Welcome to ClearVolume.
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.
The main ClearVolume wiki is the place to start for in-depth installation instructions, documentation, examples, building guide, and more...
To get started even faster please go:
- Here if you are Microscope builder using LabView
- Here if you are an OpenSPIMer
- Here if you are a Java coder
- Here if you are a C/C++ coder
- Here if you are a Python coder
- Here if you are a ImgLib2 user
- Here if you want to see your data in 3d within FiJi/ImageJ
- Here if you are a KNIME user
The ClearVolume project repositories are listed below:
Authors and Contributors
The ClearVolume project was initiated by Loic Royer (@royerloic) who wrote the first version, designed the core real-time rendering and streaming algorithms and wrote the bindings to C++/LabVIEW. Martin Weigert (@maweigert) helps to maintain and improve the core rendering algorithms and wrote the OpenCL pipeline. Martin also contributed the Python bindings and tools, OpenCL and CUDA real-time 3D data processors for image quality estimation and center of mass calculation. Ulrik Günther (@skalarproduktraum) developed and maintains the OpenSPIM integration, greatly contributed to the OpenGL backend, and improved C/C++ bindings. Florian Jug (@fjug) contributed the imagelib2 bridge, and wrote and maintains the Fiji and KNIME plugins. Nicola Maghelli is our optics/microscope building genie whitout whom we could never have tested ClearVolume in realistic scenarios.
How to cite
ClearVolume – Open-source live 3D visualization for light sheet microscopy.
Loic A. Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, Eugene W. Myers ,
Nature Methods 12, 480–481 (2015) doi:10.1038/nmeth.3372
The ClearVolume team brings together members of the Myers and
Sbalzarini labs at Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG).
Send us an email and we will get back to you.