C

In light-sheet microscopy, overall image content and resolution are improved by acquiring and fusing multiple views of the sample from different directions. State-of-the-art multi-view (MV) deconvolution simultaneously fuses and deconvolves the images in 3D, but processing takes a multiple of the acquisition time and constitutes the bottleneck in the imaging pipeline. Here, we show that MV deconvolution in 3D can finally be achieved in real-time by processing cross-sectional planes individually on the massively parallel architecture of a graphics processing unit (GPU). Our approximation is valid in the typical case where the rotation axis lies in the imaging plane.

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

neuTube is a collection of neuron reconstruction tools from fluorescence microscope images. It has an interactive system with a 3D viewer, which can be clicked in 3D and perform neuron tracing automatically and semi-automatically. It can automatically recognize branching points as junctions. Traced neurons can be exported to swc format, which could be imported by various software packages. neuTube has Win and Mac OS standalone executable builds and may also be installed by manual compilation. In addition, neuTube can be used as a plugin in Vaa3D.

>OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). Python and Java bindings are also available. The Python binding includes a Deep Zoom generator and a simple web-based viewer. The Java binding includes a simple image viewer.  

An exponential curve fitting library used for Fluorescence Lifetime Imaging (FLIM) and Spectral Lifetime Imaging (SLIM), available as:

• Source code as C/C++ and Java library

• ImageJ plugin

• Standalone Open-Source Windows application

Publications:

• Barber, P.R., Proc. SPIE, 5700, 2005.pdf
• Barber, P.R., J. R. Soc. Interface, 6, 2009.pdf