A root imaging system is disclosed which includes a robotic arm, a camera coupled to the robotic arm, the robotic arm configured to insert the camera into the soil at predefined coordinates, a processor system configured to receive user-defined data about a plant of interest, define insertion points about the plant of interest based on the user-defined data, control the robotic arm to thereby insert the camera into the soil at defined insertion points, obtain images from the camera positioned at the insertion points, analyze the images for presence of roots, and identify the images having roots and combine that with image 3D location information for 3D structure reconstruction of the entire root structure.