VisBio Overview

Welcome to VisBio, a tool for visualization and analysis of 4-D multispectral data (stacks of slices of biological data with multiple color values, animated across time). It's more fun than a backpack full of angry weasels.

How to import a dataset

The first step is to load your dataset into VisBio. From the File menu, choose Import Data. A dialog box will appear:

The most straightforward way to get a time series into VisBio is to number the data files across time. For example, the sample C. elegans dataset available on the VisBio web site is a collection of 12 files labeled SDUB1.PIC through SDUB12.PIC. For this dataset, you'd fill in "C:\data\SDUB" for the file prefix (where "C:\data" is the location of the dataset), "1" for start, "12" for end, and "PIC" for extension.

If desired, you can have VisBio fill in the fields automatically by clicking the "Choose file" button and selecting one timestep of the dataset. So, you could select any one of the SDUB files using the file chooser, and VisBio would automatically detect that there are 12 timesteps in the series.

Lastly, if you have a series of images that you wish to import as a single stack of slices rather than an animation across time, choose to "treat each file as a slice" instead of as a timestep. Note that VisBio does not currently support treating each file as a slice if each file contains more than one image.

How animation works in VisBio

To save memory, VisBio only keeps one timestep of the dataset in memory at a time, thus allowing visualization of huge datasets quickly. Unfortunately, when switching timesteps, VisBio would need to load the new timestep into memory from disk, which takes time and slows down animation.

To sidestep this problem, VisBio reads in all timesteps one at a time when it first imports the dataset. It creates a low-resolution thumbnail of each slice of every timestep, keeping all these thumbnails in memory at once.

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 timestep is loaded from disk. When you switch timesteps, VisBio uses lo-res mode by default to avoid the slowdown of going to disk for the next timestep. Thus, animation is still quick.

Controlling low-resolution thumbnailing

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

You can specify the thumbnail resolution by altering the values next to the "Create low-resolution thumbnails" checkbox when first importing a dataset (the default is 64 x 64 pixels). Making these numbers smaller will result in lo-res mode looking blockier but taking less memory, whereas larger numbers will require more memory to store the thumbnails but look crisper while animating.

You can also choose to disable low-resolution support completely by unchecking the checkbox. When thumbnails are disabled, the dataset will load more quickly (VisBio only needs to load the current timestep instead of loading them all and profiling them), but animation will be disabled as well, and switching timesteps will be slow since the new timestep must be loaded from disk.

Exporting a dataset

VisBio contains powerful features for exporting data to different formats. To export the current dataset, choose "Export" from the File menu. A dialog box will appear:

Choose the output format of the data (Bio-Rad PIC, TIFF, or QuickTime), enter the desired filename prefix, and pick a data orientation--treating each file as a timestep results in each file containing all slices from a given timestep, whereas treating each file as a slice results in each file containing all timesteps from a given slice.


Note: If "QuickTime movie" is grayed out, you'll need to install QuickTime for Java on your machine. See the "QuickTime" tab for more information.

If you have made color or alignment adjustments, you can preserve them in the exported data by checking "Save color adjustments" or "Save alignment," respectively. [coming soon]

You can also choose to limit which slices and timesteps get exported using the "Save current" and "Only export" checkboxes. In particular, if you have computed an arbitrary slice (using the "Arbitrary data slice" checkbox in the View controls), you can export it by checking "Save current slice only."

Lastly, you can change the export resolution using the "Use alternate resolution" checkbox. The dataset's slices will be resampled to match the specified resolution.

Taking a snapshot

You can take a "snapshot" of the displays currently onscreen, saving it to a file that matches the current appearance of the displays exactly. To take a snapshot, choose "Take snapshot" from the File menu. You can save the snapshot as TIFF, RAW or JPEG.