17,233 research outputs found
Identifying stochastic oscillations in single-cell live imaging time series using Gaussian processes
Multiple biological processes are driven by oscillatory gene expression at
different time scales. Pulsatile dynamics are thought to be widespread, and
single-cell live imaging of gene expression has lead to a surge of dynamic,
possibly oscillatory, data for different gene networks. However, the regulation
of gene expression at the level of an individual cell involves reactions
between finite numbers of molecules, and this can result in inherent randomness
in expression dynamics, which blurs the boundaries between aperiodic
fluctuations and noisy oscillators. Thus, there is an acute need for an
objective statistical method for classifying whether an experimentally derived
noisy time series is periodic. Here we present a new data analysis method that
combines mechanistic stochastic modelling with the powerful methods of
non-parametric regression with Gaussian processes. Our method can distinguish
oscillatory gene expression from random fluctuations of non-oscillatory
expression in single-cell time series, despite peak-to-peak variability in
period and amplitude of single-cell oscillations. We show that our method
outperforms the Lomb-Scargle periodogram in successfully classifying cells as
oscillatory or non-oscillatory in data simulated from a simple genetic
oscillator model and in experimental data. Analysis of bioluminescent live cell
imaging shows a significantly greater number of oscillatory cells when
luciferase is driven by a {\it Hes1} promoter (10/19), which has previously
been reported to oscillate, than the constitutive MoMuLV 5' LTR (MMLV) promoter
(0/25). The method can be applied to data from any gene network to both
quantify the proportion of oscillating cells within a population and to measure
the period and quality of oscillations. It is publicly available as a MATLAB
package.Comment: 36 pages, 17 figure
Motion clouds: model-based stimulus synthesis of natural-like random textures for the study of motion perception
Choosing an appropriate set of stimuli is essential to characterize the
response of a sensory system to a particular functional dimension, such as the
eye movement following the motion of a visual scene. Here, we describe a
framework to generate random texture movies with controlled information
content, i.e., Motion Clouds. These stimuli are defined using a generative
model that is based on controlled experimental parametrization. We show that
Motion Clouds correspond to dense mixing of localized moving gratings with
random positions. Their global envelope is similar to natural-like stimulation
with an approximate full-field translation corresponding to a retinal slip. We
describe the construction of these stimuli mathematically and propose an
open-source Python-based implementation. Examples of the use of this framework
are shown. We also propose extensions to other modalities such as color vision,
touch, and audition
Modeling of evolving textures using granulometries
This chapter describes a statistical approach to classification of dynamic texture images, called parallel evolution functions (PEFs). Traditional classification methods predict texture class membership using comparisons with a finite set of predefined texture classes and identify the closest class. However, where texture images arise from a dynamic texture evolving over time, estimation of a time state in a continuous evolutionary process is required instead. The PEF approach does this using regression modeling techniques to predict time state. It is a flexible approach which may be based on any suitable image features. Many textures are well suited to a morphological analysis and the PEF approach uses image texture features derived from a granulometric analysis of the image. The method is illustrated using both simulated images of Boolean processes and real images of corrosion. The PEF approach has particular advantages for training sets containing limited numbers of observations, which is the case in many real world industrial inspection scenarios and for which other methods can fail or perform badly. [41] G.W. Horgan, Mathematical morphology for analysing soil structure from images, European Journal of Soil Science, vol. 49, pp. 161ā173, 1998. [42] G.W. Horgan, C.A. Reid and C.A. Glasbey, Biological image processing and enhancement, Image Processing and Analysis, A Practical Approach, R. Baldock and J. Graham, eds., Oxford University Press, Oxford, UK, pp. 37ā67, 2000. [43] B.B. Hubbard, The World According to Wavelets: The Story of a Mathematical Technique in the Making, A.K. Peters Ltd., Wellesley, MA, 1995. [44] H. Iversen and T. Lonnestad. An evaluation of stochastic models for analysis and synthesis of gray-scale texture, Pattern Recognition Letters, vol. 15, pp. 575ā585, 1994. [45] A.K. Jain and F. Farrokhnia, Unsupervised texture segmentation using Gabor filters, Pattern Recognition, vol. 24(12), pp. 1167ā1186, 1991. [46] T. Jossang and F. Feder, The fractal characterization of rough surfaces, Physica Scripta, vol. T44, pp. 9ā14, 1992. [47] A.K. Katsaggelos and T. Chun-Jen, Iterative image restoration, Handbook of Image and Video Processing, A. Bovik, ed., Academic Press, London, pp. 208ā209, 2000. [48] M. KĀØoppen, C.H. Nowack and G. RĀØosel, Pareto-morphology for color image processing, Proceedings of SCIA99, 11th Scandinavian Conference on Image Analysis 1, Kangerlussuaq, Greenland, pp. 195ā202, 1999. [49] S. Krishnamachari and R. Chellappa, Multiresolution Gauss-Markov random field models for texture segmentation, IEEE Transactions on Image Processing, vol. 6(2), pp. 251ā267, 1997. [50] T. Kurita and N. Otsu, Texture classification by higher order local autocorrelation features, Proceedings of ACCV93, Asian Conference on Computer Vision, Osaka, pp. 175ā178, 1993. [51] S.T. Kyvelidis, L. Lykouropoulos and N. Kouloumbi, Digital system for detecting, classifying, and fast retrieving corrosion generated defects, Journal of Coatings Technology, vol. 73(915), pp. 67ā73, 2001. [52] Y. Liu, T. Zhao and J. Zhang, Learning multispectral texture features for cervical cancer detection, Proceedings of 2002 IEEE International Symposium on Biomedical Imaging: Macro to Nano, pp. 169ā172, 2002. [53] G. McGunnigle and M.J. Chantler, Modeling deposition of surface texture, Electronics Letters, vol. 37(12), pp. 749ā750, 2001. [54] J. McKenzie, S. Marshall, A.J. Gray and E.R. Dougherty, Morphological texture analysis using the texture evolution function, International Journal of Pattern Recognition and Artificial Intelligence, vol. 17(2), pp. 167ā185, 2003. [55] J. McKenzie, Classification of dynamically evolving textures using evolution functions, Ph.D. Thesis, University of Strathclyde, UK, 2004. [56] S.G. Mallat, Multiresolution approximations and wavelet orthonormal bases of L2(R), Transactions of the American Mathematical Society, vol. 315, pp. 69ā87, 1989. [57] S.G. Mallat, A theory for multiresolution signal decomposition: the wavelet representation, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 11, pp. 674ā693, 1989. [58] B.S. Manjunath and W.Y. Ma, Texture features for browsing and retrieval of image data, IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 18, pp. 837ā842, 1996. [59] B.S. Manjunath, G.M. Haley and W.Y. Ma, Multiband techniques for texture classification and segmentation, Handbook of Image and Video Processing, A. Bovik, ed., Academic Press, London, pp. 367ā381, 2000. [60] G. Matheron, Random Sets and Integral Geometry, Wiley Series in Probability and Mathematical Statistics, John Wiley and Sons, New York, 1975
Pigment Melanin: Pattern for Iris Recognition
Recognition of iris based on Visible Light (VL) imaging is a difficult
problem because of the light reflection from the cornea. Nonetheless, pigment
melanin provides a rich feature source in VL, unavailable in Near-Infrared
(NIR) imaging. This is due to biological spectroscopy of eumelanin, a chemical
not stimulated in NIR. In this case, a plausible solution to observe such
patterns may be provided by an adaptive procedure using a variational technique
on the image histogram. To describe the patterns, a shape analysis method is
used to derive feature-code for each subject. An important question is how much
the melanin patterns, extracted from VL, are independent of iris texture in
NIR. With this question in mind, the present investigation proposes fusion of
features extracted from NIR and VL to boost the recognition performance. We
have collected our own database (UTIRIS) consisting of both NIR and VL images
of 158 eyes of 79 individuals. This investigation demonstrates that the
proposed algorithm is highly sensitive to the patterns of cromophores and
improves the iris recognition rate.Comment: To be Published on Special Issue on Biometrics, IEEE Transaction on
Instruments and Measurements, Volume 59, Issue number 4, April 201
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