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TeraStitcher is a free tool that enables the stitching of Teravoxel-sized tiled microscopy images even on workstations with relatively limited resources of memory (<8 GB) and processing power. It exploits the knowledge of approximate tile positions and uses ad-hoc strategies and algorithms designed for such very large datasets. The produced images can be saved into a multiresolution representation to be efficiently visualized (e.g. Vaa3D-TeraFly) and processed.

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.

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

OpenCL (Open Computing Language) is a framework for writing programs that execute across heterogeneous platforms consisting of central processing units (CPUs), graphics processing units (GPUs), digital signal processors (DSPs), field-programmable gate arrays (FPGAs) and other processors or hardware accelerators. OpenCL specifies programming languages (based on C99 and C++11) for programming these devices and application programming interfaces (APIs) to control the platform and execute programs on the compute devices. OpenCL provides a standard interface for parallel computing using task- and data-based parallelism.

OpenCL is an open standard maintained by the non-profit technology consortium Khronos Group. Conformant implementations are available from Altera, AMD, Apple, ARM, Creative, IBM, Imagination, Intel, Nvidia, Qualcomm, Samsung, Vivante, Xilinx, and ZiiLABS.[7][8]

Source: https://en.wikipedia.org/wiki/OpenCL

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.