Using Advances in Digital Pathology to Transform Teaching and Research

Cummings School faculty and students are taking advantage of new technology for remote learning and more
Amanda Martinot looking at a computer screen. Cummings School faculty and students are taking advantage of new digital pathology technology for remote learning and more
Digital pathology “is a very useful tool in preclinical studies,” said Amanda Martinot, an assistant professor in the Cummings School Department of Infectious Diseases and Global Health. Photo: Alonso Nichols
January 19, 2021

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Digital pathology—scanning a slide containing a blood, fluid, or tissue sample so it can be viewed onscreen and shared or stored electronically—is not new.

But it has had some serious shortcomings that have limited its use for teaching—especially during a time when remote learning suddenly became important. Cummings School of Veterinary Medicine recently invested in a new online platform that overcomes those problems to revolutionize how its faculty can use it for teaching and research.

Cummings School has owned a scanner that digitally replicates the abilities of the best clinical microscopes for many years. “Being able to view slides at 100 times magnification is really important,” said veterinary clinical pathologist Francisco Conrado. “For example, there are some really tiny bacteria that attach to red blood cells that you might miss in a blood smear otherwise.”

Scanning slides at this resolution results in gigantic digital files that, until now, made digital pathology largely impractical for teaching. 

“Previously, if I wanted to use a digital sample for a course, I would have to ask a hundred students to download a five-gigabyte or larger file,” said Conrado, an assistant professor in the Department of Biomedical Sciences. “They’d also each have to download and install special software to open it—just so they could see one slide. It was impossible.”

Because of that, Cummings School veterinarians were really only using digital pathology to scan slides related to research and to send the occasional digital sample for a second opinion.

However, in June Cummings School began subscribing to a new online platform called Scopio that allows faculty and researchers to upload and store an unlimited number of scanned slides, regardless of their massive size. The service allows any user with a basic web browser to open and view the slides online without having to download or install anything.

“It is a complete game changer, because now we have all these digital pathology samples available for students to view at just one click,” said Conrado. “They can then move around inside the scan just as though they were using a microscope to zoom in.”

Improving Teaching

Cummings School invested in the Scopio digital service during COVID-19 to help keep veterinary students’ pathology instruction on track while learning remotely, but its benefits will continue long after the pandemic.

“Digital pathology is not going to completely replace conventional microscopy—at least not for now,” said Conrado. “We still need to teach students how to use a microscope. But it enhances the learning experience and increases the possibilities that we have.”

“Before, once a student left the microscope and that slide in the classroom, they were never going to see that slide again,” he said. “Now, they have it available to them forever. They can study it at their own convenience whenever they have time.”

Francisco Conrado gives a video tour of how the new digital pathology platform is being used in teaching.

This creates a more equitable learning environment. “There are students who cannot physically sit at a microscope for a long time, struggle with background noise in class, or need extra time to go over the material,” Conrado said. “This platform can make learning pathology more comfortable and accessible for everyone.”

The digital slides also can be annotated for teaching, research, and requesting a second clinical opinion, said Conrado. “If I want to point to something specific, I can note, ‘Please check these cells out,’ and when students click that spot in image, it takes them directly to that area.”

The new digital pathology platform also allows sharing that wasn’t possible before. If there is even one “textbook image” available, all students can now learn from that one ideal teaching sample.

“Before, if a really interesting blood sample was submitted to the lab, I’d need enough volume for a hundred smears if I wanted to ever use it in class,” Conrado said. “Now I can scan one good smear and that single slide is then available for every student.”

Advancing Research

At the most basic level, digital pathology is allowing researchers across Cummings School to easily store and access relevant samples without having to sort through millions of physical slides in boxes.

It also offers exciting new avenues for discovery—particularly when combined with artificial intelligence (AI).

The use of AI cannot replace what a pathologist’s work interpreting and investigating the mechanisms of a disease, said Cummings School assistant professor Gillian Beamer. However, she said, human and artificial intelligence certainly complement each other when deployed in tandem.

For example, Beamer is using AI technology to advance her research on tuberculosis and the role of host genetics in individual outcomes of disease. Her studies involve visually inspecting hundreds of slides to evaluate for a very specific lung pathology. By training a computer program to recognize and quantify the specific features she is looking for, Beamer can now compile within just days data that would normally not be possible to collect by a human in a lifetime of work.

AI analysis also can detect pathology patterns that are not apparent to the human eye, revealing microscopic features of disease that were previously unknown. As the computer can operate 24/7, Beamer also can set data-extraction and high-level analytical tasks to run overnight.

This frees up her research group to spend their time on more critical functions—such as interpreting results and publishing new research findings—and increases the team’s capacity to analyze archived samples.

Meanwhile, Cumming School assistant professor Amanda Martinot and postdoctoral researcher Cesar Piedra-Mora are using the new digital pathology platform for research on new therapies and vaccines for COVID-19.

As part of their work with Beth Israel Deaconess Medical Center immunologist Dan H. Barouch, the two veterinary pathologists are digitally analyzing the body’s response to infection.

For example, using samples from animal studies on COVID-19, the pathologists can choose to apply an antibody that will stain all T lymphocytes—a type of immune cell potentially involved in controlling the infection or causing disease—brown on a slide, which is scanned through the new digital pathology platform. Piedra-Mora can then run the digital scans through an image analysis program optimized to detect the brown signal accurately to provide an exact measurement of how many of those cells are present.

“We are able to perform this kind of quantitation for a number of immune-system markers,” said Martinot. “It is a very useful tool in preclinical studies, where you may, for example, be using the hamster model to assess if a potential COVID-19 therapy is modulating the body’s inflammatory response in a specific way.”

Genevieve Rajewski can be reached at genevieve.rajewski@tufts.edu.