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ClearVolume is a real-time live 3D visualization library designed for high-end volumetric microscopes such as SPIM and DLSM microscopes. With ClearVolume you can see live on your screen the stacks acquired by your microscope instead of waiting for offline post-processing to give you an intuitive and comprehensive view on your data. The biologists can immediately decide whether a sample is worth imaging. ClearVolume can easily be integrated into existing Java, C/C++, Python, or LabVIEW based microscope software. It has a dedicated interface to MicroManager/OpenSpim/OpenSpin control software. ClearVolume supports multi-channels, live 3D data streaming from remote microscopes, and uses a multi-pass Fibonacci rendering algorithm that can handle large volumes. Moreover, ClearVolume is integrated into the Fiji/ImageJ2/KNIME ecosystem. You can now open your stacks with ClearVolume from within these popular frameworks for offline viewing.

NeuroGPS-Tree is a workflow developed to reconstruct a neuronal population from a dense, large-scale data set. NeuroGPS-Tree is suitable for processing image stacks acquired by different image modalities.

Shiny is an R package that makes it easy to build interactive web apps straight from R.

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.

MTrack is a tool, which detects, tracks, and measures the behavior of fluorescently labeled microtubules imaged by TIRF (total internal reflection fluorescence) microscopy. In such an in vitro reconstitution approach, stabilized, non-dynamic microtubule seeds serve as nucleation points for dynamically growing microtubules.

MTrack is a bi-modular tool. The first module detects and tracks the growing microtubule ends and creates trajectories. The second module uses these trajectories to fit models of dynamic behavior (polymerization and depolymerization velocities, catastrophe and rescue frequencies). It also computes statistics such as length and lifetime distributions when analyzing more than one movie (batch mode).