microscopy and neuroscience

  1. Multiphoton fluorescence microscopy for in vivo imaging.

    Xu C, Nedergaard M, Fowell DJ, Friedl P, Ji N

    Cell (2024) 187, 4458-4487. Invited Review. https://doi.org/10.1016/j.cell.2024.07.036

  2. A dendritic mechanism for balancing synaptic flexibility and stability.

    Yaeger CE, Vardalaki D, Zhang Q, Pham TLD, Brown NJ, Ji N, Harnett MT

    Cell Reports (2024) 43, 114638. https://doi.org/10.1016/j.celrep.2024.114638

  3. Frequency-multiplexed aberration measurement for confocal microscopy.

    Pan D, Ge X, Liu Y, Ferger L, Shcherbakova D, Isacoff E, Ji N

    Optics Express (2024) 32, 28655-28665. https://doi.org/10.1364/OE.525479

  4. Adaptive optical third-harmonic generation microscopy for in vivo imaging of tissues.

    Rodríguez C, Pan D, Natan R, Mohr M, Miao M, Chen X, Northen T, Vogel J, Ji N

    Biomedical Optics Express (2024) 15, 4513-4524. https://doi.org/10.1364/BOE.527357

    Also see: bioRxiv (2024) 2024.05.02.592275. https://doi.org/10.1101/2024.05.02.592275

  5. Coordinate-based neural representations for computational adaptive optics in widefield microscopy.

    Kang I*, Zhang Q*, Yu SX, Ji N

    Nature Machine Intelligence (2024) 6, 714–725. https://doi.org/10.1038/s42256-024-00853-3

    Also see arXiv (2023) 2307.03812. https://doi.org/10.48550/arXiv.2307.03812

    *Contributed equally and co-correspondence authors

  6. High-throughput volumetric mapping of synaptic transmission.

    Chen W, Ge X, Zhang Q, Natan RG, Fan JL, Scanziani M, Ji N

    Nature Methods (2024) 21, 1298–1305. https://doi.org/10.1038/s41592-024-02309-3 (Link to a view-only version)

  7. Label-free structural imaging of plant roots and microbes using third-harmonic generation microscopy.

    Pan D*, Rivera JA*, Kim P, Miao M, Tyml T, Rodríguez C, Wang B, Yoshikuni Y, Elisabeth NH, Northen T, Vogel JP, Ji N

    bioRxiv (2024) https://doi.org/10.1101/2024.04.13.589377 (*Contributed equally)

  8. Deep-brain optical recording of neural dynamics during behavior.

    Zhou ZC, Gordon-Fennell A, Piantadosi SC, Ji N, Smith SL, Bruchas MR, Stuber GD

    Neuron (2023) 111, 3716. https://doi.org/10.1016/j.neuron.2023.09.006

  9. maskNMF: A denoise-sparsen-detect approach for extracting neural signals from dense imaging data.

    Pasarkar A, Kinsella I, Zhou P, Wu M, Pan D, Fan JL, Wang Z, Abdeladim L, Peterka DS, Adesnik H, Ji N, Paninski L

    bioRxiv (2023) https://doi.org/10.1101/2023.09.14.557777

  10. Stimulus edges induce orientation tuning in superior colliculus.

    Liang Y*, Lu R*, Borges K, Ji N

    Nature Communications (2023) 14, 4756. https://doi.org/10.1038/s41467-023-40444-1 *Contributed equally

  11. A positively tuned voltage indicator for extended electrical recordings in the brain.

    Evans SW, Shi DQ, Chavarha M, Plitt MH, Taxidis J, Madruga B, Fan JL, Hwang FJ, van Keulen SC, Suomivuori CM, Pang MM, Su S, Lee S, Hao YA, Zhang G, Jiang D, Negrean A, Losonczy A, Makinson CD, Wang S, Clandini TR, Dror RO, Ding JB, Ji N, Golshani P, Giocomo LM, Bi GQ, Lin MZ

    Nat Methods (2023) 20, 1104–1113. https://doi.org/10.1038/s41592-023-01913-z

  12. Adaptive optical two-photon fluorescence microscopy probes cellular organization of ocular lenses in vivo.

    Paidi SK, Zhang Q, Yang Y, Xia CH, Ji N, Gong X

    Investigative Ophthalmology & Visual Science (2023) 64, 20. https://doi.org/10.1167/iovs.64.7.20

    Also see bioRxiv (2023) 524320; https://doi.org/10.1101/2023.01.17.524320

  13. The mitochondrial unfolded protein response regulates hippocampal neural stem cell aging.

    Wang CL, Ohkubo R, Mu WC, Chen W, Fan JL, Song Z, Maruichi A, Sudmant PH, Pisco AO, Dubal DB, Ji N, Chen D

    Cell Metabolism (2023) 23, 00139-0. https://doi.org/10.1016/j.cmet.2023.04.012

  14. Adaptive optics for optical microscopy.

    Zhang Q, Hu Q, Berlage C, Kner P, Judkewitz B, Booth M, Ji N

    Biomedical Optics Express (2023) 14, 1732-1756. Invited Review. https://doi.org/10.1364/BOE.479886

  15. Retinal microvascular and neuronal pathologies probed in vivo by adaptive optical two-photon fluorescence microscopy.

    Zhang Q, Yang Y, Cao KJ, Chen W, Paidi S, Xia CH, Kramer RH, Gong X, Ji N

    Elife (2023) 12, e84853. https://doi.org/10.7554/eLife.84853

  16. High-Speed Neural Imaging with Synaptic Resolution: Bessel Focus Scanning Two-Photon Microscopy and Optical-Sectioning Widefield Microscopy.

    Meng G, Zhang Q, Ji N

    Chapter 10. In: Papagiakoumou E, editor. All-Optical Methods to Study Neuronal Function. New York: Humana; (2023).

  17. Ultrafast two-photon fluorescence imaging of cerebral blood circulation in the mouse brain in vivo.

    Meng G, Zhong J, Zhang Q, Wong JSJ, Wu J, Tsia KK, Ji N.

    Proceedings of the National Academy of Sciences of the United States of America (2022) 119, e2117346119. https://doi.org/10.1073/pnas.2117346119

    Also see a great commentary by Bruno Weber and Franca Schmid on our paper!

  18. Neurophotonic tools for microscopic measurements and manipulation: status report.

    Abdelfattah AS, et al.

    Neurophotonics (2022) 9, 013001. https://doi.org/10.1117/1.NPh.9.S1.013001

  19. Roadmap on wavefront shaping and deep imaging in complex media.

    Gigan S, et al.

    Journal of Physics: Photonics (2022) 4, 042501. https://doi.org/10.1088/2515-7647/ac76f9

  20. Speed scaling in multiphoton fluorescence microscopy.

    Wu J, Ji N, Tsia KK

    Nature Photonics (2021) 15, 800–812. https://doi.org/10.1038/s41566-021-00881-0

  21. Adaptive optics for high-resolution imaging.

    Hampson KM, Turcotte R, Miller DT, Kurokawa K, Males JR, Ji N, Booth MJ

    Nature Review Methods Primers (2021) 1, 68. https://doi.org/10.1038/s43586-021-00066-7

  22. In vivo volumetric imaging of calcium and glutamate activity at synapses with high spatiotemporal resolution.

    Chen W, Natan RG, Yang Y, Chou SW, Zhang Q, Isacoff EY, Ji N

    Nature Communications (2021) 12, 6630. https://doi.org/10.1038/s41467-021-26965-7

  23. An adaptive optics module for deep tissue multiphoton imaging in vivo.

    Rodríguez C, Chen A, Rivera JA, Mohr MA, Liang Y, Natan RG, Sun W, Milkie DE, Bifano TG, Chen X, Ji N

    Nature Methods (2021)18, 1259-1264. https://doi.org/10.1038/s41592-021-01279-0

  24. High-speed laser-scanning biological microscopy using FACED.

    Lai QTK, Yip GGK, Wu J, Wong JSJ, Lo MCK, Lee KCM, Le TTHD, So HKH, Ji N, Tsai KK

    Nature Protocols (2021) 16, 4227–4264. https://doi.org/10.1038/s41596-021-00576-4

  25. One wavelength to excite them all: deep tissue imaging going multicolor.

    Rodríguez C, Ji N

    Trends in Neurosciences (2021) 44, 689-691. https://doi.org/10.1016/j.tins.2021.07.001

  26. A distinct population of L6 neurons in mouse V1 mediate cross-1 callosal communication.

    Liang Y, Fan JL, Sun W, Lu R, Chen M, Ji N

    Cerebral Cortex (2021) 31, 4259–4273. https://doi.org/10.1093/cercor/bhab084

  27. Adaptive optics enables aberration-free single-objective remote focusing for two-photon fluorescence microscopy.

    Yang Y, Chen W, Fan JL, Ji N

    Biomedical Optics Express (2021) 12, 354-366. https://doi.org/10.1364/BOE.413049

  28. Bright near-infrared genetically encoded calcium indicator for in vivo imaging.

    Shemetov AA*, Monakhov MV*, Zhang Q, Canton-Josh JE, Kumar M, Chen M, Matlashov MM, Li X, Yang W, Nie L, Shcherbakova DM, Kozorovitskiy Y, Yao J, Ji N, Verkhusha VV

    Nature Biotechnology (2021) 39, 368–377. https://doi.org/10.1038/s41587-020-0710-1 (*Contributed equally)

  29. An adaptive optics module for deep tissue multiphoton imaging in vivo.

    Rodríguez C, Chen A, Rivera JA, Mohr MA, Liang Y, Sun W, Milkie DE, Bifano TG, Chen X, Ji N

    BioRxiv (2020) https://doi.org/10.1101/2020.11.25.397968

  30. High-speed volumetric two-photon fluorescence imaging of neurovascular dynamics.

    Fan JL, Rivera JA, Sun W, Peterson J, Haeberle H, Rubin S, Ji N

    Nature Communications (2020) 11, 6020. https://doi.org/10.1038/s41467-020-19851-1

  31. High-resolution in vivo optical-sectioning widefield microendoscopy.

    Zhang Q, Pan D, Ji N

    Optica (2020) 7, 1287-1290. https://doi.org/10.1364/OPTICA.397788

  32. Practical sensorless aberration estimation for 3D microscopy with deep learning.

    Saha D, Schmidt U, Zhang Q, Barbotin A, Hu Q, Ji N, Booth M, Weigert M, Myers EW

    Optics Express (2020) 28, 29044-29053. https://doi.org/10.1364/OE.401933

  33. Fast widefield imaging of neuronal structure and function with optical sectioning in vivo.
    Li Z*, Zhang Q*, Chou S-W, Newman Z, Turcotte R, Natan R, Dai Q, Isacoff EY, Ji N

    Science Advances (2020) 6, eaaz3870. https://doi.org/10.1126/sciadv.aaz3870 (*Contributed equally)

  34. Kilohertz two-photon fluorescence microscopy imaging of neural activity in vivo.
    Wu J, Liang Y, Chen S, Hsu C-L, Chavarha M, Evans SW, Shi D, Lin MZ, Tsia KK, Ji N.

    Nature Methods (2020) 17, 287–290. https://doi.org/10.1038/s41592-020-0762-7

  35. Rapid mesoscale volumetric imaging of neural activity with synaptic resolution.
    Lu R*, Liang Y*, Meng G*, Zhou P, Svoboda K, Paninski L, Ji N

    Nature Methods (2020) 17, 291–294. https://doi.org/10.1038/s41592-020-0760-9 (*Contributed equally)

  36. A distinct population of L6 neurons in mouse V1 mediate cross-callosal communication.
    Liang Y, Sun W, Lu R, Chen M, Ji N
    bioRxiv (2019) https://doi.org/10.1101/778019

  37. Dynamic super-resolution structured illumination imaging in the living brain.
    Turcotte R, Liang Y, Tanimoto M, Zhang Q, Li Z, Koyama M, Betzig E, Ji N
    Proceedings of the National Academy of Sciences of the United States of America (2019) 116, 9586-9591. doi:10.1073/pnas.1819965116

  38. Kilohertz in vivo imaging of neural activity.
    Wu J, Liang Y, Hsu C-L, Chavarha M, Evans S, Shi D, Lin M, Tsia K, Ji N
    bioRxiv (2019) 543058. doi:10.1101/543058

  39. High-throughput synapse-resolving two-photon fluorescence microendoscopy for deep-brain volumetric imaging in vivo.
    Meng G, Liang Y, Sarsfield S, Jiang WC, Lu R, Dudman JT, Aponte Y, Ji N
    Elife (2019) e40805. doi: 10.7554/eLife.40805

  40. Optical alignment device for two-photon microscopy.
    Galiñanes GL, Marchand PJ, Turcotte R, Pellat S, Ji N, Huber D
    Biomedical Optics Express (2018) 9, 3624-3639. doi: 10.1364/BOE.9.003624

  41. In vivo measurement of afferent activity with axon-specific calcium imaging.
    Broussard G, Liang Y, Fridman M, Unger E, Meng G, Xiao X, Ji N, Petreanu L, Tian L
    Nature Neuroscience (2018) 21, 1272-1280. doi: 10.1038/s41593-018-0211-4

  42. 50 Hz volumetric functional imaging with continuously adjustable depth of focus.
    Lu R, Taminoto M, Koyama M, Ji N
    Biomedical Optics Express (2018) 9, 1964-1976. doi: 10.1364/BOE.9.001964 bioRxiv (2017) doi: 10.1101/240069

  43. Adaptive optical microscopy for neurobiology.
    Rodriguez C, Ji N
    Current Opinion in Neurobiology (2018) 6, 83-91. doi: 10.1016/j.conb.2018.01.011

  44. Three-photon fluorescence microscopy with an axially elongated Bessel focus.
    Rodriguez C, Liang Y, Lu R, Ji N
    Optics Letters (2018) 43, 1914-1917. doi: 10.1364/OL.43.001914 bioRxiv (2017) doi: 10.1101/240960

  45. A general method to fine-tune fluorophores for live-cell and in vivo imaging.
    Grimm JB, Muthusamy AK, Liang Y, Brown TA, Lemon WC, Patel R, Lu R, Macklin JJ, Keller PJ, Ji N, Lavis LD
    Nature Methods (2017) 14, 987-994. doi: 10.1038/nmeth.4403

  46. Adaptive optical versus spherical aberration corrections for in vivo brain imaging.
    Turcotte R, Liang Y, Ji N
    Biomedical Optics Express (2017) 8, 3891-3902. doi: 10.1364/BOE.8.003891

  47. Near-infrared fluorescent protein iRFP713 as a reporter protein for optogenetic vectors, a transgenic Cre-reporter rat, and other neuronal studies.
    Richie CT, Whitaker LR, Whitaker KW, Necarsulmer J, Baldwin HA, Zhang Y, Fortuno L, Hinkle JJ, Koivula P, Henderson MJ, Sun W, Wang K, Smith JC, Pickel J, Ji N, Hope BT, Harvey BK
    Journal of Neuroscience Methods (2017) 284, 1-14. doi: 10.1016/j.jneumeth.2017.03.020

  48. Adaptive optical fluorescence microscopy.
    Ji N
    Nature Methods (2017) 14, 374-380. doi:10.1038/nmeth.4218

  49. Video-rate volumetric functional imaging of the brain at synaptic resolution.
    Lu R, Sun W, Liang Y, Kerlin A, Bierfeld J, Seelig J, Wilson DE, Scholl B, Mohar B, Tanimoto M, Koyama M, Fitzpatrick D, Orger MB, Ji N
    Nature Neuroscience (2017) 20, 620-628. doi:10.1038/nn.4516 http://biorxiv.org/content/biorxiv/early/2016/06/12/058495.full.pdf

  50. Opportunities for Technology and Tool Development.
    Neuron (2016) 92, 564-566. (Voices) doi: 10.1016/j.neuron.2016.10.042

  51. Technologies for imaging neural activity in large volumes.
    Ji N, Freeman J, Smith SL
    Nature Neuroscience (2016) 19, 1154-64. doi: 10.1038/nn.4358

  52. Thalamus provides layer 4 of primary visual cortex with orientation- and direction-tuned inputs.
    Sun W, Tan Z, Mensh BD, Ji N
    Nature Neuroscience (2016) 19, 308–315. doi: 10.1038/nn.4196

  53. Minimally invasive microendoscopy system for in vivo functional imaging of deep nuclei in the mouse brain.
    Bocarsly ME, Jiang W, Wang C, Dudman JT, Ji N, Aponte Y
    Biomedical Optics Express (2015) 6, 4546-56. doi: 10.1364/BOE.6.004546

  54. Neuronal Representation of Ultraviolet Visual Stimuli in Mouse Primary Visual Cortex.
    Tan Z, Sun W, Chen T, Kim D, Ji N
    Scientific Reports (2015) 5, 12597. doi: 10.1038/srep12597

  55. Direct wavefront sensing for high-resolution in vivo imaging in scattering tissue.
    Wang K, Sun W, Richie CT, Harvey BK, Betzig E, Ji N
    Nature Communications (2015) 6, 7276. doi: 10.1038/ncomms8276

  56. Label-free spectroscopic detection of membrane potential using stimulated Raman scattering.
    Liu B, Lee HJ, Zhang D, Liao C, Ji N, Xia Y, Cheng J
    Applied Physics Letters (2015) 106, 173704. doi: 10.1063/1.4919104

  57. The Practical and Fundamental Limits of Optical Imaging in Mammalian Brains.
    Ji N
    Neuron (2014) 83, 1242-1245. doi: 10.1016/j.neuron.2014.08.009

  58. Multiplexed aberration measurement for deep tissue imaging in vivo.
    Wang C, Liu R, Milkie DE, Sun W, Tan Z, Kerlin A, Chen T, Kim DS, Ji N
    Nature Methods (2014) 11, 1037–1040. doi: 10.1038/nmeth.3068

  59. Direct phase measurement in zonal wavefront reconstruction using multidither coherent optical adaptive technique.
    Liu R, Milkie DE, Kerlin A, Maclennan B, Ji N
    Optics Express (2014) 22, 1619-1628. doi: 10.1364/OE.22.001619

  60. Characterization and improvement of three-dimensional imaging performance of GRIN-lens-based two-photon fluorescence endomicroscopes with adaptive optics.
    Wang C, Ji N
    Optics Express (2013) 21, 27142-54. doi: 10.1364/OE.21.027142

  61. Pupil-segmentation-based adaptive optical correction of a high-numerical-aperture gradient refractive index lens for two-photon fluorescence endoscopy.
    Wang C, Ji N
    Optics Letters (2012) 37, 2001-3. doi: 10.1364/OL.37.002001

  62. Characterization and adaptive optical correction of aberrations during in vivo imaging in the mouse cortex.
    Ji N, Sato TR, Betzig E
    Proceedings of the National Academy of Sciences of the United States of America (2012) 109, 22-7. doi: 10.1073/pnas.1109202108

  63. Pupil-segmentation-based adaptive optical microscopy with full-pupil illumination.
    Milkie DE, Betzig E, Ji N
    Optics Letters (2011) 36, 4206-8. doi: 10.1364/OL.36.004206

  64. Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues.
    Ji N, Milkie DE, Betzig E
    Nature Methods (2010) 7, 141-7. doi: 10.1038/nmeth.1411

  65. Advances in the speed and resolution of light microscopy.
    Ji N, Shroff H, Zhong H, Betzig E
    Current Opinion in Neurobiology (2008) 18, 605-16. doi: 10.1016/j.conb.2009.03.009

  66. High-speed, low-photodamage nonlinear imaging using passive pulse splitters.
    Ji N, Magee JC, Betzig E
    Nature Methods (2008) 5, 197-202. doi: 10.1038/nmeth.1175

chemical physics & nonlinear optics

  1. Interfacial Structures of Acidic and Basic Aqueous Solutions.
    Tian C, Ji N, Waychunas GA, Shen YR
    Journal of the American Chemical Society (2008) 130, 13033-13039. https://doi.org/10.1021/ja8021297

  2. Characterization of vibrational resonances of water-vapor interfaces by phase-sensitive sum-frequency spectroscopy.
    Ji N, Ostroverkhov V, Tian CS, Shen YR
    Physical Review Letters (2008) 096102. https://doi.org/10.1103/PhysRevLett.100.096102

  3. Phase-sensitive sum-frequency vibrational spectroscopy and its application to studies of interfacial alkyl chains.
    Ji N, Ostroverkhov V, Chen CY, Shen YR
    Journal of the American Chemical Society (2007) 129, 10056-10057. https://doi.org/10.1021/ja071989t

  4. Atomic and molecular parity nonconservation and sum frequency generation solutions to the Ozma problem.
    Ji N, Harris RA
    Journal of Physical Chemistry B (2006) 110, 18744-18747. https://doi.org/10.1021/jp055038i

  5. Towards chiral sum frequency spectroscopy.
    Ji N, Ostroverkhov V, Belkin MA, Shiu YJ, Shen YR
    Journal of the American Chemical Society (2006) 128, 8845-8848. https://doi.org/10.1021/ja060888c

  6. Three-dimensional chiral imaging by sum frequency generation.
    Ji N, Zhang K, Yang H, Shen YR
    Journal of the American Chemical Society (2006) 128, 3482-3483. https://doi.org/10.1021/ja057775y

  7. A novel spectroscopic probe for molecular chirality.
    Ji N, Shen YR
    Chirality (2006) 18, 146-158. https://doi.org/10.1002/chir.20238

  8. A dynamic coupling model for sum frequency chiral response from liquids composed of molecules with a chiral side chain and an achiral chromophore.
    Ji N, Shen YR
    Journal of the American Chemical Society (2005) 127, 12933-12942. https://doi.org/10.1021/ja052715d

  9. Optically active sum frequency generation from molecules with a chiral center - amino acids as model systems.
    Ji N, Shen YR
    Journal of the American Chemical Society (2004) 126, 15008-15009. https://doi.org/10.1021/ja045708i

  10. Sum frequency vibrational spectroscopy of leucine molecules adsorbed at air-water interface.
    Ji N, Shen YR
    Journal of Chemical Physics (2004) 120, 7107-7112. https://doi.org/10.1063/1.1669375

  11. Surface vibrational spectroscopy on shear-aligned poly(tetrafluoroethylene) films.
    Ji N, Ostroverkhov V, Lagugne-Labarthet F, Shen YR
    Journal of the American Chemical Society (2003) 125, 14218-14219. https://doi.org/10.1021/ja037964l

  12. Sum-frequency vibrational spectroscopic study of surface glass transition of poly(vinyl alcohol).
    Zhang C, Hong SC, Ji N, Wang YP, Wei KH, Shen YR
    Macromolecules (2003) 36, 3303-3306. https://doi.org/10.1021/ma025681s

  13. Intense laser induced eld ionization of C2H2, C2H4, and C2H6.
    Gao L, Ji N, Xiong YJ, Tang XP, Kong F
    Chinese Science Bulletin (2003) 48, 1713. https://ur.art1lib.org/book/11486935/253f54

  14. Sum-frequency spectroscopy of electronic resonances on a chiral surface monolayer of bi-naphthol.
    Han SH, Ji N, Belkin MA, Shen YR
    Physical Review B (2002) 66, 165415. https://doi.org/10.1103/PhysRevB.66.165415

  15. Field ionization of aliphatic ketones by intense femtosecond laser.
    Wu CY, Xiong YJ, Ji N, He Y, Gao Z, Kong F
    Journal of Physical Chemistry A (2001) 105, 374. https://doi.org/10.1021/jp0024165