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 (Kubernetes)

The underlying Kubernetes-based infrastructure providing foundational services.

  • Multi-Tenancy: Strict logical and physical namespace separation.
  • Deployment: Deploy as standalone VMs/MicroK8s or integrate into existing Kubernetes clusters.
  • IAM (OIDC): Centralized authentication using Keycloak and OAuth2.
  • Network Policies: Zero-trust network segmentation.
  • Clinical Servers: Includes native FHIR, OMOP, DICOM, and OMERO servers.
📂

Medical FUSE VFS

Unified virtual file system abstracting complex medical data sources.

  • POSIX Translation: Treat OMOP, FHIR, and DICOM as local files.
  • Performance: Aggressive caching and read-ahead pre-fetching.
  • Zero-Copy: Direct access for training models without duplicating data.
🔬

Pathology Viewer (cb_path_viewer)

Next-generation clinical visualization for gigapixel Whole Slide Images.

  • Zero-Footprint: Pure HTML5 WebGL/Canvas rendering, no plugins.
  • Real-time AI: Dynamic overlay of diagnostic attention heatmaps.
  • OMERO Integration: Native integration with OMERO servers.
⚡

MLOps & Inference Engine

End-to-end lifecycle management for deep learning models.

  • NVIDIA Triton: GPU-accelerated dynamic inference server.
  • MLflow Registry: Centralized model versioning and tracking.
  • NVFlare: Transparent federated learning aggregator.
🧩

SlideLab Preprocessing

High-performance pipeline for WSI preparation before AI training.

  • Tissue Masking: Automated extraction of relevant tissue regions.
  • Normalization: Macenko and Vahadane color normalization.
  • Tile Extraction: Efficient H5 embedding generation for MIL.
🔄

End-to-End Pipelines

Complete automation from raw data to clinical insights.

  • Ingestion & Processing: Automated ETL pipelines for clinical and multi-omics data.
  • Training & Registration: Orchestrated model training and automated registry tracking.
  • Multi-modal Inference: Seamless deployment to the multi-modal viewer for clinical use.

Interoperability Standards

Native support for global healthcare data standards ensures seamless integration with existing hospital IT infrastructure.

HL7 FHIR
OMOP CDM
DICOMweb
OIDC / OAuth2