Not yet reviewed by Pith; the record is open.

Current in vivo microscopy allows us detailed spatiotemporal imaging (3D+t) of complete organisms and offers insights into their development on the cellular level. Even though the imaging speed and quality is steadily improving, fully-automated segmentation and analysis methods are often not accurate enough. This is particularly true while imaging large samples (100um - 1mm) and deep inside the specimen. Drosophila embryogenesis, widely used as a developmental paradigm, presents an example for such a challenge, especially where cell outlines need to imaged - a general challenge in other systems as well. To deal with the current bottleneck in analyzing quantitatively the 3D+t light-sheet microscopy images of Drosophila embryos, we developed a collection of semi-automatic open-source tools. The presented methods include a semi-automatic masking procedure, automatic projection of non-convex 3D isosurfaces to 2D representations as well as cell segmentation and tracking.