Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

In vivo imaging of neural activity

An Erratum to this article was published on 29 June 2017

A Corrigendum to this article was published on 29 June 2017

This article has been updated


Since the introduction of calcium imaging to monitor neuronal activity with single-cell resolution, optical imaging methods have revolutionized neuroscience by enabling systematic recordings of neuronal circuits in living animals. The plethora of methods for functional neural imaging can be daunting to the nonexpert to navigate. Here we review advanced microscopy techniques for in vivo functional imaging and offer guidelines for which technologies are best suited for particular applications.

Access options

Rent or Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Figure 1
Figure 2: Wide-field imaging.
Figure 3: Two-photon microscopy.
Figure 4: Multiplexing two-photon microscopy.
Figure 5: Deep brain imaging.
Figure 6: Imaging freely behaving animals.

Change history

  • 21 June 2017

    In the version of this article initially published, the formula for rz_confocal in Box 1 incorrectly had a coefficient of 0.4. The correct coefficient is 1.4. The error has been corrected in the HTML and PDF versions of the article.

  • 21 June 2017

    In the version of this article initially published, reference 76 was incorrectly classified as direct wavefront sensing. It should be classified as indirect wavefront sensing. The error has been corrected in the HTML and PDF versions of the article.


  1. 1

    Crick, F.H.C. Thinking about the brain. Scientific American 241, 219–232 (1979).

    CAS  PubMed  Google Scholar 

  2. 2

    Smetters, D., Majewska, A. & Yuste, R. Detecting action potentials in neuronal populations with calcium imaging. Methods 18, 215–221 (1999).

    CAS  PubMed  Google Scholar 

  3. 3

    Ahrens, M.B., Orger, M.B., Robson, D.N., Li, J.M. & Keller, P.J. Whole-brain functional imaging at cellular resolution using light-sheet microscopy. Nat. Methods 10, 413–420 (2013). Example of whole-brain functional imaging in vivo.

  4. 4

    Denk, W., Strickler, J.H. & Webb, W.W. Two-photon laser scanning fluorescence microscopy. Science 248, 73–76 (1990). Invention of two-photon microscopy.

    CAS  Google Scholar 

  5. 5

    Yuste, R. & Denk, W. Dendritic spines as basic functional units of neuronal integration. Nature 375, 682–684 (1995).

    CAS  PubMed  Google Scholar 

  6. 6

    Stosiek, C., Garaschuk, O., Holthoff, K. & Konnerth, A. In vivo two-photon calcium imaging of neuronal networks. Proc. Natl. Acad. Sci. USA 100, 7319–7324 (2003).

    CAS  PubMed  Google Scholar 

  7. 7

    Hasan, M.T. et al. Functional fluorescent Ca2+ indicator proteins in transgenic mice under TET control. PLoS Biol. 2, e163 (2004).

    PubMed  PubMed Central  Google Scholar 

  8. 8

    Chen, T.-W. et al. Ultrasensitive fluorescent proteins for imaging neuronal activity. Nature 499, 295–300 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  9. 9

    Yuste, R. ed. Imaging: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 2011). Theory and practice of optical imaging methods.

  10. 10

    Helmchen, F. & Konnerth, A. ed. Imaging in Neuroscience: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 2011). Review of optical imaging methods in neuroscience.

  11. 11

    Lanni, F. & Keller, H.E. in Imaging: A Laboratory Manual (ed. Yuste, R.) 1–56 (Cold Spring Harbor Laboratory Press, 2011).

  12. 12

    Ferezou, I. et al. Spatiotemporal dynamics of cortical sensorimotor integration in behaving mice. Neuron 56, 907–923 (2007).

    CAS  PubMed  Google Scholar 

  13. 13

    Mohajerani, M.H. et al. Spontaneous cortical activity alternates between motifs defined by regional axonal projections. Nat. Neurosci. 16, 1426–1435 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. 14

    Carandini, M. et al. Imaging the awake visual cortex with a genetically encoded voltage indicator. J. Neurosci. 35, 53–63 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  15. 15

    Pawley, J.B. Handbook of Biological Confocal Microscopy 3rd edn. (Springer, 2006).

  16. 16

    Petran, M., Hadravsk, M., Egger, M.D. & Galambos, R. Tandem-scanning reflected-light microscope. J. Opt. Soc. Am. 58, 661–664 (1968).

    Google Scholar 

  17. 17

    Mertz, J. Optical sectioning microscopy with planar or structured illumination. Nat. Methods 8, 811–819 (2011).

    CAS  PubMed  Google Scholar 

  18. 18

    Chen, B.C. et al. Lattice light-sheet microscopy: imaging molecules to embryos at high spatiotemporal resolution. Science 346, 1257998 (2014).

    PubMed  PubMed Central  Google Scholar 

  19. 19

    Fahrbach, F.O., Voigt, F.F., Schmid, B., Helmchen, F. & Huisken, J. Rapid 3D light-sheet microscopy with a tunable lens. Opt. Express 21, 21010–21026 (2013).

    PubMed  Google Scholar 

  20. 20

    Tomer, R. et al. SPED light sheet microscopy: fast mapping of biological system structure and function. Cell 163, 1796–1806 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. 21

    Quirin, S. et al. Calcium imaging of neural circuits with extended depth-of-field light-sheet microscopy. Opt. Lett. 41, 855–858 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. 22

    Bouchard, M.B. et al. Swept confocally-aligned planar excitation (SCAPE) microscopy for high speed volumetric imaging of behaving organisms. Nat. Photonics 9, 113–119 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  23. 23

    Power, R.M. & Huisken, J. A guide to light-sheet fluorescence microscopy for multiscale imaging. Nat. Methods 14, 360–373 (2017).

  24. 24

    Papagiakoumou, E., de Sars, V., Oron, D. & Emiliani, V. Patterned two-photon illumination by spatiotemporal shaping of ultrashort pulses. Opt. Express 16, 22039–22047 (2008).

    CAS  PubMed  Google Scholar 

  25. 25

    Oron, D., Tal, E. & Silberberg, Y. Scanningless depth-resolved microscopy. Opt. Express 13, 1468–1476 (2005).

    PubMed  Google Scholar 

  26. 26

    Zhu, G., van Howe, J., Durst, M., Zipfel, W. & Xu, C. Simultaneous spatial and temporal focusing of femtosecond pulses. Opt. Express 13, 2153–2159 (2005).

    PubMed  Google Scholar 

  27. 27

    Papagiakoumou, E., de Sars, V., Emiliani, V. & Oron, D. Temporal focusing with spatially modulated excitation. Opt. Express 17, 5391–5401 (2009).

    CAS  PubMed  Google Scholar 

  28. 28

    Schrödel, T., Prevedel, R., Aumayr, K., Zimmer, M. & Vaziri, A. Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light. Nat. Methods 10, 1013–1020 (2013).

    PubMed  Google Scholar 

  29. 29

    Dana, H. et al. Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks. Nat. Commun. 5, 3997 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. 30

    Nikolenko, V. et al. SLM microscopy: scanless two-photon imaging and photostimulation with spatial light modulators. Front. Neural Circuits 2, 5 (2008).

    PubMed  PubMed Central  Google Scholar 

  31. 31

    Rickgauer, J.P., Deisseroth, K. & Tank, D.W. Simultaneous cellular-resolution optical perturbation and imaging of place cell firing fields. Nat. Neurosci. 17, 1816–1824 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. 32

    Hernandez, O. et al. Three-dimensional spatiotemporal focusing of holographic patterns. Nat. Commun. 7, 11928 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  33. 33

    Quirin, S., Peterka, D.S. & Yuste, R. Instantaneous three-dimensional sensing using spatial light modulator illumination with extended depth of field imaging. Opt. Express 21, 16007–16021 (2013).

    PubMed  PubMed Central  Google Scholar 

  34. 34

    Quirin, S., Jackson, J., Peterka, D.S. & Yuste, R. Simultaneous imaging of neural activity in three dimensions. Front. Neural Circuits 8, 29 (2014).

    PubMed  PubMed Central  Google Scholar 

  35. 35

    Yang, S.J. et al. Extended field-of-view and increased-signal 3D holographic illumination with time-division multiplexing. Opt. Express 23, 32573–32581 (2015).

    PubMed  PubMed Central  Google Scholar 

  36. 36

    Broxton, M. et al. Wave optics theory and 3-D deconvolution for the light field microscope. Opt. Express 21, 25418–25439 (2013).

    PubMed  PubMed Central  Google Scholar 

  37. 37

    Prevedel, R. et al. Simultaneous whole-animal 3D imaging of neuronal activity using light-field microscopy. Nat. Methods 11, 727–730 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. 38

    Zipfel, W.R., Williams, R.M. & Webb, W.W. Nonlinear magic: multiphoton microscopy in the biosciences. Nat. Biotechnol. 21, 1369–1377 (2003). Nonlinear microscopies and their applications in biological imaging.

    CAS  PubMed  PubMed Central  Google Scholar 

  39. 39

    Helmchen, F. & Denk, W. Deep tissue two-photon microscopy. Nat. Methods 2, 932–940 (2005). Review of two-photon microscopy.

    CAS  Google Scholar 

  40. 40

    Briggman, K.L., Helmstaedter, M. & Denk, W. Wiring specificity in the direction-selectivity circuit of the retina. Nature 471, 183–188 (2011).

    CAS  PubMed  Google Scholar 

  41. 41

    Göbel, W. & Helmchen, F. New angles on neuronal dendrites in vivo. J. Neurophysiol. 98, 3770–3779 (2007).

    PubMed  Google Scholar 

  42. 42

    Grewe, B.F., Voigt, F.F., van 't Hoff, M. & Helmchen, F. Fast two-layer two-photon imaging of neuronal cell populations using an electrically tunable lens. Biomed. Opt. Express 2, 2035–2046 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  43. 43

    Beaurepaire, E. & Mertz, J. Epifluorescence collection in two-photon microscopy. Appl. Opt. 41, 5376–5382 (2002).

    PubMed  Google Scholar 

  44. 44

    Yang, W. et al. Simultaneous multi-plane imaging of neural circuits. Neuron 89, 269–284 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. 45

    Kong, L. et al. Continuous volumetric imaging via an optical phase-locked ultrasound lens. Nat. Methods 12, 759–762 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  46. 46

    Botcherby, E.J., Juskaitis, R., Booth, M.J. & Wilson, T. An optical technique for remote focusing in microscopy. Opt. Commun. 281, 880–887 (2008).

    CAS  Google Scholar 

  47. 47

    Anselmi, F., Ventalon, C., Bègue, A., Ogden, D. & Emiliani, V. Three-dimensional imaging and photostimulation by remote-focusing and holographic light patterning. Proc. Natl. Acad. Sci. USA 108, 19504–19509 (2011).

    CAS  PubMed  Google Scholar 

  48. 48

    Botcherby, E.J. et al. Aberration-free three-dimensional multiphoton imaging of neuronal activity at kHz rates. Proc. Natl. Acad. Sci. USA 109, 2919–2924 (2012).

    CAS  PubMed  Google Scholar 

  49. 49

    Kaplan, A., Friedman, N. & Davidson, N. Acousto-optic lens with very fast focus scanning. Opt. Lett. 26, 1078–1080 (2001).

    CAS  PubMed  Google Scholar 

  50. 50

    Duemani Reddy, G., Kelleher, K., Fink, R. & Saggau, P. Three-dimensional random access multiphoton microscopy for functional imaging of neuronal activity. Nat. Neurosci. 11, 713–720 (2008).

  51. 51

    Grewe, B.F., Langer, D., Kasper, H., Kampa, B.M. & Helmchen, F. High-speed in vivo calcium imaging reveals neuronal network activity with near-millisecond precision. Nat. Methods 7, 399–405 (2010).

    CAS  PubMed  Google Scholar 

  52. 52

    Kirkby, P.A., Nadella, K.M..N.S & Silver, R.A. A compact acousto-optic lens for 2D and 3D femtosecond based 2-photon microscopy. Opt. Express 18, 13720–13744 (2010).

    CAS  Google Scholar 

  53. 53

    Katona, G. et al. Fast two-photon in vivo imaging with three-dimensional random-access scanning in large tissue volumes. Nat. Methods 9, 201–208 (2012).

    CAS  PubMed  Google Scholar 

  54. 54

    Tsai, P.S. et al. Ultra-large field-of-view two-photon microscopy. Opt. Express 23, 13833–13847 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. 55

    McConnell, G. et al. A novel optical microscope for imaging large embryos and tissue volumes with sub-cellular resolution throughout. eLife 5, e18659 (2016).

    PubMed  PubMed Central  Google Scholar 

  56. 56

    Sofroniew, N.J., Flickinger, D., King, J. & Svoboda, K. A large field of view two-photon mesoscope with subcellular resolution for in vivo imaging. eLife 5, e14472 (2016).

    PubMed  PubMed Central  Google Scholar 

  57. 57

    Stirman, J.N., Smith, I.T., Kudenov, M.W. & Smith, S.L. Wide field-of-view, multi-region, two-photon imaging of neuronal activity in the mammalian brain. Nat. Biotechnol. 34, 857–862 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. 58

    Cheng, A., Gonçalves, J.T., Golshani, P., Arisaka, K. & Portera-Cailliau, C. Simultaneous two-photon calcium imaging at different depths with spatiotemporal multiplexing. Nat. Methods 8, 139–142 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  59. 59

    Kim, K.H. et al. Multifocal multiphoton microscopy based on multianode photomultiplier tubes. Opt. Express 15, 11658–11678 (2007).

    PubMed  PubMed Central  Google Scholar 

  60. 60

    Bewersdorf, J., Pick, R. & Hell, S.W. Multifocal multiphoton microscopy. Opt. Lett. 23, 655–657 (1998).

    CAS  PubMed  Google Scholar 

  61. 61

    Watson, B.O. et al. Front. Neurosci. Two-photon microscopy with diffractive optical elements and spatial light modulators. Front. Neurosci. 4, 29 (2010).

    PubMed  PubMed Central  Google Scholar 

  62. 62

    Mahou, P. et al. Multicolor two-photon tissue imaging by wavelength mixing. Nat. Methods 9, 815–818 (2012).

    CAS  PubMed  Google Scholar 

  63. 63

    Inoue, M. et al. Rational design of a high-affinity, fast, red calcium indicator R-CaMP2. Nat. Methods 12, 64–70 (2015).

    CAS  PubMed  Google Scholar 

  64. 64

    Ducros, M., Goulam Houssen, Y., Bradley, J., de Sars, V. & Charpak, S. Encoded multisite two-photon microscopy. Proc. Natl. Acad. Sci. USA 110, 13138–13143 (2013).

    CAS  PubMed  Google Scholar 

  65. 65

    Pnevmatikakis, E.A. et al. Simultaneous denoising, deconvolution, and demixing of calcium imaging data. Neuron 89, 285–299 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  66. 66

    Prevedel, R. et al. Fast volumetric calcium imaging across multiple cortical layers using sculpted light. Nat. Methods 13, 1021–1028 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  67. 67

    Mukamel, E.A., Nimmerjahn, A. & Schnitzer, M.J. Automated analysis of cellular signals from large-scale calcium imaging data. Neuron 63, 747–760 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. 68

    Friedrich, J. et al. Multi-scale approaches for high-speed imaging and analysis of large neural populations. Preprint at (2016).

  69. 69

    Lu, R. et al. Video-rate volumetric functional imaging of the brain at synaptic resolution. Nat. Neurosci. (2017).

  70. 70

    Song, A. et al. Volumetric two-photon imaging of neurons using stereoscopy (vTwINS). Nat. Methods 14, 420–426 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. 71

    Podgorski, K. & Ranganathan, G. N. Brain heating induced by near-infrared lasers during multi-photon microscopy. J. Neurophysiol. 116, 1012–1023 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. 72

    Horton, N.G. et al. In vivo three-photon microscopy of subcortical structures within an intact mouse brain. Nat. Photonics 7, 205–209 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. 73

    Combs, C.A. et al. Optimizing multiphoton fluorescence microscopy light collection from living tissue by noncontact total emission detection (epiTED). J. Microsc. 241, 153–161 (2011).

    CAS  PubMed  Google Scholar 

  74. 74

    Crosignani, V. et al. Deep tissue fluorescence imaging and in vivo biological applications. J. Biomed. Optics 17, 116023 (2012).

    Google Scholar 

  75. 75

    Booth, M.J. Adaptive optical microscopy: the ongoing quest for a perfect image. Light-Sci Appl. 3, e165 (2014).

    Google Scholar 

  76. 76

    Wang, K. et al. Rapid adaptive optical recovery of optimal resolution over large volumes. Nat. Methods 11, 625–628 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  77. 77

    Ji, N., Milkie, D.E. & Betzig, E. Adaptive optics via pupil segmentation for high-resolution imaging in biological tissues. Nat. Methods 7, 141–147 (2010).

    CAS  Google Scholar 

  78. 78

    Débarre, D., Booth, M.J. & Wilson, T. Image based adaptive optics through optimisation of low spatial frequencies. Opt. Express 15, 8176–8190 (2007).

    PubMed  Google Scholar 

  79. 79

    Débarre, D. et al. Image-based adaptive optics for two-photon microscopy. Opt. Lett. 34, 2495–2497 (2009).

    PubMed  PubMed Central  Google Scholar 

  80. 80

    Neil, M.A.A., Booth, M.J. & Wilson, T. New modal wave-front sensor: a theoretical analysis. J. Opt. Soc. Am. A Opt. Image Sci. Vis. 17, 1098–1107 (2000).

    CAS  PubMed  Google Scholar 

  81. 81

    Sun, W., Tan, Z., Mensh, B.D. & Ji, N. Thalamus provides layer 4 of primary visual cortex with orientation- and direction-tuned inputs. Nat. Neurosci. 19, 308–315 (2016).

    CAS  Google Scholar 

  82. 82

    Ji, N. Adaptive optical fluorescence microscopy. Nat. Methods 14, 374–380 (2017).

    CAS  PubMed  Google Scholar 

  83. 83

    Ouzounov, D.G. et al. In vivo three-photon imaging of activity of GCaMP6-labeled neurons deep in intact mouse brain. Nat. Methods 14, 388–390 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  84. 84

    Levene, M.J., Dombeck, D.A., Kasischke, K.A., Molloy, R.P. & Webb, W.W. In vivo multiphoton microscopy of deep brain tissue. J. Neurophysiol. 91, 1908–1912 (2004).

    Google Scholar 

  85. 85

    Andermann, M.L. et al. Chronic cellular imaging of entire cortical columns in awake mice using microprisms. Neuron 80, 900–913 (2013).

    CAS  PubMed  Google Scholar 

  86. 86

    Low, R.J., Gu, Y. & Tank, D.W. Cellular resolution optical access to brain regions in fissures: imaging medial prefrontal cortex and grid cells in entorhinal cortex. Proc. Natl. Acad. Sci. USA 111, 18739–18744 (2014).

    CAS  PubMed  Google Scholar 

  87. 87

    Attardo, A., Fitzgerald, J.E. & Schnitzer, M.J. Impermanence of dendritic spines in live adult CA1 hippocampus. Nature 523, 592–596 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  88. 88

    Ghosh, K.K. et al. Miniaturized integration of a fluorescence microscope. Nat. Methods 8, 871–878 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. 89

    Ziv, Y. et al. Long-term dynamics of CA1 hippocampal place codes. Nat. Neurosci. 16, 264–266 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. 90

    Flusberg, B.A. et al. High-speed, miniaturized fluorescence microscopy in freely moving mice. Nat. Methods 5, 935–938 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. 91

    Szabo, V., Ventalon, C., De Sars, V., Bradley, J. & Emiliani, V. Spatially selective holographic photoactivation and functional fluorescence imaging in freely behaving mice with a fiberscope. Neuron 84, 1157–1169 (2014).

    CAS  PubMed  Google Scholar 

  92. 92

    Helmchen, F., Fee, M.S., Tank, D.W. & Denk, W. A miniature head-mounted two-photon microscope. high-resolution brain imaging in freely moving animals. Neuron 31, 903–912 (2001).

    CAS  PubMed  Google Scholar 

  93. 93

    Flusberg, B.A. et al. Fiber-optic fluorescence imaging. Nat. Methods 2, 941–950 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. 94

    Myaing, M.T., MacDonald, D.J. & Li, X. Fiber-optic scanning two-photon fluorescence endoscope. Opt. Lett. 31, 1076–1078 (2006).

    PubMed  Google Scholar 

  95. 95

    Rivera, D.R. et al. Compact and flexible raster scanning multiphoton endoscope capable of imaging unstained tissue. Proc. Natl. Acad. Sci. USA 108, 17598–17603 (2011).

    CAS  PubMed  Google Scholar 

  96. 96

    Göbel, W., Kerr, J.N.D., Nimmerjahn, A. & Helmchen, F. Miniaturized two-photon microscope based on a flexible coherent fiber bundle and a gradient-index lens objective. Opt. Lett. 29, 2521–2523 (2004).

    PubMed  Google Scholar 

  97. 97

    Chen, Z., Wei, L., Zhu, X. & Min, W. Extending the fundamental imaging-depth limit of multi-photon microscopy by imaging with photo-activatable fluorophores. Opt. Express 20, 18525–18536 (2012).

    CAS  PubMed  Google Scholar 

  98. 98

    Akerboom, J. et al. Genetically encoded calcium indicators for multi-color neural activity imaging and combination with optogenetics. Front. Mol. Neurosci. 6, 2 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. 99

    Theis, L. et al. Benchmarking spike rate inference in population calcium imaging. Neuron 90, 471–482 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  100. 100

    Insel, T.R., Landis, S.C. & Collins, F.S. The NIH BRAIN Initiative. Research priorities. Science 340, 687–688 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. 101

    Yuste, R. & Bargmann, C. Towards a global BRAIN Initiative. Cell (2017).

  102. 102

    Robertson, M. Biology in the 1980s, plus or minus a decade. Nature 285, 358–359 (1980).

    CAS  PubMed  Google Scholar 

Download references


The authors thank D. Peterka and other members of R.Y.'s lab for fruitful discussions. W.Y. holds a Career Award at the Scientific Interface from Burroughs Wellcome Fund. Our work is supported by the National Eye Institute (NEI) under grants number DP1EY024503, R01EY011787 (R.Y.); National Institute of Mental Health (NIMH) under grants numbers R01MH101218, R01MH100561 (R.Y.) and the Defense Advanced Research Projects Agency (DARPA) under contracts number N66001-15-C-4032 (SIMPLEX) (R.Y.) and HR0011-17-C-0026 (R.Y.). This material is based upon work supported by, or in part by, the US Army Research Laboratory and the US Army Research Office under contract number W911NF-12-1-0594 (MURI) (R.Y.).

Author information



Corresponding authors

Correspondence to Weijian Yang or Rafael Yuste.

Ethics declarations

Competing interests

The authors have patent applications related to holographic microscopy.

Supplementary information

Supplementary Text and Figures

Supplementary Table 1 (PDF 201 kb)

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Yang, W., Yuste, R. In vivo imaging of neural activity. Nat Methods 14, 349–359 (2017).

Download citation

Further reading


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing