Bioimage analysis

Bioimage analysis

Our group develops bioimage analysis tools that blend continuous mathematical models and computer vision (e.g., learning-based) algorithms.

We are interested in flexible contour representations that allow identifying and precisely characterizing biological objects in a large variety of image data. These models can then be applied to quantify phenotypical variations at the single-cell or single-individual level in experiments ranging from genome-wide knockout screens to population dynamics studies.

We are recruiting students who have a good background in computer vision and image processing, with interests in optimisation, approximation and sampling theory.

Our group will start at EMBL-EBI on 15 September 2018.

Selected publications

Uhlmann V, Ramdya P, Delgado-Gonzalo R, Benton R, Unser M (2017) FlyLimbTracker: An active contour based approach for leg segment tracking in unmarked, freely behaving Drosophila. PLOS ONE 12:1-21.

Uhlmann V, Fageot J, Unser M (2016) Hermite snakes with control of tangents. IEEE Transactions on Image Processing 25:2803-2816.

Delgado-Gonzalo R, Uhlmann V, Schmitter D, Unser M (2015) Snakes on a plane: A perfect snap for bioimage analysis. IEEE Signal Processing Magazine 32:41-48.

Uhlmann V, Haubold C, Hamprecht FA, Unser M (2018) DiversePathsJ: Diverse shortest paths for bioimage analysis. Bioinformatics 34:538–540.