Structural Informatics Group
Department of Biological Structure
Division of Biomedical and Health Informatics
Department of Medical Education
University of Washington School of Medicine
lober@u.washington.edu
Now. Functional development versions of the authoring application and client image viewing applet are available below. They will get much better, I promise! Only the class & jar files are posted at present. Contact me via email if you want the poorly documented, preliminary source which I'm working from at present... Or, wait until the end of June...
Of course there's a mailing list for PAIS. You can sign yourself up here: http://ohana.org/mailman/listinfo/pais
Last major software content update 6/2000. This page edited 6/26/2000.
Release Date Description 6/2000 0.9beta, uses Image Markup Language 1.0,
which I've submitted to the XML.org registry.5/2000 0.7beta, still "IA7" client code, but updates to home page. 3/2000
Original PAIS, using Digital Anatomist Frame Format
PAIS is an easy way to add comments to your images, and publish those commented images over the web. It is aimed at medical educators, but the principles are generally applicable to anyone with images.
More precisely, PAIS is a simple system for creating a linked series of annotated images, and making them viewable over the web.
By "linked series", I mean that author can specify a navigation structure that will allow the user to easily move from image to image. By "annotated images", I mean that, using the PAIS authoring tool, an author can add information to an image. This annotation information is stored independently from the image data, and combined with the image data at display time, which allowing both the author and the user to control how it is viewed. Finally, by "viewable over the web", I mean that access to the images is controlled through a simple HTML web page, which downloads the image viewing client software.
An "annotated image" is the combination of an annotation file and its associated image. The annotation file contains the name of the image file, and is treated by PAIS as its primary object. These files are created using the authoring tool included with this system. Presently, they use the same format as the Digital Anatomist in-line interactive atlases. The format is described in detail here.
In brief, the annotation format of the Digital Anatomist supports an item of information text about an image, and a series of individual image annotations. The annotation metaphor is that of a gross dissection, with a label connected by a pin to a region of interest in the image. More specifically, each annotation consists of a text "label", a colored "string" connecting the label with a "pin" on the image, and an "outline" - a closed polygon "drawn" over some portion of the image.
The annotation files are text files, so it is easy to examine this format.
The format will be extended to allow a richer expression of the annotation concept, and will be expressed in XML for portability.
Yes, you can look at a demo page, and see a sample image collection (an anatomic atlas of the knee).
Second, you can download the image collection components yourself, and publish either a different sample collection, or build your own. You can view the test image collection online here, if you want to know what it should look like.
A reasonable question.
Look at the What are the pieces section to see what components comprise a publishable image collection, and the What do I need section to make sure you've got the both the client and server requirements covered.. The How do I get started section after that contains the instructions for downloading and installing the components.
Client Components
The server side consists of a directory or folder whose files are served by a standard web server. This directory contains the images and annotation files that comprise the published image collection, and at least the following five files:
index.html - a sample HTML home page for an atlas. This does nothing more than jump to the Japplet page.
JappletAppl.PlugIn1.3.html - a sample HTML home page for an atlas. This version was produced with Sun's HTML Converter 1.3, and based on a dynamic check of browser versions, tries to offer a download of the Swing Plug-In, if needed.
IA9.jar - a java archive file containing the client viewer applet.
jdom-b4.jar and xerxes.jar - XML support files
and, if you want, you can download the Java source (91 Kbytes)
Test Image Collection (download 903 Kbytes)
DemoPAIS.IML1.zip - contains a simple set of test images and annotations, as well as the executable versions of the client and authoring tools. See "How do I get started?", below.
You can view the test image collection online here, if you want to know what it should look like.
Authoring Components
The authoring side consists of a Java 2 environment, which you download from Sun, and the following four files. The XML support files are also used by the Client.
AI.jar - a java archive file containing the authoring application.
jdom-b4.jar and xerxes.jar - XML support files
AnnoteImage - a shortcut containing the command line "java -cp AI.jar;jdom-b4.jar;xerxes.jar AnnoteImage".
For the authoring code to work, you will need to have Sun's Java Software Development Kit (SDK) or Java Runtime Environment (JRE) installed on your computer. Java 1.1 will work, but you might as well install Java 2, which the client requires. You can find them, and a whole lot of other Java stuff, here for Windows, Solaris, and Linux.
Let me know if you have problems with this. I have started working on an installer version for Windows, but it is lower on my list than features at the present. If no one can figure out how to run this stuff, that will change. Please let me know.
and, if you want, you can download the Java source (35 Kbytes)
To serve the images, you need only a computer with a standard web server. There are no special language support or scripting requirements for the server.
To author the annotations, you need a computer with the Java Runtime Environment installed. This is available without cost from Sun Microsystems for the Windows and Solaris platforms. I'll get around to posting Mac and Linux instructions soon.
To view the annotated images, you need a client computer with a web browser which either includes Swing for Java, or which can use a Swing Plug-in. Windows is supported with at least IE 5 and Netscape 4.7, I'm pretty sure Netscape 4.5 and IE 4 will work, and maybe earlier versions too. (But, you really should upgrade your browser!) The details of how the plug-in works are to be found on the Sun Java Plug-In page.
You might want to print a copy of the Slice of Life 2000 conference poster, which has an overview of the steps to create an annotated image collection.
Download it. Unzip it. Move the entire folder where your web server expects to see it (C:\Inetpub\wwwroot under Windows 2000 Professional, for example). Access it from your browser by a url like http://yourserver.edu/DemoPAIS.IML1.
You should be asked about downloading the Java 1.3 Plug-In, and then you should see the client run with a trial image collection of 5 images.
You can view the same test image collection online here, if you want to know what it should look like.
If so, you're all set to make an image collection of your own. Make a copy of the DemoPAIS.IML1 folder called, for instance MyImages, also located where the web server can see it.
If you don't already have Java, go to http://java.sun.com/j2se, and download either the Java 1.3 standard edition or runtime environment.. Install it.
Go back to your MyImages folder. You should be able to start the annotation tool by clicking on the AnnoteImage shortcut.
Now close the application, and drag some GIF or JPEG images of your choosing into the folder. Open the AnnoteImage application again, and create annotations as you desire. Look to the existing annotations for examples. As with all early release authors, I promise a tutorial will be coming soon...
- If this all looks like Greek to you, and you really want to get an image collection going, show it to a web administrator at your site - it really should not be too hard to get running. If it is, let me know and I'll figure out why.
Tutorial link here, by end of June.
Until then, download the sample image collection, as above, look at the .iml files with the authoring tool, and give it a try....
The PAIS mailing list, see the top of the page.
The images in the test image collection are copyrighted, as noted above and in the collection itself. The code is available under the GNU public license (GPL). For more information, see: the GNU Project. The code was developed while I was pursuing a fellowship funded by the National Library of Medicine, and while I was employed by the University of Washington. Those two entities may or may not have policies which are either more or less restrictive than the GPL, and those policies may or may not apply to this code. I'll try to find out.