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.

Getting started

The main ClearVolume wiki is the place to start for in-depth installation instructions, documentation, examples, building guide, and more...

• 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

Repositories

The ClearVolume project repositories are listed below:

• ClearVolume Main Project repository.
• ClearGL - Object Oriented facade API on top of OpenGL.
• ClearCUDA - Object Oriented facade API on top of CUDA.
• ClearVolume Fiji plugin and imglib2 bridge interface.
• ClearVolume plugin to OpenSPIM.
• ClearVolume Python bindings and toolset.

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

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

Affiliations

The ClearVolume team brings together members of the Myers and Sbalzarini labs at Max Planck Institute of Molecular Cell Biology and Genetics (MPI-CBG).

Contact

Send us an email and we will get back to you.