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Remastering info

First Run Instructions

Place the CD into the CD drive of any (reasonably modern) PC and reboot. The PC must be able to boot from the CD drive: if your own boot loader or windows starts up, reboot again and check your bios settings (you will probably be prompted to press DEL during start-up). On the bios settings screen, check the boot devices: the first should be the floppy drive, the second the CD drive and the third the hard drive (possibly with a fourth option of booting from a network device). Check you motherboard manual for more details.

Description

The Knoppix CD contains a live linux distribution based on Debian, using the LXDE desktop. TINA Knoppix is a remastered version of the Knoppix CD containing the TINA machine vision and medical image analysis software.

TINA consists of two sets of packages; libraries and toolkits. The libraries provide the basic code resource of TINA and are themselves divided into two packages; the low-level tina-libs libraries, which handle memory allocation, file I/O, basic image processing etc., and the high-level tina-tools libraries, which handle interfaces to widget sets and algorithmic functionality. The libraries on the TINA Knoppix CD are located in /usr/local/Tina6/tina-libs and tina-tools. In order to make use of the code contained within the libraries, an interface program known as a toolkit is used. Several are included on the CD; more are available via the TINA website.

The latest version of the TINA Knoppix CD has been specifically created to showcase the TINA Geometric Morphometrics toolkit. This software has been developed in collaboration with the Max Planck Institute for Evolutionary Biology, and allows the identification of morphometric landmarks in 3D medical image volumes such as micro-CT, for subsequent use with techniques such as Procrustes analysis. The toolkit is located in /usr/local/Tina6/max_planck_toolkit-2.0.

The TINA Geometric Morphometrics toolkit can be launched by clicking on the blue TINA icon on the desktop. This will launch the software, load a relatively low-resolution, micro-CT image volume of a Mus musculus skull, set up 2D and 3D views of the data, and load and display a set of example landmarks located on the mandible; this may take a couple of minutes to complete. Note that the macro file was designed for a 15.7-inch widescreen laptop; if your screen is a different size then you may need to move some of the windows around. Also note that you may need to refresh the image displays; simply click on the "Repaint" buttons in the four Tv tools (the windows on the left-hand side of the screen). The TINA Geometric Morphometrics Toolkit User's Guide contains full instructions on how to use the software.

In order to actually mark up a set of morphometric landmarks, the software requires an ASCII text file listing the landmark names. An example file is located in /usr/local/Tina6/max_planck_toolkit-2.0/extra_files/mouse_mandible_point_list.txt; this can be loaded using the landmark list dialog box, as described in the TINA Geometric Morphometrics Toolkit User's Guide.

After having experimented with the example data set, the User may wish to analyse their own data. Clicking on the green TINA icon will start the Geometric Morphometrics toolkit without loading any data or setting up any windows. Data can then be loaded e.g. from a USB memory stick.

Finally, clicking on the red TINA icon provides access to a standard example toolkit distributed with the TINA libraries. This does not incorporate the Geometric Morphometrics tool for compatibility reasons, but provides access to most of the other medical image and machine vision functionality contained within the TINA libraries; see the Tina User's Guide for more information.