WISRD Research & Engineering Journal

Functions to find objects and outline their shape are then applied. Figure 45 shows objects that were found are highlighted in pink and the outline of objects are drawn in blue. More time will be required outside this internship to adjust the segmentation to remove the edges of rulers and surfaces of the plugs and to include the tips of this thin, pointy species of coral.

Figure 45 . PlantCV identifies the objects (top) and outlines the shape (bottom).

4.2.4.2 Parallelization

The workflow from a single image is then run in parallel for many images. To parallelize the workflow, the Jupyter Notebook is opened as a python script, which removes all the outputs such that only the code and comments remain. A package called argparse is imported to the python script, which allows the user to communicate from the command line. Another function called main is added before the body of the workflow code. To set the batch processing parameters and create the .json Batch File, the following short script was written and run:

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