 (2014). (Download | arXiv preprint)
    Nature Methods cover

2013

  • T. Schrödel*, R. Prevedel*, K. Aumayr, M. Zimmer, and A. Vaziri
    Brain-wide 3D imaging of neuronal activity Caenorhabditis elegans with sculpted light
    Nature Methods 10, 1013-1020 (2013). (Download | arXiv preprint)
  • A. Tedeschi, G. Wutz, S. Huet, M. Jaritz, A.  Wuensche, E.Schirghuber, I.Finley Davidson, W. Tang, D. Cisneros, V. Bhaskara, T. Nishiyama, A. Vaziri, A. Wutz, J. Ellenberg, and J. Peters
    Wapl is an essential regulator of chromatin structure and chromosome segregation
    Nature 501, 564-568 (2013). (Download)

2012

  • A. Vaziri and V. Emiliani
    Reshaping the Optical dimension in optogenetics
    Current Opinion in Neurobiology 22, 128-137 (Download)

2011

  • Z. Ganim, A. Tokmakoff, and A. Vaziri
    Vibrational excitons in ionophores Experimental  probes for quantum coherence-assisted ion transport and selectivity in ion channels
    New J. Phys. 31, 113030 (2011). (Download)
  • York, AG., Ghitani, A., Vaziri, A., Davidson, MW., and Shroff, H.
    Confined activation and subdiffractive localization enables whole-cell PALM with genetically expressed probes
    Nature Methods 8, 327-333 (2011). (Download)

2010

  • B. K. Andrasfalvy, B. V. Zemelman, J. Tang, and A. Vaziri,
    Two-photon single-cell optogenetic control of neuronal activity by sculpted light
    Proc. Natl. Acad. Sci. USA 107(26), 11981-11986 (2010). (Download)
  • Losonczy, A., Zemelman, BV., Vaziri, A., and Magee, JC.
    Network mechanisms of theta related neuronal activity in hippocampal CA1 pyramidal neurons
    Nature Neuroscience 13(8), 967-972 (2010). (Download)
  • Tang, J., Akerboom, J., Vaziri, A., Looger, LL., and Shank, CV.
    Near-isotropic 3D optical nanoscopy with photon-limited chromophores
    Proc. Natl. Acad. Sci. USA 107(22), 10068-10073 (2010). (Download)
  • Vaziri, A. and Plenio, M.
    Quantum coherence in ion channels: resonances, transport and verification
    New Journal of Physics 12, 085001 (2010). (Download)
  • Vaziri, A. and Shank, CV.
    Ultrafast widefield optical sectioning microscopy by multifocal temporal focusing
    Opt Express. 18(19), 19645-19655 (2010). (Download)

2009

  • K. Helmerson, M. F. Andersen, P. Cladé, V. Natarajan, W. D. Phillips, A. Ramanathan, C. Ryu, and A. Vaziri
    Vortices and Persistent Currents: Rotating a Bose-Einstein Condensate Using Photons with Orbital Angular Momentum
    Topologica 2:1 002 (2009). (Download)

2008

  • Vaziri, A., Tang, J., Shroff, H., and Shank, CV.
    Multilayer three-dimensional super resolution imaging of thick biological samples
    Proc. Natl. Acad. Sci. USA 105(51), 20221-20226 (2008). (Download)

2007

  • K. Helmerson, M. F. Andersen, C. Ryu, V. Nararajan, A. Vaziri, and W. D. Phillips
    Generating Persistent Currents States of Atoms Using Orbital Angular Momentum of Photons
    Nucl. Phys. A 790, 705C-712C (2007). (Download)

2006

  • Andersen, MF., Ryu, C., Cladé, P., Natarajan, V., Vaziri, A., Helmerson, K., and Phillips, WD.
    Quantized rotation of atoms from photons with orbital angular momentum
    Phys Rev Lett. 97(17), 170406 (2006). (Download)
  • K. Helmerson, M. F. Andersen, C. Ryu, P. Cladé, V. Natarajan, A. Vaziri, A. Hansen, and W. D. Phillips
    Rotating a Bose-Einstein condensate using photons with orbital angular momentum
    Proc. SPIE 6326, Optical Trapping and Optical Micromanipulation III, 632603 (2006). (Download)
  • Gröblacher S., Jennewein T., Vaziri A., Weihs G., and Zeilinger A.
    Experimental quantum cryptography with qutrits
    New Journal of Physics 8 75 (2006). (Download)
  • Ryu, C., Andersen, MF., Vaziri, A., d’Arcy, MB., Grossman, JM., Helmerson, K., and Phillips, WD.
    High-order quantum resonances observed in a periodically kicked Bose-Einstein condensate
    Phys Rev Lett. 96(16), 160403 (2006). (Download)

2005

  • Molina-Terriza, G., Vaziri, A., Ursin, R., and Zeilinger, A.
    Experimental quantum coin tossing
    Phys Rev Lett. 94(4), 040501 (2005). (Download)

2004

  • Molina-Terriza, G., Vaziri, A., Rehácek, J., Hradil, Z., and Zeilinger, A.
    Triggered qutrits for quantum communication protocols
    Phys Rev Lett. 92(16), 167903 (2004). (Download)

2003

  • Vaziri, A., Pan, JW., Jennewein, T., Weihs, G., and Zeilinger, A.
    Concentration of higher dimensional entanglement: qutrits of photon orbital angular momentum
    Phys Rev Lett. 91(22), 227902 (2003). (Download)

2002

  • Vaziri A., Weihs G., and Zeilinger A.
    Superpositions of the orbital angular momentum for applications in quantum experiments
    Journal of Optics B: Quantum and Semiclassical Optics 4(2), S1-S5 (2002). (Download)
  • Vaziri, A., Weihs, G., and Zeilinger, A.
    Experimental two-photon, three-dimensional entanglement for quantum communication
    Phys Rev Lett. 89(24), 240401 (2002). (Download)

2001

  • Mair, A., Vaziri, A., Weihs, G., and Zeilinger, A.
    Entanglement of the orbital angular momentum states of photons
    Nature 412(6844), 313-316 (2001). (Download)