Organization of PlantCV Outputs

During parallel processing, outputs from PlantCV analysis functions are collected into an SQLite database. The database is used to collect information about each PlantCV pipeline command that is used in conjunction with the database (runinfo table), image metadata (metadata table), object size and shape measurements (features table), object color or intensity measurements (signal table), and output image paths (analysis_images table). The database structure is updated as new features are added. The current schema is shown below.

Database schema

Screenshot
 For each table, the diagram shows three columns: the field names, data types, and index types. Index types are Primary Key (PK) and Foreign Key (FK). Foreign Keys are used to join tables in queries.

Summary of Output Measurements and Units

Analyze object function (features table)

Measurement Units Description
area pixels object area
hull-area pixels convex hull area
solidity none ratio of object area divided by convex hull area
perimeter pixels object perimeter length
width pixels maximum object width (horizontal)
height pixels maximum object height (vertical)
longest_axis pixels longest path between convex hull vertices through the center of mass
center-of-mass-x none x-axis coordinate of the object center of mass
center-of-mass-y none y-axis coordinate of the object center of mass
hull_vertices none number of convex hul vertices
in_bounds none true of false (false if the object is touching the border of the image)
ellipse_center_x none x-axis coordinate of the center of the minimum bounding ellipse
ellipse_center_y none y-axis coordinate of the center of the minimum bounding ellipse
ellipse_major_axis pixels length of the major axis of the minimum bounding ellipse
ellipse_minor_axis pixels length of the minor axis of the minimum bounding ellipse
ellipse_angle degrees degrees of rotation of the bounding ellipse major axis
ellipse_eccentricity none eccentricity of the bounding ellipse

Analyze bound function (features table), either horizontal or vertical

Measurement Units Description
y-position none y-axis reference position used for measurements (boundary line)
height_above_bound pixels maximum object height (vertical) above the y-position
height_below_bound pixels maximum object height (vertical) below the y-position
above_bound_area pixels area of object above the y-position
percent_above_bound_area none percentage of total object area above the y-position
below_bound_area pixels area of object below the y-position
percent_below_bound_area none percentage of total object area below the y-position

Report size marker function (features table)

Measurement Units Description
marker_area pixels area of reference object (marker)
marker_major_axis_length pixels length of the major axis of the marker bounding ellipse
marker_minor_axis_length pixels length of the minor axis of the marker bounding ellipse
marker_eccentricity none eccentricity of the bounding ellipse

Watershed segmentation function (features table)

Measurement Units Description
estimated_object_count none number of segmented objects (e.g. leaves)

Analyze color function (signal table)

Measurement Units Description
channel_name none possible values: red, green, blue, hue, saturation, value, lightness, green-magenta, blue-yellow
frequency none list of pixel counts per signal value
signal_values none list of channel signal range values (bins)
hue_circular_mean degrees Circular mean of the hue values (0-359 degrees)
hue_circular_std degrees Standard deviation of the circular mean of the hue values
hue_median degrees Median hue value (0-359 degrees)

Analyze NIR intensity function (signal table)

Measurement Units Description
channel_name none possible values: nir
frequency none list of pixel counts per NIR signal value
signal_values none list of signal range values (bins)