Alexis Boucharin

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UNLABELLED SMeagol is a software tool to simulate highly realistic microscopy data based on spatial systems biology models, in order to facilitate development, validation and optimization of advanced analysis methods for live cell single molecule microscopy data. AVAILABILITY AND IMPLEMENTATION SMeagol runs on Matlab R2014 and later, and uses compiled(More)
The use of regional connectivity measurements derived from diffusion imaging datasets has become of considerable interest in the neuroimaging community in order to better understand cortical and subcortical white matter connectivity. Current connectivity assessment methods are based on streamline fiber tractography, usually applied in a Monte-Carlo fashion.(More)
This paper proposes a new method to compute connectivity information from diffusion weighted images. It is inspired by graphbased approaches to connectivity definition, but formulates the estimation problem in the continuum. In particular, it defines the connectivity through the minimum cut in tensor-weighted space. It is therefore closely related to prior(More)
Regional connectivity measurements derived from diffusion imaging datasets are of considerable interest in the neuroimaging community for better understanding white matter connectivity. Current connectivity measurements are usually either based on fiber tractography applied in Monte-Carlo fashion, or variations of the Hamilton-Jacobi approach, or are(More)
The emergence and spread of antibiotic-resistant bacteria are aggravated by incorrect prescription and use of antibiotics. A core problem is that there is no sufficiently fast diagnostic test to guide correct antibiotic prescription at the point of care. Here, we investigate if it is possible to develop a point-of-care susceptibility test for urinary tract(More)
Fast Antibiotic Susceptibility Testing (FASTest) based on single cell growth rate measurements. Short Title: Fast Antibiotic Susceptibility Testing (FASTest) Özden Baltekin , Alexis Boucharin , Dan I. Andersson , Johan Elf a,1 a Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, SE-751 24 Uppsala, Sweden; and b(More)
In this paper, we have developed tools to analyze prokaryotic cells growing in monolayers in a microfluidic device. Individual bacterial cells are identified using a novel curvature based approach and tracked over time for several generations. The resulting tracks are thereafter assessed and filtered based on track quality for subsequent analysis of(More)
The emergence and spread of antibiotic resistant bacteria is a global threat to human health. The problem is aggravated by unnecessary and incorrect use of broad-spectrum antibiotics. One way to provide correct treatment and to slow down the development of antibiotic resistance is to assay the susceptibility profile of the infecting bacteria before(More)
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