Source: http://virginieuhlmann.com/
Timestamp: 2019-04-25 11:58:20+00:00

Document:
I am a life scientist fond of image data who fell in love with computers and mathematics. I hold a MSc in Bioengineering and a PhD in Electrical Engineering, with a focus on applied maths for image processing.
My work focuses on the development of continuous models for the segmentation, tracking and quantitative analysis of bioimages. My research interests include approximation and spline theory, image processing, computer vision, machine learning and life sciences.
I am leading a Bioimage Analysis research group at the EMBL-EBI in Cambridge, UK. We are interdisciplinary, doing theoretical research on continuous representations for image analysis, engaging in collaborative projects with biologists, and developing image analysis software tools. I am looking for enthusiastic researchers with an electrical engineering, applied maths or computer science backgound to join the team, at the PhD or Post-doc level. If you like blending maths and computer science and enjoys beautiful bioimages, drop me an e-mail!
I currently serve as an associate member in the Bio Imaging and Signal Processing Technical Committee of the IEEE Signal Processing Society.
Apart from scientific stuff, my mind is full of drawings of strange animals, novels and various types of music. I also tend to regularly climb on cliffs or random big rocks.
For more details, please refer to my curriculum vitae. Please note that this is my personal website and is not related to the institution I currently work in.
I warmly thank the Stack Overflow user community for their precious advice and help in designing this webpage.
J. Fageot, V. Uhlmann, M. Unser, "Gaussian and Sparse Processes Are Limits of Generalized Poisson Processes," arXiv:1702.05003 [math.PR].
V. Uhlmann, "A Guided Tour of Spline-based Active Contours," Invited Talk, 3rd NEUBIAS Training School, Edinburgh, UK, October 16-19, 2018.
V. Uhlmann, "Mathematical Models for Bioimage Analysis," Invited Talk, Bioimage Computing Workshop, 15th European Conference on Computer Vision, Munich, Germany, September 8-14, 2018.
V. Uhlmann, J. Fageot, H. Gupta, M. Unser, "Statistical Optimality of Hermite Splines for the Reconstruction of Self-Similar Signals," Invited Talk and Mini-Symposium Organizer, SIAM Conference on Imaging Science (IS'18), Bologna, Italy, June 5-8, 2018.
V. Uhlmann, M. Unser, "Spline-based Models in Bioimage Analysis: Cells beyond Pixels," Invited Talk, Trends in Microscopy: Bridging the Worlds, Düsseldorf, Germany, March 12-14, 2018.
V. Uhlmann, "Continuous Representations in Bioimage Analysis: a Bridge from Pixels to the Real World," Invited Talk, 2nd NEUBIAS Conference, Szeged, Hungary, January 27-February 2, 2018.
V. Uhlmann, "A Tale of Points and Curves in Bioimage Analysis," Invited Public Seminar, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK, September 4, 2017.
V. Uhlmann, M. Unser, "Bioimage Segmentation with Active Contours," Invited Talk, 4th Swiss Imaging Core Facility Day, Geneva, Switzerland, September 16, 2016.
V. Uhlmann, M. Unser, "Spline-based Models for Image Segmentation," Plenary Talk, 1st European Machine Vision Forum, Heidelberg, Germany, September 8-9, 2016.
V. Uhlmann, D. Schmitter, M. Unser, "Shape-constrained Tracking with Active Contours," Invited Talk, SIAM Conference on Imaging Science (IS'16), Albuquerque, NM, USA, May 23-26, 2016.
V. Uhlmann, D. Sage, M. Unser, "Directional Image Analysis in Icy," Contributed Talk, Second Icy Coding Party, Paris, France, May 4-6, 2015.
V. Uhlmann, M. Unser, "Open Active Contours with Tangent-Based Controls and Energies, " Contributed Talk, 1st International Conference on Subdivision, Geometric and Algebraic Methods, Isogeometric Analysis and Refinability in Tuscany (SMART'14), Pontignano, Italy, September 28-October 1, 2014.
V. Uhlmann, S. Singh, C. Wählby, J. McKinney, A. Carpenter, "Whole Image-Based Classification Using CellProfiler," Poster, BioImage Informatics 2012 (BI'12), Dresden, Germany, September 16-19, 2012, pp. 59-60.
I develop mostly Java-based plug-ins for the open-source image analysis softwares ImageJ, Fiji and Icy. I also regularly work with the Python-based softwares CellProfiler and ilastik.
FlyLimbTracker: a fly limb and body tracking plug-in for Icy.
ChromosomeJ and ChromosomeK: a chromosome segmentation and annotation suite for ImageJ.
DiversePathsJ: a dynamic programming approach for the general task of finding diverse shortest paths between two end-points, implemented as a plug-in for ImageJ.
Hermite Active Contours: a generic semi-automated multi-purpose segmentation algorithm for ImageJ. A unified version is currently under development. In the meantime, the more specific Open Hermite Snake and Exponential Hermite Snake plug-ins for ImageJ remain available.
CP-CHARM: a WND-CHARM-like pipeline for whole-image-based classification in CellProfiler.
TA for Continuous Signal Processing for Life Scientists and Microengineers (Prof. Michael Unser), 3rd year Bachelor students, 2009 and 2012-2016.
TA for Digital Signal Processing for Life Scientists and Microengineers (Prof. Pierre Vandergheynst), 3rd year Bachelor students, 2012-2016.
Anna Song (co-advised with Dr. J. Fageot and Prof. M. Unser), "Analysis of planar shapes through shape dictionary learning with an extension to splines," Master's thesis, 2018.
Julien Rüegg (co-advised with Prof. P. Ramdya and Prof. M. Unser), "Tracking animal behavior in neuroimaging studies," Master's thesis, 2018.
Alexandre Cherqui (co-advised with Prof. M. Unser), "A study of the tip detection problem," semester project, 2018.
Julien Rüegg (co-advised with Dr. J. Fageot and Prof. M. Unser), "A study of Hermite spline interpolation," semester project, 2017.
Gaëlle Thurre (co-advised with Prof. John McKinney), "Modeling single-cell behavior of Mycobacteria," semester project, 2015.
Bertrand Vermot (co-advised with Dr. J. Fageot and Prof. M. Unser), "Corner detection based on PDE methods," semester project, 2015.
Miryam Chaabouni (co-advised with Dr. J. Fageot, Dr. D. Schmitter and Prof. M. Unser), "Design of active contour models using NURBS," semester project, 2015.
Arik Girsault (co-advised with Dr. E. Bostan and Prof. M. Unser), "A nonlinear model of phase contrast microscopy," semester project, 2015.
Lucas Amoudruz (co-advised with Prof. M. Unser), "Refining leg movement extraction in high-speed videos of insect locomotion," semester project, 2014.
Amicie de Pierrefeu (co-advised with Dr. D. Sage, and Prof. M. Unser), "Tracking flagella endulations in microscopy images," semester project, 2014.
Laurène Donati (co-advised with Prof. M. Unser), "Modeling Mycobacteria behavior in time-lapse microscopy images," semester project, 2014.
Pritish Chakravarty (co-advised with Prof. M. Unser), "Designing tip detectors," semester project, 2014.
Loïc Perruchoud (co-advised with Dr. C. Vonesch and Prof. M. Unser), "Tracking leg movements in high-speed videos of insect locomotion," semester project, 2013.
Olivia Mariani (co-advised with Prof. M. Unser), "Segmentation and tracking of growing colonies of Mycobacteria," Master's thesis, 2013.
I think and explain better when I doodle. Below are some illustrations of this tendency.
These are personal scribbles. In the unlikely event you would like to reuse some of them, I would appreciate to be asked first.
Illustrations of differences between cubic B-spline and cubic Hermite snakes.
Illustrations of the ability of different spline bases to approximate complex shapes by "linking the dots" and serving as a bridge between the analog and the digital worlds.
Illustrations of the real, mathematical and digital worlds.
Illustrations around Ls=w, the magical formula of my Doktorvater, Michael Unser, concieved together with Julien Fageot for the 20th birthday of the Biomedical Imaging Group at EPFL.
Illustration of Stuart's moods. Stuart is a cockatiel living in my flat.
Illustrations of a conference trip to Novossibirsk.

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