Volumetric spatial transcriptomics for 3D culture-innovated drug development

Objective

Spatial biology is bottlenecked by 2D-based platforms that cannot profile intact 3D tissues, such as organoids, at scale. This gap is acute in drug discovery, where organoids and other 3D culture models in 96/384-well format are increasingly adopted, accelerated by EU and FDA roadmaps to reduce animal use. Spatial Fuseseq directly addresses this unmet need with an entirely new way to spatially barcode molecules inside intact 3-dimensional tissue samples for downstream DNA sequencing and computational volumetric (3D) reconstruction at high resolution and low cost. Building on results of an ERC PoC and subsequent improvements that together established feasibility on cells and tissue sections (TRL4), this EIC Transition project will advance Spatial Fuseseq to TRL6 and a first market-ready configuration for organoid-based drug development. Technologically, we will (i) develop and automate sample-preparation for organoids (96/384-well), (ii) expand to whole-transcriptome profiling, (iii) deliver validated computational pipelines for 3D reconstruction and visualization, and (iv) produce prototype reagent kits with QC assays and a beta software version for user testing. Commercially, we will (v) validate problem–solution fit via voice-of-customer interviews, and (vi) run early-access pilots—first in-house, then at user sites—to demonstrate the technology in relevant environment (TRL6) and its readiness for scale. The global spatial biology market is dominated by US players, while Europe leads in novel 3D culture models for translational drug discovery. Anchoring Spatial Fuseseq in Europe ensures that the enabling spatial platform for 3D culture model analysis is not imported but developed, owned, and commercialized within the EU, securing high-value IP, skilled jobs, and economic growth, strengthening EU sovereignty and positions European SMEs and Pharma to lead globally.