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Install and run

Choose the path that matches how you intend to use MedDeID:

Goal Start here
De-identify a note or a batch of files Run MedDeID locally
Add de-identification to a Python application Use the Python API
Explore the browser interface or HTTP API Try MedDeID in your browser
Operate a shared institutional service Production deployment

Training, evaluation, and annotation tools are separate workflows linked at the end of this page.

Run MedDeID locally

This is the shortest path for individual notes, scripts, and batches. It requires Python 3.10 or newer but does not require writing Python code.

Install

python3 -m venv .venv
source .venv/bin/activate
python -m pip install meddeid
meddeid models

meddeid models lists the available models and their validation scope. Select one explicitly with --model; it is downloaded once and used locally.

Choose Dutch or English

meddeid deidentify note.txt \
  --model stighellemans/meddeid-dutch-synth

meddeid deidentify note.txt \
  --model stighellemans/meddeid-english-synth \
  --language-profile en-GB  # Use en-US for US formats

The current public Dutch model declares nl-BE; the English model supports en-GB and en-US.

Use the Python API

from meddeid import Deidentifier

deidentifier = Deidentifier.from_pretrained(
    "stighellemans/meddeid-dutch-synth"
)
result = deidentifier("Patiënt Alex Voorbeeld kwam op controle.")

print(result.deid_text)
print(result.spans)
deidentifier.close()

Process a batch of notes

meddeid batch documents.jsonl \
  --output predictions.jsonl \
  --model stighellemans/meddeid-dutch-synth

The batch command keeps document order and records how the results were produced.

Try MedDeID in your browser

Install and start Docker Desktop. Clone MedDeID once:

git clone https://github.com/stighellemans/meddeid.git
cd meddeid

Choose the language you want to test:

./scripts/start-local.sh \
  --model stighellemans/meddeid-dutch-synth \
  --language-profile nl-BE

./scripts/start-local.sh \
  --model stighellemans/meddeid-english-synth \
  --language-profile en-GB

When MedDeID is ready, the browser opens with the API key already filled in. Paste a note and select De-identify. The English model also lets you switch between en-GB and en-US in the browser.

API documentation is available at http://127.0.0.1:8000/docs.

Stop the service with ./scripts/stop-local.sh.

Developers testing source changes can add --build. For a shared service, see production deployment.

Reproducible or offline runs

Inspect and record the exact model version when results must be reproducible:

meddeid model-info --model stighellemans/meddeid-dutch-synth

To stage and manage a model bundle yourself, pass its local directory with --model. The local inference guide covers revision pinning, complete local bundles, and air-gapped environments.

Next steps