ISBI 2016
Michael Unser, Denis Fortun, EPFL STI LIB

Test Run • 06 April 2016 • BM 4 233

Abstract
Title 1: User-Friendly Image-Based Segmentation and Analysis of Chromosomes Presenter: Prof. Unser Abstract 1: 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. Title 2: Isotropic resolution in fluorescence imaging by single particle reconstruction Presenter: Denis Abstract 2: Low axial resolution is a major limitation of fluorescence imaging modalities. We propose a methodology to achieve high isotropic resolution by reconstructingfluorescence volumes from observations of multiple particle replicates with different orientations. The challenge is to conciliate high reconstruction accuracy, requiring a large amount of input 3D data, with computational tractability. We achieve this goal by designing an iterative joint deconvolution and multiview reconstruction algorithm with an efficient augmented-Lagrangian based optimization. The computational cost is limited to only two FFTs per iterations, regardless of the number of input particles. We also adopt the nuclear norm of the Hessian as regularizer to avoid the usual staircase artifacts of the more standard total-variation. Experimental validation on realistic simulated data demonstrate the efficiency and accuracy of our method.