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bioRxiv · 10.64898/2026.04.12.717982

U-Probe: universal agentic probe design for imaging-based spatial-omics

Zhang, Q.·Cai, H.·Zhang, J.·Zhang, L.·Wu, X.·Wei, Y.·Chen, Y.·Su, W.·Qi, W.·Qiu, X.·Cao, G.·Xu, W.
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Abstract

Probe design for fluorescence in situ hybridization (FISH) underpins spatial transcriptomics, three-dimensional genome studies, and clinical diagnostics, yet remains constrained by two challenges: dependence on expert knowledge for parameter selection and quality evaluation, and the inability of existing tools to accommodate the diverse probe architectures introduced by rapidly emerging methods. Here we present U-Probe, a universal and agentic probe design platform. U-Probe employs a declarative configuration system with a directed acyclic graph (DAG)-based assembly engine that supports arbitrary probe structures from established protocols such as MERFISH, seqFISH, and MiP-seq to entirely novel architectures without code modifications. Integrated LLM-based AI agents enable conversational design workflows, allowing users to specify experimental goals in natural language and receive synthesis-ready probe sequences. We validated U-Probe in three scenarios: agent-driven MiP-seq panel design for influenza-infected mouse lung tissue, genome-tiling DNA-FISH for herpesvirus detection, and a novel RCA-based ligation probe for single-nucleotide mutation discrimination. U-Probe is available as an open-source tool with CLI, Web, and agent interfaces.

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Zhang, Q., Cai, H., Zhang, J., Zhang, L., Wu, X., Wei, Y., Chen, Y., Su, W., Qi, W., Qiu, X., Cao, G., Xu, W.. 2026-04-15. U-Probe: universal agentic probe design for imaging-based spatial-omics. https://doi.org/10.64898/2026.04.12.717982

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