Going European
Three million and beyond
Right mindset
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Looking for the big picture

Within the span of the past five years, a casual “What if?” conversation among two Novartis scientists has become one of the boldest European-wide research efforts to transform the field of pathology and provide medicine with a deeper understanding of cellular mechanisms. Collaborative science and the cultivation of bold mindsets were instrumental for this success.

Text by K.E.D. Coan and Goran Mijuk, photos by Bjoern Myhre

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Step-by-step sample preparation in the pathology...

arrow-rightGoing European
arrow-rightThree million and beyond
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Published on 07/10/2022

Back in 2016, when Novartis launched Genesis Labs as a sort of internal startup incubator, the idea was to give researchers space, time and money to single-mindedly follow an idea that could potentially pave the way for medical breakthroughs.

Part human resource exercise to provide talented scientists with a means to develop extra-curricular ideas, part effort to accelerate research dynamic in fringe fields that are outside of the core focus areas of Novartis, Genesis Labs attracted an ever-growing number of scientists over the past few years.

The program, which was co-initiated by Novartis researcher Ian Hunt, who runs Genesis Labs to this day, now includes engineers and technicians who work outside the lab and want to test fresh avenues in areas such as medical production, packaging or quality assurance, among many others.

All of them are craving for impact like Pierre Moulin, a former pathologist at the Novartis Institutes for BioMedical Research (NIBR), and Tobias Sing, a NIBR data scientist, who back in 2017 dreamed of tapping into the unrealized potential of the vast reserves of pathology data within the company.

Five years later, their idea has not only turned into a European flagship research project. Their success has also proven that giving researchers freedom to pursue bold and courageous ideas can make all the difference.

Thinking digital

Since the invention of the microscope, pathology has involved the careful microscopic examination of paper-thin slices of biological tissue encased in glass slides. This process is key to understanding what healthy cells look like, as well as identifying signs of disease, for example in clinical biopsies.

Pathologists spend years training to decipher these images and they spend their careers carefully annotating each one. And then, all of these images and findings are largely kept stored away – an immense and ever-increasing untapped resource.

Novartis alone collects over 300000 preclinical pathology slides each year. But these were typically used only within isolated development programs and there was no company-wide effort to bring everything under one roof.

But what if these could be combined into a centralized, shared tool for researchers across the company? And – even more ambitious – what if this could be combined with artificial intelligence, or AI, and machine learning, which have the potential to mine immense volumes of information that are beyond the ability of human minds to comprehensively analyze?

This was the thinking of Moulin and Sing when they were discussing their idea back in 2017. While pursuing such an idea was outside of Moulin and Sing’s typical business priorities, their idea was a perfect match for Genesis Labs, which supported their project, allowing the two to set up a team of researchers that brought lab, analysis and AI skills to the table.

In record time, the team formed by Moulin and Sing used the Novartis collection of pathology slides to develop AI training models to rapidly identify different tissue types. The outcomes were so convincing that the project was perpetuated even after their Genesis funding had ended with its 18-month timeframe.

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...department on the Novartis Campus.

Go­ing Eu­ro­pean

The team, and particularly Moulin, knew that so much more could be done for the entire field of pathology if they could apply similar approaches to even larger data sets. Hence, Moulin proposed his ideas to the Innovative Medicines Initiative (IMI), which is one of the flagships of Horizon 2020 health research – the world’s biggest facilitator of life science public-private partnerships.

Moulin’s project won support from the IMI as well as the European Federation of Pharmaceutical Industries and Associations, which helped launch Bigpicture, a program with the aim to create Europe’s largest digital repository of pathology slides – 3 million images – as well as the tools for fusing AI and machine learning into the field.

Forty-five partners from 15 European countries have joined Bigpicture, which officially launched in February 2021. The participating members include AI experts, biobanks, universities, hospitals and companies of every size. The project has received nearly 70 million euros in funding – roughly half from the European Commission and half from the 10 participating pharmaceutical companies, including Novartis.

Once complete, the resulting Bigpicture platform will provide a shared global resource of unprecedented size. It will also include training sets and tools for AI developers, pharmaceutical researchers and pathologists for years to come.

Assembling the building blocks

In 2021, Julie Boisclair, Director of Digital and Computational Pathology at Novartis, replaced Pierre Moulin, who left the company, as one of the four members of the Bigpicture leadership team overseeing the coordination and management of the collaboration. Beyond Boisclair’s team, there are five additional Bigpicture working groups, each responsible for one of the building blocks of the program.

“We knew that we could achieve great things if we could work in close collaboration with the best experts and the best universities, and share the vast resources that exist in academia, public organizations and small and large companies,” says Julie Boisclair. “Many people have told me that this is one of the most ambitious IMI projects to date. And we do believe that this will revolutionize the world of pathology.”

An integral first step has been creating the infrastructure and database to securely transfer and host the digital slide images. The team calculates that they will need 4.5 petabytes – around 4.5 million gigabytes – of storage and much of this framework has been put in place during the first year of the project in preparation for receiving the slides.

Developing the tools to upload, view, annotate, analyze, mine and download the slides is another foundational step and Holger Hoefling, Associate Director Data Science and one of the core members of Moulin’s original group, is part of the leadership team responsible for this work. As a starting point, they have begun with an open-source viewer software, but there are many adaptations that will be needed to suit the project’s needs.

“The final web interface will be a very dynamic platform,” says Hoefling. “Users will need to nicely zoom in and zoom out and we need to make sure that users can overlay annotations and that it will display correctly. And, of course, the platform needs to be capable of providing the 3 million slides relatively fast and easily so that users can pick and choose whatever they need.”

Perhaps most importantly, the software also needs to give users the ability to run machine learning algorithms to display results such as identifying lesions or signs of toxicity.

“One idea is that algorithms could highlight anything that doesn’t match normal tissue or that AI could make it easier to annotate slides by anticipating exactly which parts of an image a user intends to outline,” adds Hoefling.

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Classic pathology samples before they are readied to be cut in thin slices and digitized.

Three mil­li­on and bey­ond

Collecting the 3 million digital slides is planned to begin in late 2022. Two million of these will be preclinical slides provided by the partnering pharmaceutical companies (where preclinical studies are key for determining the toxicity of drug candidates). On the clinical side, participating university hospitals will contribute the remaining 1 million slides – the largest collection of clinical slides to date. The slides will also represent a broad range of diseases, as well as a nearly complete spectrum of cancer types.

Guaranteeing that the repository is safe, ethical and compliant with General Data Protection Regulation (GDPR) is also a high priority for Bigpicture and there are dedicated teams establishing the necessary precautions and regulatory framework. The platform will incorporate the strictest measures for protecting patient anonymity, as well as any proprietary data.

“Cybersecurity is critical to our efforts so that we can make sure that only the right people with good intentions have access to the slides,” says Boisclair. “Some of the biggest hurdles will be reassuring health authorities and pharmaceutical companies that the slides will be carefully protected and that no identifying data or intellectual property will be included.”

The final piece of the project is ensuring that the resulting platform is built to become an enduring and sustainable resource for the future. Bigpicture is intended to provide a community-based platform that will continue to expand and provide training data for AI pathology tools for decades to come. To accomplish this, the team will comprehensively analyze the needs of all potential participants and users, and, based on this analysis, develop a business model for the continuing growth and operation of Bigpicture.

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NIBR's pathology team (from left to right): Aline Piequet, Geraldine Greiner, Esther Erard, Julie Boisclair, Holger Hoefling and Magali Jivkov.

Right mind­set

“Bigpicture is really the legacy of Pathology 2.0,” says Hoefling. “It came from the idea that we needed much more data to develop good and useful algorithms and that no one – not Novartis or universities or AI startups – had access to enough data to build models that could transform and accelerate the use of AI in pathology.”

Since the inception of the Genesis Labs, the initiative has inspired 500 proposals, 15 of which have received funding. This represents the collaborative work of over 5000 associates. In addition to Bigpicture, these projects have resulted in scientific publications and patents, and close to half have become ongoing projects within the company.

“It’s been incredibly gratifying to see how the Genesis Labs initiative has taken nascent ideas such as Pathology 2.0 and nurtured and grown the concepts, not just for Novartis, but also the broader biomedical community,” says Ian Hunt, Head of Novartis Genesis Labs, and one of the founders of the initiative. “When we launched Genesis Labs, we really wanted to support cross-functional collaborations. Seeing this happen with Pathology 2.0, one of the first Genesis projects, has been wonderful to watch and it’s been amazing what this team has achieved, not just scientifically, but also how they’ve used their internal and external networks to scale their idea – a truly entrepreneurial mindset.”

The ultimate goal of helping patients is also at the heart of Bigpicture, as well as many other Genesis projects. It may take years for these innovations to reach the clinic, but the team is confident that they are laying the groundwork to help patients receive faster, more accurate diagnoses, and to add new tools and resources for the drug discovery pipeline.

“From our perspective, Bigpciture has great potential to promote research, improve toxicological screens and diagnoses and accelerate drug development because currently pathology readouts are a limiting step in the process,” says Boisclair. “It will take time to validate the tools and receive approval from the authorities, but eventually this pro­ject could be a real advantage for bringing drugs to patients faster.”

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