Dive deep into the data | EurekAlert!

In a glance:

  • Researchers have developed a tool that makes it easier to understand and use high-resolution imaging data on human tissue.
  • The tool, called Minerva, enables users to explore key features of tissue samples at their own pace or using the built-in narration.
  • The researchers hope that Minerva will be used by other scientists, journals, clinicians, medical students, and non-scientists.

For many of us, Google Maps has become an indispensable everyday tool: we open a web browser and instantly access a powerful map where we can get directions, zoom, pan, and overlay features like traffic and terrain, and search for specific landmarks. But what if there was a tool with similar functions for exploring a completely different type of map? What if we had the ability of the Magic School Bus to delve deeper into the details of the tissues that make up the human body?

That’s exactly the idea behind Minerva, a software tool developed by Harvard Medical School researchers in the Systems Pharmacology Laboratory in the Department of Systems Biology at the Blavatnik Institute at HMS.

Minerva, available online to anyone, is named after the Roman goddess of wisdom. It gives users access to in-depth maps of tissue samples collected during research, ranging from cancerous tumors to distressed myocardium. On each map, users can zoom in and out, overlay features such as immune cells, and explore noteworthy areas. The maps also include the expertise of scientists and clinicians who can create stories to guide users through samples.

The researchers hope that as Minerva’s tissue sample library grows, the tool will be used by other scientists, journals, clinicians, interns, medical students, or simply anyone curious, allowing scientific information – and scientific expertise – to be shared on a large scale. wider.

“We collect a lot of research data, but not a lot of it is easily accessible yet, so the question is how do you crowd the complex data so that people can access it in a useful way,” said Peter Sorger, Director of HMS Otto Krayer, Professor of Systems Pharmacology. , who co-led the project with Sandro Santagata, associate professor of pathology at HMS at Brigham and Women’s Hospital. “That’s really what Minerva is about.”

drowning in data

As imaging technology has advanced, so has the ability for scientists to collect extremely high-resolution data about tissues in the human body. Using multiplex imaging techniques, researchers can collect such details at the single-cell level—and this data can contain 50 or 60 layers of information about protein tags and other features. Several years ago, Surger, Santagata and their team developed their own multiplex imaging technology, cyclic immunofluorescence, or CI, which is freely available and uses tools and chemicals found in most laboratories.

Because the scientists used CyCIF for their own research, they were frustrated by the fact that terabytes of complex high-resolution imaging data were routinely cut into a few small still images when they published papers in scientific journals.

“What you’re posting is a postage stamp – a very small JPEG format, 600 pixels wide – while the real photo is more than a few billion pixels wide, but it’s stuck on someone’s computer,” said Surger.

In recent years, the research community has increasingly emphasized the importance of sharing full data, or so-called “FAIR” data: findable, accessible, interoperable, and repeatable. In January 2023, a new NIH policy on data management and sharing will take effect, requiring all scientists who receive NIH funding to submit a plan outlining how their data will be managed and shared.

However, despite these efforts, “our work has shown us that there is not enough investment in what is really needed to access any of this data,” Sorger said. “We continue to collect more and more data, and we continue to look to make it more accessible and shareable, but we are not building the necessary software tools to do so.”

In part, this is because scientific data is often large and useless and difficult for even experts to understand without evidence (like Google Maps without labels), so designing tools that support sharing information in a meaningful way is easier said than done.

“You can download one of our images, and then you’ll be on your computer running your hard drive,” Sorger explained. “Without specialized software, a lot of it still in development, you can’t look at it. You can’t interact with it. And even if you could, you wouldn’t necessarily know what it is.”

This is where Minerva comes in.

understand things

Based in the cloud, Minerva is organized into stories, each focused on a single tissue sample or group of related samples. When users interact with an image, they can pan from one place to another and zoom in or out to explore. They can also turn on and off different layers of information, including immune cells and other cell types, protein markers, or the physical structure of tissues, among other things.

Minerva Stories also include a ‘Digital Speaker’, a narrative element made up of a text panel that appears next to each image. The idea is inspired by the museum’s tours – both personal viewing audio tours and online tours developed during the COVID-19 pandemic – which guide visitors through an exhibition by providing a narrative introduction to various pieces of art. The Minerva Stories narrative panel guides users through the main features of a sample, providing additional information about each feature along the way. Users can pause to explore the sample freely at any time, and come back to the narration later.

Users can also create their own Minerva stories with narration.

Sorger and Santagata describe Minerva – and the idea of ​​online anecdotal evidence of tissue samples – in a recent perspective in The nature of biomedical engineering.

To date, many of Minerva’s stories focus on cancer, including skin cancer, lung cancer, and colorectal cancer. Cancer provides an obvious starting point, said Surger, because it’s diagnosed largely based on tissue samples — in 85 to 90 percent of cases, he estimates. However, Minerva stories can be created for any condition that appears or leaves its traces in tissues, including heart disease, tuberculosis, neurodegeneration, and COVID-19.

Sorger and Santagata have created Minerva Stories from images linked to research papers they publish in scientific journals, as well as images from unpublished research, resulting in about two hundred stories to date. “These are basically small publications” that allow scientists to access much more information than is available in the paper, Sorger explained.

For example, researchers created the Minerva story about skin cancer in a recent research paper in Cancer discovery They created micro-scale spatial maps showing how individual cells interact with the progression of cancer. In the future, researchers envision every small, static image in a scientific paper becoming an entry point into the full-length story of Minerva. “We see it complimenting a traditional character by providing more content and context,” Sorger said.

Pictures in medical textbooks can likewise become the stories of Minerva. For example, instead of a textbook providing a single snapshot of tissue from myocardial infarction, a student can click on the image and use Minerva to freely explore the most visually dynamic and most detailed representation of that sample. “It provides participatory engagement with images that we hope will enhance medical education,” Santagata said.

Minerva may also be useful for pathologists in training who are learning to analyze tissue samples. Currently, pathology students sit at a multihead microscope and look at a slide of tissue as a teacher guides them through the condition and points out features critical to making a diagnosis. Minerva Stories contains a lot of this information, with the advantage that it can be accessed on demand and from anywhere. “With Minerva, we can get the expertise of a wide range of people and spread it widely,” Santagata said. “It really expands our reach, and it also provides more types of data that we can use to educate people.”

Sorger and Santagata believe that Minerva could also support a broader push to digitize pathology. Currently, pathology is still largely dependent on physical tissue slides, which have to be mailed whenever colleagues at different institutions want to consult with each other. In fact, Santagata estimates that about 1 million slices of about 100,000 cases travel through the Brigham and Gynecology Department each year. With Minerva, pathologists can easily share digital copies of tissue samples, along with key information needed for their interpretation.

In keeping with their goal of making Minerva widely available, Sorger and Santagata have made the tool and all of its code open to access. They estimate that 10 research groups from different universities have built their own Minerva stories, and about 25 laboratories actively use Minerva — including several that are connected to the National Cancer Institute’s Human Tumor Atlas Network. The researchers are currently working on integrating Minerva into existing tools, including cBioPortal, an open-access tool for exploring cancer genomics data sets — a move they anticipate will greatly expand the use of Minerva. They also believe that Minerva may attract non-scientists interested in learning more about a particular condition, including cancer advocates or the scientifically curious general public.

Our mission is to create public goods. “We’re talking about education and research, and they’re both in the public domain,” Surger said. “If we want to create something to be useful in class or in research, we don’t want to put up barriers to using it.”

In addition to making scientific data easier to access, the researchers hope that Minerva will spark greater interest in science and scientific research.

“It’s great to be able to capture what was essentially a still image and bring it to life. There is a certain wonder and magic that is part of the experience of engaging and interacting with data in this way,” Santagata said. to other scientists, to the public in general, and even to ourselves.”

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