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12-15 August 2018
Europe/Berlin timezone

Interactive Analysis of Cell Tracks in Light Sheet Microscopy Images using EmbryoMiner

Not scheduled


Pfotenhauerstraße 108 01307 Dresden Germany
Poster Posters


Mr Tim Scherr (Karlsruhe Institute of Technology)Mr Ralf Mikut (Karlsruhe Institute of Technology)


Light sheet microscopy imaging allows recording entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be tracked automatically in these 3D+t images [1-4]. Analyzing the resulting cell migration trajectories can provide detailed insights in large-scale tissue reorganization and morphological changes in early developmental stages at the cellular level. With the open-source framework EmbryoMiner in-depth analyses and comparisons of entire embryos in unprecedented detail are possible [5]. Iteratively focusing on a region of interest within the embryo allows investigating and testing specific trajectory-based hypotheses. After a selection process, quantitative features can be computed from isolated trajectories. All steps can be interactively refined to cope with different data sets. A study with unexperienced users indicated that even complex analysis tasks can be done in a time range less than 5 minutes. In future works, deep learning approaches for 3D+t microscopy data will be applied in order to improve the segmentation accuracy and to yield more valid cell trajectories for the subsequent analysis with EmbryoMiner.

1. Ulman et al., 2017, Nat. Meth., 14, 1141-1152
2. Bartschat et al., 2016, Bioinformatics, 32, 315-317
3. Stegmaier et al., 2016, Dev. Cell., 36, 225-240
4. Amat et al., 2014, Nat. Meth., 11, 951-958
5. Schott et al., 2018, PLoS Comput Biol, 14(4)

Affiliation Karlsruhe Institute of Technology / RWTH Aachen University
Terms and Conditions Yes

Primary authors

Mr Tim Scherr (Karlsruhe Institute of Technology) Mr Benjamin Schott (Karlsruhe Institute of Technology) Mr Manuel Traub (Karlsruhe Institute of Technology) Mr Masanari Takamiya (Karlsruhe Institute of Technology) Mr Andreas Bartschat (Karlsruhe Institute of Technology) Mr Andrei Y. Kobitski (Karlsruhe Institute of Technology) Mr G. Ulrich Nienhaus (Karlsruhe Institute of Technology) Mr Uwe Strähle (Karlsruhe Institute of Technology) Mr Johannes Stegmaier (RWTH Aachen University) Mr Ralf Mikut (Karlsruhe Institute of Technology)

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