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 (Set (mathematics), sets of pixels). The goal of segmen ...

. 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 (where it should not be confused with power creep) and consumer and business electronics. These extra feature ...

. 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. 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 Software, computer software that is released under a Open-source license, license in which the copyright holder grants users the rights to use, study, change, and Software distribution, distribute the software an ...

distributed under the

GNU General Public License The GNU General Public Licenses (GNU GPL or simply GPL) are a series of widely used free software licenses, or ''copyleft'' licenses, that guarantee end users the freedom to run, study, share, or modify the software. The GPL was the first ...

. It is written in C++ and it leverages the

Insight Segmentation and Registration Toolkit Insight is the understanding of a specific cause and effect within a particular context. The term insight can have several related meanings: *a piece of information *the act or result of understanding the inner nature of things or of seeing intu ...

(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 **

Cysts A cyst is a closed Wikt:sac, sac, having a distinct Cell envelope, envelope and cell division, division compared with the nearby Biological tissue, tissue. Hence, it is a cluster of Cell (biology), cells that have grouped together to form a sac ...

** 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 ...

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 (vision), contrast ...

Analysis * Target definition for cancer

radiotherapy Radiation therapy or radiotherapy (RT, RTx, or XRT) is a treatment using ionizing radiation, generally provided as part of cancer therapy to either kill or control the growth of malignant cells. It is normally delivered by a linear particle ...

lung cancer Lung cancer, also known as lung carcinoma, is a malignant tumor that begins in the lung. Lung cancer is caused by genetic damage to the DNA of cells in the airways, often caused by cigarette smoking or inhaling damaging chemicals. Damaged ...

radiotherapy *

Prenatal Prenatal development () involves the embryonic development, development of the embryo and of the fetus during a viviparity, viviparous animal's gestation. Prenatal development starts with fertilization, in the germinal stage of embryonic develop ...

Image Analysis ** Diagnosis of

spina bifida Spina bifida (SB; ; Latin for 'split spine') is a birth defect in which there is incomplete closing of the vertebral column, spine and the meninges, membranes around the spinal cord during embryonic development, early development in pregnancy. T ...

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

in Medicine * Orthodontics * Brain morphometry **

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 ...

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 (: hippocampi; via Latin from Ancient Greek, Greek , 'seahorse'), also hippocampus proper, is a major component of the brain of humans and many other vertebrates. In the human brain the hippocampus, the dentate gyrus, and the ...

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 founded by Geoffrey B. Jeffery, Tim Perdue, and Drew Streib in November 1999. SourceForge provides a centralized software discovery platform, including an online platform for managing and hosting open-source soft ...

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