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 Software is a set of computer programs and associated documentation and data. This is in contrast to hardware, from which the system is built and which actually performs the work. At the lowest programming level, executable code consists ...

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 Scientific visualization ( also spelled scientific visualisation) is an interdisciplinary branch of science concerned with the visualization of scientific phenomena.Michael Friendly (2008)"Milestones in the history of thematic cartography, stat ...

. Slicer is used in a variety of

medical Medicine is the science and practice of caring for a patient, managing the diagnosis, prognosis, prevention, treatment, palliation of their injury or disease, and promoting their health. Medicine encompasses a variety of health care practic ...

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 Lung cancer, also known as lung carcinoma (since about 98–99% of all lung cancers are carcinomas), is a malignant lung tumor characterized by uncontrolled cell growth in tissue (biology), tissues of the lung. Lung carcinomas derive from tran ...

breast cancer Breast cancer is cancer that develops from breast tissue. Signs of breast cancer may include a lump in the breast, a change in breast shape, dimpling of the skin, milk rejection, fluid coming from the nipple, a newly inverted nipple, or a re ...

schizophrenia Schizophrenia is a mental disorder characterized by continuous or relapsing episodes of psychosis. Major symptoms include hallucinations (typically hearing voices), delusions, and disorganized thinking. Other symptoms include social withdra ...

orthopedic Orthopedic surgery or orthopedics ( alternatively spelt orthopaedics), is the branch of surgery concerned with conditions involving the musculoskeletal system. Orthopedic surgeons use both surgical and nonsurgical means to treat musculoskeletal ...

biomechanics Biomechanics is the study of the structure, function and motion of the mechanical aspects of biological systems, at any level from whole organisms to organs, cells and cell organelles, using the methods of mechanics. Biomechanics is a branch of ...

COPD Chronic obstructive pulmonary disease (COPD) is a type of progressive lung disease characterized by long-term respiratory symptoms and airflow limitation. The main symptoms include shortness of breath and a cough, which may or may not produce mu ...

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 Neurosurgery or neurological surgery, known in common parlance as brain surgery, is the medical specialty concerned with the surgical treatment of disorders which affect any portion of the nervous system including the brain, spinal cord and peri ...

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 Computerized batch processing is a method of running software programs called jobs in batches automatically. While users are required to submit the jobs, no other interaction by the user is required to process the batch. Batches may automatically ...

tools for a variety of applications. 3D Slicer provides

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, times, depths, or viewpoints. It is used in computer vision, medical imaging, milit ...

, processing of DTI (diffusion tractography), an interface to external devices for image guidance support, and

GPU A graphics processing unit (GPU) is a specialized electronic circuit designed to manipulate and alter memory to accelerate the creation of images in a frame buffer intended for output to a display device. GPUs are used in embedded systems, mobil ...

-enabled

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, typically a 3D scalar field. A typical 3D data set is a group of 2D slice images ...

, 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

s * Manual editing * Fusion and co-registering of data using rigid and non-rigid algorithms * Automatic

image segmentation In digital image processing and computer vision, image segmentation is the process of partitioning a digital image into multiple image segments, also known as image regions or image objects ( sets of pixels). The goal of segmentation is to simpl ...

* 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 Windows is a group of several proprietary graphical operating system families developed and marketed by Microsoft. Each family caters to a certain sector of the computing industry. For example, Windows NT for consumers, Windows Server for serv ...

Linux Linux ( or ) is a family of open-source Unix-like operating systems based on the Linux kernel, an operating system kernel first released on September 17, 1991, by Linus Torvalds. Linux is typically packaged as a Linux distribution, which ...

, and

macOS macOS (; previously OS X and originally Mac OS X) is a Unix operating system developed and marketed by Apple Inc. since 2001. It is the primary operating system for Apple's Mac computers. Within the market of desktop and lapt ...

. Slicer is distributed under a

BSD The Berkeley Software Distribution or Berkeley Standard Distribution (BSD) is a discontinued operating system based on Research Unix, developed and distributed by the Computer Systems Research Group (CSRG) at the University of California, Berk ...

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 A thesis ( : theses), or dissertation (abbreviated diss.), is a document submitted in support of candidature for an academic degree or professional qualification presenting the author's research and findings.International Standard ISO 7144: ...

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 The GUI ( "UI" by itself is still usually pronounced . or ), graphical user interface, is a form of user interface that allows users to interact with electronic devices through graphical icons and audio indicator such as primary notation, inste ...

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 To publish is to make content available to the general public.Berne Conve ...

, all aimed at improving image analysis. This significant software project has been enabled by the participation of several large-scale

NIH The National Institutes of Health, commonly referred to as NIH (with each letter pronounced individually), is the primary agency of the United States government responsible for biomedical and public health research. It was founded in the late ...

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 NSF may stand for: Political organizations *National Socialist Front, a Swedish National Socialist party *NS-Frauenschaft, the women's wing of the former German Nazi party *National Students Federation, a leftist Pakistani students' political gr ...

and the DOD.

Users

Slicer's platform provides functionalities for segmentation, registration and

three-dimensional Three-dimensional space (also: 3D space, 3-space or, rarely, tri-dimensional space) is a geometric setting in which three values (called ''parameters'') are required to determine the position of an element (i.e., point). This is the informal ...

visualization of multimodal image data, as well as advanced image analysis

algorithms In mathematics and computer science, an algorithm () is a finite sequence of rigorous instructions, typically used to solve a class of specific problems or to perform a computation. Algorithms are used as specifications for performing c ...

for diffusion tensor 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 An Image file format is a file format for a digital image. There are many formats that can be used, such as JPEG, PNG, and GIF. Most formats up until 2022 were for storing 2D images, not 3D ones. The data stored in an image file format may be c ...

are supported, and the application integrates interface capabilities to biomedical research software. Slicer has been used in a variety of

clinical research Clinical research is a branch of healthcare science that determines the safety and effectiveness ( efficacy) of medications, devices, diagnostic products and treatment regimens intended for human use. These may be used for prevention, treatm ...

. 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 ...

spinal cord The spinal cord is a long, thin, tubular structure made up of nervous tissue, which extends from the medulla oblongata in the brainstem to the lumbar region of the vertebral column (backbone). The backbone encloses the central canal of the spi ...

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 Paleontology (), also spelled palaeontology or palæontology, is the scientific study of life that existed prior to, and sometimes including, the start of the Holocene epoch (roughly 11,700 years before present). It includes the study of fossi ...

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 The Visualization Toolkit (VTK) is an open-source software system for 3D computer graphics, image processing and scientific visualization.''Visualization Handbook'', Academic Press, 2005, Chapter 30: the Visualization Toolkit/ref> VTK is distrib ...

, a pipeline-based graphical library that is widely used in scientific visualization and

ITK Itk is a framework for building mega-widgets using the Incr Tcl incr Tcl (commonly stylised as '' ncr Tcl/nowiki>'', and often abbreviated to ''itcl'') is a set of object-oriented extensions for the Tcl programming language. It is widely us ...

, a framework widely used for the development of

and

. In version 4, the core application is implemented in

C++ C++ (pronounced "C plus plus") is a high-level general-purpose programming language created by Danish computer scientist Bjarne Stroustrup as an extension of the C programming language, or "C with Classes". The language has expanded significan ...

, and the API is available through a

Python Python may refer to: Snakes * Pythonidae, a family of nonvenomous snakes found in Africa, Asia, and Australia ** ''Python'' (genus), a genus of Pythonidae found in Africa and Asia * Python (mythology), a mythical serpent Computing * Python (pro ...

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 Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable. T ...

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 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 anothe ...

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

* CPack *

Nrrd Nrrd ("nearly raw raster data") is a library and file format for the representation and processing of n-dimensional raster graphics, raster data. It was developed by Gordon Kindlmann to support scientific visualization and image processing applica ...

* MRML * IGSTK * 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