Skip to main content

Phlox Overview

Welcome to the Phlox documentation. Phlox is a free, open-source, local-first AI scribe with a built-in patient management system and agentic AI capabilities. It is designed as a local alternative to SaaS medical scribes that you can run on your own hardware.

Before using Phlox, read Limitations & Warnings. Phlox is experimental, is not a certified medical device, and is not suitable for production clinical use as provided.

Phlox encounter workspacePhlox encounter workspace

What is Phlox?​

Phlox is a local-first clinical tool with the following capabilities:

  • Patient Profiles & Encounters — stable demographics per patient, with individual encounter notes, transcripts, and tasks grouped by UR number. See Patients.
  • Ambient Medical Transcription — record or upload audio; Phlox transcribes it and generates a structured note from your chosen template. Uses Whisper-compatible endpoints or the bundled parakeet.cpp engine. See Transcription.
  • Adaptive Refinement — Phlox learns from the edits you make to generated notes and adapts future output to your style. See AI Features → Adaptive Refinement.
  • Flexible Templates — customisable note and letter templates with per-field prompts, formatting rules, and persistence. Generate templates automatically from an example note. See Templates.
  • Task Manager — action items are extracted from the Plan section of notes and tracked per patient; plus a separate workspace to-do list. See Task Manager.
  • Correspondence — one-click generation of patient letters from a note or from dictation, with interactive refinement. See Correspondence.
  • PDF Form Filling — draw fields on a PDF template (or auto-detect them with vision) and have the AI fill them from encounter data. See PDF Forms.
  • Agentic AI Assistant — chat with built-in tools (note/transcript/literature search, task management, form filling, and more), interleaved thinking, inline citations, and downloadable artifacts. See AI Features.
  • Knowledge Base — build a local, searchable corpus of reference literature (guidelines, journals) and have chat answer with inline citations. See Knowledge Base.
  • Agent Dashboard — a chat-driven hub for clinic management with a to-do panel, specialty-aware suggestions, and document upload. See Agent Dashboard.
  • MCP Server Support — connect external tool servers via the Model Context Protocol (SSE transport), with optional PHI filtering. See Settings → Tools.
  • Vision-Enhanced Document Processing — hybrid pipeline that uses vision models directly when available, falling back to text extraction and OCR.
  • 100% Local & Private — runs entirely on your machine; all data stays local. Optional local LLM (bundled llama.cpp), transcription (bundled parakeet.cpp), and embedding (bundled Qwen3-Embedding) servers.

Design​

  • Runs locally on standard hardware (GPU or Apple Silicon strongly recommended).
  • Customisable templates, prompts, and LLM settings.
  • Clinical data is encrypted at rest with SQLCipher (reference literature lives in a separate file — see Security).
  • Extensible via MCP server integration for custom tools and agentic workflows.

Philosophy​

The core idea is to use LLMs to automate administrative tasks by:

  • Surfacing relevant information from guidelines and journals
  • Automating documentation tasks
  • Organising and structuring clinical notes
  • Providing an agentic chat interface that can take actions on your behalf (search notes, manage tasks, create encounters, fill forms)

Important Caveats​

  • LLMs can hallucinate plausible but incorrect information.
  • Verification against primary medical sources is mandatory.
  • Clinical judgment remains supreme; Phlox is an administrative aid, not a clinical decision-support tool.
  • Models can misinterpret or omit important context.
  • External MCP servers and external tools (PubMed, Wikipedia) may receive PHI depending on configuration — use the sensitive-data filtering toggle. See Security.

This is an experimental administrative tool designed to assist with documentation and reference, not to provide clinical decision support.