Supplementary Material 2Supplementary Material 1 Supplementary Figures and Tables 1.1 Supplementary Figures Supplementary Figure 1: Graphical illustration of the quantification pipeline including example methods pertaining to the corresponding processing step. The categories are performed in order left to right order, top to bottom. Each category textbox lists exemplary steps which can be performed in relation to each processing category. Sub-steps marked with an asterisk (*) were not performed in this study. Circular inset graphics show examples of the data type and appearance subsequent to the corresponding processing step. For a detailed description of the processing steps, see Methods. 3Supplementary Figure 2: Successful tissue-level segmentation of injured plant tissue Illustrative example of a successful segmentation of an injured Arabidopsis thaliana SAM. (A) Summed projection of the raw confocal data. The shoot was injured during acquisition, and the subsequent propidium iodide staining dyed the entire cells, rendering an opaque tissue. Consequently, single-cell segmentation would not have been possible. Scale bar: 75 μm. (B) 3D Volume render of the raw confocal data. (C) Successful surface segmentation of the tissue substructures following application of our protocol (Methods). Individual substructures are coloured according to their corresponding segmentation label. Scale in (B-C) further to (A). Colouring in (A-B) shows the corresponding signal intensity magnitude in arbitrary units; (C) is coloured by integer label value. 4Supplementary Material Supplementary Figure 3: Illustration of capabilities for surface generation on a diverse set of plant tissues Collection of raw confocal data and generated surfaces for a collection of different plant tissues. (A-B) Protoplast and corresponding surface; (C-D) Anther and corresponding surface. (E-F) Apical hook and corresponding surface. (G-H) Leaf blade and corresponding surface. Approximate scales in terms of maximal extent, left to right: (A-B) 10 μm, (C-D) 350 μm, (E-F) 300 μm, (G-H) 400 μm. Colouring in (A, C, E, H) shows the signal intensity magnitude in arbitrary units; (B, D, F, H) are false-coloured. For data origins, see Data Availability Statement. Supplementary Figure 4: Conceptual 2D illustration of the apex coordinate quantification framework Graphical illustration of the plant shoot. A paraboloid is fitted to a surface mesh of the inflorescence meristem, and the corresponding apex coordinates are subsequently derived by projection to the mesh (Methods). In wild-type plants, the tissue is first segmented to remove flower organs (yellow and blue), and isolate the SAM (green); in NPA-treated plants, no initial organ-removal is needed (Methods). The paraboloid fit is exaggerated for illustrative purposes. 5Supplementary Figure 5: ABCB19 expression is upregulated in early flower primordia (A) Summed projection in the apical-basal direction of fluorescent expression of a SAM expressing pABCB19::ABCB19-GFP. Early flower primordia of developmental stage 1 to early stage 3 exhibit upregulated expression. Wassilewskija ecotype. (B-E) Same as (A), but for propidium iodide stained plants, illustrating the shoot morphology in representative Col-0 (B), abcb1 (C), abcb19 (D) and abcb1abcb19 (E) plants. Mutations in the ABCB gene family perturb the shoot morphology relative to the wild type plants. Scale bars: 50 μm. 6Supplementary Material Supplementary Figure 6: P-value outcome for significance tests between genotype distributions Corresponding p-values for the distributions of various statistical variables, namely the (A) Divergence angle standard deviation for the extended auxin transport dataset; (B) First organ distance for the auxin transport dataset; (C) Gaussian curvatures for the auxin transport dataset; (D) Gaussian curvatures for the mechanical dataset; (E) Principal curvatures for the auxin transport dataset; (F) Principal curvatures for the mechanical dataset. All statistical tests refer to MWW tests (Methods). Red dashed lines are refer to the canonical significance threshold, p = 0.05 (*). 71.2 Supplementary Tables Supplementary Table 1: Plant material, abbreviations and origin Genotype In-text abbreviation Reference Col-0 abcb1 van Rongen et al., 2019 abcb19 van Rongen et al., 2019 abcb1abcb19 abcb1,19 van Rongen et al., 2019 aux1 Bainbridge et al., 2008 aux1lax1lax2lax3 aux1lax1,2,3 Bainbridge et al., 2008 pin3 van Rongen et al., 2019 pin4 van Rongen et al., 2019 pin7 van Rongen et al., 2019 pin3pin4 pin3,4 van Rongen et al., 2019 pin3pin7 pin3,7 van Rongen et al., 2019 pin4pin7 pin4,7 van Rongen et al., 2019 pin3pin4pin7 pin3,4,7 van Rongen et al., 2019 cesa1any1 Fujita et al., 2013 cesa3eli1 Caño-Delgado et al., 2003 cesa3je5 Desprez et al., 2007 cesa6prc1-1 Fagard et al., 2000 xxt1xxt2 xxt1,2 Xiao et al., 2016 xxt1xxt2xxt5 xxt1,2,5 Xiao et al., 2016 pCLV3::dsRed x pUBQ10::myr-YFP pCLV3::dsRed x myr-YFP Willis et al., 2016 pABCB19::ABCB19-GFP van Rongen et al., 2019