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User-Friendly Image-Based Segmentation and Analysis of Chromosomes

V. Uhlmann, R. Delgado-Gonzalo, M. Unser, P.O. Michel, L. Baldi, F.M. Wurm

Proceedings of the Thirteenth IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI'16), Prague, Czech Republic, April 13-16, 2016, pp. 395-398.

We designed two efficient and user-friendly tools for the segmentation and analysis of images containing chromosomes or, more generally, rod-shaped elements that are spread on microscopic slides. The segmentation tool allows to automatically extract the profile of each chromosome and to sort the collection of profiles in a karyotype image. The analysis tool is interactive and allows to extract quantitative measurements and annotate the relative position of the centromere to the chromosome extremities in a fast and reproducible way. The two methods rely on custom variants of parametric active contours. Both have been designed as user-friendly plug-ins for the open-source software ImageJ.

AUTHOR="Uhlmann, V. and Delgado-Gonzalo, R. and Unser, M. and Michel,
        P.O. and Baldi, L. and Wurm, F.M.",
TITLE="User-Friendly Image-Based Segmentation and Analysis of
BOOKTITLE="Proceedings of the Thirteenth {IEEE} International Symposium
        on Biomedical Imaging: {F}rom Nano to Macro ({ISBI'16})",
address="Prague, Czech Republic",
month="April 13-16,",

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