Computational protocol: OSCILLATOR: A system for analysis of diurnal leaf growth using infrared photography combined with wavelet transformation

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Protocol publication

[…] From the obtained digital image stack of multiple plants, single plant frames were cropped using ImageJ freeware (Figure c). For Arabidopsis, for each individual plant, the 11th and 12th real leaves (5 ~ 7 mm long at t = 0) were selected in the first frame and used for measurement of the projected distance between leaf tip to rosette centre throughout the image stack (Figure c). This can be achieved in two ways: 1: ImageJ “manual tracking” plugin allows manual tracking of the leaf tip position. 2: ImageJ “Particle tracker []” allows measurement of the position of a small dot of inert paint placed on the leaf tip at the start of imaging (this did not affect growth). Both methods provide Microsoft Excel compatible files containing the leaf tip coordinates in pixels (Figure c). The rosette centre coordinates were similarly determined in the first frame. For Arabidopsis these remained fixed throughout the experiment. The projected distance in pixels between leaf tip and rosette centre was calculated and converted into millimetres according to a scale marker (placed at average plant height) included in the images. This distance is plotted against time and represents projected leaf length (Figure d). […]

Pipeline specifications

Software tools ImageJ, Particle Tracker
Applications Laser scanning microscopy, Microscopic phenotype analysis
Organisms Arabidopsis thaliana, Solanum lycopersicum