Real-time multi-view deconvolution


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.

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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 AlteraAMDAppleARMCreativeIBMImaginationIntelNvidiaQualcommSamsungVivanteXilinx, and ZiiLABS.[7][8]


neuTube (or NeuTu)


neuTube is an open source software for reconstructing neurons from fluorescence microscope images. It has a nice interactive system. It has 3D viewer, which can be clicked in 3D and perform neuron tracing semi-automatically. It can automatic 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.

Source Code available at:


FLIM / SLIM Analysis


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