Fig. 1

Schematic outline of typical processing and analysis steps for 3D plant phenotyping. Through an active (1.a) or passive (1.b) 3D acquisition method, either a depth map (2.a), a point cloud (2.b ) or a voxel grid (2.c) is obtained. After a number of preprocessing steps consisting of background subtraction, outlier removal, denoising and/or downsampling, the primary 3D representation may be transformed into a secondary representation, such as a polygon mesh (4.a), an octree (4.b), or an undirected graph (4.c), which facilitates further analysis. The main analysis steps, which may consist of skeletonization (5.a) segmentation (5.b) and/or surface fitting (5.c), precede measurements on the canopy (6.a), plant (6.b), or plant organ (6.c) level. 1.a [30], 1.b [169], 2.b [35], 2.c [101], 4.a [164], 4.b [104], 4.c, 6.a [108], and 6.b [85] reprinted under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0). 2.a, reprinted from [79], ©2015, with permission from Elsevier. 5.a [179] reprinted with permission from the American Society for Photogrammetry and Remote Sensing, Bethesda, Maryland (https://www.asprs.org/). 5.b, ©2017 IEEE, reprinted with permission from [227]. 5.c [348] and 6.c [248] reprinted with permission from the author