Scope of this guide

The purpose of the MIPAV software program is to allow medical researchers to extract quantitative information from image datasets of various medical image modalities.

The primary purpose of the MIPAV User's Guide is to provide medical researchers the information they need to use the MIPAV software program.

A secondary goal is to give researchers the information needed to extend, if desired, the software's capabilities through the development of new functions in plug-in applications via use of the software's application program interface (API).

Medical researchers, medical technicians, and other people who are involved in analyzing medical images or maintaining and supporting the equipment used to produce images form the audience for the User's Guide.

Depending on the platform-Windows, MacIntosh, or Unix-that is running your workstation, it is recommended that you are familiar with installing and using software programs for that platform.

If you plan to create plug-in applications for MIPAV to add new functionality, you must have software programming skills and be familiar with Java.

The MIPAV User's Guide is divided into two volumes:

• Volume 1, Basics, explains how to use the basic features and functions of MIPAV and how to incorporate plug-in applications.
  
• Algorithms, presents detailed information about the purpose, background, and function of the algorithms packaged with MIPAV and gives instructions for using them.
  

The MIPAV User's Guide, Volume 1 includes the following:

• Chapter 1, Introducing MIPAV, presents an overview of the MIPAV software program.
• Chapter 2, Installing MIPAV, explains how to install, remove, and upgrade the MIPAV software program. It also explains how to subscribe to the MIPAV mail list and how to search the MIPAV archive.
• Chapter 3, Getting Started Quickly with MIPAV, explains how to use MIPAV to perform common functions, such as opening an image file, saving the file, and printing a log file.
• Chapter 4, Understanding Image Basics, provides background information on image file formats. It also provides information on how to view and adjust image file attributes.
• Chapter 5, Working with DICOM Images, explains how to access DICOM databases, perform queries, and retrieve image files. In addition, it explains how to send files to a database.
• Chapter 6, Visualizing Images, provides instruction on how to customize the way image files are displayed, how to magnify and minify images, how to view images together, how to view a portion of the image, and how to change image brightness and contrast by generating histograms and adjusting color look-up tables (LUTs).
• Chapter 7, Segmenting Images Using Contours and Masks, explains how to create, group, rearrange, and modify volumes of interest (VOIs); how to create masks; and how to use paint to further identify VOIs.
• Chapter 8, Analyzing Images, discusses how to calculate statistics for VOIs and masks and how to generate intensity profiles, or graphs, for images.
• Chapter 9,Changing Image Datasets Using MIPAV Utilities . . ., explains how to use the utilities included in the software.
• Chapter 10,Using Scripts (Macros) in MIPAV, describes how to develop scripts, which you can use to customize the program.
• Chapter 11, Developing Plugin Programs, and Appendix D explain how to incorporate plug-in programs into MIPAV.
• Chapter 12, Technical Support provides information about MIPAV technical support and also explains how to use the debug mode.
• Appendix A, References, provides a list of references that can be used to learn more about MIPAV functions.
• Appendix B, DICOM Conformance, provides a copy of the formal DICOM Conformance Statement, which specifies MIPAV's service classes, information objects, communications protocols, and media storage application profiles.
• Appendix C, Supported Formats lists graphical and file formats supported by MIPAV. It also provides examples of MIPAV system files (such as the preference file) and explains how the user can interpret them; provides limited instruction on how to modify specific files.
• Appendix D, PlugIn Algorithm Median gives an example of MIPAV plug in.

The guide also includes a glossary of terms and acronyms.

Volume 2, Algorithms, includes two chapters:

• Understanding MIPAV capabilities, which discusses the tools and application programming interface provided with MIPAV
  
• Using MIPAV Algorithms, provides detailed information about the algorithms packaged in MIPAV
  

In addition, this guide includes the glossary of terms and acronyms.

Both volumes 1 and 2 of the MIPAV User's Guide are available as Acrobat PDF, which you can view, download, and print. You can either print each volume, or you can print individual chapters separately. For PDFs of this guide, go to the MIPAV web site:
http://mipav.cit.nih.gov