The three-dimensional (3D) organization of chromosomes of Crepis capillaris (2n = 6) has been investigated. Root tips were fixed, macerated with enzymes and gently separated without squashing. The cells were then stained with DAPI and optically sectioned under computer control. Sections were stored as video images and processed to remove noise and out-of-focus information. Computer modelling was then used to trace the paths of each chromosome and to display the paths as a 3D wire diagram. In

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... , 88 sets of anaphase chromosomes were modelled from 47 optically sectioned cells. The models and the coordinates of the chromosomes were then analysed to detect non-random arrangements or preferential associations of particular pairs of chromosomes. The methods used have significant advantages over electron microscope tomography for the analysis of 3D chromosome arrangement; in particular, the large number of samples allowed more thorough statistical tests to be performed on the data obtained. No evidence was found for either non-random arrangements or homologous association and, moreover, the distances between the two larger pairs of homologues were larger than for other pairs of chromosomes. These results conflict with previous results for this and other plant species where the material was squashed before measurements were taken. We found no evidence of haploid genome separation.