Image Analysis Algorithms for Single-Cell Study in Systems Biology
Research output: Book/Report › Doctoral thesis › Collection of Articles
|Publisher||Tampere University of Technology|
|Number of pages||70|
|Publication status||Published - 13 May 2016|
|Publication type||G5 Doctoral dissertation (article)|
|Name||Tampere University of Technology. Publication|
First, a study evaluates several methods for focusing microscopes and proposes a novel strategy to perform focusing in time-lapse imaging. The method relies on the nature of the focus-drift and its predictability. The study shows that focus-drift is a dynamical system with a small randomness. Therefore, a prediction-based method is employed to track the focus-drift overtime. A prototype implementation of the proposed method is created by extending the Nikon EZ-C1 Version 3.30 (Tokyo, Japan) imaging platform for acquiring images with a Nikon Eclipse (TE2000-U, Nikon, Japan) microscope.
Second, a novel method is formulated to segment individual cells from a dense cluster. The method incorporates multi-resolution analysis with maximum-likelihood estimation (MAMLE) for cell detection. The MAMLE performs cell segmentation in two phases. The initial phase relies on a cutting-edge ﬁlter, edge detection in multi-resolution with a morphological operator, and threshold decomposition for adaptive thresholding. It estimates morphological features from the initial results. In the next phase, the ﬁnal segmentation is constructed by boosting the initial results with the estimated parameters. The MAMLE method is evaluated with de novo data sets as well as with benchmark data from public databases. An empirical evaluation of the MAMLE method conﬁrms its accuracy.
Third, a comparative study is carried out on performance evaluation of state-ofthe-art methods for the detection of subcellular organelles. This study includes eleven algorithms developed in different ﬁelds for segmentation. The evaluation procedure encompasses a broad set of samples, ranging from benchmark data to synthetic images. The result from this study suggests that there is no particular method which performs superior to others in the test samples. Next, the effect of tetracycline on transcription dynamics of tetA promoter in Escherichia coli (E. coli ) cells is studied. This study measures expressions of RNA by tagging the MS2d-GFP vector with a target gene. The RNAs are observed as intracellular spots in confocal images. The kernel density estimation (KDE) method for detecting the intracellular spots is employed to quantify the individual RNA molecules.
The thesis summarizes the results from ﬁve publications. Most of the publications are associated with different methods for imaging and analysis of microscopy. Confocal images with E. coli cells are targeted as the primary area of application. However, potential applications beyond the primary target are also made evident. The ﬁndings of the research are conﬁrmed empirically.