Figure 1. Extracting cell positions, shapes and trajectories from limages.
a. Segmentation of cells by intensity thresholding. Left: raw image of fluorescent Listeria bacteria. Right: segmentation result (each colour corresponds to a distinct segmented object). Note that the two touching cells (arrow) are not distinguished.
b. Detection and localization of cells by optimizing a model of multiple rods. From left to right: raw image of Shigella bacteria, raw image with detected rods shown as red bars, corresponding model image, and segmentation by thresholding for comparison.
c. Segmentation and tracking by active contours. A differential interference contrast image of Entamoeba histolytica cells is shown. Each superposed coloured curve is a distinct active contour. Inset: trajectories of five cells tracked by active contours.
d. Segmentation by level sets. A fluorescence micoscopy image of three Plasmodium falciparum sporozoites is shown with superposed level set contours (red curves). The level set evolves from an automatically defined initialization (left) to the final segmentation (right, green curves).
e. Simulated images of a fluorescent rod with added noise (SNR as indicated).
f. Quantitative validation of the rod-detection algorithm on the simulated images. CDR indicates rate of correct detection, RMSE indicates random mean square error (a measure of accuracy) in estimations of the rod's centre (x,y), orientation (θ) and intensity (A).
g. Fluorescence image of a yeast nucleus (two projections of a 3D image stack). The bright green dot (arrow) corresponds to a single GFP-labelled chromatin locus. The nuclear envelope is also stained with GFP, while the nucleolus is labelled with mCherry (red). Scale bar, 1 μm.
h. Qualitative validation of a method to map the nuclear territories of chromosomal loci in yeast by automated analysis of images such as shown in panel g.
The heat maps show the positioning probability of the spindle pole body (SPB) and a ribosomal DNA gene (rDNA) in a co-ordinate system defined by the centre of the nucleus (centre of yellow dashed circle) and the centre of the nucleolus (centre of dotted red curve). The SPB is known to be embedded in the nuclear envelope, and the rDNA in the nucleolus, which is known to occupy a crescent-shaped region located opposite the SPB. The computed maps agree with this expectation, thus qualitatively validating the method. Panels b, e and f are reproduced from (Zhang et al., 2006) (Copyright © 2006, IEEE), panel c (inset) from Zimmer et al. (2002) (Copyright © 2002, IEEE) and panels g and h from (Berger et al., 2008).
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