Cubase Bio AB is a Stockholm-based spatial biology company that develops reagent-based technology for measuring gene expression in three dimensions within intact organoids, tissues and whole organisms. Its workflow barcodes neighboring transcripts inside the sample, forming a proximity network that is extracted and sequenced with standard DNA sequencers. Proprietary software then decodes the network and reconstructs the 3D location of transcripts within the original tissue, without optical imaging. The approach is built on DNA microscopy developed by scientific advisory co-founders Joshua Weinstein of the University of Chicago and Björn Högberg of the Karolinska Institute.

The company was founded in 2024 by Malte Kühnemund, Xiaoyan Qian, Toon Verheyen and Paulius Mielinis, who previously worked on in situ sequencing at CARTANA, a SciLifeLab spinout acquired by 10x Genomics in 2020. Cubase Bio emerged from stealth in February 2026 with €5.9 million in blended financing, comprising a €2 million non-dilutive EIC Transition grant and €3.9 million in private capital and convertibles led by Voima Ventures and Nordic Science Investments. The company is targeting high-throughput drug discovery and disease research, with native compatibility with 96- and 384-well plate formats and an early access program for its reagent kits.

In September 2026 Cubase Bio and Vienna-based HeartBeat.bio launched the FACTS-3D project, supported by roughly €1 million in Eurostars funding, to apply 3D spatial transcriptomics to human cardiac organoids and myocardial fibrosis. Cubase Bio also joined the OvCaNAM consortium, a Horizon Europe project focused on ovarian cancer, in April 2026, and expanded its board of directors in May 2026.