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 representations to quantify, describe, and model objects in bioimages. My research interests include approximation and information 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 approximation theory, engaging in collaborative projects with biologists, and developing image analysis software tools. We have internship opportunities in the team for enthusiastic researchers with an electrical engineering, applied maths or computer science backgound. If you like blending maths and computer vision and enjoy beautiful bioimages, drop me an e-mail!

I currently serve my second term as an associate member in the Bio Imaging and Signal Processing Technical Committee of the IEEE Signal Processing Society.

If you don't find me in the lab, I am most likely either climbing or doing something bird-related.

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. As I enjoy the analog life more than the digital one, be aware that this website might not be up to date. Fortunately, Google Scholar does a decent job at keeping track of my publications.

^{I am grateful to the Stack Overflow user community for their precious advice and help in designing this webpage.}

Preprints

• J. Fageot, V. Uhlmann, Z. Püspöki, B. Beck, M. Unser, A. Depeursinge, "Principled design and implementation of steerable detectors," arXiv: 1811.00863 [eess.IV]. [pdf]

Journals

• A. Song, V. Uhlmann, J. Fageot, M. Unser, "Sparse dictionary learning for 2D Kendall shapes," SIAM Journal on Imaging Science, in press. [pdf]
• J. Fageot, S. Aziznejad, M. Unser, V. Uhlmann, "Support and Approximation Properties of Hermite Splines," Journal of Computational and Applied Mathematics, vol. 268, pp. 112503, April 2020. [pdf]
• D. Nguyen, V. Uhlmann, A.L. Planchette, P.J. Marchand, D. Van De Ville, T. Lasser, A. Radenovic, "Supervised learning to quantify amyloidosis in whole brains of an Alzheimer’s disease mouse model acquired with optical projection tomography," Biomedical Optics Express, vol. 10, no. 6, pp. 3041-3060, June 2019. [pdf]
• J. Fageot, V. Uhlmann, M. Unser, "Gaussian and Sparse Processes Are Limits of Generalized Poisson Processes," Applied and Computational Harmonic Analysis, in press. [pdf]
• V. Uhlmann, C. Haubold, F.A. Hamprecht, M. Unser, "DiversePathsJ: Diverse Shortest Paths for Bioimage Analysis," Bioinformatics, vol. 34, no. 3, pp. 538-540, February 2018. [pdf]
• V. Uhlmann, P. Ramdya, R. Delgado-Gonzalo, R. Benton, M. Unser, "FlyLimbTracker: An Active Contour Based Approach for Leg Segment Tracking in Unmarked, Freely Behaving Drosophila," PLoS ONE, vol. 12, no. 4, pp. 1-21, April 28, 2017. [pdf]
• A. Badoual, D. Schmitter, V. Uhlmann, M. Unser, "Multiresolution Subdivision Snakes," IEEE Transactions on Image Processing, vol. 26, no. 3, pp. 1188-1201, March 2017. [pdf]
• V. Uhlmann, S. Singh, A.E. Carpenter, "CP-CHARM: Segmentation-Free Image Classification Made Accessible," BMC Bioinformatics, vol. 17, no. 1, paper no. 51, December 2016. [pdf]
• V. Uhlmann, J. Fageot, M. Unser, "Hermite Snakes with Control of Tangents," IEEE Transactions on Image Processing, vol. 25, no. 6, pp. 2803-2816, June 2016. [pdf]
• P. Pad, V. Uhlmann, M. Unser, "Maximally Localized Radial Profiles for Tight Steerable Wavelet Frames," IEEE Transactions on Image Processing, vol. 25, no. 5, pp 2275-2287, May 2016. [pdf] [co-first-authorship]
• Z. Püspöki, V. Uhlmann, C. Vonesch, M. Unser, "Design of Steerable Wavelets to Detect Multifold Junctions," IEEE Transactions on Image Processing, vol. 25, no. 2, pp. 643-657, February 2016. [pdf]
• R. Delgado-Gonzalo, D. Schmitter, V. Uhlmann, M. Unser, "Efficient Shape Priors for Spline-Based Snakes," IEEE Transactions on Image Processing, vol. 24, no. 11, pp. 3915-3926, November 2015. [pdf]
• R. Delgado-Gonzalo, V. Uhlmann, D. Schmitter, M. Unser, "Snakes on a Plane: A Perfect Snap for Bioimage Analysis," IEEE Signal Processing Magazine, vol. 32, no. 1, pp. 41-48, January 2015. [pdf]

Conference Proceedings

• C. Haubold, V. Uhlmann, M. Unser, F.A. Hamprecht, "Diverse M-Best Solutions by Dynamic Programming," Proceedings of the 39th German Conference on Pattern Recognition (GCPR'17), Basel, Switzerland, September 13-15, 2017, [Lecture Notes on Image Processing, Computer Vision, Pattern Recognition, and Graphics, vol. 10496, Springer, 2016], pp. 255-267. [pdf] [supplementary]
  [nominated for best paper award]
• V. Uhlmann, R. Delgado-Gonzalo, M. Unser, P.O. Michel, L. Baldi, F.M. Wurm, "User-Friendly Image-Based Segmentation and Analysis of Chromosomes," Proceedings of the 13th IEEE International Symposium on Biomedical Imaging (ISBI'16), Prague, Czech Republic, April 13-16, 2016, pp. 395-398. [pdf]
• V. Uhlmann, J. Fageot, H. Gupta, M. Unser, "Statistical Optimality of Hermite Splines," Proceedings of the 11th International Workshop on Sampling Theory and Applications (SampTA'15), Washington DC, USA, May 25-29, 2015, pp. 226-230. [pdf]
• V. Uhlmann, M. Unser, "Tip-Seeking Active Contours for Bioimage Segmentation," Proceedings of the 12th IEEE International Symposium on Biomedical Imaging (ISBI'15), Brooklyn NY, USA, April 16-19, 2015, pp. 544-547. [pdf]
  [nominated for best paper award]
• P. Pad, V. Uhlmann, M. Unser, "VOW: Variance-Optimal Wavelets for the Steerable Pyramid," Proceedings of the 2014 IEEE International Conference on Image Processing (ICIP'14), Paris, France, October 27-30, 2014, pp. 2973-2977. [pdf]
  [best student paper award]
• V. Uhlmann, R. Delgado-Gonzalo, C. Conti, L. Romani, M. Unser, "Exponential Hermite Splines for the Analysis of Biomedical Images," Proceedings of the 39th IEEE International Conference on Acoustics, Speech, and Signal Processing (ICASSP'14), Firenze, Italy, May 4-9, 2014, pp. 1650-1653. [pdf]
• V. Uhlmann, R. Delgado-Gonzalo, M. Unser, "Snakes with Tangent-Based Control and Energies for Bioimage Analysis," Proceedings of the 11th IEEE International Symposium on Biomedical Imaging (ISBI'14), Beijing, China, April 29-May 2, 2014, pp. 806-809. [pdf]

Thesis

• V. Uhlmann, "Landmark Active Contours for Bioimage Analysis: A Tale of Points and Curves," Swiss Federal Institute of Technology Lausanne, EPFL Thesis no. 7951 (2017), 263 p., December 1, 2017. [pdf]
  [best 2018 doctoral thesis in electrical engineering]

2020

• TBD, Invited Seminar, Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), Dresden, Germany, October 1, 2020.
• TBD, Invited Talk, Computational Challenges in Very Large-Scale Omics Workshop, Simons Institute, Berkeley (CA), USA, July 27-30, 2020.
• TBD, Contributed Talk, 5th IM-Workshop on Applied Approximation, Signals and Images, Bernried, Germany, February 24-28, 2020.
• TBD, Invited Seminar, University of Dundee, Dundee, UK, February 7, 2020.
• TBD, Invited Seminar, CRUK Cambridge Institute, Cambridge, UK, February 17, 2020.
• TBD, Invited Talk, Applied Machine Learning Days, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland, January 27, 2020.

2019

• TBD, Invited Seminar, University of Leeds, Leeds, UK, December 13, 2019.
• "Mathematical Models for Bioimage Analysis," Invited Talk, Women in Computational Biology Workshop, Janelia Research Campus, Ashburn (VA), USA, November 10-13, 2019.
• "Deformable Spline-Based Models for Bioimage Analysis," Invited Talk, European Numerical Mathematics and Advanced Applications Conference (ENUMATH'19), Egmond aan Zee, The Netherlands, September 30-October 4, 2019.
• "Continuous Models in Bioimage Analysis," Invited Talk, Microscience Microscopy Congress (MMC'19), Manchester, UK, July 5-8, 2019.
• "A Guided Tour of Spline-Based Deformable Contours," Invited Talk, Crick Advanced Imaging and Analysis Forum, The Francis Crick Institute, London, UK, May 31, 2019.
• "A Guided Tour of Spline-Based Deformable Contours," Invited Seminar, University of Birmingham, Birmingham, UK, February 25, 2019.
• A. Song, V. Uhlmann, J. Fageot, M. Unser, "Sparse Dictionary Learning for Bioimage Analysis of 2D Shapes," Contributed Talk, 3rd NEUBIAS Conference, Luxembourg, Luxembourg, February 2-8, 2019.

2018

• "Mathematical Models for Bioimage Analysis," Invited Talk, From Images to Knowledge with ImageJ & Friends (I2K'18), Heidelberg, Germany, December 6-8, 2018.
• "A Guided Tour of Spline-based Active Contours," Invited Talk, 3rd NEUBIAS Training School, Edinburgh, UK, October 16-19, 2018.
• "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.
• "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.

2017

• "A Tale of Points and Curves in Bioimage Analysis," Invited Seminar, European Bioinformatics Institute (EMBL-EBI), Hinxton, UK, September 4, 2017.

2016

• 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.

2015

• V. Uhlmann, D. Sage, M. Unser, "Directional Image Analysis in Icy," Contributed Talk, Second Icy Coding Party Pasteur Institute, Paris, France, May 4-6, 2015.

2014

• 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.

2012

• 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.

2019

• "Choices", StoryCollider UK, December 2019.
• "Human VS computer vision in biomedicine," Café Sci Cambridge, May 2019.

I develop mostly Python scripts and pipelines, and 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.

I am still in the process of creating a decent code base, please bear with me in the meantime, and don't hesitate to get in touch if you are struggling to use something I developed.

• Interactive Spline Models: small ImageJ/Fiji plugins to spawn different kind of spline models in an image and interactively deform them. Can be used to generate continuous annotations of object contours.
• 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.

Lectures

• Teacher at the EMBO course on Advanced Methods in Bioimage Analysis, October 2020.
• Teacher at the MBL course on Deep Learning for Microscopy Image Analysis, October 2020.
• Lecturer at Cambridge University's course NST Part II BBS Bioinformatics, February 2020.
• Lecturer at Cambridge University's course IAFIG-RMS: Bioimage analysis with Python, December 2019.
• Lecturer at the Quantitative Biology Module of the EMBL International PhD Programme Predoc Course, October 2019.
• Lecturer at the EMBL Lautenschläger Summer School 2019: Visualising Life - Interdisciplinary Approaches to Biology, July 2019.
• Teacher at the EMBL-EBI / Wellcome Trust Bioinformatics Summer School 2019, June 2019.
• Teaching Assistant for Continuous Signal Processing for Life Scientists and Microengineers (Prof. Michael Unser), 3rd year Bachelor students, 2009 and 2012-2016.
  [2013 EPFL School of Life Sciences best teaching team award]
• Teaching Assistant for Digital Signal Processing for Life Scientists and Microengineers (Prof. Pierre Vandergheynst), 3rd year Bachelor students, 2012-2016.

Students

• Jules Mabon, "Deep learning for mycobacteria tracking on time-lapse images," Master's thesis, 2019.
• Yoann Pradat, "A unified view of Hermite splines," Master's thesis, 2019.
• 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.

• Spline-based deformable models (historically called "snakes")

  Illustrations of differences between cubic B-spline and cubic Hermite snakes.

  

• Spline interpolation

  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.

  

• Worlds of knowledge

  Illustrations of the real, mathematical and digital worlds.

  

• Ls=w

  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.

  

• Weird animals

  

• Stuart impressions

  Illustration of Stuart's moods. Stuart is a cockatiel living in my flat.

  

• Life impressions

  

• Russian impressions

  Illustrations of a conference trip to Novossibirsk.

  

• Climbing impressions