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Subsections

1. Introduction

Figure: An example BioImage Suite Application.
Image example_app

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 chapters are particularly useful to a first time user:

1.1 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 [108]. 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. (Some of 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).

1.2 BioImage Suite Software Infrastructure

BioImage Suite is developed using a combination of C++ and Tcl in the same fashion as that pioneered by VTK. In practice, most of the underlying computationally expensive algorithms are implemented in C++ (as classes deriving from related VTK or ITK classes) and the user interface is for the most part developed in the Tcl/Tk scripting environment. Further, a custom written C++ wrapper around the Tk graphical user interface library enables the creation of complex graphical components from C++.

1.3 A Brief History

BioImage Suite started life as a tool for interactive 4D cardiac segmentation and the original surface editor was presented at the 47th Annual Scientific Session of the American College of Cardiology in 1998. It run exclusively on the Silicon Graphics IRIX platform (6.2,6.3) and used a combination of MOTIF and Open Inventor.

It was subsequently adapted and extended for neuroimaging applications primarily for the needs of an epilepsy image-guided neurosurgery project (2001-). At this point development switched to an explicit multi-platform setup and MOTIF was replaced by a Tcl/Tk environment and Open Inventor was replaced by VTK. (then version 3.1).

Progressively, diffusion weighted imaging (DTI) functionality was added (2002 + M. Jackowski), as well as the development of our fMRI tools (2003 + N. Rajeevan) It was subsequently extended for use in abdominal fat quantification work (2004-) and for use in vascular tree extraction for a mouse hindlimb angiogenesis project. (2005-).

Recently, we have obtained funding from the NIH/NIBIB (R01 EB006494-01 PI: Papademetris, X.) to continue, in the words of the program announcement, ``to support the continued development, maintenance, testing and evaluation of existing software''. The BioImage Suite webpage went live in early 2006 and a support forum was established soon afterwards. A first beta version was made publicly available in January 2006. We are (July 2006) in the process of releasing BioImage Suite 2.0 - version 1 was never publicly available but in use at Yale since 2002.

BioImage Suite was originally developed for the needs of the following, NIH-funded, projects at Yale:

If you use BioImage Suite for a publication please cite it as: 

X. Papademetris, M. Jackowski, N. Rajeevan, R.T. Constable, and
L.H Staib. BioImage Suite: An integrated medical image analysis suite,
Section of Bioimaging Sciences, Dept. of Diagnostic Radiology, Yale
School of Medicine. http://www.bioimagesuite.org.

next up previous contents
Next: 2. Background Up: 1 A. Overview Previous: 1 A. Overview   Contents