Release Notes

This live DVD contains a collection of software packages and sample images to accompany and support the book Advanced Biomedical Image Analysis by M. Haidekker, John Wiley (2010), ISBN 978-0-470-62458-6 link to publisher's Web site.

The DVD is based on Kubuntu, a flavor of the GNU/Linux operating system. The Live DVD is bootable, that is, you can boot your computer from this DVD, use it without affecting your hard drive, and reboot from your hard drive into your previous operating system once you are done. Alternatively, you may install the operating system and the included software on a free hard disk partition.

Note that the Live DVD is markedly slower than any hard-disk-based operating system, because CD/DVD drives are much slower than hard disks.

The GNU/Linux operating system and the programs on this DVD are free software, released under the GNU Public License, a license that gives you a number of freedoms (rights), most prominently the right to install this software on as many computers as you like, to copy this DVD and give it to as many people as you like, and the right to access the source code of the programs on this DVD. To obtain the source code, please consult the individual package's home pages. An overview of the philosophy behind Free Software can be accessed here.

Key software provided on this DVD includes:

GIMP: The GNU Image manipulation program. Software to edit images and photos on the pixel level, much like Adobe Photoshop. Link to the GIMP homepage.
ImageJ: Image analysis program sponsored by the National Institutes of Health. Link to ImageJ home page
Crystal Image: The author's image analysis program, which contains algorithms for most of the methods described in this book. Link to Crystal Image home page
OpenDX: Arguably one of the best visualization tools available. Link to OpenDX home page
FSL: A comprehensive library of image analysis and statistical tools for FMRI, MRI and DTI brain imaging data.
CTSIM: Simulation program for computed tomography image formation and image reconstruction.
AMIDE (Amide's a Medical Imaging Data Examiner): A tool for viewing and analyzing medical image data sets. Its capabilities include the simultaneous handling of multiple data sets imported from a variety of file formats, image fusion, 3D region of interest drawing and analysis, volume rendering, and rigid body alignments.

Some of these programs (ImageJ, Crystal Image, OpenDX, AMIDE) are covered in Chapter 14 of the book. Other software is available and can be explored by using the "K" start button to the left of the task bar.

Ubuntu and Kubuntu offer very large and comprehensive software repositories. These can be accessed with the "Add/Remove Software" function in the start menu or, based on user preference - with the Synaptic package manager. Presently, the Ubuntu repositories offer nearly 30,000 Free software packages in numerous categories from office and productivity tools to scientific and engineering applications.