3DSlicer
Encyclopedia
3D Slicer is a free
, open source
software package for image analysis
and scientific visualization
. Slicer is used in a variety of medical applications, including autism
, multiple sclerosis
, systemic lupus erythematosus
, prostate cancer
, schizophrenia
, orthopedic biomechanics
, COPD
, cardiovascular disease
and neurosurgery
.
tools for a variety of applications.
3D Slicer provides image registration
, processing of DTI (diffusion tractography)
, an interface to external devices for image guidance support, and GPU
-enabled volume rendering
, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools.
The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials
and measurement widgets, customized colormaps).
Slicer's capabilities include:
Slicer is compiled for use on multiple platforms, including Windows
, Linux
, and Mac OS X
.
Slicer is distributed under a BSD style, free, open source license. The license has no restrictions on use of the software. However, no claims are made on the software being useful for any particular task. It is entirely the responsibility of the user to ensure compliance with local rules and regulations. Slicer has not been approved for clinical use in the US or elsewhere.
project between the Surgical Planning Laboratory at the Brigham and Women's Hospital and the MIT Artificial Intelligence Laboratory in 1998. 3D Slicer version 2 has been downloaded several thousand times. In 2007 a completely revamped version 3 of Slicer was released. The next major refactoring of Slicer was initiated in 2009, which aims to transition the GUI
of Slicer from using KWWidgets to Qt. Qt-enabled Slicer version 4 is expected to be released in 2010–2011.
Slicer software has enabled a variety of research publications
, all aimed at improving image analysis
.
This significant software project has been enabled by the participation of several large-scale NIH
funded efforts, including the NA-MIC, NAC, BIRN
, CIMIT, Harvard Catalyst and NCIGT communities. The funding support comes from several federal funding sources, including NCRR
, NIBIB
, NIH
Roadmap, NCI
, NSF
and the DOD
.
, registration
and three-dimensional
visualization of multimodal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging
and image-guided radiation therapy
. Standard image file formats
are supported, and the application integrates interface capabilities to biomedical research software.
Slicer has been used in a variety of clinical research
. In image-guided therapy research, Slicer is frequently used to construct and visualize collections of MRI data that are available pre- and intra-operatively to allow for the acquiring of spatial coordinates
for instrument tracking. In fact, Slicer has already played such a pivotal role in image-guided therapy, it can be considered as growing up alongside that field, with over 200 publications referencing Slicer since 1998.
In addition to producing 3D models from conventional MRI images, Slicer has also been used to present information derived from fMRI (using MRI to assess blood flow in the brain related to neural
or spinal cord
activity), DTI (using MRI to measure the restricted diffusion of water in imaged tissue), and electrocardiography. For example, Slicer's DTI package allows the conversion and analysis of DTI images. The results of such analysis can be integrated with the results from analysis of morphologic
MRI, MR angiograms and fMRI. Other uses of Slicer include paleontology
and neurosurgery planning.
, a graphical library that provides a high-level interface to OpenGL
and a pipeline mechanism to connect graphical filters. The library is implemented in C++
but provides a Tcl
wrapper to instantiate and execute its methods. Tcl/Tk comprises the rest of 3D Slicer user interface and event handling.
Slicer software supports automatic testing and employs an extreme programming approach with nightly builds natively on multiple platforms. Recent accomplishments include added capability for plugging-in external modules using an XML
-based command line interface. The Slicer effort also incorporates a light-weight user-centered design effort to promote overall software usability.
Slicer.org offers resources for those who would like to improve or modify Slicer designs and applications. Various tutorials and instructions, along with access to a community of other developers can be found there.
Development still in progress, Slicer is sometimes accused by academic users of being poorly documented and a lack of automation facilities (which is useful in batch processing). Although bugs can be reported to the mail list, they are not guaranteed to be fixed timely, which is determined by its freely available nature. A new version would come out every few weeks, but is only available as a fresh installation in lieu of an in-place manner, which adds to maintenance difficulty.
Free software
Free software, software libre or libre software is software that can be used, studied, and modified without restriction, and which can be copied and redistributed in modified or unmodified form either without restriction, or with restrictions that only ensure that further recipients can also do...
, open source
Open source
The term open source describes practices in production and development that promote access to the end product's source materials. Some consider open source a philosophy, others consider it a pragmatic methodology...
software package for image analysis
Image analysis
Image analysis is the extraction of meaningful information from images; mainly from digital images by means of digital image processing techniques...
and scientific visualization
Scientific visualization
Scientific visualization is an interdisciplinary branch of science according to Friendly "primarily concerned with the visualization of three-dimensional phenomena , where the emphasis is on realistic renderings of volumes, surfaces, illumination sources, and so forth, perhaps...
. Slicer is used in a variety of medical applications, including autism
Autism
Autism is a disorder of neural development characterized by impaired social interaction and communication, and by restricted and repetitive behavior. These signs all begin before a child is three years old. Autism affects information processing in the brain by altering how nerve cells and their...
, multiple sclerosis
Multiple sclerosis
Multiple sclerosis is an inflammatory disease in which the fatty myelin sheaths around the axons of the brain and spinal cord are damaged, leading to demyelination and scarring as well as a broad spectrum of signs and symptoms...
, systemic lupus erythematosus
Systemic lupus erythematosus
Systemic lupus erythematosus , often abbreviated to SLE or lupus, is a systemic autoimmune disease that can affect any part of the body. As occurs in other autoimmune diseases, the immune system attacks the body's cells and tissue, resulting in inflammation and tissue damage...
, prostate cancer
Prostate cancer
Prostate cancer is a form of cancer that develops in the prostate, a gland in the male reproductive system. Most prostate cancers are slow growing; however, there are cases of aggressive prostate cancers. The cancer cells may metastasize from the prostate to other parts of the body, particularly...
, schizophrenia
Schizophrenia
Schizophrenia is a mental disorder characterized by a disintegration of thought processes and of emotional responsiveness. It most commonly manifests itself as auditory hallucinations, paranoid or bizarre delusions, or disorganized speech and thinking, and it is accompanied by significant social...
, orthopedic biomechanics
Biomechanics
Biomechanics is the application of mechanical principles to biological systems, such as humans, animals, plants, organs, and cells. Perhaps one of the best definitions was provided by Herbert Hatze in 1974: "Biomechanics is the study of the structure and function of biological systems by means of...
, COPD
Chronic obstructive pulmonary disease
Chronic obstructive pulmonary disease , also known as chronic obstructive lung disease , chronic obstructive airway disease , chronic airflow limitation and chronic obstructive respiratory disease , is the co-occurrence of chronic bronchitis and emphysema, a pair of commonly co-existing diseases...
, cardiovascular disease
Cardiovascular disease
Heart disease or cardiovascular disease are the class of diseases that involve the heart or blood vessels . While the term technically refers to any disease that affects the cardiovascular system , it is usually used to refer to those related to atherosclerosis...
and neurosurgery
Neurosurgery
Neurosurgery is the medical specialty concerned with the prevention, diagnosis, treatment, and rehabilitation of disorders which affect any portion of the nervous system including the brain, spine, spinal cord, peripheral nerves, and extra-cranial cerebrovascular system.-In the United States:In...
.
About Slicer
3D Slicer is a free open source software (BSD license) that is a flexible, modular platform for image analysis and visualization. 3D Slicer can be easily extended to enable development of both interactive and batch processingBatch processing
Batch processing is execution of a series of programs on a computer without manual intervention.Batch jobs are set up so they can be run to completion without manual intervention, so all input data is preselected through scripts or command-line parameters...
tools for a variety of applications.
3D Slicer provides image registration
Image registration
Image registration is the process of transforming different sets of data into one coordinate system. Data may be multiple photographs, data from different sensors, from different times, or from different viewpoints. It is used in computer vision, medical imaging, military automatic target...
, processing of DTI (diffusion tractography)
Diffusion MRI
Diffusion MRI is a magnetic resonance imaging method that produces in vivo images of biological tissues weighted with the local microstructural characteristics of water diffusion, which is capable of showing connections between brain regions...
, an interface to external devices for image guidance support, and GPU
Graphics processing unit
A graphics processing unit or GPU is a specialized circuit designed to rapidly manipulate and alter memory in such a way so as to accelerate the building of images in a frame buffer intended for output to a display...
-enabled volume rendering
Volume rendering
In scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set.A typical 3D data set is a group of 2D slice images acquired by aCT, MRI, or MicroCT scanner....
, among other capabilities. 3D Slicer has a modular organization that allows the easy addition of new functionality and provides a number of generic features not available in competing tools.
The interactive visualization capabilities of 3D Slicer include the ability to display arbitrarily oriented image slices, build surface models from image labels, and high performance volume rendering. 3D Slicer also supports a rich set of annotation features (fiducials
Fiduciary marker
A fiducial marker or fiducial is an object used in the field of view of an imaging system which appears in the image produced, for use as a point of reference or a measure...
and measurement widgets, customized colormaps).
Slicer's capabilities include:
- Handling DICOM images and reading/writing a variety of other formats
- Interactive visualization of volumetric Voxel imagesVoxelA voxel is a volume element, representing a value on a regular grid in three dimensional space. This is analogous to a pixel, which represents 2D image data in a bitmap...
, polygonal meshesPolygonal modelingIn 3D computer graphics, polygonal modeling is an approach for modeling objects by representing or approximating their surfaces using polygons. Polygonal modeling is well suited to scanline rendering and is therefore the method of choice for real-time computer graphics...
, and volume renderingVolume renderingIn scientific visualization and computer graphics, volume rendering is a set of techniques used to display a 2D projection of a 3D discretely sampled data set.A typical 3D data set is a group of 2D slice images acquired by aCT, MRI, or MicroCT scanner....
s - Manual editing
- Fusion and co-registering of data using rigid and non-rigid algorithms
- Automatic image segmentationSegmentation (image processing)In computer vision, segmentation refers to the process of partitioning a digital image into multiple segments . The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze...
- Analysis and visualization of diffusion tensor imaging data
- Tracking of devices for image-guided procedures.
Slicer is compiled for use on multiple platforms, including Windows
Microsoft Windows
Microsoft Windows is a series of operating systems produced by Microsoft.Microsoft introduced an operating environment named Windows on November 20, 1985 as an add-on to MS-DOS in response to the growing interest in graphical user interfaces . Microsoft Windows came to dominate the world's personal...
, Linux
Linux
Linux is a Unix-like computer operating system assembled under the model of free and open source software development and distribution. The defining component of any Linux system is the Linux kernel, an operating system kernel first released October 5, 1991 by Linus Torvalds...
, and Mac OS X
Mac OS X
Mac OS X is a series of Unix-based operating systems and graphical user interfaces developed, marketed, and sold by Apple Inc. Since 2002, has been included with all new Macintosh computer systems...
.
Slicer is distributed under a BSD style, free, open source license. The license has no restrictions on use of the software. However, no claims are made on the software being useful for any particular task. It is entirely the responsibility of the user to ensure compliance with local rules and regulations. Slicer has not been approved for clinical use in the US or elsewhere.
History
Slicer started as a masters thesisThesis
A dissertation or thesis is a document submitted in support of candidature for an academic degree or professional qualification presenting the author's research and findings...
project between the Surgical Planning Laboratory at the Brigham and Women's Hospital and the MIT Artificial Intelligence Laboratory in 1998. 3D Slicer version 2 has been downloaded several thousand times. In 2007 a completely revamped version 3 of Slicer was released. The next major refactoring of Slicer was initiated in 2009, which aims to transition the GUI
Gui
Gui or guee is a generic term to refer to grilled dishes in Korean cuisine. These most commonly have meat or fish as their primary ingredient, but may in some cases also comprise grilled vegetables or other vegetarian ingredients. The term derives from the verb, "gupda" in Korean, which literally...
of Slicer from using KWWidgets to Qt. Qt-enabled Slicer version 4 is expected to be released in 2010–2011.
Slicer software has enabled a variety of research publications
Academic publishing
Academic publishing describes the subfield of publishing which distributes academic research and scholarship. Most academic work is published in journal article, book or thesis form. The part of academic written output that is not formally published but merely printed up or posted is often called...
, all aimed at improving image analysis
Image analysis
Image analysis is the extraction of meaningful information from images; mainly from digital images by means of digital image processing techniques...
.
This significant software project has been enabled by the participation of several large-scale NIH
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
funded efforts, including the NA-MIC, NAC, BIRN
Biomedical Informatics Research Network
The Biomedical Informatics Research Network is a national initiative to assist biomedical research through data sharing and online collaboration. BIRN provides data-sharing infrastructure, software tools and techniques, and advisory services from a single source...
, CIMIT, Harvard Catalyst and NCIGT communities. The funding support comes from several federal funding sources, including NCRR
National Center for Research Resources
The National Center for Research Resources or NCRR, is a United States government agency. NCRR provides funding to laboratory scientists and researchers for facilities and tools in the goal of curing and treating diseases.-Organization and history:...
, NIBIB
National Institute of Biomedical Imaging and Bioengineering
The National Institute of Biomedical Imaging and Bioengineering is the newest of the National Institutes of Health research institutes and centers and was formed in the United States when President Bill Clinton signed it into law on December 29, 2000.The Institute is committed to integrating the...
, NIH
National Institutes of Health
The National Institutes of Health are an agency of the United States Department of Health and Human Services and are the primary agency of the United States government responsible for biomedical and health-related research. Its science and engineering counterpart is the National Science Foundation...
Roadmap, NCI
National Cancer Institute
The National Cancer Institute is part of the National Institutes of Health , which is one of 11 agencies that are part of the U.S. Department of Health and Human Services. The NCI coordinates the U.S...
, NSF
National Science Foundation
The National Science Foundation is a United States government agency that supports fundamental research and education in all the non-medical fields of science and engineering. Its medical counterpart is the National Institutes of Health...
and the DOD
United States Department of Defense
The United States Department of Defense is the U.S...
.
Users
Slicer's platform provides functionalities for segmentationSegmentation (image processing)
In computer vision, segmentation refers to the process of partitioning a digital image into multiple segments . The goal of segmentation is to simplify and/or change the representation of an image into something that is more meaningful and easier to analyze...
, registration
Image registration
Image registration is the process of transforming different sets of data into one coordinate system. Data may be multiple photographs, data from different sensors, from different times, or from different viewpoints. It is used in computer vision, medical imaging, military automatic target...
and three-dimensional
Three-dimensional space
Three-dimensional space is a geometric 3-parameters model of the physical universe in which we live. These three dimensions are commonly called length, width, and depth , although any three directions can be chosen, provided that they do not lie in the same plane.In physics and mathematics, a...
visualization of multimodal image data, as well as advanced image analysis algorithms for diffusion tensor imaging, functional magnetic resonance imaging
Magnetic resonance imaging
Magnetic resonance imaging , nuclear magnetic resonance imaging , or magnetic resonance tomography is a medical imaging technique used in radiology to visualize detailed internal structures...
and image-guided radiation therapy
Image-guided radiation therapy
Highly trained oncologists called radiation oncologists use image guided radiation therapy, or IGRT, to help better deliver radiation therapy to cancerous tumors. This is very useful since tumors can move between treatments due to differences in organ filling or movements while breathing...
. Standard image file formats
Image file formats
Image file formats are standardized means of organizing and storing digital images. Image files are composed of either pixels, vector data, or a combination of the two. Whatever the format, the files are rasterized to pixels when displayed on most graphic displays...
are supported, and the application integrates interface capabilities to biomedical research software.
Slicer has been used in a variety of clinical research
Clinical research
Clinical research is a branch of medical science that determines the safety and effectiveness of medications, devices, diagnostic products and treatment regimens intended for human use...
. In image-guided therapy research, Slicer is frequently used to construct and visualize collections of MRI data that are available pre- and intra-operatively to allow for the acquiring of spatial coordinates
Coordinate system
In geometry, a coordinate system is a system which uses one or more numbers, or coordinates, to uniquely determine the position of a point or other geometric element. The order of the coordinates is significant and they are sometimes identified by their position in an ordered tuple and sometimes by...
for instrument tracking. In fact, Slicer has already played such a pivotal role in image-guided therapy, it can be considered as growing up alongside that field, with over 200 publications referencing Slicer since 1998.
In addition to producing 3D models from conventional MRI images, Slicer has also been used to present information derived from fMRI (using MRI to assess blood flow in the brain related to neural
Nervous system
The nervous system is an organ system containing a network of specialized cells called neurons that coordinate the actions of an animal and transmit signals between different parts of its body. In most animals the nervous system consists of two parts, central and peripheral. The central nervous...
or spinal cord
Spinal cord
The spinal cord is a long, thin, tubular bundle of nervous tissue and support cells that extends from the brain . The brain and spinal cord together make up the central nervous system...
activity), DTI (using MRI to measure the restricted diffusion of water in imaged tissue), and electrocardiography. For example, Slicer's DTI package allows the conversion and analysis of DTI images. The results of such analysis can be integrated with the results from analysis of morphologic
Morphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....
MRI, MR angiograms and fMRI. Other uses of Slicer include paleontology
Paleontology
Paleontology "old, ancient", ὄν, ὀντ- "being, creature", and λόγος "speech, thought") is the study of prehistoric life. It includes the study of fossils to determine organisms' evolution and interactions with each other and their environments...
and neurosurgery planning.
Developers
Slicer is based on VTKVTK
The Visualization Toolkit is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. Kitware, whose team created and continues to...
, a graphical library that provides a high-level interface to OpenGL
OpenGL
OpenGL is a standard specification defining a cross-language, cross-platform API for writing applications that produce 2D and 3D computer graphics. The interface consists of over 250 different function calls which can be used to draw complex three-dimensional scenes from simple primitives. OpenGL...
and a pipeline mechanism to connect graphical filters. The library is implemented in C++
C++
C++ is a statically typed, free-form, multi-paradigm, compiled, general-purpose programming language. It is regarded as an intermediate-level language, as it comprises a combination of both high-level and low-level language features. It was developed by Bjarne Stroustrup starting in 1979 at Bell...
but provides a Tcl
Tcl
Tcl is a scripting language created by John Ousterhout. Originally "born out of frustration", according to the author, with programmers devising their own languages intended to be embedded into applications, Tcl gained acceptance on its own...
wrapper to instantiate and execute its methods. Tcl/Tk comprises the rest of 3D Slicer user interface and event handling.
Slicer software supports automatic testing and employs an extreme programming approach with nightly builds natively on multiple platforms. Recent accomplishments include added capability for plugging-in external modules using an XML
XML
Extensible Markup Language is a set of rules for encoding documents in machine-readable form. It is defined in the XML 1.0 Specification produced by the W3C, and several other related specifications, all gratis open standards....
-based command line interface. The Slicer effort also incorporates a light-weight user-centered design effort to promote overall software usability.
Slicer.org offers resources for those who would like to improve or modify Slicer designs and applications. Various tutorials and instructions, along with access to a community of other developers can be found there.
Development still in progress, Slicer is sometimes accused by academic users of being poorly documented and a lack of automation facilities (which is useful in batch processing). Although bugs can be reported to the mail list, they are not guaranteed to be fixed timely, which is determined by its freely available nature. A new version would come out every few weeks, but is only available as a fresh installation in lieu of an in-place manner, which adds to maintenance difficulty.
Components of Slicer
- VTKVTKThe Visualization Toolkit is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. Kitware, whose team created and continues to...
- ITKInsight Segmentation and Registration ToolkitITK is a cross-platform, open-source application development framework widely used for the development of image segmentation and image registration programs. Segmentation is the process of identifying and classifying data found in a digitally sampled representation. Typically the sampled...
- CMakeCMakeCMake is a cross-platform, open-source system for managing the build process of software using a compiler-independent method. It is designed to support directory hierarchies and applications that depend on multiple libraries, and for use in conjunction with native build environments such as Make,...
- CPackCPackCPack is a packaging system for software distributions which is tightly integrated with CMake, but can function without it.It allows you to generate:* Linux RPM, deb and gzip distributions of both binaries and source code.* NSIS files...
- PythonPython (programming language)Python is a general-purpose, high-level programming language whose design philosophy emphasizes code readability. Python claims to "[combine] remarkable power with very clear syntax", and its standard library is large and comprehensive...
- TclTclTcl is a scripting language created by John Ousterhout. Originally "born out of frustration", according to the author, with programmers devising their own languages intended to be embedded into applications, Tcl gained acceptance on its own...
- nrrd
- MRML
- IGSTKIGSTKThe Image-Guided Surgery Toolkit is a software package oriented to facilitate the development of image-guided surgery applications....
- KWWidgets
- Qt