Developer(s) | Paul A. Yushkevich, Guido Gerig, and the researchers at UPenn, UNC, Utah, and Kitware |
---|---|
Initial release | 2004 |
Written in | C++ |
Platform | Cross-platform |
Available in | English |
Type | Health software |
License | GNU General Public License |
Website | http://www.itksnap.org |
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. 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. ITK-SNAP is most frequently used to work with magnetic resonance imaging (MRI), cone-beam computed tomography (CBCT) and computed tomography (CT) data sets.
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
ITK-SNAP is open-source software distributed under the GNU General Public License. It is written in C++ and it leverages the Insight Segmentation and Registration Toolkit (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) and multi-variate imaging data.
ITK-SNAP has been applied in the following areas
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 waves to generate images of the organs in the body. MRI does not involve X-rays or the use of ionizing radiation, which distinguishes it from computed tomography (CT) and positron emission tomography (PET) scans. MRI is a medical application of nuclear magnetic resonance (NMR) which can also be used for imaging in other NMR applications, such as NMR spectroscopy.
A brain tumor occurs when abnormal cells form within the brain. There are two main types of tumors: malignant tumors and benign (non-cancerous) tumors. These can be further classified as primary tumors, which start within the brain, and secondary tumors, which most commonly have spread from tumors located outside the brain, known as brain metastasis tumors. All types of brain tumors may produce symptoms that vary depending on the size of the tumor and the part of the brain that is involved. Where symptoms exist, they may include headaches, seizures, problems with vision, vomiting and mental changes. Other symptoms may include difficulty walking, speaking, with sensations, or unconsciousness.
A computed tomography scan is a medical imaging technique used to obtain detailed internal images of the body. The personnel that perform CT scans are called radiographers or radiology technologists.
Radiology is the medical discipline that uses medical imaging to diagnose diseases and guide their treatment, within the bodies of humans and other animals. It began with radiography, but today it includes all imaging modalities, including those that use no electromagnetic radiation, as well as others that do, such as computed tomography (CT), fluoroscopy, and nuclear medicine including positron emission tomography (PET). Interventional radiology is the performance of usually minimally invasive medical procedures with the guidance of imaging technologies such as those mentioned above.
Medical imaging is the technique and process of imaging the interior of a body for clinical analysis and medical intervention, as well as visual representation of the function of some organs or tissues (physiology). Medical imaging seeks to reveal internal structures hidden by the skin and bones, as well as to diagnose and treat disease. Medical imaging also establishes a database of normal anatomy and physiology to make it possible to identify abnormalities. Although imaging of removed organs and tissues can be performed for medical reasons, such procedures are usually considered part of pathology instead of medical imaging.
Tomography is imaging by sections or sectioning that uses any kind of penetrating wave. The method is used in radiology, archaeology, biology, atmospheric science, geophysics, oceanography, plasma physics, materials science, astrophysics, quantum information, and other areas of science. The word tomography is derived from Ancient Greek τόμος tomos, "slice, section" and γράφω graphō, "to write" or, in this context as well, "to describe." A device used in tomography is called a tomograph, while the image produced is a tomogram.
Spinal tumors are neoplasms located in either the vertebral column or the spinal cord. There are three main types of spinal tumors classified based on their location: extradural and intradural. Extradural tumors are located outside the dura mater lining and are most commonly metastatic. Intradural tumors are located inside the dura mater lining and are further subdivided into intramedullary and extramedullary tumors. Intradural-intramedullary tumors are located within the dura and spinal cord parenchyma, while intradural-extramedullary tumors are located within the dura but outside the spinal cord parenchyma. The most common presenting symptom of spinal tumors is nocturnal back pain. Other common symptoms include muscle weakness, sensory loss, and difficulty walking. Loss of bowel and bladder control may occur during the later stages of the disease.
Image-guided surgery (IGS) is any surgical procedure where the surgeon uses tracked surgical instruments in conjunction with preoperative or intraoperative images in order to directly or indirectly guide the procedure. Image guided surgery systems use cameras, ultrasonic, electromagnetic or a combination of fields to capture and relay the patient's anatomy and the surgeon's precise movements in relation to the patient, to computer monitors in the operating room or to augmented reality headsets. This is generally performed in real-time though there may be delays of seconds or minutes depending on the modality and application.
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 digitally sampled representation. Typically the sampled representation is an image acquired from such medical instrumentation as CT or MRI scanners. Registration is the task of aligning or developing correspondences between data. For example, in the medical environment, a CT scan may be aligned with an MRI scan in order to combine the information contained in both.
In medicine, a biomarker is a measurable indicator of the severity or presence of some disease state. It may be defined as a "cellular, biochemical or molecular alteration in cells, tissues or fluids that can be measured and evaluated to indicate normal biological processes, pathogenic processes, or pharmacological responses to a therapeutic intervention." More generally a biomarker is anything that can be used as an indicator of a particular disease state or some other physiological state of an organism. According to the WHO, the indicator may be chemical, physical, or biological in nature - and the measurement may be functional, physiological, biochemical, cellular, or molecular.
Computer-aided detection (CADe), also called computer-aided diagnosis (CADx), are systems that assist doctors in the interpretation of medical images. Imaging techniques in X-ray, MRI, Endoscopy, and ultrasound diagnostics yield a great deal of information that the radiologist or other medical professional has to analyze and evaluate comprehensively in a short time. CAD systems process digital images or videos for typical appearances and to highlight conspicuous sections, such as possible diseases, in order to offer input to support a decision taken by the professional.
3D Slicer (Slicer) is a free and 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, lung cancer, breast cancer, schizophrenia, orthopedic biomechanics, COPD, cardiovascular disease and neurosurgery.
Preclinical imaging is the visualization of living animals for research purposes, such as drug development. Imaging modalities have long been crucial to the researcher in observing changes, either at the organ, tissue, cell, or molecular level, in animals responding to physiological or environmental changes. Imaging modalities that are non-invasive and in vivo have become especially important to study animal models longitudinally. Broadly speaking, these imaging systems can be categorized into primarily morphological/anatomical and primarily molecular imaging techniques. Techniques such as high-frequency micro-ultrasound, magnetic resonance imaging (MRI) and computed tomography (CT) are usually used for anatomical imaging, while optical imaging, positron emission tomography (PET), and single photon emission computed tomography (SPECT) are usually used for molecular visualizations.
Positron emission tomography–magnetic resonance imaging (PET–MRI) is a hybrid imaging technology that incorporates magnetic resonance imaging (MRI) soft tissue morphological imaging and positron emission tomography (PET) functional imaging.
Magnetic resonance imaging of the brain uses magnetic resonance imaging (MRI) to produce high quality two-dimensional or three-dimensional images of the brain and brainstem as well as the cerebellum without the use of ionizing radiation (X-rays) or radioactive tracers.
EEG microstates are transient, patterned, quasi-stable states or patterns of an electroencephalogram. These tend to last anywhere from milliseconds to seconds and are hypothesized to be the most basic instantiations of human neurological tasks, and are thus nicknamed "the atoms of thought". Microstate estimation and analysis was originally done using alpha band activity, though broader bandwidth EEG bands are now typically used. The quasi-stability of microstates means that the "global [EEG] topography is fixed, but strength might vary and polarity invert."
Medical image computing (MIC) is an interdisciplinary field at the intersection of computer science, information engineering, electrical engineering, physics, mathematics and medicine. This field develops computational and mathematical methods for solving problems pertaining to medical images and their use for biomedical research and clinical care.
The Dextroscope is a medical equipment system that creates a virtual reality (VR) environment in which surgeons can plan neurosurgical and other surgical procedures.
In the field of medicine, radiomics is a method that extracts a large number of features from medical images using data-characterisation algorithms. These features, termed radiomic features, have the potential to uncover tumoral patterns and characteristics that fail to be appreciated by the naked eye. The hypothesis of radiomics is that the distinctive imaging features between disease forms may be useful for predicting prognosis and therapeutic response for various cancer types, thus providing valuable information for personalized therapy. Radiomics emerged from the medical fields of radiology and oncology and is the most advanced in applications within these fields. However, the technique can be applied to any medical study where a pathological process can be imaged.
Studierfenster or StudierFenster (SF) is a free, non-commercial open science client/server-based medical imaging processing online framework. It offers capabilities, like viewing medical data (computed tomography (CT), magnetic resonance imaging (MRI), etc.) in two- and three-dimensional space directly in standard web browsers, like Google Chrome, Mozilla Firefox, Safari, and Microsoft Edge. Other functionalities are the calculation of medical metrics (dice score and Hausdorff distance), manual slice-by-slice outlining of structures in medical images (segmentation), manual placing of (anatomical) landmarks in medical image data, viewing medical data in virtual reality, a facial reconstruction and registration of medical data for augmented reality, one click showcases for COVID-19 and veterinary scans, and a Radiomics module.