SIMBA Image Viewers

 

The image viewer is a very important component of the SIMBA system. It provides three very important functions:

1.     It facilitates convenient viewing of image data including review of three-dimensional images.

2.     It provides for detailed image inspection of image intensity values at the pixel level.

3.     It facilitates the creation of human annotations and boundary markings on images to a geometric precision of better than one pixel.

 

There three different viewers available with the SIMBA system:

 

All viewers are integrated into the SIMBA Image analysis web system. All viewers perform similar functions; however, the interactive user controls are a little different for each.

 

1.     The Standard viewer. Created in 2018 the standard viewer is based on JavaScript technology and therefore runs in a web browser. For Linux workstation use there is a version of the viewer supported by a python web server that makes it available for reviewing images in a specified directory. The viewer uses the left mouse button and the mouse scroll-wheel only and is very slow for image windowing since most of the image processing operations are performed in the web server.

2.     The Advanced viewer. Created in 2020 the advance viewer takes advantage of the cornerstone.js library and more advanced JavaScript features than the standard viewer. It is also available for viewing images on a Linux workstation using a python web server. It is much faster than the standard viewer for image windowing; However, it is very new and some of its features may be subject to changes and updates. This viewer takes advantage of all the mouse buttons: left, right, center and mouse-wheel.

3.     The java viewer. Originally created in 2000. This viewer is written in native java and comes in two versions: one for the workstation and one as a java applet. All modern web browsers no longer support java applets so its use in the web system is depreciated. It still works with Internet Explorer on PCs if java is installed and appropriate security settings are made. On a Linux workstation it is directly and efficiently implemented as a compiled java application. For interactive interaction only the left mouse button and the scroll wheel are used.

 

Viewer Recommendations

 

SIMBA web use: In general, the advanced viewer is recommended; however, it currently requires a 3 button mouse. The standard viewer is currently preferable for some annotation and inspection tasks and only requires a single button mouse. The java reviewer is not recommended even though it has the most complete implementation due to the security issues in enabling java applets and the limited web browser support.

 

Linux V4 use: On a workstation the advanced viewer and standard viewer are good options as for the web environment. In this case, they require a local python web server to be run and display requires a local web browser; thus, some setup is required.  The java viewer has the advantage of direct implementation and, currently, slightly better system integration with vview. For remote workstation access using x2go there may be some speed advantage in using the java viewer depending upon the speed of the internet connection.

 

Task-Specific Recommendations

 

SIMBA Tasks	Recommendation
Image review	For image review the advanced viewer is best, in general, as it has fast windowing, fast multi-image management and makes use of a 3-button mouse. The standard viewer may be preferable when only a single button  mouse is available.
Annotations and Boundary marking	The standard viewer has a more complete capabilities for point, line and boundary annotations. The advanced viewer has a more convenient tool for closed boundary creation but can only create closed boundaries. The standard viewer can also create isolated points, lines and open boundaries.
Data Inspection	The standard viewer currently has best tools for pixel data inspection for small image ROIs.
Medical Image Review	The advanced viewer is recommended