ITK-SNAP is an interactive software application that allows users to navigate three-dimensional medical images, manually delineate anatomical regions of interest, and perform 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 ...

. The software was designed with the audience of clinical and basic science researchers in mind, and emphasis has been placed on having a user-friendly interface and maintaining a limited feature set to prevent

feature creep Feature creep is the excessive ongoing expansion or addition of new features in a product, especially in computer software, video games and consumer and business electronics. These extra features go beyond the basic function of the product and ...

. ITK-SNAP is most frequently used to work with magnetic resonance imaging (MRI), cone-beam computed tomography (CBCT) and computed tomography (CT) data sets.

Features

The purpose of the tool is to make it easy for researchers to delineate anatomical structures and regions of interest in imaging data. The set of features is kept to a minimum. The main features of the program are ; Image navigation: three orthogonal cut planes through the image volume are shown at all times. The cut planes are linked by a common cursor, so that moving the cursor in one cut plane updates the other cut planes. The cursor is moved by dragging the mouse over the cut planes, making for smooth navigation. The linked cursor also works across ITK-SNAP sessions, making it possible to navigate multimodality imaging data (e.g., two MRI scans of a subject from a single session). ; Manual segmentation : ITK-SNAP provides tools for manual delineation of anatomical structures in images. Labeling can take place in all three orthogonal cut planes and results can be visualized as a three-dimensional rendering. This makes it easier to ensure that the segmentation maintains reasonable shape in 3D. ; Automatic segmentation: ITK-SNAP provides automatic functionality segmentation using the

level-set method Level-set methods (LSM) are a conceptual framework for using level sets as a tool for numerical analysis of surfaces and shapes. The advantage of the level-set model is that one can perform numerical computations involving curves and surfaces on a ...

. This makes it possible to segment structures that appear somewhat homogeneous in medical images using very little human interaction. For example, the lateral ventricles in MRI can be segmented reliably, as can some types of tumors in CT and MRI. ITK-SNAP is

open-source software Open-source software (OSS) is computer software that is released under a license in which the copyright holder grants users the rights to use, study, change, and distribute the software and its source code to anyone and for any purpose. Op ...

distributed under the

GNU General Public License The GNU General Public License (GNU GPL or simply GPL) is a series of widely used free software licenses that guarantee end users the Four Freedoms (Free software), four freedoms to run, study, share, and modify the software. The license was th ...

. It is written 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 it leverages the

Insight Segmentation and Registration Toolkit __NOTOC__ ITK 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 dig ...

(ITK) library. ITK-SNAP can read and write a variety of medical image formats, including DICOM, NIfTI, and Mayo Analyze. It also offers limited support for multi-component (e.g.,

diffusion tensor imaging 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 ...

) and multi-variate imaging data.

Applications

ITK-SNAP has been applied in the following areas * Craniofacial pathologies and anatomical studies ** KCOT **

Ameloblastoma Ameloblastoma is a rare, benign or cancerous tumor of odontogenic epithelium (ameloblasts, or outside portion, of the teeth during development) much more commonly appearing in the lower jaw than the upper jaw. It was recognized in 1827 by Cusack. ...

Cysts A cyst is a closed sac, having a distinct envelope and division compared with the nearby tissue. Hence, it is a cluster of cells that have grouped together to form a sac (like the manner in which water molecules group together to form a bubble) ...

** Condyle Volumes *

Carotid artery Carotid artery may refer to: * Common carotid artery, often "carotids" or "carotid", an artery on each side of the neck which divides into the external carotid artery and internal carotid artery * External carotid artery, an artery on each side of t ...

segmentation *

Diffusion MRI 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 ...

Analysis * Target definition for cancer

radiotherapy Radiation therapy or radiotherapy, often abbreviated RT, RTx, or XRT, is a therapy using ionizing radiation, generally provided as part of cancer treatment to control or kill malignant cells and normally delivered by a linear accelerator. Radia ...

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 ...

radiotherapy *

Prenatal Prenatal development () includes the development of the embryo and of the fetus during a viviparous animal's gestation. Prenatal development starts with fertilization, in the germinal stage of embryonic development, and continues in fetal devel ...

Image Analysis ** Diagnosis of

spina bifida Spina bifida (Latin for 'split spine'; SB) is a birth defect in which there is incomplete closing of the spine and the membranes around the spinal cord during early development in pregnancy. There are three main types: spina bifida occulta, me ...

Virtual reality Virtual reality (VR) is a simulated experience that employs pose tracking and 3D near-eye displays to give the user an immersive feel of a virtual world. Applications of virtual reality include entertainment (particularly video games), educ ...

in Medicine * Orthodontics *

Brain morphometry Brain morphometry is a subfield of both morphometry and the brain sciences, concerned with the measurement of brain structures and changes thereof during development, aging, learning, disease and evolution. Since autopsy-like dissection is gener ...

Corpus callosum The corpus callosum (Latin for "tough body"), also callosal commissure, is a wide, thick nerve tract, consisting of a flat bundle of commissural fibers, beneath the cerebral cortex in the brain. The corpus callosum is only found in placental mam ...

and ventricle analysis in

22q11.2 deletion syndrome DiGeorge syndrome, also known as 22q11.2 deletion syndrome, is a syndrome caused by a microdeletion on the long arm of chromosome 22. While the symptoms can vary, they often include congenital heart problems, specific facial features, frequent i ...

Hippocampus The hippocampus (via Latin from Greek , 'seahorse') is a major component of the brain of humans and other vertebrates. Humans and other mammals have two hippocampi, one in each side of the brain. The hippocampus is part of the limbic system, a ...

size and shape measurement in neurodegenerative disorders. **Human brain tumors (e.g., Meningioma)

References

External links

Main ITK-SNAP website
(downloads, bugs, mailing lists)
ITK-SNAP
on

SourceForge SourceForge is a web service that offers software consumers a centralized online location to control and manage open-source software projects and research business software. It provides source code repository hosting, bug tracking, mirrorin ...

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