• Bowen Tan, Tobias Nöbauer, Caleb J. Browne, Eric J. Nestler, Alipasha Vaziri, and Jeffrey M. Friedman
    Dynamic Processing of Hunger and Thirst by Common Mesolimbic Neural Ensembles
    PNAS 119 (43) e2211688119 (2022) (Download)                      
  • Ahmed Abdelfattah, Sapna Ahuja, Taner Akkin, Srinivasa Rao Allu, David Boas, Joshua Brake, Erin Buckley, Robert Campbell, Anderson Chen,et. al.
    Neurophotonic tools for microscopic measurements and manipulation: status report
    Neurophoton. 9 (S1), 013001 (2022). (Download)


  • Jeffrey Demas, Jason Manley, Frank Tejera, Kevin Barber, Hyewon Kim, Francisca Martínez Traub, Brandon Chen, and Alipasha Vaziri
    High-Speed, Cortex-Wide Volumetric Recording of Neuroactivity at Cellular Resolution using Light Beads Microscopy
    Nature Methods 18, 1103-1111 (2021). (Download)
  • Robert G. Alexander, Ronald J. Mintz, Paul J. Custodio, Stephen L. Macknik, Alipasha Vaziri, Ashwin Venkatakrishnan, Sofya Gindina, and Susana Martinez-Conde
    Gaze mechanisms enabling the detection of faint stars in the night sky
    European Journal of Neuroscience 54, 5357-5367 (2021). (Download)

  • Jeffrey Demas, Jason Manley, Frank Tejera, Hyewon Kim, Francisca Martínez Traub, Brandon Chen, Alipasha Vaziri
    High-Speed, Cortex-Wide Volumetric Recording of Neuroactivity at Cellular Resolution using Light Beads Microscopy
    BioRxiv (2021), (Download


  • Qian Lin, Jason Manley, Magdalena Helmreich, Friederike Schlumm, Jennifer M. Li, Drew N. Robson, Florian Engert, Alexander Schier, Tobias Nöbauer, and Alipasha Vaziri
    Cerebellar Neurodynamics Predict Decision Timing and Outcome on the Single-Trial Level.
    Cell 180, 1-16 (2020). (Download)
  • Tobias Nöbauer and Alipasha 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)


  • Qian Lin, Magdalena Helmreich, Friederike Schlumm, Jennifer Li, Drew Robson, Florian Engert, Alexander Schier, Tobias Nöbauer, and Alipasha Vaziri
    Cerebellar Neurodynamics during Motor Planning Predict Decision Timing and Outcome on Single-Trial Level
    BioRxiv, (Download
  • Siegfried Weisenburger, Frank Tejera, Jeffrey Demas, Brandon Chen, Jason Manley, Fraser T. Sparks, Francisca Martínez Traub, Tanya Daigle, Hongkui Zeng, Attila Losonczy, and Alipasha 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


  • Oliver Skocek, Tobias Nöbauer, Lukas Weilguny, Francisca Martínez Traub, Chuying Naomi Xia, Maxim I. Molodtsov, Abhinav Grama, Masahito Yamagata, Daniel Aharoni, David D. Cox, Peyman Golshani, and Alipasha Vaziri
    High-speed volumetric imaging of neuronal activity in freely moving rodents
    Nature Methods 15, 429–432 (2018). (Download)
  • Siegfried Weisenburger and Alipasha 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)
  • Michael A. Taylor, Tobias Nöbauer, Alejandro Pernia-Andrade, Friederike Schlumm, and Alipasha Vaziri
    Brain-wide 3D light-field imaging of neuronal activity with speckle-enhanced resolution
    Optica 5, 345-353 (2018). (Download, Open Access)


  • Tobias Nöbauer, Oliver Skocek, Alejandro J Pernía-Andrade, Lukas Weilguny, Francisca Martínez Traub, Maxim I Molodtsov, and Alipasha Vaziri
    Video rate volumetric Ca2+ imaging across cortex using seeded iterative demixing (SID) microscopy
    Nature Methods 14, 811-818 (2017). (Download | bioRxiv preprint)
  • Siegfried Weisenburger*, Robert Prevedel* and Alipasha Vaziri
    Quantitative evaluation of two-photon calcium imaging modalities for high-speed volumetric calcium imaging in scattering brain tissue
    Submitted (2017). (bioRxiv preprint)


  • Iain F. Davidson, Daniela Goetz, Maciej P. Zaczek, Maxim I. Molodtsov, Pim J. Huis in’t Veld, Florian Weissmann, Gabriele Litos, David A. Cisneros, Maria Ocampo‐Hafalla, Rene Ladurner, Frank Uhlmann, Alipasha Vaziri, and Jan‐Michael Peters
    Rapid movement and transcriptional re‐localization of human cohesin on DNA
    The EMBO Journal 35, 2671-2685 (2016). (Download, Open Access)
  • Robert Prevedel, Aart J Verhoef, Alejandro J Pernía-Andrade*, Siegfried Weisenburger*, Ben S Huang, Tobias Nöbauer, Alma Fernández, Jeroen E Delcour, Peyman Golshani, Andrius Baltuska, and Alipasha Vaziri
    Fast volumetric calcium imaging across multiple cortical layers using sculpted light
    Nature Methods 13, 1021-1028 (2016). (Download | PMC Full text)
  • Maxim I. Molodtsov, Christine Mieck, Jeroen Dobbelaere, Alexander Dammermann, Stefan Westermann and Alipasha Vaziri
    A force-induced directional switch of a molecular motor enables parallel microtubule bundle formation
    Cell 176:2, 539 (2016). (Download, Open Access)
  • Jonathan N. Tinsley, Maxim I. Molodtsov, Robert Prevedel, David Wartmann, Jofre Espigulé-Pons, Mattias Lauwers, and Alipasha Vaziri
    Direct Detection of a Single Photon by Humans
    Nature Communications 7, 12172 (2016). (Download, Open Access)


  • 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)
  • Paul Stevenson, Christoph Götz, Carlos R. Baiz, Jasper Akerboom, Andrei Tokmakoff, and Alipasha Vaziri
    Visualizing KcsA Conformational Changes upon Ion Binding by Infrared Spectroscopy and Atomistic Modeling
    J. Phys. Chem. B 119 (18), 5824–5831 (2015). (Download)
  • Ugur Sezer, Lisa Wörner, Johannes Horak, Lukas Felix, Jens Tüxen, Christoph Götz, Alipasha Vaziri, Marcel Mayor, and Markus Arndt
    Laser-induced acoustic desorption of natural and functionalized biochromophores
    Anal. Chem., 87 (11), 5614-5619 (2015). (Download)
  • Tobias Nöbauer, Robert Prevedel, Friederike Schlumm, Maximilian Hoffmann, Maxim Molodtsov, and Alipasha 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. 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)


  • Jofre Espigulé-Pons, Christoph Goetz, Alipasha Vaziri, and Markus 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


  • 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)


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


  • 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)


  • BK. Andrasfalvy, BV. 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)


  • 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)


  • 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)


  • 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)


  • 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)
  • Kristian Helmerson, Mikkel F. Andersen, Changhyun Ryu, Pierre Cladé, Vasant Natarajan, Alipasha Vaziri, Azure Hansen, and William 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)


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


  • 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)


  • 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)


  • 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)


  • 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)