Image Processing Tools In BioImage Suite Web

The applications in BioImage Suite Web can do many standard medical image analysis processing tasks. These are available from the Image Processing menu of the main orthogonal viewer application and the dual viewer applications.

Tools Summary

In the Orthogonal Viewer Tool these appear as:


These tools perform the following tasks:

Note: All of these modules can be run on the command line as well — see the Command Line Tools document for more information. You can also regression test the modules — see the Testing document for more on this.

Using a Tool — Single Viewer Mode

All the tools listed above can run on the viewer. Consider the case of the Flip Image tool, as explained in the figure below.

flipimage Figure 1: The full diagram explaining how to use a module in the viewer. (A) The Flip Image menu item (B) the Flip Image module in the sidebar (C) a cutaway of the Flip Image module (D) the inputs and outputs tab of Flip Image (E) advanced options for Flip Image (F) extra options for the module (G) the close button for the module in the sidebar.

The tool is accessed using the Flip Image option under the Image Processing Menu (A). This opens the tool and places it in the viewer sidebar (B).

An expanded version of B is shown in C. The tool control consists of the following options:

Note: Outputs from a module will overwrite whatever is currently in their destination viewer. Be sure that you save your data as you go! Images can be moved from image to overlay and back, using the Advanced Transfer Tool, accessible under the Edit menu (see its section in the documentation).

The extra options under F merit some explanation. These are:

One advanced usage scenario is to configure parameter sets in the GUI (web-applications), especially for complex tasks, and to reuse these on the command line. The command line tools have a flag (—paramfile) that can be used to load all parameters from a such a parameter file and use them while running the module.

G highlights the close button. The sidebar can show only up to four tools (see the figure below). If an additional tool is opened, at this point, then the least recently opened module — in this case below Normalize Image — will be removed from the sidebar. The user may manually remove a control from the sidebar using the x button in its title bar.

closebutton Figure 2: A sidebar full of modules.

Using a Tool — Dual Viewer Mode

In the Dual Viewer application, there is an additional set of options for setting the input and the output image. As shown in Figure 3, both the input and the output have an additional “Viewer” tab with which you can choose to flip the image in viewer 1 and send the output to viewer 2 or any one the other possible combinations. The rest of the functionality is identical.

dualviewer Figure 3: The input and output options in the dual viewer

[BioImage Suite Web Manual Table Of Contents]    [BioImage Suite Web Main Page]

This page is part of BioImage Suite Web. We gratefully acknowledge support from the NIH Brain Initiative under grant R24 MH114805 (Papademetris X. and Scheinost D. PIs, Dept. of Radiology and Biomedical Imaging, Yale School of Medicine.)