A Modular Ecosystem for Next-Generation Precision Medicine
ColabBio provides a comprehensive suite of interoperable modules built for strict data governance, scalable AI, and clinical research.
Base Platform & Provisioning
The foundational Kubernetes and VM infrastructure providing scalable, zero-trust services.
- Declarative Provisioning: 2-Files Stack (
vfs.yaml+study.yaml) across Local, VM, and K8s. - Multi-Tenancy: Strict logical and physical namespace isolation.
- Deployment: Deploy as standalone VMs/MicroK8s or integrate into enterprise clusters.
- IAM (OIDC): Centralized authentication using Keycloak and OAuth2.
- Network Policies: Zero-trust network segmentation.
Medical FUSE VFS (Zero-Copy)
Unified POSIX virtual file system abstracting complex medical data sources.
- POSIX Translation: Treat OMOP, FHIR, and DICOM as native local files.
- Streaming Cache: Aggressive caching, tile pre-fetching, and read-ahead acceleration.
- Zero-Copy: Direct GPU training access without duplicating gigapixel datasets.
Clinical MCP Servers
Standardized medical microservices over Anthropic's Model Context Protocol (FastMCP/SSE).
- mcp-omop: Longitudinal cohort querying and SNOMED-CT/RxNorm translation.
- mcp-dicom: PACS search (QIDO-RS) and series resolution (WADO-RS).
- mcp-fhir & mcp-omero: EHR clinical records and gigapixel WSI slide connectors.
SlideLab Preprocessing
High-performance computational pathology pipeline for WSI preparation before AI training.
- Tissue Masking: Automated extraction of relevant tissue regions.
- Normalization: Macenko and Vahadane color normalization algorithms.
- Tile Extraction: Efficient H5 embedding generation for MIL.
Enterprise MLOps & Inference
End-to-end lifecycle management for deep learning models and distributed training.
- NVIDIA Triton: GPU-accelerated dynamic inference server.
- MLflow Registry: Centralized model versioning, artifacts, and tracking.
- NVFlare: Privacy-preserving federated learning aggregator.
End-to-End Pipelines
Complete automation from raw data ingestion to clinical insights.
- Ingestion & Processing: Automated Nextflow ETL pipelines for clinical data.
- Training & Registration: Orchestrated model training and automated registry tracking.
- Multi-modal Inference: Automated deployment to Triton for clinical consumption.
Clinical Companion & Tools
Deterministic agentic AI copilot for pathologists and oncologists powered by LangGraph4j.
- 19 Clinical Tools: Fact-checked, auditable reasoning without hallucinations.
- Cyclic State Graph: Adaptive planning, prerequisite validation, and execution.
- Real-Time Streaming: WebSocket event broadcast for heatmaps, ROI focus, and cards.
Pathology Viewer (cb_path_viewer)
Next-generation clinical visualization canvas for gigapixel Whole Slide Images.
- Zero-Footprint: Pure HTML5 WebGL/Canvas rendering, no browser plugins.
- Real-time AI: Dynamic overlay of diagnostic attention heatmaps.
- OMERO Integration: Native integration with institutional OMERO servers.
Interoperability Standards
Native support for global healthcare data standards ensures seamless integration with existing hospital IT infrastructure.