Visualisation

vmtk is a collection of libraries and tools for 3D reconstruction, geometric analysis, mesh generation and surface data analysis for image-based modeling of blood vessels.

vmtk is composed of

• C++ classes (VTK and ITK -based algorithms)
• Python classes (high-level functionality - each class is a script)
• PypeS - Python pipeable scripts, a framework which enables vmtk scripts to interact with each other

Facade API on top of JOGL (http://jogamp.org/jogl/www/) offering a simple interface for creating OpenGL contexts/windows, GLSL shader programs, and textures. Use it in your favourite JVM-based language.

scenery is a scenegraphing and rendering library. It allows you to quickly create high-quality 3D visualisations based on mesh data. scenery contains both a OpenGL 4.1 and Vulkan renderer. The rendering pipelines of both renderers are configurable using YAML files, so it's easy to switch between e.g. Forward Shading and Deferred Shading, as well as stereo rendering. Rendering pipelines can be switched on-the-fly.

Both renderers support rendering to head-mounted VR goggles like the HTC Vive or Oculus Rift via OpenVR/SteamVR.

The Multiview Reconstruction software package enables users to register, fuse, deconvolve and view multiview microscopy images. The software is designed for lightsheet fluorescence microscopy (LSFM), but is applicable to any form of three or higher dimensional imaging modalities like confocal timeseries or multicolor stacks. 

The BigDataViewer is a re-slicing browser for terabyte-sized multi-view image sequences. BigDataViewer was developed with multi-view light-sheet microscopy data in mind and integrates well with Fiji's SPIMage processing pipeline.