Denoising two-photon calcium imaging data

PLoS ONE

Volumn 6, Issue 6, 2011, Pages

  Malik, Wasim Q ^a,b   Schummers, James ^b   Sur, Mriganka ^b   Brown, Emery N ^a,b  

^a MASSACHUSETTS GENERAL HOSPITAL   (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; CONFIDENCE INTERVAL; DATA ANALYSIS; IMAGE ANALYSIS; IMAGING SYSTEM; MICROSCOPY; PARSIMONY ANALYSIS; REGRESSION ANALYSIS; RELIABILITY; SIGNAL NOISE RATIO; STATISTICAL MODEL; TWO PHOTON CALCIUM IMAGING; ANIMAL; CYTOLOGY; FERRET; IMAGE PROCESSING; METABOLISM; METHODOLOGY; MOLECULAR IMAGING; NERVE CELL; PHOTON; PHOTOSTIMULATION; SPECTROFLUOROMETRY; THEORETICAL MODEL; VISUAL CORTEX;

MUSTELA;

CALCIUM;

ALGORITHMS; ANIMALS; CALCIUM; FERRETS; IMAGE PROCESSING, COMPUTER-ASSISTED; LIKELIHOOD FUNCTIONS; MODELS, THEORETICAL; MOLECULAR IMAGING; NEURONS; PHOTIC STIMULATION; PHOTONS; SPECTROMETRY, FLUORESCENCE; VISUAL CORTEX;

EID: 79958078924     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0020490     Document Type: Article

References (54)

1. Wilt B, Burns LD, Ho ETW, Ghosh KK, Mukamel EA, et al. (2009) Advances in light microscopy for neuroscience. Annu Rev Neurosci 32: 435-506.
2. Denk W, Svoboda K, (1997) Photon upmanship: why multiphoton imaging is more than a gimmick. Neuron 18: 351-357.
3. Homma R, Baker BJ, Jin L, Garaschuk O, Konnerth A, et al. (2009) Dynamic Brain Imaging: Multi-Modal Methods and In Vivo Applications, Humana Pres., chapter Wide-field and two-photon imaging of brain activity with voltage- and calcium-sensitive dyes.
4. Helmchen F, Denk W, (2005) Deep tissue two-photon microscopy. Nature Methods 2: 932-940.
5. Kerr JND, Denk W, (2008) Imaging in vivo: watching the brain in action. Nature Neuroscience 9: 195-205.
6. Majewska A, Sur M, (2003) Motility of dendritic spines in visual cortex in vivo: Changes during the critical period and effects of visual deprivation. Proc Natl Acad Sci 100: 16024-16029.
7. Barretto RPJ, Messerschmidt B, Schnitzer MJ, (2009) In vivo uorescence imaging with highresolution microlenses. Nature Methods 6: 511-512.
8. Holtmaat A, Bonhoeffer T, Chow DK, Chuckowree J, Paola VD, et al. (2009) Long-term, highresolution imaging in the mouse neocortex through a chronic cranial window. Nat Protoc 4: 1128-1144.
9. Ohki K, Chung S, Ch'ng YH, Kara P, Reid CR, (2005) Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. Nature 433: 597-603.
10. Göbel W, Kampa BM, Helmchen F, (2006) Imaging cellular network dynamics in three dimensions using fast 3D laser scanning. Nature Methods 4: 73-79.
11. Kerr JND, Greenberg D, Helmchen F, (2005) Imaging input and output of neocortical networks in vivo. Proc Natl Acad Sci 102: 14063-14068.
12. Greenberg DS, Houweling AR, Kerr JND, (2008) Population imaging of ongoing neuronal activity in the visual cortex of awake rats. Nature Neuroscience 11: 749-751.
13. Yaksi E, Friedrich RW, (2006) Reconstruction of firing rate changes across neuronal populations by temporally deconvolved Ca2+ imaging. Nature Methods 3: 377-383.
14. Mukamel EA, Nimmerjahn A, Schnitzer MJ, (2009) Automated analysis of cellular signals from large-scale calcium imaging data. Neuron 63: 747-760.
15. Garaschuk O, Linn J, Eilers J, Konnerth A, (2000) Large-scale oscillatory calcium waves in the immature cortex. Nature 3: 452-459.
16. Mironov SL, (2008) Metabotropic glutamate receptors activate dendritic calcium waves and TRPM channels which drive rhythmic respiratory patterns in mice. J Physiol 586: 2277-2291.
17. Basole A, White LE, Fitzpatrick D, (2003) Mapping multiple features in the population response of visual cortex. Nature 423: 986-990.
18. Schummers J, Yu H, Sur M, (2008) Tuned responses of astrocytes and their inuence on hemodynamic signals in the visual cortex. Science 320: 1638-1643.
19. Martinez LM, Alonso JM, Reid CR, Hirsch JA, (2002) Laminar processing of stimulus orientation in cat visual cortex. J Physiol 540: 321-333.
20. Gabbay M, Brennan C, Kaplan E, Sirovich L, (2000) A principal components-based method for the detection of neuronal activity maps: application to optical imaging. NeuroImage 1: 313-325.
21. Kalatsky VA, Stryker MP, (2003) New paradigm for optical imaging: temporally encoded maps of intrinsic signal. Neuron 38: 529-545.
22. Mrsic-Flogel T, Hübener M, Bonhoeffer T, (2003) Brain mapping: New wave optical imaging. Curr Biol 13: R778-R780.
23. Sornborger A, Sailstad C, Kaplan E, Sirovich L, (2003) Spatiotemporal analysis of optical imaging data. NeuroImage 18: 610-621.
24. Purdon PL, Solo V, Weisskoff RM, Brown EN, (2001) Locally regularized spatiotemporal modeling and model comparison for functional MRI. NeuroImage 14: 912-923.
25. Kantz H, Schreiber T, (2004) Nonlinear Time Series Analysis. Cambridge University Press.
26. Kantz H, Schreiber T, (1993) Nonlinear noise reduction: A case study on experimental data. Phys Rev E 48.
27. Schreiber T, Grassberger, (1991) A simple noise-reduction method for real data. Phys Lett A 160: 411-418.
28. Effern A, Lehnertz K, Schreiber T, Grunwald T, David P, et al. (2000) Nonlinear denoising of transient signals with application to event-related potentials. Physica D 140: 257-266.
29. Corradi C, (1979) A note on the computation of maximum likelihood estimates in linear regression models with autocorrelated errors. J Econometrics 11: 303-317.
30. Perc M, Green AK, Marhl M, (2008) Establishing the stochastic nature of intracellular calcium oscillations from experimental data. Biophys Chem 132: 33-38.
31. Perc M, Rupnik M, Gosak M, Marhl M, (2009) Prevalence of stochasticity in experimentally observed responses of pancreatic acinar cells to acetylcholine. Chaos 19: 037113.
32. Marhl M, Gosak M, Perc M, Roux E, (2010) Importance of cell variability for calcium signaling in rat airway myocytes. Biophys Chem 148: 42-50.
33. Bullmore E, Long C, Suckling J, Fadili J, Calvert G, et al. (2001) Colored noise and computational inference in neurophysiological (fMRI) time series analysis: Resampling methods in time and wavelet domains. Human Brain Mapping 12: 61-78.
34. Chen Y, Geisler WS, Seidemann E, (2008) Optimal temporal decoding of neural population responses in a reaction-time visual detection task. J Neurophysiol 99: 1366-1379.
35. Brown EN, Choe Y, Luithardt H, Czeisler CA, (2000) A statistical model of the human coretemperature circadian rhythm. Am J Physiol Endocrinol Metab 279: E669-E683.
36. Brunel N, Latham PE, (2003) Firing rate of the noisy quadratic integrate-and-fire neuron. Neural Comput 15: 2281-2306.
37. Destexhe A, Rudolph M, Fellous JM, Sejnowski TJ, (2001) Fluctuating synaptic conductances recreate in vivo-like activity in neocortical neurons. Neuroscience 107: 13-24.
38. Sakai Y, Funahashi S, Shinomoto S, (1999) Temporally correlated inputs to leaky integrate-and-fire models can reproduce spiking statistics of cortical neurons. Neural Networks 12: 1181-1190.
39. Huang MC, Wu JW, Luo YP, Petrosyan KG, (2010) Fluctuations in gene regulatory networks as Gaussian colored noise. J Chem Phys 132: 155101.
40. Gibson JD, Koo B, Gray SD, (1991) Filtering of colored noise for speech enhancement and coding. IEEE Trans Sig Proc 39: 1732-1742.
41. Shenderov AD, Sheetz MP, (1997) Inversely correlated cycles in speed and turning in an ameba: An oscillatory model of cell locomotion. Biophys J 72: 2382-2389.
42. Everson RM, Prashanth AK, Gabbay M, Knight BW, Sirovich L, et al. (1998) Representation of spatial frequency and orientation in the visual cortex. Proc Natl Acad Sci 95: 8334-8338.
43. Friston KJ, Josephs O, Rees G, Turner R, (1998) Nonlinear event-related responses in fMRI. Magn Reson Med 39: 41-52.
44. Sjulson L, Miesenböck G, (2007) Optical recording of action potentials and other discrete physiological events: a perspective from signal detection theory. Physiology 22: 47-55.
45. Vogelstein JT, Watson BO, Packer AM, Yuste R, Jedynak B, et al. (2009) Spike inference from calcium imaging using sequential Monte Carlo methods. Biophys J 97: 636-655.
46. Ozden I, Lee HM, Sullivan MR, Wang SH, (2008) Identification and clustering of event patterns from in vivo multiphoton optical recordings of neuronal ensembles. J Neurophysiol 100: 495-503.
47. Stosiek C, Garaschuk O, Holthoff K, Konnerth, (2003) In vivo two-photon calcium imaging of neuronal networks. Proc Natl Acad Sci 100: 7319-7324.
48. Majewska A, Yiu G, Yuste R, (2000) A custom-made two-photon microscope and deconvolution system. Eur J Physiol 441: 398-408.
49. Brainard DH, (1997) The Psychophysics Toolbox. Spatial Vision 10: 433-436.
50. Schetzen M, (2006) The Volterra and Wiener Theories of Nonlinear Systems. Krieger.
51. Box GEP, Jenkins GM, Reinsel GC, (2008) Time Series Analysis. Wiley.
52. Kay SM, (1999) Modern Spectral Estimation. Prentice Hall.
53. Myers RH, Montgomery DC, Vining GG, (2002) Generalized Linear Models. Wiley.
54. Fisher NI, (1993) Statistical Analysis of Circular Data. Cambridge.