We are in the process of updating the manual for the new version 2.5 Some parts of this may be a little bit out-of-date.
BioImage Suite is a collection of image analysis programs which use the same underlying code infrastructure and have the same look and feel but are tuned to specific imaging applications. The current version of BioImage Suite consists of a number of graphical applications (GUI) and a set of command-line utilities providing support for both interactive and batch-mode processing. All software has been tested on Linux, Windows, MAC OS X 10.4 (and at least cursorily run on IRIX 6.5, Free BSD 6.0 and Solaris 10.0).
This manual describes the basic concepts in BioImage Suite. The following pages are particularly useful to a first time user:
- The Starting and Running BioImage Suite page describes how to start BioImage Suite and how to configure user preferences.
- The Application Structure (Framework) page describes the overall structure of all BioImage Suite applications.
- The Viewers page describes the BioImage Suite viewers which are at the heart of all applications.
BioImage Suite Functionality
BioImage Suite has facilities for:Pre-processing: Standard image smoothing/filtering, reslicing, cropping reorienting etc. In addition, for bias field correction, it includes a custom reimplementation of the bias field correction method of Styner et al. which incorporates automated histogram fitting for determining the appropriate numbers of classes, and additional spatial constraints.
Voxel Classification: Methods for voxel classification are available using simple histogram, single channel MRF and exponential-fit methods.
Deformable Surface Segmentation: BioImage Suite has a strong and unique interactive deformable surface editor tool which allows for easy semi-interactive segmentation of different anatomical structures and embeds common snake-like deformable models.
Registration: BioImage Suite includes a clean reimplementation of the work of Studholme et al. for rigid/affine registration using a highly efficient conjugate gradient optimization scheme. These methods have been successfully used to align serial MRI data as well as multimodal data (e.g. CT/PET/SPECT to MRI). It also includes a full complement of non-rigid point-based registration methods, intensity-only and integrated feature intensity methods.
Diffusion Weighted MR Image Analysis: BioImage Suite includes methods for the computation and visualization of basic voxel-wise measures from diffusion tensor images (e.g. fractional anisotropy) as well as fiber tracking methods using traditional (streamlining) and novel (anisotropic front propagation) methods.
Cardiac Image Analysis: The shape-based cardiac deformation method of Papademetris et al. is included in BioImage Suite. This functionality, however, requires the presence of the Abaqus finite element package and license).
fMRI Activation Detection: BioImage Suite has a clean and fast reimplementation of the standard General Linear Model (GLM) method for fMRI activation detection, in addition to tools for performing region of interest analysis (ROI), multisubject composite maps, etc. The registration tools (described above) can be used for motion correction, distortion correction and intra-subject registration. (The fMRI tools are not included in the current released version of BioImage Suite because they still use VTK 4.0 and an older set of the common libraries -- the rest of BioImage Suite is based on VTK 4.4. We anticipate adding this soon).