Quantitative Bioimage Computation — Computer Vision and Machine Learning to Facilitate Biological Research

The overarching goal of research conducted in my lab aims at pushing the boundary of what image analyses and machine learning can do for quantifying biological data. Projects we are currently pursuing aim at understanding e.g. apical constriction during gastrulation in C.elegans, mitotic cluster formation in Drosophila and Tribolium, or morphological tissue changes in the green alga Volvox. The common denominator of such projects is the undisputable necessity to analyze large amounts of light microscopy data without causing impossible amounts of manual data curation and processing – often the one major bottleneck.

From a computational point of view we are interests in (i) object segmentation and tracking, e.g. cells or nuclei, that enables easy and powerful data curation workflows (‘leveraged editing’), (ii) building feature rich ‘downstream’ quantification pipelines, and (iii) casting those functionalities in reusable and modular software packages. More technical aspects of our daily work are: (i) developing and applying novel, scalable solvers for the graphical models that underlie the automated data processing, and (ii) enabling so called ‘deep learning’ techniques to be applied to biological data.

Results in the field show that the next generation of quantification algorithms and (semi-)automated pipelines will have a big impact on cell and developmental biology, enabling research that is to date simply not feasible. At the same time I am convinced that recent advances in image analysis and machine learning, once applicable to biologically relevant data, will allow us to make big strides towards gaining a deeper understanding of a wide range of cellular and developmental processes.

Future plans

In order to work on relevant biological problems, the lab usually starts tight and fruitful collaborations with colleagues around the world. The projects we take on are therefore relatively diverse, spanning various model organisms and aim at answering a series of fundamental questions in cell and developmental biology. However all these projects share the need for an effective quantification of tremendous amounts of biological (image-)data. Developing algorithms and computational solutions that make this possible lies right at the heart of our mission.

A screenshot of one of our final ‘software products’. The underlying segmentation, tracking, and proofreading capabilities (‘leveraged editing’) make this a unique tool that helps analyzing large microscopy time-lapses. Next to the scientific staff that tackles the many open computer vision and machine learning problems to be solved, we also employ software developers that help making such technological advances become accessible to our collaborators.

Methodological and Technical Expertise

  • Graphical Models (Bayesian Networks/ Factor Graphs)
  • Deep Learning (Classification, Domain Adaptation, etc.)
  • Discrete Optimization
  • Efficient Algorithms
  • Software Design and Development

Selected Publications


Kaiser Matthias, Florian Jug, Olin Silander, Siddharth Deshpande, Thomas Pfohl, Thomas Julou, Gene Myers, Erik van Nimwegen
Tracking single-cell gene regulation in dynamically controlled environments using an integrated microfluidic and computational setup
bioRxiv, Art. No. 076224 (2016)
Florian Jug, Evgeny Levinkov, Corinna Blasse, Eugene W Myers, Bjoern Andres
Moral Lineage Tracing
In: Proceedings 29th IEEE Conference on Computer Vision and Pattern Recognition (CVPR 2016) (2016), Piscataway, N.J., IEEE (2016), 5926-5935


Loic Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, Eugene W Myers
ClearVolume: open-source live 3D visualization for light-sheet microscopy.
Nat Methods, 12(6) 480-481 (2015)


Florian Jug, Tobias Pietzsch, Dagmar Kainmueller, Jan Funke, Matthias Kaiser, Erik van Nimwegen, Carsten Rother, Gene Myers
Optimal Joint Segmentation and Tracking of Escherichia Coli in the Mother Machine
In: Bayesian and grAphical models for biomedical imaging first international workshop, BAMBI 2014, Cambridge, MA, USA, September 18, 2014 ; revised selected papers (2014) Lecture Notes in Computer Science ; 8677, New York, Springer (2014), 25-36
Florian Jug, Tobias Pietzsch, Stephan Preibisch, Pavel Tomancak
Bioimage Informatics in the context of Drosophila research.
Methods, 68(1) 60-73 (2014)
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