An imaging system is disclosed herein. The imaging system includes an imaging apparatus and a computing system. The imaging apparatus includes a plurality of light sources positioned at a plurality of positions and a plurality of angles relative to a stage configured to support a specimen. The imaging apparatus is configured to capture a plurality of images of a surface of the specimen. The computing system in communication with the imaging apparatus. The computing system configured to generate a 3D-reconstruction of the surface of the specimen by receiving, from the imaging apparatus, the plurality of images of the surface of the specimen, generating, by the imaging apparatus via a deep learning model, a height map of the surface of the specimen based on the plurality of images, and outputting a 3D-reconstruction of the surface of the specimen based on the height map generated by the deep learning model.