Year: 2014

  • Amat, F., Lemon, W., Mossing, D., McDole, K., Wan, Y., Branson, K. et al. (2014). Fast, accurate reconstruction of cell lineages from large-scale fluorescence microscopy data. Nature Methods, 11(9), 951-958. [More] [Online version]
  • Khairy, K., Lemon, W., Amat, F. & Keller, P. J. (2014). Light sheet-based imaging and analysis of early embryogenesis in the fruit fly. Methods in Molecular Biology, 1189, 79-97. [More] [Online version]
  • Preibisch, S., Amat, F., Stamataki, E., Sarov, M., Singer, R. H., Myers, E. W. et al. (2014). Efficient Bayesian-based multiview deconvolution. Nature Methods, 11(6), 645-648. [More] [Online version]

Year: 2013

  • Amat, F. & Keller, P. J. (2013a). Towards comprehensive cell lineage reconstructions in complex organisms using light‐sheet microscopy. Development, Groth & Differentiation, 55(4), 563-578. [More] [Online version]
  • Amat, F. & Keller, P. J (2013b). 3D Haar-Like Elliptical Features for Object Classification in Microscopy. In IEEE (editor), International Symposium on Biomedical Imaging (ISBI). IEEE. [More] [Full text]
  • Amat, F., Myers, E. W. & Keller, P. J. (2013). Fast and robust optical flow for time-lapse microscopy using super-voxels. Bioinformatics, 29(3), 373-380. [More] [Online version]

Year: 2012

  • Tomer, R., Khairy, K., Amat, F. & Keller, P. J. (2012). Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy. Nature Methods. [More] [Online version]

Year: 2011

  • Myamichi, K., Amat, F., Moussavi, F., Wang, C., Wickersham, I., Wall, N. R. et al. (2011). Cortical representations of olfactory input by trans-synaptic tracing. Nature, 472(7342), 191-196. [More] [Online version]
  • Zhao, T., Xie, J., Amat, F., Clack, N., Ahammad, P., Peng, H. et al. (2011). Automated Reconstruction of Neuronal Morphology Based on Local Geometrical and Global Structural Models. Neuroinformatics, 9(2-3), 247-261. [More] [Online version]

Year: 2010

  • Amat, F. (2010). Alignment of Cryo-Electron Tomography Images Using Markov Random Fields. Phd Thesis, Stanford University. [More] [Online version]
  • Amat, F., Comolli, L. R., Moussavi, F., Smit, J., Downing, K. H. & Horowitz, M. (2010a). Subtomogram alignment by adaptive Fourier coefficient thresholding. Journal of Structural Biology, 171(3), 332-344. [More] [Online version]
  • Amat, F., Castaño-Diez, D., Lawrence, A., Moussavi, F., Winkler, H. & Horowitz, M (2010b). Alignment of Cryo-Electron Tomography Datasets. In Jensen, G. (editor), Methods in Enzymology: Cryo-EM, Part B: 3-D Reconstruction. Academic Press. [More] [Online version]
  • Amat, F., Comolli, L. R., Nomellini, J. F., Moussavi, F., Downing, K. H., Smit, J. et al. (2010c). Analysis of Intact Surface Layer of Caulobacter crescentus by Cryo-Electron Tomography. Journal of Bacteriology, 192(22), JB.00747-10. [More] [Online version]
  • Moussavi, F., Heitz, G., Amat, F., Comolli, L. R., Koller, D. & Horowitz, M. (2010). 3D segmentation of cell boundaries from whole cell cryogenic electron tomography volumes. Journal of Structural Biology, 170(1), 134-145. [More] [Online version]

Year: 2009

  • Gould, S., Amat, F. & Koller, D (2009). Alphabet SOUP: A Framework for Approximate Energy Minimization. In CVPR, pages 903-910. [More]

Year: 2008

  • Amat, F., Moussavi, F., Comolli, L. R., Elidan, G., Downing, K. H. & Horowitz, M. (2008). Markov random field based automatic image alignment for electron tomography. Journal of Structural Biology, 161(3), 260-275. [More] [Online version]
  • Carneiro, G., Amat, F., Georgescu, B., Good, S. & Comaniciu, D (2008). Semantic-based indexing of fetal anatomies from 3-D ultrasound data using global/semi-local context and sequential sampling. In CVPR, pages 1-8. Anchorage, AK, USA. [More] [Online version]

Year: 2007

  • Moussavi, F., Amat, F., Comolli, L. R., Elidan, G., Downing, K. H., Koller, D. et al (2007). Markov random field based automatic image alignment for electron tomography. In NIPS workshop. [More]
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