A computer-implemented method of characterising the phenotype of a plant, including: (i) obtaining mesh data representing a surface of the plant, said mesh data including data representing a plurality of polygons having respective sets of vertices, each vertex having a spatial coordinate; and (ii) applying at least two automated segmentations (200, 300) to the mesh data to automatically assign the vertices to distinct morphological regions of the plant, wherein step (ii) includes: applying a first segmentation to the mesh data to coarsely segment the stem from the other regions of the plant, to generate first-pass segmentation data in which at least some vertices are assigned to a stem region and some of the vertices are assigned to leaf-branch regions, the first segmentation being performed using a first segmentation method using a region growing algorithm to partition the mesh data into stem region data and leaf-branch region data; applying a further segmentation to the stem region data, to refine the stem region, using primitive shape fitting to define a boundary for the stem region where vertices lying within the boundary are assigned to the stem region; if the plant comprises petioles determined on the basis of a plant type indicator, applying a segmentation to the leaf-branch region data to separate the leaf-branch regions into separate leaf and branch sub-regions, using primitive shape fitting to define a boundary for the branch sub-region, where vertices lying within the boundary are assigned to the branch sub-region, and vertices lying outside the boundary are assigned to the leaf sub-region; wherein the boundary for the stem region and the leaf-branch regions are directly retrieved from the boundary of a primitive shape of the primitive shape fitting, and the boundary is substantially tubular; and wherein the segmented mesh data is used to extract quantitative phenotypic data of the plant. (i) obtaining mesh data representing a surface of the plant, said mesh data including data representing a plurality of polygons having respective sets of vertices, each vertex having a spatial coordinate; and (ii) applying at least two automated segmentations (200, 300) to the mesh data to automatically assign the vertices to distinct morphological regions of the plant, wherein step (ii) includes: applying a first segmentation to the mesh data to coarsely segment the stem from the other regions of the plant, to generate first-pass segmentation data in which at least some vertices are assigned to a stem region and some of the vertices are assigned to leaf-branch regions, the first segmentation being performed using a first segmentation method using a region growing algorithm to partition the mesh data into stem region data and leaf-branch region data; applying a further segmentation to the stem region data, to refine the stem region, using primitive shape fitting to define a boundary for the stem region where vertices lying within the boundary are assigned to the stem region; if the plant comprises petioles determined on the basis of a plant type indicator, applying a segmentation to the leaf-branch region data to separate the leaf-branch regions into separate leaf and branch sub-regions, using primitive shape fitting to define a boundary for the branch sub-region, where vertices lying within the boundary are assigned to the branch sub-region, and vertices lying outside the boundary are assigned to the leaf sub-region; wherein the boundary for the stem region and the leaf-branch regions are directly retrieved from the boundary of a primitive shape of the primitive shape fitting, and the boundary is substantially tubular; and wherein the segmented mesh data is used to extract quantitative phenotypic data of the plant. applying a first segmentation to the mesh data to coarsely segment the stem from the other regions of the plant, to generate first-pass segmentation data in which at least some vertices are assigned to a stem region and some of the vertices are assigned to leaf-branch regions, the first segmentation being performed using a first segmentation method using a region growing algorithm to partition the mesh data into stem region data and leaf-branch region data; applying a further segmentation to the stem region data, to refine the stem region, using primitive shape fitting to define a boundary for the stem region where vertices lying within the boundary are assigned to the stem region; if the plant comprises petioles determined on the basis of a plant type indicator, applying a segmentation to the leaf-branch region data to separate the leaf-branch regions into separate leaf and branch sub-regions, using primitive shape fitting to define a boundary for the branch sub-region, where vertices lying within the boundary are assigned to the branch sub-region, and vertices lying outside the boundary are assigned to the leaf sub-region; wherein the boundary for the stem region and the leaf-branch regions are directly retrieved from the boundary of a primitive shape of the primitive shape fitting, and the boundary is substantially tubular; and wherein the segmented mesh data is used to extract quantitative phenotypic data of the plant.