Various

quickstart-template.yaml
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# phenopype quickstart template
# ------------------------------
# This template is intended to go with the phenopype quickstart materials 
# - for details see https://www.phenopype.org/docs/quickstart/ and refer to
# Figure 2 in Lürig 2021 (https://doi.org/10.1111/2041-210X.13771) or 
# phenopype tutorial 3 (https://www.phenopype.org/docs/tutorials/tutorial_3)

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - create_mask:
            tool: polygon
            label: plate-area
        - blur:
            kernel_size: 9
    - segmentation:
        - threshold:
            method: adaptive
            blocksize: 99
            constant: 5
            channel: red
        - detect_contour:
            retrieval: ext
            min_area: 150
    - measurement:
        - compute_shape_features:
    - visualization:
        - select_canvas:
            canvas: raw
        - draw_contour
        - draw_mask
    - export:
        - save_canvas
        - save_annotation:
            overwrite: true