PLEXI (PLugin EXtensible Image) Viewer
Overview
PlexiViewer is a java based tool developed at Washington University, St Louis to view MR images. Built using ImageJ and the XNAT engine, PlexiViewer has a web-based interface and a command line interface.
PlexiViewer displays three categories of images: standard, low resolution and thumbnails. Low resolution images are used in web-based applications to reduce transfer time. PlexiViewer creates the low resolution and thumbnail images from the standard resolution image. PlexiViewer supports the following formats: Siemens IMA, ANALYZE and DICOM, and Interfile (4dfp).
PlexiViewer's web-based interface consists of a Java applet user interface and a Java servlet component (Fig 1). The applet provides tools for selecting and viewing images. The servlet queries the XNAT database to determine what images are viewable for a particular imaging session and subsequently loads and manipulates images requested by the user. The command line interface of the PlexiViewer allows creation of thumbnail and low resolution images for each of three orientations viz. Transverse, Sagittal and Coronal.
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Fig 1. The PlexiViewer architecture (left) and user interface (right). The steps to retrieving an image are as follows: (1) Requests from the applet are received by the servlet. (2) The Loader class queries the database to determine where the files are located, and (3) reads the image data from the appropriate files. (4) Additional processing steps crop and compress the images according to a specification file. (5) The image is sent to the applet using HTTP tunneling. |
Setting up PlexiViewer in XNAT
PlexiViewer relies on an XML specification file to populate the user interface, to launch the appropriate image processing classes, and to display images. The PlexiViewerSpec file is generated during the setup step and is located at XNAT_HOME/deployments/PROJECT_NAME/PlexiViewerSpec.xml.
PlexiViewer uses XNAT engine to find the location of the high resolution image and depending on the contents of PlexiViewerSpec file, looks for the low resolution file for an orientation in the location specified by the xdat.project.image.lo_res.location property in the build.properties file. If the appropriate low resolution file is not present, PlexiViewer creates and delivers the low resolution image. The thumbnail images are searched in the location specified by the xdat.project.image.thumbnail.location property in the build.properties file.
In order to setup the viewer with XNAT, follow the steps mentioned here.
More info about PlexiViewerSpec file
Command line interface
The command line interface enables to pre build the low-resolution and thumbnail files for a session(s). To use the command line interface, execute:
java –jar <WEBSERVERHOME>/webapps/PROJECT_NAME/WEB-INF/lib/PlexiViewer-1.jar plexiConverter [-all] [-file <path to file containing session ids>] [-session <session id>] -o <overwrite existing files [Default: false]> -r <radiologic convention [Default non-radiologic]> -x <path to XNAT project>
The low resolution and the thumbnail files are created for the sessions based on the following options:
- all: generate files for all the sessions in the database
- file: generate files for the sessions in the input file
- session: generate files only for the single session id
- o: overwrite any existing files. Default is false
- r: generate all the files as per radiologic convention. Default is non-radiologic
- x: path to the XNAT project
Customizing viewer
To customize the viewer, follow the documentation here.
