Installation

macOS (Current Release)

Download the .dmg file from the download page. Open the disk image and drag ClinicalFlow into your Applications folder. On first launch, macOS may ask you to confirm you want to open an app from an identified developer — click Open.

Supported on macOS 11.0 (Big Sur) or later. Optimized for Apple Silicon (M1, M2, M3, M4).

Windows

Download the .exe installer from the download page. Run the installer and follow the setup wizard. ClinicalFlow installs to your user profile (no admin required) and creates a Start Menu shortcut.

Supported on Windows 10 (version 1903+) and Windows 11, x86_64.

Linux

Linux builds are in development. Sign up for notifications on the download page to be notified when Linux support becomes available.

First Launch & PIN Setup

When you open ClinicalFlow for the first time, you’ll be asked to create a numeric PIN (4–8 digits). This PIN encrypts all clinical data stored on your device using AES-256 encryption.

You’ll enter this PIN every time you open the app. ClinicalFlow never stores your PIN in plaintext — only an Argon2id cryptographic hash is saved for verification.

After creating your PIN, the Welcome Wizard guides you through initial setup.

Welcome Wizard

The Welcome Wizard runs once after PIN creation and walks you through a 5-screen setup flow:

After completing the wizard, it never appears again. The welcomeCompleted flag is saved in your configuration. To re-run the setup, delete your auth.json file (see Log Files for file locations).

Demo Mode

ClinicalFlow includes four built-in demo encounters to help you explore the app without a real patient visit. Each demo covers a different specialty to showcase the full range of templates and features.

Accessing Demo Mode

Triple-click the Help button (3 clicks within 400ms). A picker modal appears with four demo scenarios.

General Medical Visit (Animated)

A multi-problem internal medicine encounter with James Robinson (patient), Dr. Patel (physician), and Maria (medical assistant). Covers Type 2 diabetes, hypertension, peripheral neuropathy, and left knee osteoarthritis. The transcript plays back word-by-word with waveform animation (~24 entries).

Dental Examination (Instant)

A comprehensive dental encounter with Ms. Ramirez (patient) and Dr. Chen (dentist). Covers MOD caries, endodontic failure, impacted wisdom tooth, and a 4-phase treatment plan. The transcript loads instantly (15 entries), the dental chart auto-populates with findings, and the dental_general template is auto-selected.

Radiology Report (Instant)

A CT abdomen/pelvis with contrast demonstrating appendicitis findings. The transcript loads instantly and the radiology_diagnostic template is auto-selected, generating a structured radiology report with technique, findings, and impression sections.

Behavioral Health Session (Instant)

A psychiatry follow-up encounter covering panic disorder, medication adjustment, and CBT therapy progress. The transcript loads instantly and the DAP (Data, Assessment, Plan) template is auto-selected, showcasing behavioral health documentation with mental status exam and treatment planning.

Demo mode is a great way to test different note templates, dental charting, medical coding, and the verification system before using ClinicalFlow in a real encounter.

System Requirements

Online Mode (Minimum)

Offline Mode (Recommended)

Recording Basics

The record button is the large circular button at the bottom center of the app. Press it or hit Space to start recording. The button pulses red and a timer counts up in the header.

Controls

During Recording

• The timer in the header counts up (MM:SS format)
• The waveform visualizer animates at 60 FPS to show audio input level
• Transcript entries appear in real time in the left panel
• Each entry shows the speaker name, timestamp, and transcribed text
• The transcript auto-scrolls to the latest entry (can be toggled off in Settings)

Maximum Session Duration

Sessions are limited to 4 hours of continuous recording. When this limit is reached, recording stops automatically.

Crash Recovery

ClinicalFlow writes audio data to disk continuously during recording (flushing every ~10 seconds). If the app crashes mid-recording, your audio is preserved up to the last flush. On restart, ClinicalFlow recovers the session automatically.

Online Transcription (Deepgram)

Online mode uses Deepgram Nova-3 Medical, a cloud-based speech recognition model optimized for clinical encounters. It provides the highest accuracy and real-time speaker diarization.

Setup

1. Sign up at deepgram.com (free tier includes $200 of credit)
2. Create an API key in your Deepgram dashboard
3. Open ClinicalFlow Settings → Transcription → paste your API key → click Save

The connection indicator in the header will show Online — connected when the key is valid.

How It Works

Audio is captured from your microphone, encoded as 16-bit PCM at 16 kHz mono, and streamed to Deepgram over an encrypted WebSocket connection (WSS). Deepgram returns transcription results with word-level timestamps and speaker labels. A keepalive signal is sent every 8 seconds, and utterance boundaries are detected after 1,500ms of silence.

Keyterm Boosting

ClinicalFlow sends up to 100 medical terms to Deepgram as keyterm parameters, drawn from the corrections dictionary and medical dictionary. This improves recognition accuracy for clinical terminology.

Speaker Diarization

Deepgram automatically identifies different speakers in the audio stream. ClinicalFlow maps these speaker IDs to the speakers you’ve defined in the sidebar.

Offline Transcription (Whisper)

Offline mode uses a local Whisper large-v3-turbo model (574 MB, multilingual, quantized) running via a Metal GPU-accelerated whisper-server HTTP sidecar. No audio ever leaves your machine.

How It Works

Audio is captured in 2-second chunks with 0.3-second overlap. Each chunk is sent as a 16 kHz mono WAV to the local whisper-server via HTTP POST. The server stays alive between recordings (no cold start) and uses adaptive chunk sizing based on inference performance. Chunks below a 200 RMS silence threshold are skipped to avoid processing silence.

Model Details

Microphone Setup

ClinicalFlow uses your system’s default audio input device. Audio is captured at 16 kHz, 16-bit signed mono via the native audio stack (cpal on Rust).

For best results, use an external USB microphone positioned between you and the patient. Built-in laptop microphones work but capture more ambient noise.

On macOS, you’ll need to grant microphone permission on first launch: System Settings → Privacy & Security → Microphone → enable ClinicalFlow.

Languages (37)

ClinicalFlow supports 37 languages across the full pipeline: transcription, medical term corrections, note generation, and date formatting.

Correction Dictionaries

Medical term corrections are available for 6 languages, totaling 325+ patterns:

Languages without dedicated correction dictionaries use the base transcription engine output without post-processing.

Medical Term Corrections

Speech-to-text engines frequently garble medical terminology. ClinicalFlow applies a post-processing step after transcription that fixes common errors using 325+ regex patterns across 6 languages.

What Gets Corrected

Custom Dictionary

Corrections are loaded from language-specific JSON files in the app’s data directory (corrections.json for English, corrections-es.json for Spanish, etc.). You can edit these files to add corrections specific to your specialty:

[
  { "pattern": "\\bmetforming\\b", "flags": "gi", "replacement": "metformin" },
  { "pattern": "\\byour-custom-term\\b", "flags": "gi", "replacement": "CorrectTerm" }
]

ClinicalFlow reloads the corrections file on each app launch. Changes take effect on the next recording.

Hallucination Filtering

Whisper occasionally produces false positive text output from silence or background noise. ClinicalFlow filters these automatically before they reach the transcript.

What Gets Filtered

• Whisper meta-tags: [blank_audio], (silence), (blank audio), (no audio)
• Background sounds: (music), (laughter), (coughing), (breathing), (footsteps), and similar
• YouTube/social media artifacts: “subscribe”, “like and subscribe”, “thank you for watching” (training data leakage from Whisper)
• Generic filler: “thank you.”, “goodbye.”, “the end.”, single-word outputs
• Structural patterns: Fully parenthesized strings, repeated words/phrases, empty output

Medical Vocabulary Conditioning

ClinicalFlow conditions the Whisper model with a prompt containing 55+ medical terms to improve recognition of clinical terminology. This prompt is passed to whisper-server via the --prompt flag.

Term Categories

Speaker Management

The sidebar’s Speakers section lets you define who is in the encounter. Each speaker gets a name, a role, and a unique color that appears in the transcript.

Adding a Speaker

Click the + button in the Speakers section. Enter a name (e.g., “Dr. Martinez”) and select a role. ClinicalFlow automatically assigns a color.

Switching the Active Speaker

Click a speaker’s name in the sidebar to make them the active speaker. All subsequent transcript entries will be attributed to this speaker until you switch again or auto-detection switches for you.

Removing a Speaker

Click the × button next to a speaker’s name. Existing transcript entries from that speaker are preserved.

Roles & Colors

Each speaker can be assigned one of three roles. The role determines how the speaker’s words are categorized in the generated clinical note:

Each speaker has a unique color in the transcript, displayed as a left border on each entry for easy visual scanning.

Auto-Detection

When Auto-detect speakers is enabled (Settings → Recording), ClinicalFlow uses two methods to automatically switch speakers:

• Diarization data (online mode) — Deepgram provides speaker IDs with each transcript segment, and ClinicalFlow maps these to your defined speakers.
• Silence detection (both modes) — After 1.5 seconds of silence, ClinicalFlow may switch the active speaker. This works best in clear turn-taking conversations.

Auto-detection is not perfect. You can always manually click a speaker in the sidebar to correct it.

Cloud AI (Claude Haiku 4.5)

Cloud AI uses Anthropic’s Claude Haiku 4.5 (claude-haiku-4-5-20251001) to generate clinical notes. It provides the highest quality output with the most natural clinical language.

Setup

1. Sign up at console.anthropic.com
2. Create an API key (starts with sk-ant-)
3. Open ClinicalFlow Settings → AI Note Generation → select Cloud AI
4. Paste your API key and click Save
5. Click Test to verify the connection

Technical Details

Cost

A full online encounter (Deepgram transcription + Claude note generation with verification) costs approximately $0.10–$0.15 per encounter for a 15-minute visit. This is separate from your ClinicalFlow subscription — you pay Deepgram and Anthropic directly through your own API keys.

How It Works

When you click Generate Note (or press G), ClinicalFlow sends the full transcript to Claude along with a detailed clinical prompt that specifies the note template, evidence-extraction rules, safety constraints, and output structure. Claude’s response streams back in real time — you see the note being written section by section.

Ollama (Local AI)

Ollama runs AI models entirely on your local machine. No data leaves your computer. It’s free, open-source, and supports dozens of models.

Installation — macOS

1. Go to ollama.com/download/mac and download the installer.
2. Open the downloaded .dmg file and drag Ollama to your Applications folder.
3. Launch Ollama from Applications. You’ll see a small llama icon appear in your menu bar — this means Ollama is running in the background.
4. Open Terminal (search “Terminal” in Spotlight) and run:
   ollama pull llama3.1:8b
   This downloads the recommended model (~4.7 GB). Wait for it to complete.
5. Verify it worked by running: ollama list — you should see llama3.1:8b in the list.
6. Open ClinicalFlow → Settings → AI Note Generation → select Ollama.
7. Click Test to verify the connection, then Refresh to load your models.

Installation — Windows

1. Go to ollama.com/download/windows and download the installer.
2. Run OllamaSetup.exe and follow the prompts. Ollama will start automatically and appear in your system tray.
3. Open Command Prompt or PowerShell (search “cmd” in Start) and run:
   ollama pull llama3.1:8b
   This downloads the recommended model (~4.7 GB). Wait for it to complete.
4. Verify it worked by running: ollama list — you should see llama3.1:8b in the list.
5. Open ClinicalFlow → Settings → AI Note Generation → select Ollama.
6. Click Test to verify the connection, then Refresh to load your models.

Recommended Models

For most clinical use, llama3.1:8b provides the best balance of quality and speed. It runs well on machines with 8 GB of RAM.

Making Ollama Start Automatically

macOS: Ollama starts automatically on login by default. If it doesn’t, open Ollama from Applications and check “Start at login” in the menu bar icon preferences.

Windows: Ollama runs as a background service and starts automatically after installation. If it’s not running, search for “Ollama” in the Start menu and launch it.

Configuration

Default server URL: http://localhost:11434. ClinicalFlow includes 3 automatic retries for transient failures. You can change the URL in Settings if you run Ollama on a different machine or port.

Rule-Based Fallback

If both Cloud AI and Ollama are unavailable, ClinicalFlow falls back to a rule-based note generator. This deterministic system extracts information using pattern matching: vital sign patterns, medication mentions, symptom descriptions, and exam findings.

Rule-based notes are less polished than AI-generated ones but provide a reliable baseline that captures key data points. Select it explicitly in Settings → AI Note Generation → Rule-Based.

Two-Pass Verification

ClinicalFlow’s verification system runs a second AI pass after generating a note. This auditor checks every claim against the original transcript.

The verification pass runs at temperature 0.1 for maximum precision. Toggle in Settings → AI Note Generation → Verification pass.

Clinical Prompt System

ClinicalFlow uses a carefully engineered prompt to guide AI note generation. The prompt includes:

• Template specification — Exact section headers and structure for the selected template (from all 22 built-in templates)
• Evidence-extraction rules — Every line must trace back to something explicitly stated in the transcript
• Omission logic — If a system or exam component was not discussed, it is omitted (not listed as “not assessed”)
• Pertinent negatives — Only negatives the patient explicitly denied are included
• Medication categorization — Separates new prescriptions, continued medications, and dosage changes
• Multilingual output — For non-English languages, an OUTPUT LANGUAGE directive generates clinical content in the target language while keeping section headers in English for the note parser
• Dental chart integration — When a dental template is selected, dental chart findings are serialized into the prompt
• Medical/dental coding — When auto-coding is enabled, a separate coding prompt generates ICD-10, CPT, E&M, or CDT codes from the note content

Template Overview

ClinicalFlow includes 22 built-in note templates across 6 categories, plus the ability to create custom templates. Select a template from the dropdown (#formatSelector) in the sidebar, or change your default in Settings.

General Templates (3)

Behavioral Health Templates (2)

Specialty Templates (10)

Radiology Templates (2)

Dental Templates (5)

Dental templates automatically enable the interactive dental chart in the sidebar.

Custom Templates

Click + Custom Template in the template dropdown to create your own. Provide a name, define section names, and optionally write a custom AI prompt. Custom templates are stored in the ms-custom-templates config key as a JSON array.

Interactive Dental Chart

When any dental template is selected, a Dental Chart section appears in the sidebar with an “Edit Chart” button. Clicking opens a full-screen SVG dental chart modal.

The chart supports both 32-tooth adult (permanent) and 20-tooth primary (deciduous) dentition with a toggle switch. Teeth use ADA Universal numbering: adult teeth 1–32, primary teeth A–T.

Tooth States (8)

Click any tooth to open a two-tier popup. Select from 8 color-coded clinical states:

Surface Marking

For states that affect specific surfaces (decay, restored, fracture), a second tier of surface buttons appears after selecting the state:

Anatomical validation prevents impossible surface combinations. Click outside the popup to save your selection.

AI Integration

Dental chart findings are automatically serialized into the AI prompt during note generation. The format includes dentition type, tooth number, state, and affected surfaces.

Response Parsing

When the AI generates a note mentioning dental findings, ClinicalFlow can parse findings back to the chart. Acronym protection prevents false surface detection for 18 common dental abbreviations: FPD, RPD, ZOE, FGC, PFM, MTA, SDF, BOP, CAL, TMD, TMJ, GBI, OHI, DI, CI, CEJ, PDL, and IPR.

Export

The dental chart SVG and findings table are included in PDF and text exports when enabled in Settings (ms-settings-dentalChartInExport and ms-settings-dentalFindingsInExport).

Periodontal Charting Overview

ClinicalFlow includes a full periodontal charting mode that overlays on the dental chart. When a dental template is active, a “Perio Mode” toggle appears in the dental chart modal. Enabling perio mode transforms the chart into a 6-point probing depth entry system.

Accessing Perio Mode

• Select any dental template (General Dental, Periodontal Exam, etc.)
• Open the dental chart modal via Edit Chart
• Toggle the Perio Mode switch at the top of the chart

What Perio Mode Adds

• 6-point probing depths per tooth (MB, B, DB, ML, L, DL)
• Bleeding on probing (BOP) markers per site
• Recession measurements per site
• Mobility grades (I, II, III) per tooth
• Furcation involvement grades (I, II, III) for multi-rooted teeth
• Clinical attachment level (CAL) auto-calculated from probing depth + recession

All perio data is serialized into the AI prompt during note generation and included in PDF/text exports.

Voice-Driven Entry

Probing depths and perio findings can be entered by voice during a live recording. The perio voice parser recognizes natural dictation patterns and maps them to specific teeth and sites.

Supported Voice Commands

Voice-entered data populates the perio chart in real time. You can also click individual sites on the chart to enter or correct values manually.

Measurements & Data Points

Each tooth in perio mode tracks the following data points:

Color Coding

Probing depths are color-coded for quick visual assessment:

Documentation Completeness Scoring

ClinicalFlow automatically calculates a documentation completeness score for each perio charting session. This helps ensure thorough documentation before generating notes or exporting.

How Scoring Works

The score is a percentage (0–100%) based on the ratio of documented data points to expected data points for the teeth present in the chart. Missing teeth are excluded from the calculation.

Score Display

The completeness score appears as a badge in the perio chart header. Scores below 80% display a warning suggesting the provider complete additional measurements before generating the note.

Automatic Billing Codes

ClinicalFlow automatically generates billing codes from the generated note content when auto-coding is enabled (ms-settings-autoCoding). Codes appear in a read-only panel (#codingPanel) below the note sections with colored confidence badges.

Confidence Levels

Codes are read-only with a copy-to-clipboard option. No direct editing of suggested codes in the UI.

Medical Coding (ICD-10 + CPT)

For medical (non-dental) templates, ClinicalFlow generates:

• Up to 8 ICD-10-CM diagnosis codes with confidence levels
• Up to 4 CPT procedure codes with confidence levels
• E&M level assessment (Level 1–5) based on number of problems addressed, data complexity, and risk of morbidity/mortality

The system uses only real, valid ICD-10-CM and CPT codes.

Dental Coding (CDT + Dental ICD-10)

For dental templates, ClinicalFlow generates CDT D-codes and dental-specific ICD-10 codes. The dental coding engine enforces 4 strict guardrails:

1. Strict Domain Gate

Only CDT D-codes and dental ICD-10 codes are allowed. CPT codes (00100–99499), E&M levels, and non-dental codes are strictly forbidden. Every procedure code must begin with “D”.

2. Depth & Severity Escalator

Never defaults to the shallowest/generic code. If “approaching pulp” or “deep caries” is documented, codes escalate to K04.0/K04.1 rather than K02.51. If “bone loss” or “deep pockets >5mm” is documented, periodontal codes escalate from K05.10 to K05.311+.

3. Structural vs. Positional Trauma

Every injury is classified into exactly one track:

• Track A (structural failure): cracked/fractured → K03.81, S02.5XXA, D2740, D7140
• Track B (positional displacement): loosened/luxated → S03.2XXA, M26.30, D7270, D4921

Codes from both tracks are never assigned to the same tooth.

4. Etiology of Absence

For every missing tooth, the reason is determined. Default is acquired (K08.111–K08.409) unless the transcript explicitly states “congenitally absent”, “agenesis”, or “hypodontia” → then congenital (K00.0).

Audit Flags

After billing codes are generated, ClinicalFlow runs an audit pass that checks for common documentation and coding issues. Audit flags appear as collapsible alerts below the coding panel.

What the Audit Checks

Interacting with Flags

Each flag is collapsible — click to expand for details and the specific code(s) involved. Flags are informational only and do not modify the suggested codes. They help providers review and correct coding before submission.

Clinical Warnings

Separate from audit flags, ClinicalFlow generates clinical warnings when the note content suggests potential safety or quality concerns. Warnings appear as highlighted alerts in the coding panel.

Warning Categories

Inline Editing

After note generation, each section is editable directly in the note panel. Every line has inline controls that appear on hover:

• Move up/down — reorder lines within a section
• Add line — insert a new blank line below
• Delete line — remove the line with a smooth animation
• Drag handle — drag and drop lines within or across sections (e.g., move a line from Subjective to Objective)
• Line dictation mic — dictate directly into any line (see Line Dictation)
• Edit button — toggle full-section editing mode for bulk changes

Click on any line’s text to edit it directly. All edits are saved to the active session automatically.

Note Line Editing Toggle

All inline editing controls — move up/down, add line, delete line, drag reorder, and line dictation mic — are bundled under a single Note Line Editing toggle in Settings → Advanced → Notes. This toggle is on by default. Turning it off hides all line-level controls for a cleaner read-only view of your notes.

Line Dictation

Dictate directly into any line of the generated note using Deepgram’s real-time streaming. This is enabled by default and can be toggled in Settings → Note Output → Line Dictation.

How to use

1. Click the microphone icon on any line to start dictating
2. Click anywhere in a line to position where text will be inserted
3. While dictating, click a different position or line to move the insertion point on the fly
4. Highlight a word or phrase, then speak to replace the selection
5. Click the microphone icon again to stop

Spoken punctuation

Say punctuation names out loud and they’ll be converted to symbols:

• “period” → .   “comma” → ,   “question mark” → ?
• “colon” → :   “semicolon” → ;   “hyphen” → -
• “open parenthesis” / “close parenthesis” → ( )

Text is lowercase by default and auto-capitalized at the start of sentences. The same medical dictionary used during transcription is applied for accurate clinical terminology.

Note: Line dictation requires an active recording to be stopped first — it cannot run simultaneously with a patient recording session.

Dictionary-Powered Features

ClinicalFlow includes a suite of dictionary-driven tools that enrich your generated notes with contextual information. All dictionary features are individually toggleable in Settings → Advanced → Notes.

Abbreviation Expansion Tooltips

Hover over abbreviated medical terms in a generated note to see their full expansion in a tooltip. Common abbreviations like “BID,” “PRN,” “HTN,” and “BMP” are recognized and explained on hover.

Medication Cross-Reference Tooltips

Hover over a medication name to see a tooltip with generic/brand name mapping, drug class, and related information. Works for both brand and generic names.

Scoring System Quick-Reference Tooltips

When clinical scoring systems appear in notes (e.g., PHQ-9, GAD-7, NIHSS, GCS), hover over the reference to see a quick-reference tooltip with score ranges and interpretation.

Dental Tooth Number Labels

In dental notes, tooth number references like “#14” or “#30” display blue badge tooltips showing the tooth name and location (e.g., “#14 — Upper Left First Premolar”).

Quick-Insert Phrase Palette (Ctrl+J)

Press Ctrl+J while editing a note to open a template-aware phrase palette. The palette presents commonly used phrases appropriate for the current note template — for example, SOAP-specific phrases when editing a SOAP note, or dental-specific phrases when working with a dental template. Click a phrase to insert it at the cursor position.

Note Autocomplete

While editing a note line, type 3 or more characters to trigger medical term suggestions. An autocomplete dropdown appears with matching terms from the medical dictionary. Select a suggestion to insert the complete term.

Enhanced ASR Corrections

The automatic speech recognition post-processor now includes 325+ correction patterns (up from 204), providing broader coverage of misrecognized drug names, conditions, procedures, and medical terminology across 6 languages.

PDF Export

Press E or click the Export PDF button. ClinicalFlow uses the headless_chrome Rust crate (Chromium DevTools Protocol) to generate a professional PDF with header, formatted sections, disclaimer footer, and optional dental chart.

PDFs are saved to the app’s exports directory with the filename ClinicalFlow_Note_YYYY-MM-DD_HH-MM.pdf.

Text Export

Press T to download the transcript as a plain text file. A native save dialog lets you choose the location. The default filename is ClinicalFlow_Transcript_YYYY-MM-DD.txt.

Copy to Clipboard

Click the Copy button in the note panel header to copy the entire note as plain text. Paste it directly into your EHR (Epic, Cerner, Athena, or any system that accepts text input).

Export Actions

ClinicalFlow provides configurable export actions that appear in the note panel toolbar after note generation. You can enable or disable individual actions to streamline your workflow.

Available Actions

PDF, Copy, and Download Transcript are always visible. The remaining actions (Copy for EHR, Export HL7, Insurance Narrative, Sync to PMS) are toggleable in Settings → Advanced → Export Actions, and hidden from the toolbar when disabled.

Session Archiving

When you click New Session (or press N), ClinicalFlow archives the current encounter. The archive includes the full transcript, generated note, audio recording, dental chart data, coding results, and all session metadata.

Archives are named YYYY-MM-DD_HH-MM_PatientName, encrypted with AES-256-GCM, and sorted newest-first in the archive browser. Audio is stored as a separate unencrypted WAV file.

The Past Sessions archive browser is accessible from the sidebar. It displays all archived encounters with date, patient name, and template used. Click any session to restore its transcript, note, dental chart, and coding data.

EHR Integration

ClinicalFlow can export clinical notes to Electronic Health Record systems using the HL7 v2 messaging standard. This allows direct transmission of generated notes into your EHR without manual copy-paste.

Setup

Configure EHR integration in Settings → Advanced → EHR Integration:

How It Works

• After note generation, click Send to EHR in the export toolbar
• ClinicalFlow packages the note into an HL7 v2 ORU^R01 message
• The message includes patient identifiers, note sections, coding data, and dental findings
• The HL7 message is sent to the configured endpoint

PMS Bridge

The Practice Management System (PMS) Bridge connects ClinicalFlow to your dental or medical practice management software for bidirectional data exchange.

Supported Systems

Configuration

Configure PMS Bridge in Settings → Advanced → PMS Bridge:

Use the Test Connection button to verify connectivity before saving. A successful test confirms ClinicalFlow can reach the PMS database.

Insurance Narrative Generation

ClinicalFlow can generate insurance-ready narratives from the clinical note and billing codes. These narratives are formatted for insurance claim submissions and pre-authorization requests.

What the Narrative Includes

• Clinical justification — summarizes the patient’s condition and why the treatment is medically/dentally necessary
• Supporting documentation — references specific findings from the examination
• Procedure rationale — links each procedure code to the clinical indication
• Diagnosis correlation — maps ICD-10 or dental ICD-10 codes to the documented findings

Generating a Narrative

After note generation with coding enabled, click Generate Narrative in the export toolbar. The AI processes the note content, billing codes, and dental chart data to produce a cohesive narrative. The narrative can be copied to clipboard or exported as part of the PDF.

General & Advanced Tabs

The Settings drawer is organized into two tabs accessible via a segmented control at the top:

Click a tab to switch views. Your selected tab is remembered for the duration of the session.

Appearance

Transcription Settings

AI Engine Settings

Notes Settings

Found in Settings → Advanced tab → Notes card.

Recording Settings

Found in Settings → Advanced tab → Recording card.

Dental Settings

Found in Settings → Advanced tab → Dental card.

EHR Integration Settings

Found in Settings → Advanced tab → EHR Integration card.

PMS Bridge Settings

Found in Settings → Advanced tab → PMS Bridge card.

Language Settings

Found in Settings → Advanced tab → Language card.

Security Settings

Keyboard Shortcuts

Encryption at Rest

ClinicalFlow encrypts all files containing protected health information using AES-256-GCM with keys derived from your PIN via PBKDF2-HMAC-SHA256 (100,000 iterations).

What Is Encrypted

Each encrypted file has a unique random salt (16 bytes) and nonce (12 bytes) prepended to the ciphertext. Total overhead: 28 bytes per file. Writes are atomic (write to .tmp, then rename) to prevent corruption.

PIN & Lock Screen

The PIN serves two purposes: authentication (proving you’re authorized) and key derivation (your PIN is the cryptographic key that unlocks encrypted files).

• PIN is verified using Argon2id hashing (memory-hard, resistant to brute force)
• Only the hash is stored (in auth.json), never the PIN itself
• PIN length: 4–8 numeric digits
• No lockout after failed attempts — the encryption itself is the protection
• Auto-lock default: 5 minutes of inactivity (60 seconds when page is hidden)
• Auto-lock is deferred during active recording to prevent data loss

Network Requests

HIPAA Considerations

ClinicalFlow implements HIPAA technical safeguards: encryption at rest (AES-256-GCM), unique user authentication (PIN), automatic logoff (auto-lock), audit logging (sanitized, no PHI), transmission security (TLS for all network requests), Content Security Policy headers, and localhost-only Whisper binding.

For full HIPAA compliance, your organization also needs Business Associate Agreements (BAAs) with Deepgram and Anthropic if using online features, plus organizational policies covering training, incident response, and access management.

Data Handling Summary

Plans & Billing

ClinicalFlow uses Supabase for authentication and Stripe for payment processing.

Subscription States

Manage your subscription through the in-app billing portal, which opens Stripe’s management interface.

Microphone Issues

“No microphone found”

Ensure a microphone is connected. Check System Settings → Sound to confirm it’s recognized. Try unplugging and replugging USB microphones.

“Microphone access denied”

macOS: System Settings → Privacy & Security → Microphone → enable ClinicalFlow.

Transcription Issues

Poor transcription accuracy

• Use an external USB microphone instead of built-in laptop mic
• Reduce ambient noise (fans, HVAC, other conversations)
• Speak clearly and at a normal pace
• Check that the correct language is selected in Settings

Deepgram connection failed

• Verify your API key in Settings
• Check your internet connection
• Check status.deepgram.com for outages
• Switch to offline mode as a workaround

Ollama Issues

“Ollama not connected”

• Make sure Ollama is running: ollama list in Terminal
• If not installed, download from ollama.com
• Check the server URL in Settings (default: http://localhost:11434)

Out of memory

Switch to a smaller model (e.g., llama3.1:8b instead of llama3.1:70b) or use Cloud AI.

Note Generation Issues

Note seems incomplete or inaccurate

• Ensure the transcript is complete before generating
• Enable the verification pass to catch omissions
• Check that speakers are correctly labeled
• Try a different template that better matches the encounter type

Cancel a stuck generation

The Generate button becomes a Cancel button during generation. Click it to abort. ClinicalFlow uses an AbortController to cleanly cancel API calls. Timeout is 120 seconds.

Export Issues

PDF export shows blank page

Try exporting again. If the issue persists, use Copy to Clipboard as an alternative.

Save dialog doesn’t appear

Check that ClinicalFlow has file access permissions in System Settings → Privacy & Security → Files and Folders.

Crashes & Recovery

App crashed during recording

Your audio is safe. ClinicalFlow writes to disk every ~10 seconds. On restart, the session is recovered automatically.

App crashed during note generation

The transcript is preserved. Regenerate the note from the saved transcript after restart.

Low memory warning

ClinicalFlow monitors available system memory. Warnings appear at <2 GB free. Close other applications or switch to a smaller model.

Log Files

ClinicalFlow writes structured logs for debugging. Logs never contain patient data.

File Locations

Log files are named clinicalflow-YYYY-MM-DD.log, rotated daily, and auto-cleaned after 30 days.

System Architecture

ClinicalFlow is a desktop application built with Tauri v2. The frontend is vanilla HTML/CSS/JavaScript (21 modules) running in a native webview. The backend is Rust (9 modules), handling audio capture, file encryption, PDF export, PMS integration, and system integration. No JavaScript frameworks are used.

Component Overview

┌─────────────────────────────────────────────────────┐
│                   Tauri Webview                      │
│                                                     │
│  ┌──────────────┐  ┌──────────────┐  ┌───────────┐ │
│  │ Transcript   │  │ Note Panel   │  │ Sidebar   │ │
│  │ Panel        │  │ (editable)   │  │           │ │
│  │              │  │              │  │ Speakers  │ │
│  │ Real-time    │  │ 22 templates │  │ Templates │ │
│  │ entries      │  │ Dental chart │  │ Settings  │ │
│  │ 1,300+ terms │  │ Coding panel │  │ Archive   │ │
│  └──────────────┘  └──────────────┘  └───────────┘ │
│                                                     │
│  21 JS modules — UI, prompts, templates, dental,   │
│  notes, coding, subscription, audio, settings       │
└─────────────────────┬───────────────────────────────┘
                      │  invoke() / listen()
                      │  (26 Tauri IPC commands)
┌─────────────────────┴───────────────────────────────┐
│                  Rust Backend                        │
│                                                     │
│  audio.rs     — cpal capture, whisper-server,       │
│                  hallucination filter, vocab prompt  │
│  storage.rs   — Encrypted sessions, config,         │
│                  archives, logging                   │
│  pdf.rs       — PDF export (headless_chrome)        │
│  pms.rs       — PMS Bridge (Dentrix/Eaglesoft/OD)   │
│  crypto.rs    — AES-256-GCM, PBKDF2 key derivation │
│  auth.rs      — Argon2id PIN, auto-lock, AppState   │
│  license.rs   — License validation, subscription    │
│  logging.rs   — Tracing, daily rotation             │
│  lib.rs       — App setup, command registration     │
└─────────────────────┬───────────────────────────────┘
                      │
          ┌───────────┼───────────┐
          ▼           ▼           ▼
┌──────────────┐ ┌───────────────┐ ┌──────────────────┐
│whisper-server│ │headless_chrome│ │  Local Storage    │
│ (3.44 GB)    │ │ Rust crate    │ │                  │
│              │ │ Chromium      │ │ auth.json        │
│ ggml-small   │ │ DevTools      │ │ config.json  🔒  │
│ 574 MB model │ │ Protocol      │ │ active.json  🔒  │
│ HTTP sidecar │ │ PDF gen       │ │ archive/*.json🔒 │
│ 127.0.0.1    │ │               │ │ archive/*.wav    │
└──────────────┘ └───────────────┘ │ logs/*.log       │
                                   └──────────────────┘

External Services (online mode only):
┌───────────────┐ ┌───────────────┐ ┌──────────────┐
│ Deepgram API  │ │ Anthropic API │ │ Supabase     │
│ WSS streaming │ │ HTTPS (Claude)│ │ Auth + Stripe│
└───────────────┘ └───────────────┘ └──────────────┘

┌───────────────┐
│ Ollama        │
│ localhost     │
│ :11434        │
└───────────────┘

🔒 = AES-256-GCM encrypted with PIN-derived key

Data Formats

File Storage Structure

~/Library/Application Support/com.clinicalflow.ai/
├── auth.json                      PIN hash + welcome flag
├── config.json                    [ENCRYPTED] Settings & API keys
├── sessions/
│   ├── active.json               [ENCRYPTED] Current session
│   └── archive/
│       ├── 2026-02-23_18-45_PatientName.json  [ENCRYPTED]
│       └── 2026-02-23_18-45_PatientName.wav   Audio recording
├── exports/
│   ├── ClinicalFlow_Note_2026-02-23.pdf
│   └── ClinicalFlow_Transcript_2026-02-23.txt
└── logs/
    └── clinicalflow-2026-02-23.log

All session data is stored as JSON files (no database). Sessions include entries, speakers, note sections, dental chart state, and coding results.

How ClinicalFlow Compares

An honest comparison of where ClinicalFlow fits relative to other AI clinical documentation tools.

ClinicalFlow’s Strengths

• Offline mode. Most AI scribes are cloud-only. ClinicalFlow runs with zero internet.
• 22 specialty templates + dental & perio charting. Covers general, behavioral health, 10 specialties, 2 radiology templates, 5 dental templates, full periodontal charting, and custom templates.
• Automatic billing codes with audit flags. ICD-10, CPT, E&M, and CDT coding with audit flags and clinical warnings.
• EHR & PMS integrations. HL7 v2 export to EHR systems, PMS Bridge for Dentrix/Eaglesoft/Open Dental, and insurance narrative generation.
• Transparent pricing. $25/month with 14-day free trial. Cloud API costs separate and pay-as-you-go.
• Data stays local. In offline mode, nothing leaves your machine. No ClinicalFlow servers.
• Open architecture. Bring your own API keys, choose your AI models.
• Encryption at rest. PIN-based AES-256 encryption is not standard in most scribe tools.

Where Others May Have an Advantage

• Deep EHR integration. Products like Nuance DAX, Abridge, and Suki offer embedded EHR integration. ClinicalFlow supports HL7 v2 export but does not embed directly inside EHR interfaces.
• Ambient listening. Some products run continuously without pressing a button. ClinicalFlow requires explicit start/stop.
• Multi-user and team features. Enterprise products offer multi-provider support, shared templates, and admin dashboards. ClinicalFlow is single-user.
• Mobile apps. Some competitors have iOS/Android apps. ClinicalFlow is a desktop application (macOS and Windows).
• Cross-platform. ClinicalFlow runs on macOS (Apple Silicon) and Windows. Linux is planned.

Summary Table

Version History

v1.0.0 — Initial Release

February 2026

• Dual-mode transcription: Deepgram Nova-3 Medical (online) and Whisper large-v3-turbo (offline, Metal GPU-accelerated, 574 MB)
• AI note generation: Claude Haiku 4.5 (cloud), Ollama (local), and rule-based fallback
• 22 built-in note templates across 6 categories (General, Behavioral Health, Specialty, Radiology, Dental, Preventive) plus custom templates
• Two-pass verification system for hallucination, contradiction, and omission detection
• Interactive dental chart: 32-tooth adult + 20-tooth primary, 8 states, 5-surface marking
• Periodontal charting: 6-point probing depths, BOP, recession, mobility, furcation, voice-driven entry
• Documentation completeness scoring for perio charting sessions
• Medical coding: ICD-10 (up to 8), CPT (up to 4), E&M level assessment
• Dental coding: CDT D-codes + dental ICD-10 with 4 guardrails
• Audit flags and clinical warnings for coding review
• Multi-speaker management with 3 roles (Physician, Patient, Other) and 1.5s silence detection
• Medical term post-processor with 325+ correction patterns across 6 languages
• Whisper hallucination filtering and medical vocabulary conditioning (55+ terms)
• PIN-based authentication with AES-256-GCM encryption at rest (PBKDF2 100k iterations, Argon2id)
• Auto-lock after configurable inactivity (default: 5 minutes)
• EHR integration via HL7 v2 export
• PMS Bridge for Dentrix, Eaglesoft, and Open Dental
• Insurance narrative generation from notes and billing codes
• PDF export (headless_chrome Rust crate, Chromium DevTools Protocol), text export, clipboard copy, configurable export actions
• Session archiving with transcript, note, audio, dental chart, and coding data
• Continuous WAV save (~10s intervals) for crash recovery
• Structured logging with PHI sanitization (30-day retention)
• Settings drawer with General/Advanced tabs — General: Account, Appearance, AI & Transcription; Advanced: Notes, Recording, Export Actions, Dental, EHR Integration, PMS Bridge, Language, Security
• Dark and light themes
• 37-language support (full pipeline: transcription + corrections + notes + UI)
• 1,300+ medical term highlighting in transcript
• Welcome wizard (5-screen setup) and 4 demo scenarios (medical, dental, radiology, behavioral health)
• Dictionary-powered features: abbreviation tooltips, medication cross-reference, scoring quick-reference, dental tooth labels, quick-insert palette (Ctrl+J), note autocomplete
• Note line editing toggle (Settings → Advanced → Notes) combining move, add, delete, drag, and dictation controls
• Subscription/licensing via Supabase + Stripe (14-day trial)
• 12 keyboard shortcuts
• Built with Tauri v2 for macOS (Apple Silicon) and Windows