메뉴 건너뛰기




Volumn 8, Issue , 2014, Pages

SIMA: Python software for analysis of dynamic fluorescence imaging data

Author keywords

Analysis software; Calcium imaging; Fluorescence imaging; In vivo GECI imaging; Motion correction; Multi photon microscopy; Python language; Segmentation

Indexed keywords

ARTICLE; ARTIFACT; AUTOMATION; CELL STRUCTURE; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER LANGUAGE; DATA ANALYSIS SOFTWARE; DOCUMENTATION; FLUORESCENCE IMAGING; IMAGE PROCESSING; LASER MICROSCOPY; LEARNING ALGORITHM; MOTION; NERVOUS SYSTEM; PYTHON; SIGNAL DETECTION; WORKFLOW;

EID: 84907286201     PISSN: 16625196     EISSN: 16625196     Source Type: Journal    
DOI: 10.3389/fninf.2014.00080     Document Type: Article
Times cited : (156)

References (23)
  • 1
    • 84893389465 scopus 로고    scopus 로고
    • ACQ4: An open-source software platform for data acquisition and analysis in neurophysiology research
    • Campagnola, L., Kratz, M. B., and Manis, P. B. (2014). ACQ4: an open-source software platform for data acquisition and analysis in neurophysiology research. Front. Neuroinform. 8:3. doi: 10.3389/fninf.2014.00003
    • (2014) Front. Neuroinform , vol.8 , pp. 3
    • Campagnola, L.1    Kratz, M.B.2    Manis, P.B.3
  • 2
    • 34748867201 scopus 로고    scopus 로고
    • Imaging large-scale neural activity with cellular resolution in awake, mobile mice
    • Dombeck, D. A., Khabbaz, A. N., Collman, F., Adelman, T. L., and Tank, D. W. (2007). Imaging large-scale neural activity with cellular resolution in awake, mobile mice. Neuron 56, 43-57. doi: 10.1016/j.neuron.2007.08.003
    • (2007) Neuron , vol.56 , pp. 43-57
    • Dombeck, D.A.1    Khabbaz, A.N.2    Collman, F.3    Adelman, T.L.4    Tank, D.W.5
  • 4
    • 34247493236 scopus 로고    scopus 로고
    • Matplotlib: A 2D graphics environment
    • Hunter, J. D. (2007). Matplotlib: a 2D graphics environment. Comput. Sci. Eng. 9, 90-95. doi: 10.1109/MCSE.2007.55
    • (2007) Comput. Sci. Eng , vol.9 , pp. 90-95
    • Hunter, J.D.1
  • 6
    • 84883448302 scopus 로고    scopus 로고
    • Septo-hippocampal GABAergic signaling across multiple modalities in awake mice
    • Kaifosh, P., Lovett-Barron, M., Turi, G. F., Reardon, T. R., and Losonczy, A. (2013). Septo-hippocampal GABAergic signaling across multiple modalities in awake mice. Nat. Neurosci. 16, 1182-1184. doi: 10.1038/nn.3482
    • (2013) Nat. Neurosci , vol.16 , pp. 1182-1184
    • Kaifosh, P.1    Lovett-Barron, M.2    Turi, G.F.3    Reardon, T.R.4    Losonczy, A.5
  • 7
    • 39549113171 scopus 로고    scopus 로고
    • Imaging in vivo: Watching the brain in action
    • Kerr, J. N. D., and Denk, W. (2008). Imaging in vivo: watching the brain in action. Nat. Rev. Neurosci. 9, 195-205. doi: 10.1038/nrn2338
    • (2008) Nat. Rev. Neurosci , vol.9 , pp. 195-205
    • Kerr, J.N.D.1    Denk, W.2
  • 8
    • 77951623793 scopus 로고    scopus 로고
    • Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice
    • Komiyama, T., Sato, T. R., O’Connor, D. H., Zhang, Y.-X., Huber, D., Hooks, B. M., et al. (2010). Learning-related fine-scale specificity imaged in motor cortex circuits of behaving mice. Nature 464, 1182-1186. doi: 10.1038/nature 08897
    • (2010) Nature , vol.464 , pp. 1182-1186
    • Komiyama, T.1    Sato, T.R.2    O’connor, D.H.3    Zhang, Y.-X.4    Huber, D.5    Hooks, B.M.6
  • 10
    • 84857690012 scopus 로고    scopus 로고
    • Genetically encoded neural activity indicators
    • Looger, L. L., and Griesbeck, O. (2012). Genetically encoded neural activity indicators. Curr. Opin. Neurobiol. 22, 18-23. doi: 10.1016/j.conb.2011.10.024
    • (2012) Curr. Opin. Neurobiol , vol.22 , pp. 18-23
    • Looger, L.L.1    Griesbeck, O.2
  • 12
    • 70349129483 scopus 로고    scopus 로고
    • Automated analysis of cellular signals from large-scale calcium imaging data
    • Mukamel, E. A., Nimmerjahn, A., and Schnitzer, M. J. (2009). Automated analysis of cellular signals from large-scale calcium imaging data. Neuron 63, 747-760. doi: 10.1016/j.neuron.2009.08.009
    • (2009) Neuron , vol.63 , pp. 747-760
    • Mukamel, E.A.1    Nimmerjahn, A.2    Schnitzer, M.J.3
  • 14
    • 34247500374 scopus 로고    scopus 로고
    • Python for scientific computing
    • Oliphant, T. E. (2007). Python for scientific computing. Comput. Sci. Eng. 9, 10-20. doi: 10.1109/MCSE.2007.58
    • (2007) Comput. Sci. Eng , vol.9 , pp. 10-20
    • Oliphant, T.E.1
  • 15
    • 0018306059 scopus 로고
    • A threshold selection method from gray-level histograms
    • Otsu, N. (1979). A threshold selection method from gray-level histograms. IEEE Trans. Syst. Man Cybern. 9, 62-66. doi: 10.1109/TSMC.1979.4310076
    • (1979) IEEE Trans. Syst. Man Cybern , vol.9 , pp. 62-66
    • Otsu, N.1
  • 17
    • 84863205849 scopus 로고    scopus 로고
    • NIH Image to ImageJ: 25 years of image analysis
    • Schneider, C. A., Rasband, W. S., and Eliceiri, K. W. (2012). NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671-675. doi: 10.1038/nmeth.2089
    • (2012) Nat. Methods , vol.9 , pp. 671-675
    • Schneider, C.A.1    Rasband, W.S.2    Eliceiri, K.W.3
  • 18
    • 84884905595 scopus 로고    scopus 로고
    • Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light
    • Schrödel, T., Prevedel, R., Aumayr, K., Zimmer, M., and Vaziri, A. (2013). Brain-wide 3D imaging of neuronal activity in Caenorhabditis elegans with sculpted light. Nat. Methods 10, 1013-1020. doi: 10.1038/nmeth.2637
    • (2013) Nat. Methods , vol.10 , pp. 1013-1020
    • Schrödel, T.1    Prevedel, R.2    Aumayr, K.3    Zimmer, M.4    Vaziri, A.5
  • 19
    • 0034244751 scopus 로고    scopus 로고
    • Normalized cuts and image segmentation
    • Shi, J., and Malik, J. (2000). Normalized cuts and image segmentation. IEEE Trans. Patt. Anal. Mach. Intell. 22, 888-905. doi: 10.1109/34.868688
    • (2000) IEEE Trans. Patt. Anal. Mach. Intell , vol.22 , pp. 888-905
    • Shi, J.1    Malik, J.2
  • 20
    • 0000825481 scopus 로고
    • A statistical method for evaluating systematic relationships
    • Sokal, R. R., and Michener, C. D. (1958). A statistical method for evaluating systematic relationships. Univer. Kansas Sci. Bull. 38, 1409-1438.
    • (1958) Univer. Kansas Sci. Bull , vol.38 , pp. 1409-1438
    • Sokal, R.R.1    Michener, C.D.2
  • 21
    • 0031647592 scopus 로고    scopus 로고
    • A pyramid approach to subpixel registration based on intensity
    • Thevenaz, P., Ruttimann, U. E., and Unser, M. (1998). A pyramid approach to subpixel registration based on intensity. IEEE Trans. Image Process. 7, 27-41. doi: 10.1109/83.650848
    • (1998) IEEE Trans. Image Process , vol.7 , pp. 27-41
    • Thevenaz, P.1    Ruttimann, U.E.2    Unser, M.3
  • 23
    • 34247882949 scopus 로고    scopus 로고
    • High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy
    • Verveer, P. J., Swoger, J., Pampaloni, F., Greger, K., Marcello, M., and Stelzer, E. H. (2007). High-resolution three-dimensional imaging of large specimens with light sheet-based microscopy. Nat. Methods 4, 311-313. doi: 10.1038/nmeth1017
    • (2007) Nat. Methods , vol.4 , pp. 311-313
    • Verveer, P.J.1    Swoger, J.2    Pampaloni, F.3    Greger, K.4    Marcello, M.5    Stelzer, E.H.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.