Introduction

Slicer is a software research tool with emphasis on: Research for guiding biopsies and craniotomies Research of diagnostic visualization and surgical planning Facilitating research into brain shift and volumetric studies in the lab

1. Overview

2. Acknowledgements

1. Overview

Slicer uniquely integrates several facets of image-guided medicine into a single environment. It provides capabilities for automatic registration (aligning data sets), semi-automatic segmentation (extracting structures such as vessels and tumors from the data), generation of 3D surface models (for viewing the segmented structures), 3D visualization, and quantitative analysis (measuring distances, angles, surface areas, and volumes) of various medical scans.

The image to the left was created by segmenting an anatomical MR scan to form 3D surface models of the skin and tumor (green). Functional MR data was segmented to build models of the motor cortex (yellow), auditory verb generation (red), and visual verb generation (blue). All these surface models are integrated in a 3D view along with 3 slices through the MR images. The slices are also shown in 2D views at the bottom. Note that the functional data is overlaid in color on the anatomical data.

top

2. Acknowledgements

Slicer is an Open Source development project begun at the MIT Artificial Intelligence Laboratory (now the Computer Science and Artificial Intelligence Laboratory) and the Surgical Planning Laboratory at Brigham and Women's Hospital, a teaching affiliate of Harvard Medical School. Slicer is now in active research use at institutions around the world with contributing developers sponsored by a variety of governmental, commercial, and institutional funding sources. MIT held the initial copyright to the source code (for Slicer 1.* and Slicer 2.0-2.3, 1999-2004), and has transferred it to BWH as of Slicer version 2.4, in 2005. The text of the copyright can be found here. The SPL coordinates the ongoing development and hosts a wide range of clinical and development efforts using Slicer.

Funding Agencies:

National Institutes of Health	National Center for Research Resources	National Institute of Biomedical Imaging and Bioengineering
National Cancer Institute	Neuroimaging Analysis Center	National Alliance for Medical Image Computing
National Center for Image Guided Therapy	Biomedical Informatics Research Network	United States Department of Defense
Center for Integration of Medicine and Innovative Technology

Contributors:

Brigham and Women's Hospital and Harvard Medical School	Massachusetts Institute of Technology	Johns Hopkins University
Georgia Institute of Technology	Harvard NeuroDiscovery Center	Massachusetts General Hospital
Laboratory of Mathematics in Imaging		Athinoula A. Martinos Center for Biomedical Imaging

The main individual contributors to this joint effort are listed below.

Area	Contributors
Overall concept	Ron Kikinis, Ferenc Jolesz, Eric Grimson, William Wells III
Major designer and implementer	Dave Gering (1997-1999), Lauren O'Donnell (1999-), Steve Pieper (2001-)
Prototype	Noby Hata (1997), Ron Kikinis
OpenMR interface	Arya Nabavi (1998-1999), Ferenc Jolesz
Measurement tools	William Lorensen (GE), Peter Everett (SPL), Krishna Yeshwant (SPL)
Robot simulation tools	Noby Hata, Oliver Schorr
3D connectivity algorithm	Andre Robatino
MI registration	William Wells III
Virtual endoscopy tool	Delphine Nain (MIT CSAIL)
DICOM functionality, robot control, volume rendering	Attila Tanacs (Johns Hopkins University)
Cryotherapy planning	Torsten Butz (EPFL)
Architecture	Michael Halle (SPL)
EMSegmenter	Kilian Pohl (MIT CSAIL)
Tetramesh, volumeMath, developer.tcl	Samson Timoner (MIT CSAIL)
Print header	Mark Anderson (SPL)
Training and Download requests	Marianna Jakab (SPL)
Model Hierarchies	Arne Hans (SPL)
Application development	Steven Haker (SPL)
Craniofacial	Krishna Yeshwant (SPL)
FreeSurfer Volume Readers	Kevin Teich (MGH), Nicole Aucoin (BWH)
Nightly Builds, Testing, QA	Kathryn Hayes (BWH)
Training Materials	Sonia Pujol (BWH)
DTI Tools	C. F. Westin, Lauren O'Donnell, Raul San Jose Estepar (BWH)
fMRI Tools	William Wells, Wendy Plesniak, Haiying Liu (BWH)

We are sincerely thankful for the grants and fellowships supporting this project, and we wish to acknowledge them here.

Contributor	Supporter
David Gering	GE Medical Systems
Lauren O'Donnell	National Science Foundation Graduate Research Fellowship
Ron Kikinis	NIH grants P41 RR13218, P01 CA67165, and R01 RR11747; ERC 9731748
William Wells III	Whitaker Foundation Biomedical Engineering Research Grant
W. Eric L. Grimson	NSF grant IIS-9610249, ERC 9731748
Attila Tanacs	ERC 9731748
Kevin Teich	NIH-NCRR grant 3 P41 RR14075-03S1

top