mede 0.0.7
De-Identification of Medical Imaging Data: A Comprehensive Tool for Ensuring Patient Privacy
Requires Python: >=3.9

# De-Identification of Medical Imaging Data: A Comprehensive Tool for Ensuring Patient Privacy

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[Getting started](#getting-started) • [Usage](#usage) • [Citation](#citation)

</div>

> [!IMPORTANT]  
> The package is now available on PyPI: `pip install mede`

> [!NOTE]
> MEDE now supports the _Enhanced DICOM_ format!


This repository contains the **De-Identification of Medical Imaging Data: A Comprehensive Tool for Ensuring Patient Privacy**, which enables the user to anonymize a wide variety of medical imaging types, including Magnetic Resonance Imaging (MRI), Computer Tomography (CT), Ultrasound (US), Whole Slide Images (WSI) or MRI raw data (twix).

<div align="center">

<img src="Figures/aam_pipeline.png" alt="Overview" width="300"/>

</div>


This tool combines multiple anonymization steps, including metadata deidentification, defacing and skull-stripping while being faster than current state-of-the-art deidentification tools.

![Computationtimes](Figures/computation_times.png)

## Getting started

You can install the anonymization tool directly via pip or Docker. 

### Installation via pip

Our tool is available via pip. You can install it with the following command:
```
pip install mede
```

#### Additional dependencies for text removal
If you want to use the text removal feature, you also need to install Google's Tesseract OCR engine. You can find the installation instructions for your operating system [here](https://tesseract-ocr.github.io/tessdoc/Installation.html).
On Ubuntu, you can install it via 
```bash
sudo apt install tesseract-ocr
sudo apt install libtesseract-dev
```
On MacOS, you can install it via Homebrew:
```bash
brew install tesseract
```

### Installation via Docker
Alternatively this tool is distributed via docker. You can find the docker images [here](https://hub.docker.com/repository/docker/morrempe/mede/). The docker image is available for Linux-based (including Mac) amd64 and arm64 platforms.

For the installation and execution of the docker image, you must have [Docker](https://docs.docker.com/get-docker/) installed on your system.

1. Pull the docker image

       docker pull morrempe/mede:[tag]   (either arm64 or amd64)

2. Run the docker container with attached volume. Your data will be mounted in the ````data```` folder:

       docker run --rm -it -v [Path/to/your/data]:/data morrempe/mede:[tag]

3. Run the script with the corresponding cli parameter, e.g.:

       mede-deidentify [your flags]

## Usage
**De-Identification CLI**
```
usage: mede-deidentify [-h] [-v | --verbose | --no-verbose] [-t | --text-removal | --no-text-removal] [-i INPUT]
                                    [-o OUTPUT] [--gpu GPU] [-s | --skull_strip | --no-skull_strip] [-de | --deface | --no-deface]
                                    [-tw | --twix | --no-twix] [-p PROCESSES]
                                    [-d {basicProfile,cleanDescOpt,cleanGraphOpt,cleanStructContOpt,rtnDevIdOpt,rtnInstIdOpt,rtnLongFullDatesOpt,rtnLongModifDatesOpt,rtnPatCharsOpt,rtnSafePrivOpt,rtnUIDsOpt} [{basicProfile,cleanDescOpt,cleanGraphOpt,cleanStructContOpt,rtnDevIdOpt,rtnInstIdOpt,rtnLongFullDatesOpt,rtnLongModifDatesOpt,rtnPatCharsOpt,rtnSafePrivOpt,rtnUIDsOpt} ...]]

options:
  -h, --help            show this help message and exit
  -v, --verbose, --no-verbose
  -t, --text-removal, --no-text-removal
  -i INPUT, --input INPUT
                        Path to the input data.
  -o OUTPUT, --output OUTPUT
                        Path to save the output data.
  --gpu GPU             GPU device number. (default 0)
  -s, --skull_strip, --no-skull_strip
  -de, --deface, --no-deface
  -tw, --twix, --no-twix
  -w, --wsi, --no-wsi
  -p PROCESSES, --processes PROCESSES
                        Number of processes to use for multiprocessing.
  -d {basicProfile,cleanDescOpt,cleanGraphOpt,cleanStructContOpt,rtnDevIdOpt,rtnInstIdOpt,rtnLongFullDatesOpt,rtnLongModifDatesOpt,rtnPatCharsOpt,rtnSafePrivOpt,rtnUIDsOpt} [{basicProfile,cleanDescOpt,cleanGraphOpt,cleanStructContOpt,rtnDevIdOpt,rtnInstIdOpt,rtnLongFullDatesOpt,rtnLongModifDatesOpt,rtnPatCharsOpt,rtnSafePrivOpt,rtnUIDsOpt} ...], --deidentification-profile {basicProfile,cleanDescOpt,cleanGraphOpt,cleanStructContOpt,rtnDevIdOpt,rtnInstIdOpt,rtnLongFullDatesOpt,rtnLongModifDatesOpt,rtnPatCharsOpt,rtnSafePrivOpt,rtnUIDsOpt} [{basicProfile,cleanDescOpt,cleanGraphOpt,cleanStructContOpt,rtnDevIdOpt,rtnInstIdOpt,rtnLongFullDatesOpt,rtnLongModifDatesOpt,rtnPatCharsOpt,rtnSafePrivOpt,rtnUIDsOpt} ...]
                        Which DICOM deidentification profile(s) to apply. (default None)
```


## Citation

If you use our tool in your work, please cite us with the following BibTeX entry.
```latex
@article{rempe2025identification,
  title={De-identification of medical imaging data: a comprehensive tool for ensuring patient privacy},
  author={Rempe, Moritz and Heine, Lukas and Seibold, Constantin and H{\"o}rst, Fabian and Kleesiek, Jens},
  journal={European Radiology},
  pages={1--10},
  year={2025},
  publisher={Springer}
}
```