Generating thumbnails

To save memory, VisBio only keeps one dimensional position of the dataset (e.g., one timestep) in memory at a time, thus allowing visualization of huge datasets quickly. Unfortunately, when switching positions, VisBio needs to load the new position into memory from disk, which takes time and slows down animation.

To sidestep this problem, VisBio reads in all data when it first imports the dataset. It creates a low-resolution thumbnail of every image, keeping all these thumbnails in memory at once. It does this in the background, so that you can begin visualizing your data even before all thumbnails have been computed. You can see how far along the computation is from the progress bar in the Tasks panel. You can stop the computation process by clicking the "Stop" button next the progress bar, if you wish to conserve memory or CPU use.

When visualizing data, VisBio has a "lo-res" mode and a "hi-res" mode. In lo-res mode the thumbnail is displayed, whereas in hi-res mode the data is loaded from disk. When you switch positions, VisBio uses lo-res mode by default to avoid the slowdown of going to disk for the data, keeping animation quick.

VisBio loads hi-res data for the current dimensional position in the background. If it finishes loading the hi-res data, it displays it. Thus, the hi-res data will eventually "burn in" if you leave the displays idle for a moment.

If there is no thumbnail for an image plane in lo-res mode (e.g., if thumbnails are not finished loading, or if you pressed the "Stop" button), the plane will be missing. Once the hi-res data for that plane is loaded, its thumbnail will be computed automatically and cached on disk.

Controlling thumbnailing

Since the thumbnails' memory footprint is much smaller than it would be at full resolution, VisBio gives you both efficient memory use and realtime animation at the expense of an initial thumbnail loading time and lower animation resolution.

The default thumbnail resolution is 96 x 96 pixels. You can adjust these values in VisBio's Options (Preferences on Mac OS X). Making these numbers smaller will result in lo-res mode looking blockier but thumbnails taking less memory, whereas larger numbers will require more memory to store the thumbnails but look crisper while animating.

Thumbnail disk cache files

For each dataset you import, VisBio creates a disk cache of computed thumbnails in a file with extension ".visbio" in the same directory as your dataset. If this file already exists, VisBio reads the thumbnails from it, greatly speeding thumbnail generation. You can even include the cache file with your dataset when distributing your data to allow others to read in your data more quickly. Lastly, if for some reason you want VisBio to regenerate thumbnails from the source data, just delete the ".visbio" cache file.

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