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...
Last major software content update 3/6/2000. This page edited 5/28/2000.
Release Date Description 5/20/2000 0.7beta, still "IA7" client code, but updates to home page. 3/6/2000
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. There are two ways.
First, you can look at this 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.
Server Side Components (download)
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 three files:
Server.zip contains
index.html - a sample HTML home page for an atlas. This version was produced with Sun's HTML Converter 1.2, and based on a dynamic check of browser versions, tries to offer a download of the Swing Plug-In, if needed.
IA7.jar - a java archive file containing the client viewer applet. Version 7, obviously...
index.an - whichever annotation file you would like your users to see first. A sample is supplied as part of the Test Image Collection.
Test Image Collection (download)
TestPAIS.zip - contains a simple set of test images and annotations. Download it. Unzip it. Copy it into a web server folder along with the Server Side components mentioned above. Accessing the default web page in that folder should allow you to download the Swing plug-in if you need it, and you should be on your way. (note: these images are copyrighted -- see the included copyright notice)
You can view the test image collection online here, if you want to know what it should look like.
Authoring Components (download)
Authoring.zip contains
AI.jar - a java archive file containing the authoring application.
AnnoteImage - a shortcut containing the command line "java -cp AI.jar AnnoteImage".
For this shortcut to work, you will need to have Sun's Java Software Development Kit (SDK) or Java Runtime Environment (JRE) installed on your computer. You can find them, and a whole lot of other Java stuff, here for Windows, Solaris, and Linux.
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. The details are to be found on the Sun Java Plug-In page.
- Look at the license stuff at the bottom of the page for details of the GNU Public License, which applies to this code.
- First, download the Server Side Components (right click on "download" and choose "save". Or, whatever.)
- Then download the Test Image Collection,
- This should give you Server.zip and TestPais.zip.
- Unzip these two files, and put their contents into the same folder. Don't just put the two folders together into a third -- the IA7.jar file has to be in the top level folder of your collection, along with index.html and index.an.
- Unzip them into the same folder and copy the contents of that folder into a folder that your web server will serve, for example MyAtlas.
- Try the URL http://mywebserver.com/MyAtlas (with the right names substituted, of course.) This the the part that varies locally, depending on your web server and how you create web sites. If it looks Greek to you, find someone nearby who understands Greek...
Tutorial link here, by end of June.
Until then, download the Authoring Components, unzip the file, dump AI.jar and AnnoteImage into the same folder you are using for publishing your atlas, install the Java Runtime Environment if you have not already, double click the AnnoteImage icon, and give it a try.
The PAIS mailing list, coming soon...
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.