When studying the three-dimensional shape of prophase chromosomes (or any other tubular structure), it is useful to represent these structures as a string of three-dimensional Cartesian coordinates along the medial ax...
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When studying the three-dimensional shape of prophase chromosomes (or any other tubular structure), it is useful to represent these structures as a string of three-dimensional Cartesian coordinates along the medial axis. This procedure was automated in order to limit the number of human interactions and to improve reproducibility. In this paper the design, implementation, and validation of the automated method is presented. From the data presented it can be concluded that the cursor algorithm provides an objective and therefore reproducible method to trace the medial axes of prophase chromosomes automatically. This method could allow a more extensive understanding of the (changes in) chromosome organisation throughout the cell cycle, its relation to cell function, and the complex process of chromosome condensation.
The problem considered is to compensate for the attenuation of light with depth when recording stacks of images with a confocal microscope, working in the epifluorescence mode. A basic assumption is that there are reg...
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The problem considered is to compensate for the attenuation of light with depth when recording stacks of images with a confocal microscope, working in the epifluorescence mode. A basic assumption is that there are regions of the specimen that are homogeneous in the sense that the attenuation is constant within the region. A method is presented to trace such regions in the stack of recordedimages. It is also shown how the attenuation factor of the traced region is determined. Its inverse is the correction factor to be used when compensating for the attenuation relevant to the region. Techniques have been implemented to perform the compensation automatically by changing the photomultiplier tube voltage during the recording, using computer control. Some results of using this technique are reported. To trace a homogeneous region, a stack of 2-d histograms of adjacent images, a histostack, is used. It usually shows distinguishable features through which homogeneous regions can be traced. A homogeneous region may be extracted from the stack of recordedimages anddealt with separately, set apart in a special stack. The residual stack of images, containing what is left over after a homogeneous region has been extracted, is also available, and can be used for further extractions of homogeneous regions. In this way the extraction procedure can be used for image segmentation in three dimensions. A review is given of the fundamentals of the extraction process.
A 3-d segmentation algorithm is presented, based on a split, merge and group approach. It uses a mixed (oct/quad)tree implementation. A number of homogeneity criteria is discussed and evaluated. An example shows the s...
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An algorithm is proposed for skeletonization of 3-dimages. The criterion to preserve connectivity is given in two versions: global and local. The latter allows local decisions in the erosion process. A table of the d...
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