KIT | KIT-Bibliothek | Impressum
Open Access Logo
DOI: 10.5445/IR/1000082328
Veröffentlicht am 02.05.2018
DOI: 10.1371/journal.pcbi.1006128

EmbryoMiner : A new framework for interactive knowledge discovery in large-scale cell tracking data of developing embryos

Schott, Benjamin; Traub, Manuel; Schlagenhauf, Cornelia; Takamiya, Masanari; Antritter, Thomas; Bartschat, Andreas; Löffler, Katharina; Blessing, Denis; Otte, Jens C.; Kobitski, Andrei Y.; Nienhaus, G. Ulrich; Strähle, Uwe; Mikut, Ralf; Stegmaier, Johannes

State-of-the-art light-sheet and confocal microscopes allow recording of entire embryos in 3D and over time (3D+t) for many hours. Fluorescently labeled structures can be segmented and tracked automatically in these terabyte-scale 3D+t images, resulting in thousands of cell migration trajectories that provide detailed insights to large-scale tissue reorganization at the cellular level. Here we present EmbryoMiner, a new interactive open-source framework suitable for in-depth analyses and comparisons of entire embryos, including an extensive set of trajectory features. Starting at the whole-embryo level, the framework can be used to iteratively focus on a region of interest within the embryo, to investigate and test specific trajectory-based hypotheses and to extract quantitative features from the isolated trajectories. Thus, the new framework provides a valuable new way to quantitatively compare corresponding anatomical regions in different embryos that were manually selected based on biological prior knowledge. As a proof of concept, we analyzed 3D+t light-sheet microscopy images of zebrafish embryos, showcasing potential user appl ... mehr

Zugehörige Institution(en) am KIT Institut für Toxikologie und Genetik (ITG)
Institut für Automation und angewandte Informatik (IAI)
Publikationstyp Zeitschriftenaufsatz
Jahr 2018
Sprache Englisch
Identifikator ISSN: 1553-734X, 1553-7358
URN: urn:nbn:de:swb:90-823282
KITopen ID: 1000082328
HGF-Programm 47.01.02; LK 01
Erschienen in PLoS Computational Biology
Band 14
Heft 4
Seiten e1006128
Bemerkung zur Veröffentlichung Gefördert durch den KIT-Publikationsfonds
KIT – Die Forschungsuniversität in der Helmholtz-Gemeinschaft KITopen Landing Page