Bioimage informatics

An R package for the (3D) visualisation and analysis of biological image data, especially tracings of single neurons. nat is the core package of a wider suite of neuroanatomy tools introduced at http://jefferislab.github.io.

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.

ClearCL is a Multi-backend Java Object Oriented Facade API for OpenCL.

OpenCL libraries come and go in Java, some are great but then one day the lead developper goes on to greener pastures and you are left with code that needs to be rewritten to take advantage of a new up-to-date library with better support. Maybe a particular library has a bug or does not support the function you need? or it does not give you access to the underlying native pointers, making difficult to process large buffers/images or interoperate with hardware? or maybe it just does not support your exotic OS of choice. To protect your code from complete rewrites ClearCL offers a very clean and complete API to write your code against. Changing backend requires just changing one line of code.

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.

FracLac is for digital image analysis. Use it to measure difficult to describe morphological features.
FracLac is a plugin for ImageJ. It is freely available software developed and maintained by our lab at the School of Community Health, Faculty of Science, Charles Sturt University, Australia. The author of the software and project lead is also the author of this document (me, Audrey Karperien). The basic box counting algorithm was originally modified from ImageJ's box counting algorithm and H. Jelinek's NIH Image plugin, and was further elaborated based on extensive research and development. The convex hull algorithm was provided by Thomas Roy, University of Alberta, Canada. As open source software, with the continuing help of a host of users and collaborators, FracLac has evolved to a suite of fractal analysis and morphology functions.