University Medicine Essen
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FHIR-PYrate
FHIR-PYrate PublicFHIR-PYrate is a package that provides a high-level API to query FHIR Servers for bundles of resources and return the structured information as pandas DataFrames. It can also be used to filter reso…
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Body-and-Organ-Analysis
Body-and-Organ-Analysis PublicBOA is a segmentation tool of CT scans by the SHIP-AI group (https://ship-ai.ikim.nrw/). Combining the TotalSegmentator and the Body Composition Analysis, this tool is capable of analyzing medical …
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saros-dataset
saros-dataset PublicSparsely Annotated Region and Organ Segmentation (SAROS) - A large, heterogeneous, and sparsely annotated segmentation dataset on CT imaging data
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Repositories
- FHIR-PYrate Public
FHIR-PYrate is a package that provides a high-level API to query FHIR Servers for bundles of resources and return the structured information as pandas DataFrames. It can also be used to filter resources using RegEx and SpaCy and download DICOM studies and series.
- Volcano-HL7-MLLP-Connector Public
A high-performance HL7 v2 MLLP listener that converts healthcare messages to JSON and publishes them to Apache Kafka.
- DeidentiFHIR-Pipeline Public
With the DeidentiFHIR-Pipeline, you can transfer FHIR based data from one source (e.g. a FHIR server) to a target (e.g. a FHIR server) and pseudonymize the data in between. Pseudonymization is based on the DeidentiFHIR library.
- PIGEON Public
This repository presents a reproducible framework for transforming structured FHIR data into synthetic German patient information texts. The generated corpus is used to fine-tune large language models for extracting structured medical information, providing a foundation for developing and evaluating clinical NLP applications.
- SALT Public
Softmax for Arbitrary Label Trees (SALT) is a framework for training segmentation networks using conditional probabilities to model hierarchical relationships in the data.
- saros-dataset Public
Sparsely Annotated Region and Organ Segmentation (SAROS) - A large, heterogeneous, and sparsely annotated segmentation dataset on CT imaging data
- BOA-Profiles Public
A collection of HL7 FHIR profiles for AI-based Body and Organ Analysis (BOA). These profiles standardize the representation of body composition biomarkers extracted from CT imaging, enabling interoperable storage, exchange, and reuse across healthcare systems.
- HYSPI Public
HYSPI is a small Python tool for turning hyperspectral hand scans into analysis-ready spectra. It detects anatomical landmarks with MediaPipe, creates reproducible palm or fingertip masks, applies those masks to hyperspectral cubes, and writes the mean spectrum per sample to CSV.
- CycleMED Public
CycleMED is a CycleGAN-based framework for medical image translation projects using MRI and CT data. The repository provides custom dataset loader including specific medical imaging preprocessings and adaptions for training runs.
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