McCormick, Alistair; Scorza, Livia; Bernotas, Gytis. (2019). Photometric stereo test data set, [dataset]. University of Edinburgh. School of Biological Sciences. Institute of Molecular Plant Sciences. https://doi.org/10.7488/ds/2513.
A test data set for extracting trait data from Arabidopsis thaliana plants using PS-Plant software. The data set included raw and processed data, and a pre-trained Mask R-CNN model. This data set forms part of work done in the BBSRC Tools and Resources Development project BB/N02334X/1. All PS-Plant software packages are available for download (https://bit.ly/2EFOk0O). Installation instructions are available on YouTube: https://youtu.be/7q6ZnJvhx6I. The PS-Plant software pipeline has seven steps: (1) PS data acquisition, (2) adaptive light source generation, (3) raw PS data processing, (4) rosette and (5) individual leaf mask generation, and (6) leaf instance tracking. The generation of compiled results (i.e. plant trait data) can be done at steps 4 and 6 to obtain rosette- and leaf-level data, respectively. Most PCs with onboard GPUs can be used to acquire and process PS data (steps 1-4 and 6). We recommend a PC with at least an Intel Core i3 equivalent CPU, and 4 GB of RAM. A GPU with a minimum Compute Unified Device Architecture (CUDA) capability of 3.5 (https://bit.ly/1Jnzfz8) is required for the generation of leaf masks (step 5) using the Leaf Segmentation GUI.
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