Supplemental Data

Files in this Data Supplement:

• Supplemental Movie 1 - Supplemental Movies 1-3. OPT data reconstructed and displayed as volumes with clipping to reveal internal morphology. Movies correspond to images labelled A, C and D in Figures 1 and 2. Movie 1. (Figures 1A and 2A) Colour OPT volume views of the Antirrhinum flower. Based on a combination of transmission (shown in blue) and fluorescence OPT (Leica TXR filter (shown in red) and GFP1 filters (shown in green)).
• Supplemental Movie 2 - Movie 2. (Figures 1C and_2C) First true leaves of an Arabidopsis seedling, volume view shows trichome cells on the adaxial leaf surface (cotyledons removed), clipping displays the vasculature. Collected with fluorescence OPT (GFP1 filter).
• Supplemental Movie 3 - Movie 3. (Figures 1D and 2D) Part of an Arabidopsis silique taken with fluorescence OPT (TXR filter). Movie shows volume and clipped views. Arabidopsis silique clipped to reveal internal structure. A piece was removed using three clipping planes to show the seeds developing within.
• Supplemental Movie 4 - Supplemental Movie 4. Virtual sectioning of an Arabidopsis silique. (Figure 3F) Movie shows orthogonal ZX sections oriented parallel to the viewing plane, with heart stage embryos. Movies were made via MAPaint with an image size of 512 x 512 x 512 pixels.
• Supplemental Movie 5 - Supplemental Movies 5 and 6. Live OPT imaging. Movies correspond with images shown in Figure 4A and B. Movie 5. (Figure 4A) Volume views of an Arabidopsis seedling growing within the OPT device. A series of OPT scans in water collected at 24, 49 and 72 hours after the start of the experiment are shown (transmission OPT channel).
• Supplemental Movie 6 - Movie 6. (Figure 4B) High resolution section views of the same root as in Figure 4A collected 30 hours after the start of the experiment. Movie was made via MAPaint, image size 512 x 512 x 512 pixels.
• Supplemental Movie 7 - Supplemental Movies 7 and 8. Visualisation of gene expression in 3D. Movies correspond with images shown in Figure 5B and D. Movie 7. (Figure 5B) .Combined volume view of a GL2:GUS Arabidopsis leaf showing GUS staining in the trichomes (m5, 13 dfs). Transmission OPT highlights GUS stained trichomes, shown in red. Fluorescence OPT highlights the remaining leaf tissue, shown in green (GFP1 filter). The two channels were combined and displayed in the same 3D space. Data collected with OPT Scanner 3001.
• Supplemental Movie 8 - Movie 8. (Figure 5D) Combined volume view of LFY:GUS Arabidopsis seedling, after leaf removal and staining to reveal GUS activity (m1-5 were removed, 8 dfs). The view was clipped to remove metamer 6 and reveal LFY:GUS staining (red) in emerging leaves (m8 and m9). Signal is also seen in the flanks of the shoot apical meristem. Red signal is from transmission OPT while green is signal from fluorescence OPT (GFP1 filter).
• Supplemental Movie 9 - Supplemental Movie 9. Extraction of morphological landmarks. Movie corresponds with the image shown in Figure 6A Movie 9. (Figure 6A). OPT fluorescence volume view of an Arabidopsis leaf (m3, 12 dfs) (GFP1 Filter).
• Supplemental Movie 10 - Supplemental Movies 10-14. Extraction of gene expression patterns from 3D datasets. Movies correspond to images labelled A to H in Figure 8. Movie 10 (Figure 8A and B) OPT volume view of mature ATHB8:GUS Arabidopsis leaf stained to reveal GUS activity (m2, 9 dfs) with the GUS signal extracted using semi-automatic segmentation tools to reveal staining in veins. Combined transmission and fluorescent (GFP1) OPT channels.
• Supplemental Movie 11 - Movie 11 (Figure 8C and D) OPT volume view of young ATHB8:GUS dissected seedling (4 dfs) with ATHB8 venation pattern extracted. Combined transmission and fluorescent (GFP1) channels. Cotyledons were removed and first true leaves are visible.
• Supplemental Movie 12 - Movie 12 (Figure 8E and F) OPT volume view of LFY:GUS Arabidopsis meristem with expression domains highlighted. Gene expression was segmented as separate domains for each metamer and colour-coded accordingly. LFY:GUS staining situated deeper within the volume is revealed. Colour-coding: m7: blue, m8: turquoise, m9: pink, m10: dark green, m11: pale blue, m12: orange.
• Supplemental Movie 13 - Movie 13 (Figure 8G) OPT volume view of DEF expression in an Antirrhinum inflorescence. Dark staining is DEF expression. Flowers are arranged with spiral phyllotaxy. Flower 1 is the most mature in this series.
• Supplemental Movie 14 - Movie 14 (Figure 8H1) A flower from Figure 8G was clipped and segmented, with intense DEF expression colour-coded in green, whilst weaker expression is displayed in yellow. Flower 1: late stage 5 (without sepals). DEF is expressed in petal and stamen primordia.