Team, Visitors, External Collaborators
Overall Objectives
Research Program
Application Domains
Highlights of the Year
New Software and Platforms
New Results
Bilateral Contracts and Grants with Industry
Partnerships and Cooperations
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Section: Research Program

From image data to motion descriptors: trajectory computation and dynamics analysis

Several particle tracking methods for intracellular analysis have been tailored to cope with different types of cellular and subcellular motion down to Brownian single molecule behavior. Many algorithms were carefully evaluated on the particle tracking challenge dataset published in the Nature Methods journal in 2014. Actually, there is no definitive solution to the particle tracking problem which remains application-dependent in most cases. The work of serpico in particle motion analysis is significant in multiple ways, and inserts within a very active international context. One of the remaining key open issues is the tracking of objects with heterogeneous movements in crowded configurations. Moreover, particle tracking methods are not always adapted for motion analysis, especially when the density of moving features hampers the individual extraction of objects of interest undergoing complex motion. Estimating flow fields can be more appropriate to capture the complex dynamics observed in biological sequences. The existing optical flow methods can be classified into two main categories: i/ local methods impose a parametric motion model (e.g. local translation) in a given neighborhood; ii/ global methods estimate the dense motion field by minimizing a global energy functional composed of a data term and a regularization term.

The serpico team has developed a strong expertise in key topics, especially in object tracking for fluorescence microscopy, optical flow computation and high-level analysis of motion descriptors and trajectories. Several algorithms proposed by the team are very competitive when compared to the state-of-the-art results, and our new paradigms offer promising ways for molecule traffic quantification and analysis. Amongst the problems that we currently address, we can mention: computation of 3D optical flow for large-size images, combination of two frame-based differential methods and sparse sets of trajectories, detection and analysis of unexpected local motion patterns in global coherent collective motion. Development of efficient numerical schemes will be central in the future but visualization methods are also crucial for evaluation and quality assessment. Another direction of research consists in exploiting deep learning to 3D optical flow so as to develop efficient numerical schemes that naturally capture complex motion patterns. Investigation in machine learning and statistics will be actually conducted in the team in the two first research axes to address a large range of inverse problems in bioimaging. Deep learning is an appealing approach since expertise of biologists, via iterative annotation of training data, will be included in the design of image analysis schemes.