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Abstract: Convolutional neural networks (CNNs) produce promising results when applied to a wide range of medical imaging tasks including the segmentation of tissue structures. However, segmentation is particularly challenging when the target structures are small with respect to the complete image data and exhibit substantial curvature as in the case of coronary arteries in computed tomography angiography (CTA). Therefore, we evaluated the impact of data representation of tubular structures on the segmentation performance of CNNs with U-Net architecture in terms of the resulting Dice coefficients and Hausdorff distances. For this purpose, we considered 2D and 3D input data in cross-sectional and Cartesian representations. We found that the data representation can have a substantial impact on segmentation results with Dice coefficients ranging from 60% to 82% reaching values similar to those of human expert annotations used for training and Hausdorff distances ranging from 1.38 mm to 5.90 mm. Our results indicate that a 3D cross-sectional data representation is preferable for segmentation of thin tubular structures