Johannes is developing software tools to help biologists analyze microscopy data. A particular interest of his is developing open source software approaches that can analyze image dimensions beyond 2D. 2D images are often not sufficient to analyze some biological phenomena and objects (organs, cells) as they don't have the spatial (space) and temporal (time) details to capture the 3D aspects over time. In LOCI and many other labs, microscopes are available to capture 3D images non-invasively over long periods of time using special optical approaches such as multiphoton microscopy. These 3D images can allow for better visualization of biological processes. In tools that he develops such as Fiji, Johannes analyze these images with emphasis on transparency and color of that image, along with quantitative information at each pixel.