CubaseBio secures €5.9m to scale 3D spatial transcriptomics

The remaining €2 million are non-dilutive grant from the European Innovation Council’s (EIC) Transition programme, which supports the maturation of promising research results toward market readiness. Just like another Swedish biotech startup, Beactica Therapeutics, CubaseBio was selected for the EIC grant as one of 40 projects from 611 submissions across 17 countries.

The grant helps selected projects to validate the technology in application-relevant environments and refine the company’s business. Beyond funding, participants of the EIC Transition programme gain access to coaching and business acceleration services.

Moving beyond thin tissue sections

The fast-evolving sector of spatial biology has reshaped how researchers study gene expression in tissues. Most established platforms, though, rely on thin two-dimensional sections. Systems such as 10x Genomics’ Visium and Xenium, imaging-based approaches and newer reconstruction tools have pushed resolution forward, but they still depend largely on slicing tissue into 5–10 micron layers. The field of 3D spatial transcriptomics, aiming to reconstruct tissue volumes at high resolution, is gaining momentum. The U.S. biotech startup Stellaromics, which raised an $80m Series B funding a few days ago, was one of the first to enter the space with its imaging-driven 3D multiomics platforms. However, this approach can miss long-range cellular interactions and distort complex structures.

CubaseBio aims to overcome these limits: its technology enables volumetric analysis of intact samples and reconstructs gene expression in three dimensions at scale. The method builds on DNA microscopy, which creates molecular networks inside specimens to encode spatial proximity between transcripts. Sequencing then generates a proximity matrix that software converts into a 3D map of gene expression.

“Biology is 3 dimensional. We want to enable measuring it in that way,” said CEO Malte Kuhnemund in a press release. He added that the company is “thrilled to be backed by strong life science tech investors and the European Innovation Council.”

From academic breakthrough to scalable platform

CubaseBio was founded in 2024 by Malte Kuhnemund, Xiaoyan Qian, Toon Verheyen and Paulius Mielinis, pioneers in spatial biology and genomics. Kuhnemund and Qian previously co-founded CARTANA, a biotech spinout acquired by 10x Genomics in 2020 for SEK 425m (around €96m at the time of the transaction).

Scientific advisory co-founders include Joshua Weinstein of the University of Chicago and Björn Högberg of the Karolinska Institute. Their work on DNA microscopy laid the foundation for CubaseBio’s platform and for the EIC-funded “Spatial Fuseseq” project.

“CubaseBio’s DNA microscopy technique offers a scalable route to spatial-transcriptomic analysis of complex 3 dimensional biological samples such as organoids and whole organisms,” commented Weinstein.

By combining EU grant support with private capital, CubaseBio positions itself in the spatial biology market. The company targets applications in drug discovery and disease research, where understanding 3D tissue architecture could reveal new biomarkers and therapeutic targets. CubaseBio will use the funding to accelerate technology development and prepare for commercialization.