Installation Overview

For installation instructions see the Installing BioImage Suite page. BioImage Suite is a collection of programs using the same underlying components. There is no main application as such. However, BioImage Suite has a main menu application which can be used as (a) a launcher for the individual component applications and (b) to access the user preferences dialog.

Operating System Selection

Please select the operating system type that you have installed BioImage Suite on:

• Microsoft Windows 98/2000/XP
• Linux/Unix/Mac OS X

For more details on the individual applications see below.

Microsoft Windows 2000/XP

Please follow the installation instructions. Once you have run c:\yale\bioimagesuite\bioimagesuite_shortcuts.bat there will be a folder in your  Start menu called BioImage Suite with two links:

1. BioImage Suite Menu -- use this to start the graphical menu application (shown below)
2. BioImage Suite Console -- starts a "DOS" console with the appropriate environment variable settings for running the programs on the command-line "Unix-style". The program names are the same as on the buttons in the menu e.g. type pxitclsimpleviewer to start the "SimpleViewer" application.

In both cases there will be a DOS/Command Window open. Do not close this window. It is used to output diagnostic messages etc. Closing it will eventually crash the software.

Linux/Unix/Mac OS X

Please follow the installation instructions. There are two ways to start BioImage Suite:

1. Execute /usr/local/bioimagesuite/start_bioimagesuite  -- this to start the graphical menu application (shown below)
2. Console mode. This allows running the programs on the command-line "Unix-style". The program names are the same as on the buttons in the menu, e.g. type pxitclsimpleviewer to start the "SimpleViewer" application. To set the paths appropriately type:
• source /usr/local/bioimagesuite/setpaths.sh   (if you are using a Bash/ksh shell)     or
• source /usr/local/bioimagesuite/setpaths.csh (if you are using the csh/tcsh shells)
3. This command may be added to your .profile or .cshrc files if desired.

Application List

To invoke each application, click on the button (i.e. pxitclsimpleviewer). If you are using the software in "console mode" with the paths properly set, you may invoke each application by simply typing its name on the command line. For example, to invoke the pxitclbrainsegment program simply type "pxitclbrainsegment"

The applications are shown in seven categories under the main tabs on the left. A brief desciption of each application is given under its button. The main tabs are:

• General -- contains the core applications which are primarily geared towards neuroimage analysis, including Registration tools and tools for the formation of Multisubject Composite Functional Maps.
• Data Tree -- accesses the new datatree tool which serves as a database-like front-end for BioImage Suite. A lot of the future growth of BioImage Suite will involve this functionality.
• DTI/Angiography -- includes tools for diffusion weighted image analysis and early versions of our angiography tools.
• Surface Editors -- contains the SurfaceEditor tool which allows for interactive segmentation of 3D images.
• Neurosurgery -- contains tools specific to epilepsy neurosurgery planning including the intracranial electrode localization tool. Much of this functionality is incorporated into the data tree tool (which started life as a surgical planning tool). In addition, there are facilities for real-time communication with the BrainLAB VectorVision Cranial system using the VectorVision Link interface tool in BioImage Suite.
• Cardiac -- has two tools for viewing and surface editing (variations on other tools) specifically adapted to 4D Image Analysis.
• Mousesuite -- includes early versions of our segmentation/registration Mouse Tools specifically adapted for small animal imaging.

The Core functionality in all applications is described here.

Preferences Editor

The User Preferences Editor enables the setting of global parameters used by the BioImage Suite Applications. The preferences are stored in a file called .pxitclpref2 in the user's home directory (in this case d:/.pxitclpref2 as the dialog itself informs the user). Changes made in the "Preferences Editor" -- which is also accessible under the Help menu in many applications only take effect once the application is restarted.

There are 5 tabs in the editor each containing different sets of options described below:

1. Look & Feel
• Color Scheme -- chose between System Default, BioImage Suite Blue, Bisque and High Contrast color schemes.
• Font Selection -- sets the font for the menus/dialog boxes
• Mirror Console -- by default in most GUI applications most "print-outs" go to the BioImage Suite Console (accessible under Help/Console in most applications). Setting Mirror to 1 also sends any printouts to the native console (e.g. the DOS Window or the xterm window from which the application was started.
2. File Formats
• Swap on Save -- saves all images as ByteSwapped -- useful only for compatibility with older Unix Systems.
• Default Import Mode -- sets the default import format for the Image Import Tool
• Minc Image Format and MincImageFormatDefault enables the use of the .mnc format and set it as the default respectively. This format however may not be supported by the binary version of BioImage Suite that you are using. This is still work in progress.
3. Image Display
• NormalizeAnatomical -- If enabled, the default windowing used for image display is automatically adjusted to improve the contrast (Also available using the "Nr" Colormap in the Viewers)
• Image Colornaps -- if enabled, the current colormap is saved  upon saving the image and reloaded afterwards. This is also work in progress.
• Interpolation -- default interpolation mode for image reslicing.
• Volume Texture Mode -- by default, the software will use hardware accelerated volume rendering. Disable on systems with older graphics cards (>5 years old -- any recent ATI/Nvidia card should work fine with this on)
• FMRI Mode -- selection of default colormap for overlay of functional images (these three choices are also available from the Overlay Tool).
4. Surface Editing
• MaxSurfaces  -- maximum number of surfaces available. Set this to the minimum requirement to speed up the application.
• ControlPointSize -- sets the default size of the control points in the spline editor.
5. Advanced/Miscellaneous
• RigidRegistration -- do not touch this unless specifically instructed to do so.
• VectorVisionLink -- enables the VectorVisionLink interface to the BrainLAB Vector Vision Cranial Image Guided navigation system.
• Enable Beta Features -- if on, additional options may be available which are considered experimental for now. Keep this off.

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