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New 3D imaging software improves precision of dental research

Lucia Cevidanes with 3D images in her lab.

U.S., international researchers collaborate on NIH-supported project

Ann Arbor, Mich., May 25, 2016 -- Researchers at the University of Michigan School of Dentistry, in collaboration with a network of scientists and engineers around the world, have released new software that significantly improves the effectiveness of using 3-dimensional images in the treatment of dental-related diseases and conditions.

The software advances current 3D imaging by precisely aligning a series of anatomical scans obtained over a period of time.  “That allows researchers to more accurately track both a disease and the effectiveness of its treatment,” said Lucia Cevidanes, assistant professor in the Department of Orthodontics and Pediatric Dentistry and the project’s principal investigator.

The software’s name, SlicerCMF, refers to its cranio maxillofacial applications in analyzing scans, or slices, of the mouth, jaws, face and head.  It works with various imaging tools, such as magnetic resonance imaging (MRI), computed tomography (CT), nuclear medicine and ultrasound.  SlicerCMF is an extension of the original 3D Slicer technology that computer scientists, software engineers and medical investigators developed over the last two decades for the visualization and analysis of medical imaging data. The work is funded by the National Institute of Health Roadmap initiative, which supports a research center, the National Alliance of Medical Image Computing, led by Ron Kikinis  at Harvard University.

Cevidanes' lab is part of the Dental and Craniofacial Bionetwork for Image Analysis, or DCBIA, which adapted the original Slicer software for more specific dental-related applications.  “It doesn’t include all the tools that are just for more general medicine, and it adds some other modules that are of specific interest for dentistry,” she said.  For example, the ability to find and quantify changes to the jaw and the soft tissues of the mouth are crucial to dental researchers.  The software identifies specific biomarkers in the scans that are registered as future images of the problem area are added.  If researchers are monitoring jaw growth or how tissue is healing after surgery, they can see not only the amount of change over time, but also the direction of the change. 

“I think what we have done is exciting,” Cevidanes said. “Our collaborative group is recognized nationally and internationally as being leaders in the field of registration, noting changes over time and quantifying them.  At the same time, (the software allows) visualization of those changes with some very nice color maps or color-coded visualizations.”

The DCBIA is working with various School of Dentistry colleagues who are either using or testing the new software, including researchers in periodontology, physiology, surgery, orthodontics and pediatric dentistry, among others.  Hector Rios, assistant professor in the department of periodontology and oral medicine at the school, calls the new release “an appealing and innovative resource for dental clinicians and scientists.”

“In periodontics, the 3D evaluation of developmental, acquired or disease-associated topographical changes to the local anatomy provides a valuable opportunity to better assess, classify and monitor a number of different clinical conditions,” Rios said. “The new software provides us with a flexible and powerful resource to support further interdisciplinary collaboration in oral health sciences.”

Because the Slicer technology is a free, “open source” resource available to any researcher around the world, the DCBIA produced a series of video tutorials posted on YouTube. Third-year dental student Nicole Pentis narrates the 18 videos and will coordinate a survey to determine their effectiveness in helping researchers master the software, which is compatible with Mac, Windows and Linux systems.

Cevidanes notes that there are many 3D imaging software programs available, but they are often used primarily to create visualizations to show patients or students about human anatomy.  SlicerCMF does that as well, but it is more focused on gathering precise data to aid researchers.  Another advantage is that it is truly “open source” compared to 3D imaging companies that are partially if not totally proprietary and sell their products.  An advantage of Slicer’s open platform, is that researchers can go into the code and change its operation to meet their unique needs.  “Our initiative is intended to use only software that is free, that spends a lot of effort in the documentation of the source code, which makes it a very flexible platform.  The purpose is truly to disseminate it and to train people as well as we can in how to use it,” Cevidanes said.

The project, now starting the third of its three years of funding (award R01DE024450), is supported by two NIH research arms – the National Institute of Dental & Craniofacial Research and the National Institute of Biomedical Imaging and Bioengineering. Other lead researchers are from the University of North Carolina and Harvard University, among some 30 U.S. and international collaborators from Australia, Brazil, Canada, Cyprus, Denmark, France, Italy, Korea, Sweden, Taiwan and Turkey.

Additional Resources:

• DCBIA here

• Link to Windows download here.

• Link to Linux download here.

• Link to MacOS download here.

• Link to YouTube tutorials here.