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