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 PI: Papademetrix, 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. The first official version of BioImage Suite 2.0 was released in February 2007. This was followed by BioImage Suite 2.5 in January 2008. We are currently (Aug 2008) in the process of releasing BioImage Suite 2.6, the first beta for which was made available in July of 2008.

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

  • Bioimaging and Intervention in Neocortical Epilepsy -- BRP R01-EB000473 PI: Duncan, J. S. 
  • Dynamic Analysis of LV Deformation from 4D Images -- R01-EB002068 PI: Duncan, J. S. 
  • Integrated Function/Structure Image Analysis in Autism -- R01-NS035193 PI: Duncan, J. S. 
  • Brain Image Segmentation, Comparison, and Measurement -- R01-EB000311 PI: Staib, L. H. 
  • Functional MRI for Neurosurgical Planning in Epilepsy -- R01-NS38467 PI: Constable, R.T. 
  • Functional Heterogeneity of the Hippocampal Formation -- R01-NS38467 PI: Constable R.T 
  • Non-invasive Methods for Imaging Angiogenesis -- R01-HL65662 PI: Sinusas, A. J. 
  • Yale Mouse Metabolic Phenotyping Center -- U24-DK59635-01 PI: Shulman, G.I. (Imaging Core PI: Behar, K.L.)
BioImage Suite

BioImage Suite has extensive capabilities for both neuro/cardiac and abdominal image analysis and state of the art visualization. Many packages are available that are highly extensible, and provide functionality for image visualization and registration, surface editing, cardiac 4D multi-slice editing, diffusion tensor image processing, mouse segmentation and registration, and much more. It can be integrated with other biomedical image processing software, such as FSL, AFNI, and SPM. This site provides information, downloads, documentation, and other resources for users of the software.

Contact Us

The e-mail addresses for those who are able to provide support for BioImage Suite are provided below. Please look through the online documentation before e-mailing us with questions. This website is updated regularly.

Xenophon Papademetris

Associate Professor of Diagnostic Radiology and Biomedical Engineering
Yale University School of Medicine
P.O. Box 208043 (TAC N119)
New Haven, CT 06520
xenophon.papademetris@yale.edu

Alark Joshi

Assistant Professor
Department of Computer Science
College of Engineering
Boise State University
alarkjoshi@boisestate.edu