IMAXT
Led by the late Professor Greg Hannon (1964 - 2026)The challenge
In 2017, the IMAXT team set out to tackle the 3D tumour mapping challenge.
At the time, the ‘single-cell revolution’ had only just begun. It was known that cancer cells exist within an increasingly complex, interactive ecosystem, and there was a growing appreciation for the role of tumour heterogeneity and the microenvironment in cancer progression, metastasis and therapeutic resistance. Yet, spatial-multi-omics was barely imagined, and single-cell technologies were emerging, difficult to interpret, and often untested in more challenging tissue-types, let alone intact tissues, such as primary tumours and metastases.
Team IMAXT proposed to develop a platform, bringing together advanced imaging approaches with cutting-edge technologies, most of which were still in their infancy, for measuring DNA, RNA and protein on a single-cell level. Importantly, the team would also preserve spatial information- location and context would be key. IMAXT then planned to integrate this complex data and visualise them in an interactive 3D map using virtual reality (VR). Creating such a precise, detailed 3D map would capture the complexity of intra-tumour architecture and provide an entirely new way to study cancer.
At a glance
IMAXT was funded by
Team and leadership
Led by the late Professor Greg Hannon (1964 - 2026), IMAXT assembled a multinational team spanning five countries, bringing together expertise in medicine, astronomy, virtual reality, statistics, programming and molecular biology. The team included pioneers of the technologies it would develop and integrate. This breadth of expertise enabled IMAXT to refine existing methods, invent new ones and combine them into a platform capable of exploring tumours in extraordinary detail.
Tackling the 3D tumour mapping challenge
The technologies developed and optimised by the team include Serial two-photon tomography (STPT), Ex-Seq, MERFISH, 3D IMC, DLP+, WILD-Seq, HiFi to name but a few. IMAXT has gone on to show that tumour mapping can yield valuable prognostic and diagnostic insights. By leveraging imaging mass spectrometry alongside mutliplatform bulk genomics to profile breast tumours from hundreds of patients, the team demonstrated that the structure of the tumour neighbourhood correlated strongly with patient outcomes. This work extended to both primary tumours and lymphatic metastases, identifying a specific tumour microenvironment motif with significant prognostic potential. IMAXT has helped lead the spatial biology revolution, developing an integrated platform to map tumours cell by cell while preserving information about each cell’s location and surroundings. The platform combines 3D imaging with measurements of DNA, RNA and proteins, supported by advanced data analysis and visualisation tools. Together, these approaches allow researchers to investigate how tumour architecture and interactions between cells influence cancer behaviour.
Among its advances, the team adapted serial two-photon tomography to image entire tumours and metastases while preserving biomolecules for further analysis. Mapping tumours in three dimensions allows researchers to identify rare features, such as small areas of invasion that may contribute to cancer spread, and examine the cells and structures surrounding them. The team also developed and refined complementary techniques to study gene activity, proteins and genomic differences between individual cells.
To explore these complex datasets, IMAXT developed Project Theia, a virtual reality viewer that allows researchers to immerse themselves in a 3D tumour map. The platform can handle datasets containing millions of cells and enables researchers in different locations to examine the same tumour together. Members of the team also established Suil Vision, the first spin-out from Cancer Grand Challenges, to further develop the viewer and explore its application to other large datasets.
Applying its technologies to breast cancer, IMAXT showed that the organisation of tumour neighbourhoods was associated with patient outcomes. The team also used single-cell genomic approaches to track how different cancer cell populations evolve and respond to treatment, demonstrating how therapy can change which populations have a growth advantage.
In 2025, work in high-grade serous ovarian cancer revealed that whole-genome doubling, in which a cell duplicates its entire genome, is an ongoing process shaping tumour evolution. By integrating single-cell genome sequencing with spatial techniques, the researchers uncovered an adaptive mechanism of immune evasion that allows tumours to sustain this process. They also developed DoubleTime, a computational approach to establish when genome doubling occurred and investigated its role in cancer evolution.
Tumour mapping in virtual reality
IMAXT launched VR software to visualise and analyse tumours, with technology provided by Suil. The digital map, with the use of a VR headset, allows the user to "go inside" a detailed, comprehensive recreation of an individual tumour.Looking ahead
The IMAXT platform, alongside the expertise developed, represents truly cutting-edge technology, allowing unprecedented exploration of the complexity of the tumour microenvironment. Importantly, its application has already yielded novel insights into cancer biology, – and these innovative tools can now also be used to address important clinical questions. We can successfully say, that Team IMAXT solved the challenge we set.
The Spatial Profiling and Annotation Centre of Excellence (SPACE) has been established at the University of Cambridge with £5.25 million in additional funding from Cancer Research UK. Bringing together technologies developed through IMAXT, SPACE is opening these approaches to the wider research community through open access, technology comparison and integrated spatial analysis.
This lasting resource extends IMAXT’s impact beyond the original team, enabling more researchers to investigate tumour complexity and address new questions in cancer biology. By making these technologies and the expertise needed to use them more widely available, SPACE aims to accelerate discoveries that could ultimately improve cancer diagnosis and treatment.
