CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2013 vol.10 Issue No.05 - Sept.-Oct.
Quantitative Analysis of Live-Cell Growth at the Shoot Apex of Arabidopsis thaliana: Algorithms for Feature Measurement and Temporal Alignment
Issue No.05 - Sept.-Oct. (2013 vol.10)
Oben M. Tataw , Univ. of California, Riverside, Riverside, CA, USA
G. Venugopala Reddy , Univ. of California, Riverside, Riverside, CA, USA
Eamonn J. Keogh , Univ. of California, Riverside, Riverside, CA, USA
Amit K. Roy-Chowdhury , Univ. of California, Riverside, Riverside, CA, USA
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2013.64
Study of the molecular control of organ growth requires establishment of the causal relationship between gene expression and cell behaviors. We seek to understand this relationship at the shoot apical meristem (SAM) of model plant Arabidopsis thaliana. This requires the spatial mapping and temporal alignment of different functional domains into a single template. Live-cell imaging techniques allow us to observe real-time organ primordia growth and gene expression dynamics at cellular resolution. In this paper, we propose a framework for the measurement of growth features at the 3D reconstructed surface of organ primordia, as well as algorithms for robust time alignment of primordia. We computed areas and deformation values from reconstructed 3D surfaces of individual primordia from live-cell imaging data. Based on these growth measurements, we applied a multiple feature landscape matching (LAM-M) algorithm to ensure a reliable temporal alignment of multiple primordia. Although the original landscape matching (LAM) algorithm motivated our alignment approach, it sometimes fails to properly align growth curves in the presence of high noise/distortion. To overcome this shortcoming, we modified the cost function to consider the landscape of the corresponding growth features. We also present an alternate parameter-free growth alignment algorithm which performs as well as LAM-M for high-quality data, but is more robust to the presence of outliers or noise. Results on primordia and guppy evolutionary growth data show that the proposed alignment framework performs at least as well as the LAM algorithm in the general case, and significantly better in the case of increased noise.
Quantitative analysis, Surface reconstruction, Time series analysis, Biological systems, Gene expression, Three-dimensional displays, Image reconstruction,growth feature measurement, Growth alignment, algorithms
Oben M. Tataw, G. Venugopala Reddy, Eamonn J. Keogh, Amit K. Roy-Chowdhury, "Quantitative Analysis of Live-Cell Growth at the Shoot Apex of Arabidopsis thaliana: Algorithms for Feature Measurement and Temporal Alignment", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.10, no. 5, pp. 1150-1161, Sept.-Oct. 2013, doi:10.1109/TCBB.2013.64