DOI: 10.5281/zenodo.7808198
title: Data from: Coronary artery segmentation in non-contrast calcium scoring CT images using deep learning

description: Abstract

Precise segmentation of coronary arteries in non-contrast Computed Tomography (CT) scans plays an important role in the assessment of the coronary artery disease, where it is the key component for evaluating the Calcium Score (Agatston et al. 1990). In the paper by Bujny et al. (2024), a deep-learning approach for high-precision segmentation of coronary arteries in non-contrast CT was proposed along with a novel method for generating Ground Truth (GT) test data (test-GT) via manual registration of high-resolution coronary tree models obtained based on contrast CT with the non-contrast CT scans. In this dataset, we present the inferences of the neural network model together with the corresponding test-GT samples, based on 6 CT scans from the openly available OrCaScore dataset (Wolterink et al. 2016). The geometrical models included in the dataset can be used both for inspection of the proposed deep learning model and for testing of new non-contrast coronary vessel segmentation approaches, which is a unique opportunity since, to the best of our knowledge, manual generation of GT for non-contrast coronary artery segmentation was not addressed so far due to very challenging character of this particular segmentation task.

 

Methods

Manual Generation of test-GT

The geometric models of coronary arteries used for the evaluation of the proposed neural network model were generated according to the manual mesh-to-image registration process as described by Bujny et al. (2024). In this approach, the high-resolution coronary artery masks obtained based on contrast CT scans are manually aligned with the corresponding non-contrast CT images using tools available in the open-source 3D computer graphics software, Blender (https://www.blender.org/). To ease the manual alignment process, specialized add-ons for medical image processing such as Cardiac add-on for Blender of Graylight Imaging (https://graylight-imaging.com/3d-modelling/) can be used, as well. The STL models in this dataset were manually generated by a medical expert with 4 years of experience.

Segmentation of Coronary Arteries using a Deep Learning Model

For each of the cases presented in this dataset, we run an inference of an nnU-Net (Isensee et al. 2021) model trained according to the process described in our paper (Bujny et al. 2024). Since we use a standard nnU-Net, which utilizes a sliding window approach for processing of the CT scan, the context information within a patch is limited, which can lead to some false-positive detections. To mitigate this problem, we additionally post-process the inferences by eliminating small vessel fragments of less than 50 [mm^3] volume and structures outside of pericardium, which we segment using another nnU-Net model, SegTHOR (Lambert et al. 2020). The resulting geometric models are stored using the STL format and presented as green masks in the HTML reports with an embedded viewer based on the K3D-jupyter library (https://k3d-jupyter.org/).

 

Dataset organization

The root folder contains 6 folders whose names correspond to the CT scans from the OrCaScore dataset (Wolterink et al. 2016). In each of the folders, there are the following 4 files available:



‘manualGT_rater1.stl’ – high-resolution STL model of coronary arteries obtained via manual alignment of the geometric model segmented in contrast CT with the corresponding non-contrast CT scan by the first rater. A sample belonging to the test-GT set (Bujny et al. 2024).

‘manualGT_rater2.stl’ – corresponding test-GT sample by the second rater.

‘ML.stl’ – post-processed inference of the nnU-Net ML model in the STL format.

‘report.html’ – interactive HTML report consisting of a manually-aligned test-GT sample (red mask), the ML segmentation based on the non-contrast CT scan (green mask), and selected slices of the non-contrast CT scan. The reports contain the relevant information related to the scanning device and present the main segmentation quality metrics for the ML model inference.