Automatic detection of large dense-core vesicles in secretory cells and statistical analysis of their intracellular distribution

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 7, Issue 1, 2010, Pages 2-11

  Díaz, Ester ^a   Ayala, Guillermo ^a   Díaz, María Elena ^a   Gong, Liang Wei ^b   Toomre, Derek ^c  

^a UNIVERSITY OF VALENCIA   (Spain)

^b UNIVERSITY OF ILLINOIS AT CHICAGO   (United States)

^c YALE UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

Biology and genetics; Bootstrap methods; Clustering; Computer vision; Correlation and regression analysis; Electron microscopy; Exocytosis; Image segmentation; Large dense core vesicles.; Pattern analysis; Replicated spatial point patterns; Stochastic processes

Indexed keywords

BIOLOGY AND GENETICS; BOOTSTRAP METHOD; BOOTSTRAP METHODS; CLUSTERING; CORRELATION AND REGRESSION ANALYSIS; DENSE CORE; PATTERN ANALYSIS; SPATIAL POINT PATTERN; STOCHASTIC PROCESS;

CELL MEMBRANES; CHROMOSOMES; COMPUTER VISION; CYTOLOGY; DIGITAL IMAGE STORAGE; DISTRIBUTION FUNCTIONS; ELECTRON MICROSCOPY; GRANULATION; IMAGE ENHANCEMENT; IMAGE SEGMENTATION; RANDOM PROCESSES; REGRESSION ANALYSIS; SIZE DISTRIBUTION; STOCHASTIC SYSTEMS;

POINT GROUPS;

ALGORITHM; ANIMAL; ARTICLE; ARTIFICIAL INTELLIGENCE; AUTOMATED PATTERN RECOGNITION; BIOLOGICAL MODEL; CELL CULTURE; CHROMAFFIN CELL; CHROMAFFIN GRANULE; COMPUTER ASSISTED DIAGNOSIS; COMPUTER SIMULATION; ELECTRON MICROSCOPY; EVALUATION; IMAGE ENHANCEMENT; INFORMATION RETRIEVAL; METHODOLOGY; MOUSE; NEWBORN; REPRODUCIBILITY; SECRETORY VESICLE; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS; STATISTICAL MODEL; ULTRASTRUCTURE;

ALGORITHMS; ANIMALS; ANIMALS, NEWBORN; ARTIFICIAL INTELLIGENCE; CELLS, CULTURED; CHROMAFFIN CELLS; CHROMAFFIN GRANULES; COMPUTER SIMULATION; DATA INTERPRETATION, STATISTICAL; IMAGE ENHANCEMENT; IMAGE INTERPRETATION, COMPUTER-ASSISTED; INFORMATION STORAGE AND RETRIEVAL; MICE; MICROSCOPY, ELECTRON; MODELS, BIOLOGICAL; MODELS, STATISTICAL; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SECRETORY VESICLES; SENSITIVITY AND SPECIFICITY;

EID: 76849092028     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.30     Document Type: Article

References (29)

1. R. Burgoyne and A. Morgan, "Calcium Sensors in Regulated Exocytosis," Cell Calcium, vol.24, no.5-6, pp. 367-376, 1998.
2. A. Garcia, A. Garcia-De-Diego, L. Gandia, and J. Garcia-Sancho, "Calcium Signaling and Exocytosis in Adrenal Chromaffin Cells," Physiological Rev., vol.86, no.4, pp. 1093-1131, 2006.
3. S. Tooze, G. Martens, and W. Huttner, "Secretory Granule Biogenesis: Rafting to the Snare," Trends in Cell Biology, vol.11, no.3, pp. 116-122, 2001.
4. R. Burgoyne and A. Morgan, "Secretory Granule Exocytosis," Physiological Rev., vol.83, pp. 581-632, 2002.
5. L. Gong, I. Hafez, G. Alvarez de Toledo, and M. Lindau, "Secretory Vesicles Membrane Area Is Regulated in Tandem with Quantal Size in Chromaffin Cells," J. Neuroscience, vol.23, no.21, pp. 7917-7921, 2003.
6. L. Gutierrez, S. Viniegra, J. Rueda, A. Ferrer-Montiel, J. Canaves, and M. Montal, "A Peptide That Mimics the C-Terminal Sequence of Snap-25 Inhibits Secretory Vesicle Docking in Chromaffin Cells," J. Biological Chemistry, vol.272, pp. 2634-2639, 1997.
7. L. Koval, E. Yavorskaya, and E. Lukyanetz, "Ultrastructural Features of Medullary Chromaffin Cell Cultures," Neuroscience, vol.96, pp. 639-649, 2000.
8. L. Koval, E. Yavorskaya, and E. Lukyanetz, "Electron Microscopic Evidence for Multiple Types of Secretory Vesicles in Bovine Chromaffin Cells," General and Comparative Endocrinology, vol.121, pp. 261-277, 2001.
9. H. Plattner, A. Artalejo, and E. Neher, "Ultrastructural Organization of Bovine Chromaffin Cell Cortex-Analysis by Cryofixation and Morphometry of Aspects Pertinent to Exocytosis," J. Cell Biology, vol.139, pp. 1709-1717, 1997.
10. E. Pothos, E. Mosharov, L. Kuo-Peing, W. Setlik, M. Haburcak, G. Baldini, M. Gershon, H. Tamir, and D. Sulzer, "Stimulation-Dependent Regulation of the PH, Volume and Quantal Size of Bovine and Rodent Secretory Vesicles," J. Physiology, vol.542.2, pp. 453-476, 2002.
11. O. Yizhar, U. Matti, R. Melamed, Y. Hagalili, D. Bruns, J. Rettig, and U. Ashery, "Tomosyn Inhibits Priming of Large Dense-Core Vesicles in a Calcium-Dependent Manner," Proc. Nat'l Academy of Sciences USA, vol.101, pp. 2578-2583, 2004.
12. P. Keller, D. Toomre, E. Diaz, J. White, and K. Simons, "Multicolor Imaging of Post-Golgi Sorting and Trafficking in Live Cells," Nature Cell Biology, vol.3, pp. 140-149, 2001.
13. R. Sebastian, M.E. Díaz, G. Ayala, K. Letinic, J. Moncho-Bogani, and D. Toomre, "Spatio-Temporal Analysis of Constitutive Exocytosis in Epithelial Cells," IEEE/ACM Trans. Computational Biology and Bioinformatics, vol.3, no.1, pp. 17-32, Jan.-Mar. 2006.
14. N. Cressie, Statistics for Spatial Data, revised ed. John Wiley & Sons, 1993.
15. P. Diggle, Statistical Analysis of Spatial Point Patterns, second ed. Arnold, 2003.
16. D. Stoyan and H. Stoyan, Fractals, Random Shapes and Point Fields: Methods of Geometrical Statistics. John Wiley & Sons, 1994.
17. D. Stoyan, W. Kendall, and J. Mecke, Stochastic Geometry and Its Applications, second ed. John Wiley & Sons, 1995.
18. L. Gong, G. Di Paolo, E. Díaz, G. Cestra, M. Díaz, M. Lindau, P. De Camilli, and D. Toomre, "Phosphatidylinositol Phosphate Kinase Type I Regulates Dynamics of Large Dense-Core Vesicle Fusion," Proc. Nat'l Academy of Sciences USA, vol.102, no.14, pp. 5204-5209, 2005.
19. M. De Graef, Introduction to Conventional Transmission Electron Microscopy. Cambridge Univ. Press, 2003.
20. J. McIntosh, "Electron Microscopy of Cells: A New Beginning for a New Century," J. Cell Biology, vol.153, no.6, pp. F25-F32, 2001.
21. B. Loo, B. Parvin, and S. Rothman, "Two-and Three-Dimensional Segmentation for Measurement of Particles in the Analysis of Microscopic Digital Images of Biological Samples," Proc. SPIE, vol.2655, pp. 209-215, 1996.
22. J. Serra, Image Analysis and Mathematical Morphology. Academic Press, 1982.
23. P. Soille, Morphological Image Analysis: Principles and Applications, second ed. Springer, 2003.
24. K. Castleman, Digital Image Processing. Prentice Hall, 1996.
25. M. Sonka and J. Fitzpatrick, Medical Image Processing and Analysis, vol.2. SPIE Press, 2000.
26. R Development Core Team, R: A Language and Environment for Statistical Computing. R Foundation for Statistical Computing, Vienna, Austria, http://www.R-project.org, 2004.
27. A. Agresti, Categorical Data Analysis, second ed. John Wiley & Sons, 2002.
28. B. Efron and R. Tibshirani, An Introduction to the Bootstrap. Chapman and Hall/CRC, 1993.
29. P. Diggle et al., "Analysis of Variance for Replicated Spatial Point Patterns in Clinical Neuroanatomy," J. Am. Statistical Assoc., vol.86, pp. 618-625, 1991.