The Data Browser is an ImageJ plugin that facilitates quick browsing of multichannel, multi-focal plane time course datasets, written by Curtis Rueden. It is integrated with the Bio-Formats importer plugin—as well as ImageJ's built-in hyperstack and virtual stack support—to provide multidimensional visualization capabilities across space, time and channels.

Data Browser in action

The Data Browser displays a 215 MB dataset (2 channels x 43 time points x 10 slices, distributed across 86 TIFF files). To conserve memory use, the Options window (left) has been used to configure the browser to cache the next 20 time points at the given slice and channel. Planes currently in the cache are represented by the blue bars beneath the Z-depth and time sliders.

The primary goal of the Data Browser is to allow quick and easy visualization of large, multidimensional data within ImageJ. It supports data spanning multiple focal planes (Z), time points (T), and channels (C), and reads a subset of image planes from the data source into memory at one time, so that datasets larger than the available RAM can be browsed effectively. The Data Browser is similar to Joachim Walter's Image5D plugin, but was developed independently.

The Z and T positions are browsed by moving sliders labeled "Z-depth" and "time" respectively, while the channel is changed with the spinner labeled "channel." In the case of 2-channel data, the spinner is replaced with a "Transmitted" checkbox for toggling between the two channels. The blue bars beneath the Z and T sliders show which image planes have been cached in memory, while the red bars indicate planes currently in the process of being cached. The "Animate" button begins cycling through the time axis at the current Z and C positions. The "Options" button displays a host of configuration parameters, such as animation speed, dimensional axis ordering, and planar caching preferences. The "Metadata" button pops up OME Notes to inspect the associated metadata.

The user can perform normal operations on the image (e.g., Process>Smooth), but they will only affect the currently visible image plane. In a future release, the software will support more dynamic application of image processing commands.

The Data Browser is available for download as part of the LOCI Tools complete bundle.

To install, drop loci_tools.jar into ImageJ's plugins folder. Next time you run ImageJ, a new LOCI submenu with several plugins will appear in the Plugins menu. To use, choose "Data Browser" from the LOCI menu and select a file when prompted.