Image processing scripts for manuscript: Control of plant organ growth through cell division orientation in inner tissues

Set of Python scripts and Fiji macros used to analyse cell geometry and orientations of cell division during early stages of stem development in the model plant Arabidopsis thaliana. The starting images were confocal image stacks of inflorescence apices. The scritps were used for cell segmentation, measurements of cell geometry, position of cells within the shoot apex, detection of recent cell divisions, measurement of division angles and manual curation. Instructions and description of each script are included, in addition to a test image to check that the downloaded scripts run correctly. These scripts were adapted and extended from previously published analysis pipelines (Bencivenga et al., 2016; Serrano-Mislata et al., 2017) to be used in the manuscript Yates et al. (2026) 'Control of plant organ growth through cell division orientation in inner tissues'. Folders containing the initial and processed images are available through links provided in the manuscript's main text and supplementary data. References: Serrano-Mislata, A., Schiessl, K., and Sablowski, R. (2015). Active control of cell size generates spatial detail during plant organogenesis. Curr. Biol. 25, 2991-2996. Bencivenga, S., Serrano-Mislata, A., Bush, M., Fox, S., and Sablowski, R. (2016). Control of Oriented Tissue Growth through Repression of Organ Boundary Genes Promotes Stem Morphogenesis. Dev. Cell 39, 198-208. Serrano-Mislata, A., Bencivenga, S., Bush, M., Schiessl, K., Boden, S., and Sablowski, R. (2017). DELLA genes restrict inflorescence meristem function independently of plant height. Nature plants 3, 749.