BigDataViewer: visualization and processing for large image data sets

Further, we demonstrated the use of ClearVolume for longterm time-lapse imaging with an OpenSPIM microscope5. ClearVolume was readily integrated into the mManager (www. micro-manager.org/) plug-in to allow live 3D visualization. We used ClearVolume to remotely monitor a developing Drosophila melanogaster embryo to check on sample drift, photobleaching and other artifacts (Supplementary Video 5). Time-shifting allows inspection of the data at any given point in time during acquisition (Supplementary Video 6). In addition, ClearVolume can be used for aligning and calibrating light-sheet microscopes. The overall 3D point spread function of the optical system and the full 3D structure of the beam (for example, Gaussian or Bessel beam) can be visualized (Supplementary Videos 7 and 8). To aid manual alignment of the microscope, ClearVolume computes image sharpness in real time and provides audiovisual feedback (Supplementary Video 9). Finally, ClearVolume computes and visualizes sample drift trajectories and makes that information available through an interface for stabilization of the sample (Supplementary Video 10). ClearVolume can also be used on other types of microscopes such as confocal microscopes (Supplementary Video 11). Going beyond microscopy, ClearVolume is integrated with the popular Fiji6 (http://fiji.sc) and KNIME (http://www.knime.org/) software packages, bringing real-time 3D+t multichannel volume visualization to a larger community (Supplementary Videos 12–14). Furthermore, ClearVolume’s modularity allows any user to implement additional CPUor GPU-based modules for image analysis and visualization. In summary, ClearVolume makes live imaging truly live by enabling direct real-time inspection of the specimen imaged in light-sheet microscopes. The source code of ClearVolume is available at http://clearvolume.github.io.