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  • Quickstart
  • Installation
    • 1. Installing Python
    • 2. Installing phenopype
    • 3. Choosing a text editor
    • 4. Installing Spyder (optional)
  • API reference
    • Project class
    • Pype class
    • Project_labelling class
    • Utility functions
    • Core modules
    • Video analysis
  • Tutorials
    • Tutorial 1: A (very) brief python introduction
    • Tutorial 2: Interacting with images in phenopype
    • Tutorial 3: The phenopype workflows
    • Tutorial 4: The Pype class
    • Tutorial 5: Projects
    • Tutorial 6: Size and colour reference
    • Tutorial 7: Video analysis
  • Templates
    • Detection
    • Landmarks
    • Gallery
    • Various
  • Resources
    • Python
    • OpenCV
    • Computer vision
    • YAML
  • Citation

    External links

  • Homepage
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  • Gallery
  • Author (luerig.net)
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Gallery¶

project_1.yaml
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# phenopype gallery project 1
# ---------------------------
# count isopods and measure their pigmentation and body size


template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - create_mask
        - detect_reference
        - blur:
            kernel_size: 15
    - segmentation:
        - threshold:
            method: adaptive
            blocksize: 149
            constant: 5
            channel: blue
        - morphology:
            operation: open
            shape: cross
            kernel_size: 9
            iterations: 2
        - detect_contour:
            min_diameter: 150
            max_diameter: 300
        - edit_contour
        - detect_contour:
            min_diameter: 150
            max_diameter: 300
    - measurement:
        - compute_shape_features
        - compute_texture_features
    - visualization:
        - select_canvas:
            canvas: image
        - draw_contour
        - draw_mask:
            line_colour: aqua
        - draw_reference:
            line_colour: crimson
    - export:
        - save_canvas
        - save_annotation:
            overwrite: true
Download
project_2.yaml
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# phenopype gallery project 2
# ---------------------------
# set landmarks on stickleback and automatically size-reference them

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - detect_reference
        - write_comment
    - measurement:
        - landmarks:
            point_size: 12
            label_size: 2
            label_width: 2
    - visualization:
        - draw_landmarks:
            point_size: 12
            label_size: 2
            label_width: 2
        - draw_reference:
            line_colour: crimson
    - export:
        - save_annotation:
            overwrite: true
Download
project_3.yaml
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# phenopype gallery project 5
# ---------------------------
# separate stickleback armour plates

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - create_mask:
            tool: polygon
    - segmentation:
        - threshold:
            method: adaptive
            blocksize: 199
            constant: 7
            channel: green
        - morphology:
            operation: close
            shape: ellipse
            kernel_size: 3
            iterations: 3
        - detect_contour
        - watershed:
            distance_cutoff: 0.9
        - detect_contour
        - edit_contour
        - detect_contour
    - visualization:
        - select_canvas:
            canvas: green
    - segmentation:
        - edit_contour:
            overlay_blend: 0
            overlay_line_width: 1
        - detect_contour:
            min_area: 100
    - measurement:
    - visualization:
        - select_canvas:
            canvas: green
        - draw_contour:
            line_width: 1
        - draw_mask:
            line_width: 2
            line_colour: aqua
    - export:
        - save_annotation:
            overwrite: true
Download
project_5.yaml
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# phenopype gallery project 3
# ---------------------------
# detect phytoplankton contours

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - blur:
            kernel_size: 9
    - segmentation:
        - threshold:
            method: adaptive
            blocksize: 299
            constant: 10
        - morphology:
            operation: open
            shape: cross
            kernel_size: 5
            iterations: 1
        - morphology:
            operation: close
            shape: ellipse
            kernel_size: 3
            iterations: 3
        - detect_contour:
            min_area: 150
        - edit_contour:
            overlay_blend: 0.1
            overlay_line_width: 1
        - detect_contour:
            min_area: 10
    - visualization:
        - select_canvas:
            canvas: raw
        - draw_contour
    - export:
        - save_canvas
        - save_annotation:
            overwrite: true
Download
project_6.yaml
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# phenopype gallery project 6
# ---------------------------
# count small freshwater snails and separate overlapping specimens

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - create_mask:
            tool: rectangle
        - create_reference
    - segmentation:
        - threshold:
            method: adaptive
            blocksize: 99
            constant: 3
        - detect_contour
        - watershed:
            distance_cutoff: 0.7
        - detect_contour:
            min_area: 100
        - edit_contour
        - detect_contour:
            min_area: 100
    - measurement:
    - visualization:
        - select_canvas:
            canvas: raw
        - draw_contour:
            line_width: 1
        - draw_mask:
            line_width: 2
            line_colour: aqua
    - export:
        - save_annotation:
            overwrite: true
Download
project_7.yaml
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# phenopype gallery project 7
# ---------------------------
# detect worms in 6-well plates

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - detect_mask:
            shape: circle
            circle_args: {max_radius: 300, min_radius: 210, param2: 100, param1: 100, min_dist: 400}
            resize: 0.5
        - blur:
            kernel_size: 5
    - segmentation:
        - threshold:
            method: adaptive
            blocksize: 29
            constant: 10
        - detect_contour
        - edit_contour
        - detect_contour:
            min_diameter: 100
    - measurement:
        - detect_skeleton
    - visualization:
        - select_canvas:
            canvas: raw
        - draw_contour:
            line_width: 1
        - draw_mask:
            line_width: 2
            line_colour: aqua
        - draw_polyline:
            line_colour: fuchsia
            line_width: 2
    - export:
        - save_annotation:
            overwrite: true
Download
project_8a.yaml
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# phenopype gallery project 6
# ---------------------------
# measure a single fish tooth on a light background

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - create_mask
        - create_reference
    - segmentation:
        - blur:
            kernel_size: 25
        - threshold:
            method: binary
            value: 170
            channel: blue
        - morphology:
            operation: close
            shape: ellipse
            kernel_size: 3
            iterations: 3
        - detect_contours:
            min_area: 500
    - measurement:
        - compute_shape_features
    - visualization:
        - select_canvas:
            canvas: blue
        - draw_contour
Download
project_8b.yaml
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# phenopype gallery project 8b
# ----------------------------
# measure multiple fish teeth on a dark background

template_locked: true  # prevents accidental overwrite - removed after loading

processing_steps:
    - preprocessing:
        - create_mask:
            include: false
        - create_reference
    - segmentation:
        - blur:
            kernel_size: 11
        - threshold:
            method: binary
            value: 180
            invert: true
        - morphology:
            operation: close
            shape: ellipse
            kernel_size: 3
            iterations: 3
        - detect_contour:
            min_area: 500
    - measurement:
        - compute_shape_features
    - visualization:
        - select_canvas:
            canvas: raw
        - draw_contour
Download
project_9.yaml
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# phenopype gallery project 9
# ----------------------------
# segment damselflies and quantify shape and texture of their body parts

template_locked: true  # prevents accidental overwrite - removed after loading


processing_steps:
    - preprocessing:
        - comment:
            label: ID
        - blur:
            kernel_size: 5
    - segmentation:
        - threshold:
            method: binary
            value: 90
            channel: red
        - morphology:
            operation: open
            shape: cross
            kernel_size: 7
            iterations: 2
        - morphology:
            operation: close
            shape: ellipse
            kernel_size: 5
            iterations: 3
        - detect_contour:
            min_diameter: 0
            min_area: 10000
        - edit_contour:
            overlay_blend: 0
            overlay_line_width: 1
        - detect_contour:
            min_diameter: 0
            min_area: 10000
        - edit_contour:
            overlay_blend: 0
            overlay_line_width: 1
        - detect_contour
    - visualization:
        - draw_contour:
            contour_id: b
        - draw_contour:
            contour_id: c
            line_colour: aqua
    - export:
        - save_canvas:
            resize: 1
        - save_annotation:
            overwrite: true
Download
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Last updated on 2024-07-03 18:34:04