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Open-source live 3D visualization for light sheet microscopy

Loic Royer
Martin Weigert
Ulrik Günther
Florian Jug
Nicola Maghelli
Ivo F. Sbalzarini
Eugene W. Myers

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.

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Package or library
Linux, Mac OSX, Windows
Java JDK (1.7); Gradle 2.1; CUDA or OpenCL requirements; A graphics card with at the very minimum 500M of GPU RAM, preferably >=1G, Linux: A recent version of Linux, tested: Ubuntu 14+ , Xubuntu 14+; Eclipse, Mac OSX: Java 8; at least Mac OSX 10.9, Windows: VisualStudio

Project development

Institution: Center for Systems Biology & Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany; Technische Universität Dresden, Dresden, Germany