Medical Computing

We are an interdisciplinary team of computer scientists, software engineers, and imaging experts who provide collaborative research, development, and technology integration services for research centers, universities and companies working in the medical and biomedical business sectors.

We have a long history leading and contributing to open source platforms such as the Insight Toolkit (ITK) or 3D Slicer, that serve as the foundation of many medical visualization and data processing applications. We work with our commercial customers to streamline their internal software and processes, by investigating new algorithms or methodologies that upgrade existing commercial offerings or develop new products. Alone or as part of partnerships, we generate results for research publications, generate prototypes for raising venture capital, conduct first-in-human trials or pursue regulatory approval such as FDA.

Customer Highlights

Exonicus and Kitware Collaborate to Develop a Trauma Simulator Using the Pulse Physiology Engine

Introduction The top three causes of preventable death on the battlefield are hemorrhage, tension pneumothorax, and airway trauma. Training to appropriately treat these injuries is … Read More

Xoran Technologies and Kitware Collaborate on Image-guided Platform for Deep Brain Stimulation Surgery

Introduction Deep brain stimulation (DBS) has become a standard of care for Parkinson’s patients and is a more effective treatment than other nonsurgical ones for … Read More

Kitware customer highlight: Radiopharmaceutical Imaging and Dosimetry, LLC (RAPID)

Introduction Radiopharmaceutical therapy (RPT) is a new and underutilized cancer therapy modality that has shown tremendous potential and is the subject of intense recent interest. … Read More

Kitware customer highlight: MuriPlan from Xstrahl – A 3D Slicer based radiotherapy treatment planning system

Introduction Kitware provides collaborative research, development, and technology-integration services for companies that work in the medical and biomedical business sectors. As part of a series … Read More

Kitware customer highlight: Optics in Medicine Laboratory

Introduction Kitware provides collaborative research, development, and custom development and technology-integration services for universities and research centers that work in the medical and biomedical business … Read More

Kitware customer highlight: Phoenix Research Labs

Phoenix Research Labs: The Company Phoenix Research Labs develops technologies to support eye and eye-brain research using mice and rats, with products which are designed … Read More

Areas of Focus

Image Guided Intervention and Surgical Planning

We develop image-guided intervention and surgical planning applications that replace traditional surgery and invasive procedures with minimally invasive techniques that incorporate medical imaging to guide the intervention. Patients prefer these procedures to open surgeries because they are typically less traumatic to the body and result in faster recovery times. Technological advancements in medical imaging, registration algorithms, visualization technologies, and tracking systems are driving forces behind increased adoption of these procedures by physicians. Software is an integral part of these image-guided intervention systems. Whether it is for interfacing with a tracking device to collect position information from surgical instruments, integrating intra-operative and pre-operative images, or generating a 3D visualization to provide visual feedback to the clinician, software has a critical role. The software platforms we are developing at Kitware is playing a major role in increasing the pace of research and discovery in image-guided intervention systems by promoting collaborations between clinicians, biomedical engineers, and software developers across the globe.  

iCSPlan is an intelligent craniosynostosis surgical treatment planning software. This screenshot of iCSPlan shows the aulti-label segmentation of a child’s skull bones, which exhibit metopic and left coronal synostosis. This is a collaborative project between Kitware and Children National Medical Center.

An interactive, patient-specific virtual surgery planning system for upper airway surgery

Computational Physiological Modeling

Our open source Pulse Physiology Suite includes a well-validated and documented computational physiology engine for real time simulations of the body’s response to trauma, disease, and treatment and the Pulse Physiology Explorer is an extendable user interface for quick exploration and experimentation with the Pulse Physiology Engine.

 

Our open source lumped-parameter model provides real-time accurate human physiological responses to injury, disease, and treatment.

 

Our dynamic physiology engine can be integrated into a variety of platforms, hardware components, and virtual environments

Ultrasound Systems

We are integrating artificial intelligence and deep learning technologies with custom ultrasound and augmented reality hardware to advance the use of ultrasound in a variety of applications. These applications include preclinical and clinical research, pre-hospital patient triage, bedside patient monitoring, and precision needle guidance. Our integrations are enabling less-experienced operators to complete the applications with confidence, in less time, and with expert-level outcomes. They have been transitioned into several consulting projects and pending commercial products.  

Ultrasound image-based mechanical strain identifies arterial plaques vulnerable to rupture

3D Slicer-based Applications

We help solve challenges by creating custom plugins, SDKs, applications, and software packages using 3D Slicer. Our 3D Slicer packages and modules have been used in a variety of medical and basic scientific applications such as dentistry, radiation oncology, surgical planning, and drug development. These custom applications can be deployed as local software, or they can be deployed on remote servers using Docker or on tablets. To support reproducible workflows, they can also be integrated with our Girder data management solution or with Jupyter notebooks.

3D Slicer is free, open source software that is available across different platforms. Its permissive license makes it even more flexible for the creation of custom commercial software.

 

Visualization of bone quality texture features as colormap extracted from a CBCT of the temporomandibular joint. It is made possible by using Slicer BoneTexture extension allowing to leverage the ITKBoneMorphometry and ITKTextureFeatures modules. For more details, see https://github.com/kitware/BoneTextureExtension#readme

 

Home module of the SlicerSALT application guiding user on how to perform geometric shape modeling for understanding shape changes. For more details, see http://salt.slicer.org/

 

SonoEQ is a custom Slicer application developer by SonoVol Inc with help of Kitware. Leveraging SonoVol research platform based on ultrasound technology, the application enables high-throughput acquisition of image data, exploration of animal anatomy and quantification of tumor size. For more details, see https://sonovol.com/products/sonoeq/

Medical Visualization

Kitware is a leader in scientific visualization, including medical data visualization. Kitware began with the open-source release of the Visualization Toolkit (VTK) in 1996, and that toolkit has become the leading visualization tool in multiple scientific domains, including medical imaging. VTK is capable of generating visualizations of exascale data using supercomputers, heterogeneous data (e.g., genomic as well as image data) using cloud resources, and composite geometric and volume rendered data on desktops; and then VTK can stream any or all of those visualizations to mobile devices, surgical microscopes, and augmented reality / virtual reality systems. Our philosophy is to innovate, promote, and support “pervasive visualization” whereby the data that you need to make a decision is presented to you in an intuitive format, when and where you need it, within your own workflows. Examples of our implementation of pervasive visualizations include the ITK-JupyterWidgets for visualizing data within the Jupyter Lab Python research environment, 3D Slicer for biomedical research data visualization, ParaView Glance for in-browser visualization of a wide variety of scientific data, and ParaView Server for visualization of high-fidelity biomedical simulations of blood flow and/or respiratory air motion.  

Visualization of a chest CT using jupyter lab python notebooks

 

ParaView Glance is a general purpose standalone Web application that can be used to visualize many data types. It is also a great framework for building custom viewers on the web that can be deployed in different platforms.

 

Image from ResearchGate submitted by Michael Papka

Virtual Surgical Simulation and Training

Our experience with developing medical skill and procedural trainers includes developing the underlying real-time technologies such as fast numerical solvers, haptic rendering algorithms, advanced rendering for 2D and virtual reality displays, collision processing and custom hardware interfacing. These technologies are embedded in our Interactive Medical Simulation Toolkit (iMSTK) which is a C++ based open-source toolkit that aids rapid prototyping of interactive multi-modal surgical simulations. iMSTK features a highly modular and easy to use framework with a comprehensive ecosystem of tools and algorithms required to develop end-to-end medical planners and trainers.

Besides access to the technologies that are exclusive to iMSTK, applications can benefit greatly from its interfacing with Kitware’s another open-source software tools such as VTK, 3D Slicer and Pulse. Such synergistic use of disparate software has broadened the range of medical applications that are possible and has already helped Kitware successfully build virtual trainers for laparoscopic camera navigation, kidney biopsy and osteotomy procedures.

 

Virtual Airway Skill Trainer (VAST) developed using iMSTK (Courtesy: CeMSIM, RPI)

 

Kidney Biopsy Virtual Trainer (KBVTrainer) developed using iMSTK

Medical Image Analysis

Our expertise in the development of custom image analysis algorithms spans brain morphology assessment associated with mental disorders, tumor volume estimation for clinical trials, vessel modeling for stroke and tumor microenvironment research, multiparametric MRI prostate cancer assessment, deep learning for interpreting histology images, and a number of other applications. Building on our role in the creation and maintenance of libraries such as the Insight Toolkit (ITK) and applications such as 3D Slicer, we lead and partner on basic research grants, small business grants, and development contracts for the National Institutes of Health and the Department of Defense. These encompass nearly every aspect of medical image segmentation, registration, quantification, and computer-aided diagnosis. In addition to working on grants and contracts, we can extend ITK and 3D Slicer with new algorithms to speed the deployment of pre-clinical and clinical products, as well as to collaborate on research investigations.

Magnetic resonance imaging of the human brain with the lateral ventricles highlighted

Cross-platform Interactive Applications

We work on a variety of cross- and multi-platform applications from desktop, to server, to mobile, to cloud, to web. The focus of these applications includes distributed 2D and 3D ultrasound, augmented reality, manual and semi-automatic segmentation and registration, quality control workflows, and surgical robotics.

At their core, these applications are built on our technologies and expertise in image processing, segmentation, registration, and surgical guidance. We work directly with customers to design workflows, user experiences, and custom interfaces from the ground up. Our development, testing, and documentation practices are aligned with FDA requirements and HIPAA technical safeguards for software products.

Digital Pathology

We are building a suite of open source web-based informatics tools that manage, visualize, and analyze massive and growing collections of data in digital pathology. The key solutions in the making include Digital Slide Archive (DSA), HistomicsTK, and Large-image. DSA is a web-based platform for the aggregation, management, and dissemination of large collections of whole-slide histopathology images, along with associated clinical and genomic metadata. HistomicsTK serves as both a web-based analytics platform and a standalone Python toolkit. It contains computer vision and machine learning algorithms for the quantitative analysis of whole-slide histopathology images and associated data. Large-image supports the web-based visualization and annotation of large multi-resolution whole-slide histopathology images. It also includes a Python API for reading/writing these images in a tiled fashion.  

Snapshot of the web-based analytics dashboard of HistomicsTK

 

A multi-resolution viewer embedded within DigitalSlideArchive for visualizing whole-slide images

Dental and Craniomaxillofacial Image Analysis

Our projects and research aim to quantitatively explore how age, disease or treatment affect structures in the craniomaxillofacial (CMF) complex. This improved knowledge can help diagnose disease early, plan and measure treatment, and monitor the progression of certain conditions.

In particular, we are experts in morphometry analysis, a technique that can be used to quantitatively plan CMF surgery or measure remodeling in the bony structures of the skull. Our dental image analysis methods, for example, can quantify bone quality or tooth integrity.

We also develop CMF-specific surgical trainers to improve procedural knowledge and surgical proficiency without sacrificing patient safety.

Craniomaxillofacial and musculoskeletal 3D image analysis

Two-dimensional multiplanar assessment or panoramic reconstructions are the main ways to detect radiological signs of disease in dental or musculoskeletal scans. Though useful, two-dimensional analysis overlooks the there-dimensional nature of anatomy and can lead to misdiagnosis.  

Kitware has designed and developed powerful image analysis algorithms that can be used for analyzing dental scans such as Cone Beam Computed Tomography or micro CT

Craniomaxillofacial and musculoskeletal morphometry analysis

Studying how the shape of anatomy changes overtime, with disease or with treatment can help characterizing disease and healthy aging as well as planning and measure treatment outcomes  

Kitware has worked in different projects that analyze shape of anatomy, and produced popular open-source platforms for shape analysis

Oral and maxillofacial surgical simulation and training

Surgical simulation and virtual reality can improve procedural knowledge and surgical proficiency in Oral and Maxillofacial surgery training. Simulation-based training can increase familiarity with surgical instruments, procedures and knowledge without sacrificing patient safety.  

Kitware has designed a first-of-its-kind, high-fidelity Oral and Maxillofacial surgery simulator that can be used to train the osteotomy step in Orthognathic Surgery

What We Offer for Your Project

We provide custom research and software development, collaboration, support, training, and books to help in the above areas of focus.

Medical Computing Platforms

The Insight Toolkit (ITK) is a software development solution for medical image processing, segmentation, and registration. ITK is a library of segmentation and registration imaging algorithms tailored for medical investigations. The toolkit supports a variety of imaging data formats.

3D Slicer is a medical image computing and visualization application. 3D Slicer works with optical imaging, MRI, CT, and ultrasound data. We have applied 3D Slicer to a range of research and commercial applications.
The Pulse Physiology Engine has an explorer with models for anaphylaxis and multi-trauma. The engine also contains physiological systems and a common data model.
The interactive Medical Simulation Toolkit (iMSTK) provides developers with software for making virtual simulators for medical procedures, including biopsies, resectioning, radiosurgery, and laparoscopy.

Publications

We have over 350 publications on topics such as surgical simulation, medical image analysis, structural shape analysis, and ultrasound image systems. These publications show up in leading conferences and journals.