Introducing U-Probe β the first agent-assisted platform for FISH probe design. π§¬
Probe design today is still fragmented and expert-heavy: different tools for different protocols, manual parameter tuning, and limited support for new probe designs.
U-Probe addresses this by:
β’ Supporting diverse protocols (MERFISH, seqFISH, DNA-FISH, etc.)
β’ Enabling custom probe architectures via a programmable framework
β’ Using AI agents to assist with panel design and parameter selection
βοΈ Built on the @PantheonOS evolvable multi-agent framework
β from experimental goal to synthesis-ready probes
Apr 16, 2026 Β· 3:18 PM UTC
1
5
20
3,628
We evaluated U-Probe across several representative use cases:
β’ Spatial transcriptomics panel design
β from scRNA-seq data to probe panels for infected mouse lung tissue
β’ Genome-scale DNA-FISH
β tiling probe sets for viral detection with high genome coverage
β’ Custom probe design
β RCA-based probes for single-nucleotide mutation detection
These examples highlight that U-Probe can handle both
established protocols and new probe architectures.
(Examples π)
1
3
179
U-Probe is available as an open source software:
β’ Web interface for interactive design
β’ CLI for batch workflows
β’ Agent interface for assisted design
It supports the full workflow from
design specification β probe generation β export.
Resources:
π Preprint: biorxiv.org/content/10.64898β¦
π Website: u-probe.org/
π» GitHub: github.com/UFISH-Team/U-Probβ¦
Feedback and use cases are very welcome!
1
2
223
Thanks to Qian Zhang (@QianZhang12138), Huaiyuan Cai (@hycai_wikk), and the team for their contributions. Qian Zhang is currently seeking a PhD position. She has strong engineering skills and a deep understanding of biological image processing and FISH probe design. If interested, please feel free to get in touch.
1
2
233