Reconstructing histological slices into 3D images

August 06, 2019

Japanese scientists report in Pattern Recognition a new method to construct 3D models from 2D images. The approach, which involves non-rigid registration with a blending of rigid transforms, overcomes several of the limitations in current methods. The researchers validate their method by applying it to the Kyoto Collection of Human Embryos and Fetuses, the largest collection of human embryos in the world, with over 45,000 specimens.

MRI and CT scans are standard techniques for acquiring 3D images of the body. These modalities can trace with unprecedented precision the location of an injury or stroke. They can even reveal the microscopic protein deposits seen in brain pathologies like Alzheimer's disease. However, for the best resolution, scientists still depend on slices of the specimen, which is why cancer and other biopsies are taken. Once the information desired is acquired, scientists use algorithms that can put together the 2D slices to recreate a simulated 3D image. In this way, they can reconstruct an entire organ or even organism.

Stacking slices together to create a 3D image is akin to putting a cake together after it has been cut. Yes, the general shape is there, but the knife will cause certain slices to break so that the reconstructed cake never looks as beautiful as the original. While this might not upset the party of five-year olds who want to indulge, the party of surgeons looking for the precise location of a tumor are harder to appease.

In fact, the specimen can undergo a series of changes when prepared for sectioning.

"The sectioning process stretches, bends and tears the tissue. The staining process varies between samples. And the fixation process causes tissue destruction," explains Nara Institute of Science and Technology (NAIST), Nara, Japan, Associate Professor Takuya Funatomi, who led the project.

Fundamentally, there are three challenges that emerge with the 3D reconstruction. First is non-rigid deformation, in which the position and orientation of various points in the original specimen have changed. Second is tissue discontinuity, where gaps may appear in the reconstruction if the registration fails. Finally, there is a scale change, where portions of the reconstruction are disproportional to their real size due to non-rigid registration.

For each of these problems, Funatomi and his research team proposed a solution that when combined resulted in a reconstruction that minimizes all three factors using less computational cost than standard methods.

"First, we represent non-rigid deformation using a small number of control points by blending rigid transforms," says Funatomi. The small number of control points can be estimated robustly against the staining variation.

"Then we select the target images according to the non-rigid registration results and apply scale adjustment," he continues.

The new method mainly focuses on a number of serial section images of human embryos from the Kyoto Collection of Human Embryos and Fetuses and could reconstruct 3D embryos with extraordinary success.

Notably, there are no MRI or CT scans of the samples, meaning no 3D models could be used as a reference for the 3D reconstruction. Further, wide variability in tissue damage and staining complicated the reconstruction.

"Our method could describe complex deformation with a smaller number of control points and was robust to a variation of staining," says Funatomi.

Title: Non-rigid registration of serial section images by blending transforms for 3D reconstruction

Authors: Takehiro Kajihara, Takuya Funatomi, Haruyuki Makishima, Takahito Aoto, Hiroyuki Kubo, Shigehito Yamada & Yasuhiro Mukaigawa

Journal: Pattern Recognition

DOI: 10.1016/j.patcog.2019.07.001

Information about Prof. Mukaigawa lab can be found at the following website:

Nara Institute of Science and Technology

Related Science Articles from Brightsurf:

75 science societies urge the education department to base Title IX sexual harassment regulations on evidence and science
The American Educational Research Association (AERA) and the American Association for the Advancement of Science (AAAS) today led 75 scientific societies in submitting comments on the US Department of Education's proposed changes to Title IX regulations.

Science/Science Careers' survey ranks top biotech, biopharma, and pharma employers
The Science and Science Careers' 2018 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Science in the palm of your hand: How citizen science transforms passive learners
Citizen science projects can engage even children who previously were not interested in science.

Applied science may yield more translational research publications than basic science
While translational research can happen at any stage of the research process, a recent investigation of behavioral and social science research awards granted by the NIH between 2008 and 2014 revealed that applied science yielded a higher volume of translational research publications than basic science, according to a study published May 9, 2018 in the open-access journal PLOS ONE by Xueying Han from the Science and Technology Policy Institute, USA, and colleagues.

Prominent academics, including Salk's Thomas Albright, call for more science in forensic science
Six scientists who recently served on the National Commission on Forensic Science are calling on the scientific community at large to advocate for increased research and financial support of forensic science as well as the introduction of empirical testing requirements to ensure the validity of outcomes.

World Science Forum 2017 Jordan issues Science for Peace Declaration
On behalf of the coordinating organizations responsible for delivering the World Science Forum Jordan, the concluding Science for Peace Declaration issued at the Dead Sea represents a global call for action to science and society to build a future that promises greater equality, security and opportunity for all, and in which science plays an increasingly prominent role as an enabler of fair and sustainable development.

PETA science group promotes animal-free science at society of toxicology conference
The PETA International Science Consortium Ltd. is presenting two posters on animal-free methods for testing inhalation toxicity at the 56th annual Society of Toxicology (SOT) meeting March 12 to 16, 2017, in Baltimore, Maryland.

Citizen Science in the Digital Age: Rhetoric, Science and Public Engagement
James Wynn's timely investigation highlights scientific studies grounded in publicly gathered data and probes the rhetoric these studies employ.

Science/Science Careers' survey ranks top biotech, pharma, and biopharma employers
The Science and Science Careers' 2016 annual Top Employers Survey polled employees in the biotechnology, biopharmaceutical, pharmaceutical, and related industries to determine the 20 best employers in these industries as well as their driving characteristics.

Three natural science professors win TJ Park Science Fellowship
Professor Jung-Min Kee (Department of Chemistry, UNIST), Professor Kyudong Choi (Department of Mathematical Sciences, UNIST), and Professor Kwanpyo Kim (Department of Physics, UNIST) are the recipients of the Cheong-Am (TJ Park) Science Fellowship of the year 2016.

Read More: Science News and Science Current Events is a participant in the Amazon Services LLC Associates Program, an affiliate advertising program designed to provide a means for sites to earn advertising fees by advertising and linking to