The Center for Advanced Systems Understanding (CASUS) co-organized the second scenery and sciview hackathon that took place in Dresden, Germany, in mid-June. Fellow organizer and provider of the venue was the Center for Systems Biology Dresden (CSBD). Sixteen participants from Germany, the USA, Italy, Czechia, India, and Tunisia – representing six different institutions – came together in the Elbe valley to work on the visualization toolkit scenery and the Fiji visualization plugin sciview, which is based on scenery. Thanks to the dedicated work, the release of the stable 1.0 version is now already planned for the end of summer.

The organizer and sponsor of the hackathon was Ivo Sbalzarini, Professor of Scientific Computing for Systems Biology at the TU Dresden, Research Group Leader at the Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG), and Dean of the Faculty of Computer Science at the TU Dresden and TU-Dresden director in the CSBD. He says, “The week together at CSBD brought both projects a great deal further. It was simply amazing to see how the participants inspired each other.”

The goal of the hackathon was to bring both software packages close to a stable 1.0 release. During the event, many contributions to both pieces of software were made; overall, 20 bugfixes and 25 new features and enhancements were contributed by the participants, some of whom were first-time contributors to the projects. The toolkit scenery has been developed by Ulrik Günther and colleagues since 2016 when Ulrik was a PhD student in the research group of Ivo Sbalzarini at the CSBD.

Ulrik now is a postdoc at CASUS. He adds, “The intensive work over the past seven days has not only led to significant improvements in the software in terms of scope and quality. Rather, we are more convinced than ever that scenery is of interest to anyone who wants to visualize their scientific data in three dimensions. This visual and interactive access to large volumetric and geometric data opens up exciting opportunities to address unanswered research questions. Moreover, 3D visualizations are simply fascinating and can help to communicate scientific results intuitively.”

With scenery, scientists have a flexible open-source visualization framework for Virtual and Augmented Reality at their disposal. Scenery can visualize large volumes of data, such as the data generated from state-of-the-art microscopes. The framework runs on the Java VM, is interoperable with a variety of tools from the popular ImageJ bioimage analysis ecosystem, and is free and open source software. The plugin sciview for the image-analysis software fiji provides 3D visualization and Virtual Reality capabilities for images and meshes to end users on the basis of scenery.

related publication:
U. Günther et al., “scenery: Flexible Virtual Reality Visualization on the Java VM,” 2019 IEEE Visualization Conference (VIS), Vancouver, BC, Canada, 2019, pp. 1-5, doi: 10.1109/VISUAL.2019.8933605

GitHub links: