3D Slicer (Slicer) is a

free Free may refer to: Concept * Freedom, having the ability to do something, without having to obey anyone/anything * Freethought, a position that beliefs should be formed only on the basis of logic, reason, and empiricism * Emancipate, to procur ...

and

open source Open source is source code that is made freely available for possible modification and redistribution. Products include permission to use the source code, design documents, or content of the product. The open-source model is a decentralized sof ...

software package for

image analysis Image analysis or imagery analysis is the extraction of meaningful information from images; mainly from digital images by means of digital image processing techniques. Image analysis tasks can be as simple as reading bar coded tags or as sophi ...

and scientific visualization. Slicer is used in a variety of medical applications, including

autism The autism spectrum, often referred to as just autism or in the context of a professional diagnosis autism spectrum disorder (ASD) or autism spectrum condition (ASC), is a neurodevelopmental condition (or conditions) characterized by difficulti ...

multiple sclerosis Multiple (cerebral) sclerosis (MS), also known as encephalomyelitis disseminata or disseminated sclerosis, is the most common demyelinating disease, in which the insulating covers of nerve cells in the brain and spinal cord are damaged. This d ...

systemic lupus erythematosus Lupus, technically known as systemic lupus erythematosus (SLE), is an autoimmune disease in which the body's immune system mistakenly attacks healthy tissue in many parts of the body. Symptoms vary among people and may be mild to severe. Comm ...

prostate cancer Prostate cancer is cancer of the prostate. Prostate cancer is the second most common cancerous tumor worldwide and is the fifth leading cause of cancer-related mortality among men. The prostate is a gland in the male reproductive system that sur ...

, lung cancer, breast cancer, schizophrenia, orthopedic biomechanics, COPD,

cardiovascular disease Cardiovascular disease (CVD) is a class of diseases that involve the heart or blood vessels. CVD includes coronary artery diseases (CAD) such as angina and myocardial infarction (commonly known as a heart attack). Other CVDs include stroke, h ...

and neurosurgery.

About

3D Slicer is a free open source software (BSD-style license) that is a flexible, modular platform for image analysis and visualization. 3D Slicer is extended to enable development of both interactive and batch processing 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 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 hardware accelerated volume rendering. 3D Slicer also supports a rich set of annotation features ( fiducials and measurement widgets, customized color maps). Slicer's capabilities include: * Handling DICOM images and reading/writing a variety of other formats * Interactive visualization of volumetric Voxel images, polygonal meshes, and volume renderings * Manual editing * Fusion and co-registering of data using rigid and non-rigid algorithms * Automatic image segmentation * Analysis and visualization of diffusion tensor imaging data * Tracking of devices for image-guided procedures. Slicer is compiled for use on multiple computing platforms, including Windows, Linux, and macOS. Slicer is distributed under a BSD style, free, open source license. The license has no restrictions on use of the software in academic or commercial projects. 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. The slicer has not been formally approved for clinical use by the FDA in the US or by any other regulatory body elsewhere.

Image gallery

Image:3DSlicer-VolumeRendering1.png , Hardware accelerated volume rendering with OpenGL. Image:3DSlicer-IGT.png , ProstateNav Module for MRI guided robot assisted biopsy of the prostate. Image:Fedorov-Supercomputing2006-fig3.png, Left: 3D rendering. Right: Open MR system Image:3DSlicer-Mahnaz-ISBI2008-fig2.jpg , Visualization of some atlas-based ROIs which correspond to major anatomical fiber tracts. The atlas was provided as part of a download o
DTI studio
Image:3DSlicer-KubickiJPR2007-fig6.jpg, High resolution data acquired on 3-Tesla magnet and post-processed using automated tracking procedure. Image:3DSlicer-odonnell-miccai2006-fig2.jpg , High-dimensional white matter atlas generation and group analysis: result of automatic segmentation of novel subjects. Image:3DSlicer-Jolley-HR2008-fig7.jpg , Patient-specific modeling in a patient with congenital heart disease. Image:3DSlicer-Margulies-ObstetGynecol2006-fig1.jpg , Left: Three-dimensional model of levator ani subdivisions including the pubic bone and pelvic viscera. Right: The same model without the pubic bone. Image:3DSlicer-Park-AJNR2004-Fig1.jpg , Cortical parcellations derived from SPGR images obtained from a tumor patient. Image:3DSlicer-Mislow-NeurosurgClinNAm2009-fig3.jpg , Intraoperative colocalization using iMRI images and 3-D Slicer software.

History

Slicer started as a master's thesis 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 transitioned the GUI of Slicer from using KWWidgets to Qt. Qt-enabled Slicer version 4 was released in 2011. As of 2022, Slicer 4 had been downloaded over one million times by users around the world. 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.

Users

Slicer's platform provides functionalities for segmentation, registration and three-dimensional visualization of multimodal image data, as well as advanced image analysis algorithms for

diffusion tensor Diffusion-weighted magnetic resonance imaging (DWI or DW-MRI) is the use of specific MRI sequences as well as software that generates images from the resulting data that uses the diffusion of water molecules to generate contrast in MR images. It ...

imaging, functional

magnetic resonance imaging Magnetic resonance imaging (MRI) is a medical imaging technique used in radiology to form pictures of the anatomy and the physiological processes of the body. MRI scanners use strong magnetic fields, magnetic field gradients, and radio wave ...

and

image-guided radiation therapy Image-guided radiation therapy is the process of frequent imaging, during a course of radiation treatment, used to direct the treatment, position the patient, and compare to the pre-therapy imaging from the treatment plan. Immediately prior to, o ...

. 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 In geometry, a coordinate system is a system that uses one or more numbers, or coordinates, to uniquely determine the position of the points or other geometric elements on a manifold such as Euclidean space. The order of the coordinates is sig ...

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 In Biology, biology, the nervous system is the Complex system, highly complex part of an animal that coordinates its Behavior, actions and Sense, sensory information by transmitting action potential, signals to and from different parts of its ...

or spinal cord activity), DTI (using MRI to measure the restricted diffusion of water in imaged tissue), and

electrocardiography Electrocardiography is the process of producing an electrocardiogram (ECG or EKG), a recording of the heart's electrical activity. It is an electrogram of the heart which is a graph of voltage versus time of the electrical activity of the hear ...

. 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. There is an active community at Slicer's

Discourse Discourse is a generalization of the notion of a conversation to any form of communication. Discourse is a major topic in social theory, with work spanning fields such as sociology, anthropology, continental philosophy, and discourse analysis. ...

server.

Developers

The Slicer Developer Orientation offers resources for developers new to the platform. Slicer development is coordinated on the Slicer Discourse forum, and a summary of development statistics is available on Ohloh. 3D Slicer is built on VTK, a pipeline-based graphical library that is widely used in scientific visualization and ITK, a framework widely used for the development of image segmentation and image registration. In version 4, the core application is implemented in C++, and the API is available through a Python wrapper to facilitate rapid, iterative development and visualization in the included Python console. The user interface is implemented in Qt, and may be extended using either C++ or Python. Slicer supports several types of modular development. Fully interactive, custom interfaces may be written in C++ or Python. Command-line programs in any language may be wrapped using a light-weight XML specification, from which a graphical interface is automatically generated. For modules that are not distributed in the Slicer core application, a system is available to automatically build and distribute for selective download from within Slicer. This mechanism facilitates the incorporation of code with different license requirements from the permissive BSD-style license used for the Slicer core. The Slicer build process utilizes CMake to automatically build prerequisite and optional libraries (excluding Qt). The core development cycle incorporates automatic testing, as well as incremental and nightly builds on all platforms, monitored using an online dashboard. Slicer's development is managed primarily through its GitHub repository.

External dependencies

* VTK * ITK * CMake *

CPack In software development, CMake is cross-platform free and open-source software for build automation, testing, packaging and installation of software by using a compiler-independent method. CMake is not a build system itself; it generates anoth ...

* Python * Nrrd * MRML *

IGSTK The Image-Guided Surgery Toolkit (IGSTK: pronounced IGStick) is a software package oriented to facilitate the development of image-guided surgery applications. IGSTK is an open-source software toolkit designed to enable biomedical researchers to r ...

* Qt

Notes

:1.For a list of publications citing Slicer usage since 1998, visit
slicer.org

References

External links

Slicer
{{Free healthcare software, state=expanded Computer vision software Free 3D graphics software Free DICOM software Free health care software Free science software Free software programmed in C++ Free software programmed in Python Free software programmed in Tcl Science software for Linux Science software that uses Qt Software that uses VTK