Alexandra Kalaitzidou

• Footage of organoids taken by means of fluorescence microscopy and segmented as well as triangulated by image analysis software like LimeSeg and Mastodon often needs to be visualized in aesthetic manner for presentation of the results in scientific papers, talks and demonstrations. The goal of this work was to create a simple to use addon “Biobox” for the open source 3D – visualization package “Blender” which would allow to import triangulated 3D data with animation over time (4D), produced by image analysis software, and optimize it for efficient usage. ”Biobox” offers several visualization tools for the creation of rendered images and animation videos by biologists. The optimization of imported data was performed by using Blender intern modifiers. The optimized data can then be visualized by using several tools built for visualizing the organoid in frozen, animated and semi-transparent manners. A dynamic link for object selection and dynamic data exchange between Blender and Mastodon was developed. Additionally, a user interface was developed for manual correction errors of segmentation and steering the object detection algorithms of LimeSeg. The benchmark of the developed addon “Biobox” was performed on real scientific data. The benchmark test demonstrated that developed optimization result in significant (~5 fold) decrease of RAM usage and acceleration of visualization more than 160 times.