Making live imaging truly live

How to smoothly navigate multiterabyte recordings
Researchers at the MPI-CBG have taken important steps in solving the big data problem. Their contributions published in Nature Methods are making volumetric microscopy more user-friendly.

A group of scientists from the labs of Gene Myers and Ivo Sbalzarini present ClearVolume, an open-source toolkit that permits the immediate 3D perception of imaged processes in microscopy.

ClearVolume creates instant multiview and multicolor renderings and enables live streaming of 3D data in real time over the Internet. This effectively decouples the physical location of the microscope from the experimenter’s location – it, for instance, enables researchers to remotely inspect the health of the embryo and the quality of the recorded volumes. Overall, ClearVolume makes live imaging truly live by enabling direct real time inspection of the specimen imaged in light sheet microscopes.

BigDataViewer is an open-source software developed by researchers of the Tomancak Lab which allows users to smoothly navigate multiterabyte recordings. BigDataViewer enables users to interactively navigate and visualize large image sequences from both local and remote data sources and thus makes it a solution for dealing with large data sets, like multiview data from light-sheet microscopy. The performance on very large data is achieved by using an efficient client-side renderer and an intelligent loading and caching scheme.

Corresponding papers:
Loic A. Royer, Martin Weigert, Ulrik Günther, Nicola Maghelli, Florian Jug, Ivo F. Sbalzarini, Eugene W. Myers: ClearVolume: open-source live 3D visualization for light sheet microscopy Nature Methods, published online on 28 May 2015 doi:10.1038/nmeth.3372

Tobias Pietzsch, Stephan Saalfeld, Stephan Preibisch & Pavel Tomancak: BigDataViewer: visualization and processing for large image data sets Nature Methods, published online on 28 May 2015 doi:10.1038/nmeth.3392