CubaseBio secures €5.9M to bring true 3D spatial transcriptomics to market
A Stockholm-based biotechnology company, CubaseBio, has emerged from stealth mode with €5.9 million in blended financing to accelerate the commercialisation of a next-generation spatial transcriptomic platform capable of analysing intact three-dimensional tissue structures — a capability that has eluded conventional spatial biology methods.
Funding structure and investor backing
The financing comprises a €2 million non-dilutive grant from the European Innovation Council (EIC) Transition programme and €3.9 million in private capital and convertibles. Lead investors Voima Ventures and Nordic Science Investments (NSI) were joined by Illumina Ventures, Almi Invest, Life Science Invest, and several undisclosed private investors from the genomics technology sector. CubaseBio was selected for the EIC Transition grant from a record 611 submissions across 17 countries, ultimately securing one of only 40 funded projects under the Horizon Europe programme.
Overcoming the limitations of 2D spatial analysis
Current spatial transcriptomic platforms — including those based on in situ sequencing — are constrained by their dependence on thin tissue sections, which inevitably sacrifice the three-dimensional context of gene expression within complex tissues. CubaseBio’s approach addresses this directly using DNA microscopy, a method that constructs molecular networks within intact specimens to encode spatial proximity between transcripts in three dimensions. These networks are resolved by DNA sequencing to generate a proximity matrix, from which a 3D image of gene expression is computationally reconstructed, capturing both spatial coordinates and nucleotide-level sequence data in a single measurement.
The scientific foundations of the technology were established by advisory co-founders Professor Björn Högberg (Karolinska Institute) and Professor Joshua Weinstein (University of Chicago), both recognised for pioneering work in DNA microscopy. Högberg’s contributions formed the basis for the EIC Transition grant, designated “Spatial Fuseseq.”
Founders bring proven track record in spatial biology
CubaseBio was founded in 2024 by Malte Kuhnemund, Xiaoyan Qian, Toon Verheyen, and Paulius Mielinis. Kuhnemund and Qian previously co-founded CARTANA, a SciLifeLab spinout that pioneered in situ sequencing and was acquired by 10x Genomics in 2020, where it formed the basis of the Xenium In Situ platform — now widely used in clinical research and translational laboratory settings.
Kuhnemund, serving as CEO, said: “Biology is 3 dimensional. We want to enable measuring it in that way. We are thrilled to be backed by strong life science tech investors and the European Innovation Council that awarded our company for the high scalability and disruptiveness of our technology.”
Professor Weinstein, who is presented work on volumetric DNA microscopy at the AGBT meeting in Orlando in February, noted that the technique “offers a scalable route to spatial-transcriptomic analysis of complex 3 dimensional biological samples such as organoids and whole organisms.”
The funds will support further technology development and commercialisation, with the platform targeting drug discovery and disease research applications.
For more information, visit: https://www.cubasebio.com/
