Documentation
ColonyAI Developer Docs
API Reference · Architecture · Deployment · ML Pipeline · User Guide
Introduction
ColonyAI — Automated Computer Vision for Microbiology
What is ColonyAI
ColonyAI is a production-grade, automated computer vision platform designed for clinical and industrial microbiology laboratories. It replaces manual colony counting with a YOLOv8-powered detection pipeline, delivering ISO-17025-compliant results with full audit traceability and zero-trust security architecture.
ColonyAI is actively used in accredited laboratory environments. All analysis outputs include uncertainty budgets per ISO 4833-1:2013.
Key Features
| Feature | Details |
|---|---|
| 5-Class Detection | colony_single, colony_merged, bubble, dust_debris, media_crack |
| CFU/ml Calculation | Auto-computed with dilution factor and plated volume |
| ISO-17025 Compliance | Full audit trail, uncertainty budget, method validation |
| Simulator | Transient analysis — test parameters without saving to DB |
| Role-Based Access | 5 roles: super_admin, admin, manager, auditor, analyst |
| PDF/Excel Export | Annotated plate images, detection tables, CFU summary |
| i18n | English and Bahasa Indonesia UI |
| Zero-Trust Security | JWT + refresh tokens, ClamAV file scanning, S3 storage |
Tech Stack
| Layer | Technology |
|---|---|
| Frontend | Next.js 14 App Router, Tailwind CSS, Lucide Icons, Zustand |
| Backend | FastAPI (async), SQLAlchemy async, Alembic, Pydantic v2 |
| ML Engine | YOLOv8n (fine-tuned), Ultralytics, OpenCV, PyTorch |
| Database | PostgreSQL 15+ with async driver (asyncpg) |
| Storage | S3-compatible (MinIO / Cloudeka Object Storage) |
| Auth | JWT HS256 access + refresh tokens, bcrypt password hashing |
| File Security | ClamAV antivirus scanning on every upload |
| Deployment | Docker Compose, NGINX reverse proxy, Redis cache |
Compliance
ColonyAI implements ISO-17025 requirements for automated colony counting methods, including measurement uncertainty, method validation records, and tamper-evident audit logs. Every analysis record is immutable once created — modifications generate new revision entries.