Additional file 22: Video 8. Exemplary segmentation and tracking of the formation process of organoids. Video shows an mPO as an excerpt of an entire culture grown within one Z1-FEP-cuvette. The organoids expressed Rosa26-nTnG (grey) as nuclei marker. The movie shows an excerpt of the first 10 h a recorded data set of 6 days. The formation starts with a conglomeration of the cells towards one compact structure and ends with the establishment of a lumen. Each coloured dot represents one cell nucleus, but not each nucleus was tracked (lines). To ensure a proper segmentation and tracking higher resolved images need to be acquired, e.g. detection objectives with a higher magnification can be used. Microscope: Zeiss Lightsheet Z.1; detection objective: W Plan-Apochromat 20x/1.0, illumination objective: Zeiss LSFM 10x/0.2; laser lines: 488 nm, 561 nm; filters: laser block filter (LBF) 405/488/561; voxel size: 1.02 × 1.02 × 2.00 μm3; recording interval: 30 min; 3D rendering and tracking software: Arivis Vision4D. (MP4 11,909 kb)
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