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Abstract. Micro computerized-tomography (micro-CT) has started being used for studying structures and textures of biological samples in three-dimensional (3D). Because of the complex essence of 3D images, conventionally, the identification of traits in 3D images is performed manually. Manual identification is, however, time-consuming and can be subjective owing to researchers‘ experience. This work proposed to identify lobe contours and vascular bundles for flowers in genus Sinningia automatically. In the study, volumetric 3D flower images were acquired using micro-CT. Denoising algorithms were applied to improve the quality of the 3D images. Vascular bundles were then detected using Hessian detectors. The volumetric images were next converted to surface images. Lobe contours were then identified using vector superposition and the surface images. The experiment showed that the proposed methods can identify first-order vascular bundles and lobe contours at rates of 85.67% and 90.87%, respectively. The overall successful detection rate for detecting both the first-order veins and corolla contours was 81.71%.