Optimal joint segmentation and tracking of Escherichia coli in the mother machine

Jug, Florian and Pietzsch, Tobias and Kainmüller, Dagmar and Funke, Jan and Kaiser, Matthias and van Nimwegen, Erik and Rother, Carsten and Myers, Gene. (2014) 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. Cham, pp. 25-36.

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Official URL: http://edoc.unibas.ch/dok/A6338900

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We introduce a graphical model for the joint segmentation and tracking of E. coli cells from time lapse videos. In our setup cells are grown in narrow columns (growth channels) in a so-called “Mother Machine” [1]. In these growth channels, cells are vertically aligned, grow and divide over time, and eventually leave the channel at the top. The model is built on a large set of cell segmentation hypotheses for each video frame that we extract from data using a novel parametric max-flow variation. Possible tracking assignments between segments across time, including cell identity mapping, cell division, and cell exit events are enumerated. Each such assignment is represented as a binary decision variable with unary costs based on image and object features of the involved segments. We find a cost-minimal and consistent solution by solving an integer linear program. We introduce a new and important type of constraint that ensures that cells exit the Mother Machine in the correct order. Our method finds a globally optimal tracking solution with an accuracy of < 95% (1.22 times the inter-observer error) and is on average 2 − 11 times faster than the microscope produces the raw data.
Faculties and Departments:05 Faculty of Science > Departement Biozentrum > Computational & Systems Biology > Bioinformatics (van Nimwegen)
UniBasel Contributors:van Nimwegen, Erik
Item Type:Book Section, refereed
Book Section Subtype:Further Contribution in a Book
Note:Also published in: Lecture notes in computer science. - Berlin : Springer. - 8677 (2014), S. 25-36 -- Publication type according to Uni Basel Research Database: Book item
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Last Modified:25 Apr 2018 08:42
Deposited On:07 Aug 2015 12:05

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