U-ProbeUniversal Agentic Probe Design Platform

A universal agentic probe design platform for imaging-based spatial-omics. Design arbitrary probe architectures via declarative configurations and execute end-to-end multi-step design pipelines guided by LLM-based AI agents.

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bioRxiv (Preprint)

🤖 AI-Driven Agentic Design

A hierarchical team of LLM-based agents interprets natural language requests, analyzes scRNA-seq data to select marker genes, and autonomously constructs configurations, significantly lowering the expertise barrier.

🧬 Universal Declarative Architecture

A DAG-based assembly engine and declarative YAML configuration system resolve architectural fragmentation, enabling the design of arbitrary probe structures (e.g., MERFISH, seqFISH, RCA-based) without code modifications.

⚡ End-to-End Automated Workflows

Provides a complete automated design pipeline from target sequence extraction, probe construction, property calculation to off-target filtering, supporting both DNA and RNA modes.

🔍 Advanced Specificity & Quality Filtering

Computes GC, Tm, secondary structure stability (ViennaRNA), off-target mapping (Bowtie2), and k-mer frequency (Jellyfish). Supports overlap removal and equal spacing for tiling designs.

📊 Rich Visual Reports

Automatically generates interactive HTML reports and PDF files containing detailed statistics and visual charts, helping you quickly evaluate and select the best probes.

🌐 Flexible Multi-Platform Interfaces

Provides an easy-to-use Command Line Interface (CLI), Python API, and a modern Web UI based on FastAPI to meet usage requirements across different scenarios.