Project: Image Multimodal Database with AI Assisted Annotation

[mariamonzon]

Draft Status

Ready - team will start page creating immediately

Category

Infrastructure

Presenter Location

In-person

Key Investigators

• Maria Monzon (ETHz, Switzerland)
• Catherine Jutzeler (ETHz, Switzerland)

Project Description

Despite various existing solutions for DICOM Medical Database, (e.g. XNAT server), the storage of medical records. However, (to the best of my limited knowledge) there exist very few open sources solutions that can store multimodal data (DICOM, Electronic Health Records, REDCAP questionaires) for clinical research. The project would comprise set up a ORTHANC PACS Server with a non-relational MongoDB database as a backend for efficient stoarage of patient multimodal data and high thoughtput for further AI analysis. This database will be designed to assist AI enabled interactive annotation. Additionally the database would include visualizing capabilities (e.g., descriptive statistics). Ideally the database will also support data retieval API for data visualization dashboard

Objective

This project aims to develop an open-source and ideally community-maintained solution for:

1. Data Standardization: All collected data will be converted and standarized into research format (e.g. BIDS format)
2. Having a multimodal research database or integration of medical records with ORTHANC Database.
3. The infrastructure would enable connection to annotation tools such as MONAI Label.

Approach and Plan

0. Define an standardize (or extended in teh community) format to optimally store multimodal data ( e.g. the Brain Imaging Data Structure BIDS format extension)
1. Create a mongoDB database for optimal storage
2. Configure ORTHANC server for visualization and integration prposes
3. (optional) Add possibility to export to an structured format, integrating Magnetic Resonance Imaging (MRI) (maybe in DICOM but would support NIFTI conversion), Electronic Health Records (EHR)...
4. Enable data anotation capabilites ( e.g. OHIF viewer with MONAI label)

Progress and Next Steps

1. Data curation
2. Basic ORTHANC server proptotyping

Illustrations

Background and References

• We can use the MIMIC-IV Dataset with genertaed in this publication: https://physionet.org/content/haim-multimodal/1.0.1/
• Orthanc database mongoDB plugin: https://github.com/Doc-Cirrus/orthanc-mongodb

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Project Page Pull Request Creation

:white_check_mark: COMPLETED: See https://github.com/NA-MIC/ProjectWeek/pull/885