Measurements ============ .. toctree:: :hidden: metadata/index .. _measurement-info-metadata-match: :doc:`METADATA_MATCH ` --------------------------------------------------------------------------- .. list-table:: Category: **QC** :header-rows: 1 * - Column label - Description - Type * - ``QC_MetadataOnly`` - True when the row came from a --metadata CSV key that matched no measured object; every measurement/info column on the row is null. - :bdg-ref-secondary:`Quality ` .. _measurement-info-bbox: :doc:`BBOX ` ------------------------------------------------------- .. list-table:: Category: **Bbox** :header-rows: 1 * - Column label - Description - Type * - ``Bbox_CenterRR`` - The row coordinate of the center of the bounding box. - :bdg-ref-muted:`Identity / design ` * - ``Bbox_MinRR`` - The smallest row coordinate of the bounding box. - :bdg-ref-muted:`Identity / design ` * - ``Bbox_MaxRR`` - The largest row coordinate of the bounding box. - :bdg-ref-muted:`Identity / design ` * - ``Bbox_CenterCC`` - The column coordinate of the center of the bounding box. - :bdg-ref-muted:`Identity / design ` * - ``Bbox_MinCC`` - The smallest column coordinate of the bounding box. - :bdg-ref-muted:`Identity / design ` * - ``Bbox_MaxCC`` - The largest column coordinate of the bounding box. - :bdg-ref-muted:`Identity / design ` * - ``Bbox_IntensityWeightedCenterRR`` - The intensity-weighted center row coordinate of the object (skimage ``centroid_weighted``). - :bdg-ref-muted:`Identity / design ` * - ``Bbox_IntensityWeightedCenterCC`` - The intensity-weighted center column coordinate of the object (skimage ``centroid_weighted``). - :bdg-ref-muted:`Identity / design ` * - ``Bbox_DistWeightedCenterRR`` - Row coordinate of the per-object Euclidean-distance-transform maximum (deepest interior point of the object mask). Robust to thin filamentous extensions that pull intensity-weighted centroids off-body. - :bdg-ref-muted:`Identity / design ` * - ``Bbox_DistWeightedCenterCC`` - Column coordinate of the per-object Euclidean-distance-transform maximum (deepest interior point of the object mask). Robust to thin filamentous extensions that pull intensity-weighted centroids off-body. - :bdg-ref-muted:`Identity / design ` .. _measurement-info-colorcomposition: :doc:`ColorComposition ` ------------------------------------------------------------------------------- .. list-table:: Category: **ColorComposition** :header-rows: 1 * - Column label - Description - Type * - ``ColorComposition_BlackPct`` - Percentage of pixels classified as black (Value < 20) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_WhitePct`` - Percentage of pixels classified as white (Saturation < 15, Value > 85) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_GrayPct`` - Percentage of pixels classified as gray (Saturation < 15, Value 20-85) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_PinkPct`` - Percentage of pixels classified as pink (Red/Magenta hue, Saturation 20-60, Value > 80) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_BrownPct`` - Percentage of pixels classified as brown (Red/Orange hue, Value 20-60) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_RedPct`` - Percentage of pixels classified as red (Hue 0-15° or 345-360°) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_OrangePct`` - Percentage of pixels classified as orange (Hue 15-45°) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_YellowPct`` - Percentage of pixels classified as yellow (Hue 45-75°) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_GreenPct`` - Percentage of pixels classified as green (Hue 75-150°) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_CyanPct`` - Percentage of pixels classified as cyan (Hue 150-180°) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_BluePct`` - Percentage of pixels classified as blue (Hue 180-250°) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorComposition_PurplePct`` - Percentage of pixels classified as purple/magenta (Hue 250-345°) - :bdg-ref-warning:`Tier 3 · Discriminative feature ` .. _measurement-info-colorhsv: :doc:`ColorHSV ` --------------------------------------------------------------- .. list-table:: Category: **ColorHSV** :header-rows: 1 * - Column label - Description - Type * - ``ColorHSV_HueRobustMean`` - Hue of the cone-embedded geometric-median robust center (circular-correct) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorHSV_SaturationRobustMean`` - Saturation of the cone-embedded geometric-median robust center - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorHSV_ValueRobustMean`` - Value (brightness) of the cone-embedded geometric-median robust center - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorHSV_HSVConeVariance`` - Trace of the HSV cone-Cartesian covariance (single 3D HSV spread scalar); spread about the arithmetic mean of the cone coordinates (NOT about the reported RobustMean center) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` .. _measurement-info-colorlab: :doc:`ColorLab ` --------------------------------------------------------------- .. list-table:: Category: **ColorLab** :header-rows: 1 * - Column label - Description - Type * - ``ColorLab_L*GeoMedian`` - L* of the ΔE76 (Euclidean) geometric-median center color of the object - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_a*GeoMedian`` - a* of the ΔE76 (Euclidean) geometric-median center color of the object - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_b*GeoMedian`` - b* of the ΔE76 (Euclidean) geometric-median center color of the object - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_L*Medoid`` - L* of the ΔE2000 medoid center color (real pixel minimizing total ΔE2000) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_a*Medoid`` - a* of the ΔE2000 medoid center color (real pixel minimizing total ΔE2000) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_b*Medoid`` - b* of the ΔE2000 medoid center color (real pixel minimizing total ΔE2000) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_DeltaE2000MedianFromMedoid`` - Median ΔE2000 of object pixels from the ΔE2000 medoid center (robust perceptual MAD) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_DeltaE2000MeanFromMedoid`` - Mean ΔE2000 of object pixels from the ΔE2000 medoid center (color-uniformity standard) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_DeltaE2000P95FromMedoid`` - 95th-percentile ΔE2000 of object pixels from the ΔE2000 medoid center (worst-case / sectoring flag) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_LabTotalVariance`` - Trace of the 3x3 L*a*b* covariance (var L* + var a* + var b*); mean-squared ΔE76 spread about the arithmetic mean (NOT about the reported GeoMedian/Medoid center) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``ColorLab_MedoidColorHex`` - sRGB hex string of the ΔE2000 medoid color; for plot visualization only (not a numeric measurement) - :bdg-ref-primary:`Tier 2 · Descriptive trait ` .. _measurement-info-colorxy: :doc:`Colorxy ` ------------------------------------------------------------- .. list-table:: Category: **Colorxy** :header-rows: 1 * - Column label - Description - Type * - ``Colorxy_xMin`` - The minimum chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_xQ1`` - The lower quartile (Q1) chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_xMean`` - The mean chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_xMedian`` - The median chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_xQ3`` - The upper quartile (Q3) chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_xMax`` - The maximum chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_xStdDev`` - The standard deviation of the chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_xCoeffVar`` - The coefficient of variation of the chromaticity x coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yMin`` - The minimum chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yQ1`` - The lower quartile (Q1) chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yMean`` - The mean chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yMedian`` - The median chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yQ3`` - The upper quartile (Q3) chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yMax`` - The maximum chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yStdDev`` - The standard deviation of the chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Colorxy_yCoeffVar`` - The coefficient of variation of the chromaticity y coordinate of the object - :bdg-ref-warning:`Tier 3 · Discriminative feature ` .. _measurement-info-colorxyz: :doc:`ColorXYZ ` --------------------------------------------------------------- .. list-table:: Category: **ColorXYZ** :header-rows: 1 * - Column label - Description - Type * - ``ColorXYZ_CieXMin`` - The minimum X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieXQ1`` - The lower quartile (Q1) X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieXMean`` - The mean X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieXMedian`` - The median X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieXQ3`` - The upper quartile (Q3) X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieXMax`` - The maximum X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieXStdDev`` - The standard deviation of the X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieXCoeffVar`` - The coefficient of variation of the X value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYMin`` - The minimum Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYQ1`` - The lower quartile (Q1) Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYMean`` - The mean Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYMedian`` - The median Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYQ3`` - The upper quartile (Q3) Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYMax`` - The maximum Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYStdDev`` - The standard deviation of the Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieYCoeffVar`` - The coefficient of variation of the Y value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZMin`` - The minimum Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZQ1`` - The lower quartile (Q1) Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZMean`` - The mean Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZMedian`` - The median Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZQ3`` - The upper quartile (Q3) Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZMax`` - The maximum Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZStdDev`` - The standard deviation of the Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``ColorXYZ_CieZCoeffVar`` - The coefficient of variation of the Z value of the object in CIE XYZ color space - :bdg-ref-warning:`Tier 3 · Discriminative feature ` .. _measurement-info-curation: :doc:`CURATION ` --------------------------------------------------------------- .. list-table:: Category: **Curation** :header-rows: 1 * - Column label - Description - Type * - ``Curation_Category`` - Error-category token assigned to a removed/triaged object. - :bdg-ref-secondary:`Quality ` .. _measurement-info-linear-cap-and-lag-model: :doc:`LINEAR_CAP_AND_LAG_MODEL ` ----------------------------------------------------------------------------------------------- .. list-table:: Category: **LinearCapAndLagModel** :header-rows: 1 * - Column label - Description - Type * - ``LinearCapAndLagModel_v`` - The post-lag phase growth rate. - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LinearCapAndLagModel_s0`` - The initial size - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LinearCapAndLagModel_lambda`` - The duration of the lag phase - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LinearCapAndLagModel_alpha`` - lag phase transition sharpness - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``LinearCapAndLagModel_smax`` - Carrying capacity used by the model. Either the user-provided scalar or the per-group observed maximum. - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LinearCapAndLagModel_beta`` - Saturation transition sharpness. Fitted per-group when a saturation shoulder is detected and ``beta`` is ``None`` at construction; held at the user-provided scalar (or the module default) when no shoulder is present. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``LinearCapAndLagModel_mode`` - Fit variant selected per-group: 'fixed_beta' (beta held at the user-provided or module-default value) or 'fitted_beta' (beta fitted as a 5th free parameter when a saturation shoulder is detected). - :bdg-ref-secondary:`Quality ` .. _measurement-info-edge-correction: :doc:`EDGE_CORRECTION ` ----------------------------------------------------------------------------- .. list-table:: Category: **EdgeCorrection** :header-rows: 1 * - Column label - Description - Type * - ``EdgeCorrection_Cap`` - The carrying capacity for the target measurement - :bdg-ref-info:`Derived ` * - ``EdgeCorrection_NewVal`` - The new value of the target measurement - :bdg-ref-info:`Derived ` .. _measurement-info-errorcategory: :doc:`ErrorCategory ` ------------------------------------------------------------------------- .. list-table:: Category: **ErrorCategory** :header-rows: 1 * - Column label - Description - Type * - ``ErrorCategory_oversegmented`` - One colony split into multiple detections. - :bdg-ref-secondary:`Quality ` * - ``ErrorCategory_undersegmented`` - A single colony under-detected — its mask captured too small or only partially covering the colony. - :bdg-ref-secondary:`Quality ` * - ``ErrorCategory_merged`` - Multiple touching colonies detected as one object. - :bdg-ref-secondary:`Quality ` * - ``ErrorCategory_background_noise`` - Not a colony — agar texture, reflection, or vignette. - :bdg-ref-secondary:`Quality ` * - ``ErrorCategory_debris`` - Dust, scratch, bubble, or other plate artifact. - :bdg-ref-secondary:`Quality ` * - ``ErrorCategory_other`` - Removed without a specified reason (the catch-all bucket). - :bdg-ref-secondary:`Quality ` .. _measurement-info-grid: :doc:`GRID ` ------------------------------------------------------- .. list-table:: Category: **Grid** :header-rows: 1 * - Column label - Description - Type * - ``Grid_RowNum`` - The row idx of the object - :bdg-ref-muted:`Identity / design ` * - ``Grid_RowIntervalStart`` - The start of the row interval of the object - :bdg-ref-muted:`Identity / design ` * - ``Grid_RowIntervalEnd`` - The end of the row interval of the object - :bdg-ref-muted:`Identity / design ` * - ``Grid_ColNum`` - The column idx of the object - :bdg-ref-muted:`Identity / design ` * - ``Grid_ColIntervalStart`` - The start of the column interval of the object - :bdg-ref-muted:`Identity / design ` * - ``Grid_ColIntervalEnd`` - The end of the column interval of the object - :bdg-ref-muted:`Identity / design ` * - ``Grid_RowMajorIdx`` - The row-major index of the object. Row major is the standard in most programming and data science array libraries. Used for indexing into 2D arrays. - :bdg-ref-muted:`Identity / design ` * - ``Grid_ColMajorIdx`` - The col-major index of the object in an array. Lab automation logic uses column-major (column-wise) indexing for well plate operations because 96-well plates are physically arranged with 8 rows (labeled A-H) and 12 columns (numbered 1-12), and this layout maps directly to how multichannel pipettes operate. - :bdg-ref-muted:`Identity / design ` .. _measurement-info-grid-linreg-stats: :doc:`GRID_LINREG_STATS ` --------------------------------------------------------------------------------- .. list-table:: Category: **GridLinReg** :header-rows: 1 * - Column label - Description - Type * - ``GridLinReg_RowM`` - Slope of row-wise linear regression fit across column positions. Measures systematic drift in row alignment. Values near 0 indicate horizontal rows; non-zero values suggest rotational misalignment or systematic row curvature across the plate. - :bdg-ref-secondary:`Quality ` * - ``GridLinReg_RowB`` - Intercept of row-wise linear regression fit. Represents the expected row coordinate when column position is 0. Combined with slope, defines the expected row trend line for quality assessment and position prediction. - :bdg-ref-secondary:`Quality ` * - ``GridLinReg_ColM`` - Slope of column-wise linear regression fit across row positions. Measures systematic drift in column alignment. Values near 0 indicate vertical columns; non-zero values suggest rotational misalignment or systematic column curvature across the plate. - :bdg-ref-secondary:`Quality ` * - ``GridLinReg_ColB`` - Intercept of column-wise linear regression fit. Represents the expected column coordinate when row position is 0. Combined with slope, defines the expected column trend line for quality assessment and position prediction. - :bdg-ref-secondary:`Quality ` * - ``GridLinReg_PredRR`` - Predicted row coordinate from column-wise linear regression. Uses the column position and column regression parameters (ColM, ColB) to estimate where the row coordinate should be if the grid were perfectly aligned. Used for calculating residual errors and detecting misaligned colonies. - :bdg-ref-secondary:`Quality ` * - ``GridLinReg_PredCC`` - Predicted column coordinate from row-wise linear regression. Uses the row position and row regression parameters (RowM, RowB) to estimate where the column coordinate should be if the grid were perfectly aligned. Used for calculating residual errors and detecting misaligned colonies. - :bdg-ref-secondary:`Quality ` * - ``GridLinReg_ResidualError`` - Euclidean distance between the actual colony centroid and the predicted position from linear regression. Quantifies how far each colony deviates from the expected grid pattern. High values indicate misdetections, off-grid growth, or local plate warping. Used by refinement operations to filter outliers and select the most plausible colony per grid cell. - :bdg-ref-secondary:`Quality ` .. _measurement-info-neighbor-dist: :doc:`NEIGHBOR_DIST ` ------------------------------------------------------------------------- .. list-table:: Category: **GridSpatial** :header-rows: 1 * - Column label - Description - Type * - ``GridSpatial_LeftNeighborObjLabel`` - The object label of the left neighbor colony - :bdg-ref-secondary:`Quality ` * - ``GridSpatial_LeftDistance`` - The minimum pixel-to-pixel distance to the left neighbor colony, computed via a Euclidean distance transform of object pixel masks - :bdg-ref-secondary:`Quality ` * - ``GridSpatial_RightNeighborObjLabel`` - The object label of the right neighbor colony - :bdg-ref-secondary:`Quality ` * - ``GridSpatial_RightDistance`` - The minimum pixel-to-pixel distance to the right neighbor colony, computed via a Euclidean distance transform of object pixel masks - :bdg-ref-secondary:`Quality ` * - ``GridSpatial_AboveNeighborObjLabel`` - The object label of the above neighbor colony - :bdg-ref-secondary:`Quality ` * - ``GridSpatial_AboveDistance`` - The minimum pixel-to-pixel distance to the above neighbor colony, computed via a Euclidean distance transform of object pixel masks - :bdg-ref-secondary:`Quality ` * - ``GridSpatial_UnderNeighborObjLabel`` - The object label of the under neighbor colony - :bdg-ref-secondary:`Quality ` * - ``GridSpatial_UnderDistance`` - The minimum pixel-to-pixel distance to the under neighbor colony, computed via a Euclidean distance transform of object pixel masks - :bdg-ref-secondary:`Quality ` .. _measurement-info-grid-spread: :doc:`GRID_SPREAD ` --------------------------------------------------------------------- .. list-table:: Category: **GridSpread** :header-rows: 1 * - Column label - Description - Type * - ``GridSpread_ObjectSpread`` - Sum of squared pairwise Euclidean distances between all unique colony pairs within a grid section. Quantifies spatial dispersion of colonies in a grid cell. Higher values indicate greater spread from the section center, suggesting over-segmentation, multi-detections, or colonies growing beyond expected boundaries. Used to identify problematic grid sections requiring refinement or quality review. - :bdg-ref-secondary:`Quality ` .. _measurement-info-intensity: :doc:`INTENSITY ` ----------------------------------------------------------------- .. list-table:: Category: **Intensity** :header-rows: 1 * - Column label - Description - Type * - ``Intensity_IntegratedIntensity`` - The sum of the object's pixels - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_Density`` - The ratio of the object's intensity to the max possible intensity of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_ConvexDensity`` - The ratio of the objects intensity to the max possible intensity of the object's convex hull - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_MinimumIntensity`` - The minimum intensity of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_MaximumIntensity`` - The maximum intensity of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_MeanIntensity`` - The mean intensity of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_MedianIntensity`` - The median intensity of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_StandardDeviationIntensity`` - The standard deviation of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_CoefficientVarianceIntensity`` - The coefficient of variation of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_LowerQuartileIntensity`` - The lower quartile intensity of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_UpperQuartileIntensity`` - The upper quartile intensity of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Intensity_InterquartileRangeIntensity`` - The interquartile range of the object - :bdg-ref-success:`Tier 1 · Direct phenotype ` .. _measurement-info-linear-lag-model: :doc:`LINEAR_LAG_MODEL ` ------------------------------------------------------------------------------- .. list-table:: Category: **LinearLagModel** :header-rows: 1 * - Column label - Description - Type - Biology * - ``LinearLagModel_v`` - The post-lag phase growth rate. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - The post-lag phase growth rate using the target metric (usually radius) * - ``LinearLagModel_s0`` - The initial value of the target metric - :bdg-ref-success:`Tier 1 · Direct phenotype ` - The initial size * - ``LinearLagModel_lambda`` - The duration of the lag phase - :bdg-ref-success:`Tier 1 · Direct phenotype ` - * - ``LinearLagModel_alpha`` - lag phase transition sharpness - :bdg-ref-primary:`Tier 2 · Descriptive trait ` - .. _measurement-info-log-growth-model: :doc:`LOG_GROWTH_MODEL ` ------------------------------------------------------------------------------- .. list-table:: Category: **LogGrowthModel** :header-rows: 1 * - Column label - Description - Type * - ``LogGrowthModel_r`` - The intrinsic growth rate - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LogGrowthModel_K`` - The carrying capacity - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LogGrowthModel_N0`` - The initial number of the colony size metric being fitted - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LogGrowthModel_lambda`` - The regularization factor applied to the max specific growth rate and initial population size - :bdg-ref-secondary:`Quality ` * - ``LogGrowthModel_beta`` - The penalty factor applied to relative difference of the carrying capacity from the largest measurement - :bdg-ref-secondary:`Quality ` * - ``LogGrowthModel_µmax`` - The growth rate of the colony calculated as (K*r)/4 - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``LogGrowthModel_Kmax`` - The upper bound of the carrying capacity for model fitting - :bdg-ref-secondary:`Quality ` .. _measurement-info-model-metrics: :doc:`MODEL_METRICS ` ------------------------------------------------------------------------- .. list-table:: Category: **ModelMetrics** :header-rows: 1 * - Column label - Description - Type * - ``ModelMetrics_MAE`` - The mean absolute error - :bdg-ref-secondary:`Quality ` * - ``ModelMetrics_MSE`` - The mean squared error - :bdg-ref-secondary:`Quality ` * - ``ModelMetrics_RMSE`` - The root mean squared error - :bdg-ref-secondary:`Quality ` * - ``ModelMetrics_R2`` - The coefficient of determination - :bdg-ref-secondary:`Quality ` * - ``ModelMetrics_NumSamples`` - The number of samples used for model fitting - :bdg-ref-secondary:`Quality ` * - ``ModelMetrics_OptimizerLoss`` - The loss of model fitting - :bdg-ref-secondary:`Quality ` * - ``ModelMetrics_OptimizerStatus`` - The output of the optimizer status - :bdg-ref-secondary:`Quality ` .. _measurement-info-object: :doc:`OBJECT ` ----------------------------------------------------------- .. list-table:: Category: **Object** :header-rows: 1 * - Column label - Description - Type * - ``Object_Label`` - Integer label uniquely identifying each detected object (colony) within its source image. Acts as the per-image primary key shared by every measurement table, letting all per-colony measurements be joined together and traced back to a single colony on the agar plate. - :bdg-ref-muted:`Identity / design ` .. _measurement-info-quality-check: :doc:`QUALITY_CHECK ` ------------------------------------------------------------------------- .. list-table:: Category: **QC** :header-rows: 1 * - Column label - Description - Type * - ``QC_Flag`` - True when the metric crosses fail_threshold in the bad direction; eligible for curation. - :bdg-ref-secondary:`Quality ` * - ``QC_Metric`` - Headline metric in the check's own units; the bad direction is set by the check's _HIGHER_IS_BAD flag. Drives Status. - :bdg-ref-secondary:`Quality ` * - ``QC_Status`` - Categorical: pass \| warn \| fail. - :bdg-ref-secondary:`Quality ` .. _measurement-info-quality-count: :doc:`QUALITY_COUNT ` ------------------------------------------------------------------------- .. list-table:: Category: **QC_Count** :header-rows: 1 * - Column label - Description - Type * - ``QC_Count_Detected`` - Detected colony count in the group. - :bdg-ref-secondary:`Quality ` * - ``QC_Count_Expected`` - Expected colony count from the metadata frame. - :bdg-ref-secondary:`Quality ` * - ``QC_Count_Delta`` - Detected − Expected (signed; negative = missing). - :bdg-ref-secondary:`Quality ` .. _measurement-info-quality-icc: :doc:`QUALITY_ICC ` --------------------------------------------------------------------- .. list-table:: Category: **QC_ICC** :header-rows: 1 * - Column label - Description - Type * - ``QC_ICC_NumSubjects`` - Distinct subjects (e.g. timepoints) in the two-way model. - :bdg-ref-secondary:`Quality ` * - ``QC_ICC_NumRaters`` - Replicates per subject in the two-way model. - :bdg-ref-secondary:`Quality ` * - ``QC_ICC_NumMembers`` - Total measurements contributing to the ICC. - :bdg-ref-secondary:`Quality ` .. _measurement-info-quality-mad: :doc:`QUALITY_MAD ` --------------------------------------------------------------------- .. list-table:: Category: **QC_MAD** :header-rows: 1 * - Column label - Description - Type * - ``QC_MAD_Median`` - Group median of the measurement. - :bdg-ref-secondary:`Quality ` * - ``QC_MAD_MAD`` - Median absolute deviation (raw, before normalization). - :bdg-ref-secondary:`Quality ` * - ``QC_MAD_NumMembers`` - Members contributing to the statistic. - :bdg-ref-secondary:`Quality ` .. _measurement-info-quality-occupancy: :doc:`QUALITY_OCCUPANCY ` --------------------------------------------------------------------------------- .. list-table:: Category: **QC_Occupancy** :header-rows: 1 * - Column label - Description - Type * - ``QC_Occupancy_Filled`` - Distinct grid cells holding at least one colony (doublets count once). - :bdg-ref-secondary:`Quality ` * - ``QC_Occupancy_Expected`` - Expected grid-cell count from the metadata frame (rows per group). - :bdg-ref-secondary:`Quality ` * - ``QC_Occupancy_Vacant`` - Expected - Filled; empty/missing grid cells in the group. - :bdg-ref-secondary:`Quality ` .. _measurement-info-quality-se: :doc:`QUALITY_SE ` ------------------------------------------------------------------- .. list-table:: Category: **QC_SE** :header-rows: 1 * - Column label - Description - Type * - ``QC_SE_Value`` - Raw SE = stddev / sqrt(n) across replicates. - :bdg-ref-secondary:`Quality ` * - ``QC_SE_Mean`` - Mean across replicates at this (group, time). - :bdg-ref-secondary:`Quality ` * - ``QC_SE_CV`` - Coefficient of variation, stddev / \|mean\|. - :bdg-ref-secondary:`Quality ` * - ``QC_SE_NumReplicates`` - Replicate count contributing to the SE. - :bdg-ref-secondary:`Quality ` .. _measurement-info-quality-tukey: :doc:`QUALITY_TUKEY ` ------------------------------------------------------------------------- .. list-table:: Category: **QC_Tukey** :header-rows: 1 * - Column label - Description - Type * - ``QC_Tukey_LowerFence`` - Lower Tukey fence, Q1 - k*IQR. - :bdg-ref-secondary:`Quality ` * - ``QC_Tukey_UpperFence`` - Upper Tukey fence, Q3 + k*IQR. - :bdg-ref-secondary:`Quality ` * - ``QC_Tukey_NumOutliers`` - Members falling outside the fences. - :bdg-ref-secondary:`Quality ` * - ``QC_Tukey_NumMembers`` - Members contributing to the statistic. - :bdg-ref-secondary:`Quality ` .. _measurement-info-quality-zmax: :doc:`QUALITY_ZMAX ` ----------------------------------------------------------------------- .. list-table:: Category: **QC_ZMax** :header-rows: 1 * - Column label - Description - Type * - ``QC_ZMax_Median`` - Group median of the measurement. - :bdg-ref-secondary:`Quality ` * - ``QC_ZMax_MAD`` - Median absolute deviation used to scale the modified Z-score. - :bdg-ref-secondary:`Quality ` * - ``QC_ZMax_NumMembers`` - Members contributing to the statistic. - :bdg-ref-secondary:`Quality ` .. _measurement-info-radial-expansion: :doc:`RADIAL_EXPANSION ` ------------------------------------------------------------------------------- .. list-table:: Category: **RadialExpansion** :header-rows: 1 * - Column label - Description - Type * - ``RadialExpansion_RobustMeanRadius`` - Trimmed mean of branch path lengths, excluding detected runner. Represents the typical radial expansion distance of hyphae from the core boundary, robust to single-runner outliers. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``RadialExpansion_MeanRadius`` - Arithmetic mean of all branch path lengths from core boundary to branch tips. Includes runner if present. Reflects overall average colony reach. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``RadialExpansion_MedianRadius`` - Median branch path length. Robust to outliers and provides a typical expansion distance. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``RadialExpansion_NumBranches`` - Number of skeleton branches extending from the core boundary to peripheral tips. Higher counts indicate denser branching morphology. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``RadialExpansion_MaxBranchLength`` - Length of the longest branch path in pixels. When a runner is detected, this equals RunnerLength. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``RadialExpansion_RunnerLength`` - Path length of the detected runner branch (the single longest outlier). NaN if no runner detected. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``RadialExpansion_RunnerDetected`` - Boolean flag (0 or 1) indicating whether an outlier runner branch was detected for this colony. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``RadialExpansion_CoreRadius`` - Radius of the dense colony core as determined by PELT changepoint detection on the radial density profile. Pixels within this radius of the intensity-weighted centroid are excluded from skeleton analysis. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` .. _measurement-info-shape: :doc:`SHAPE ` --------------------------------------------------------- .. list-table:: Category: **Shape** :header-rows: 1 * - Column label - Description - Type - Biology - Image * - ``Shape_Area`` - Total number of pixels occupied by the microbial colony. Represents colony biomass and growth extent on agar plates. Larger areas typically indicate more robust growth or longer incubation times. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - Projected 2D footprint of the colony in pixels — a common proxy for colony size and overall growth in arrayed plate assays. With matched imaging and incubation, larger area generally reflects greater proliferation or spreading; it captures only the 2D footprint, not colony height or cell density. - .. image:: /_static/measurements/shape/area.png :width: 110px * - ``Shape_Perimeter`` - Total length of the colony's outer boundary in pixels. Measures colony edge complexity and surface irregularity. Smooth, circular colonies have shorter perimeters relative to their area compared to irregular or filamentous colonies. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_Circularity`` - Calculated as :math:`\frac{4\pi*\text{Area}}{\text{Perimeter}^2}`. Measures how closely a colony approximates a perfect circle (value = 1). Values < 1 indicate irregular colony morphology, which may result from genetic mutations, environmental stress, or mixed microbial populations on agar plates. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` - - * - ``Shape_ConvexArea`` - Area of the smallest convex polygon that completely contains the colony. Represents the colony's "filled-in" appearance if all indentations and holes were removed. Useful for detecting colony spreading patterns or invasive growth characteristics. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_MedianRadius`` - Median distance from colony center to edge across all directions. Provides a robust measure of typical colony size that is less sensitive to outliers than mean width. Particularly useful for colonies with uneven growth or sectoring. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_MeanRadius`` - Average distance from colony center to edge across all directions. Represents overall colony expansion rate. In arrayed growth assays, this correlates with microbial fitness and growth kinetics under controlled conditions. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_MaxRadius`` - Maximum distance from colony center to edge across all directions. Represents the furthest extent of colony growth from its center. In arrayed microbial assays, this measurement helps identify asymmetric growth patterns or colonies extending toward neighboring positions. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_MinFeretDiameter`` - Minimum caliper diameter - the shortest distance between two parallel tangent lines touching opposite sides of the colony. Represents the narrowest dimension of the colony regardless of orientation. Useful for detecting elongated or irregular colony morphologies and measuring colony width. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_MaxFeretDiameter`` - Maximum caliper diameter - the longest distance between two parallel tangent lines touching opposite sides of the colony. Represents the maximum dimension of the colony regardless of orientation. Often exceeds major axis length for irregular shapes and helps quantify maximum colony extent. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_Eccentricity`` - Measure of colony elongation, ranging from 0 (perfect circle) to 1 (highly elongated). Values near 0 indicate compact, radially symmetric growth typical of healthy bacterial colonies, while higher values may suggest directional growth, motility, or environmental gradients on the agar surface. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` - - * - ``Shape_Solidity`` - Ratio of actual colony area to its convex hull area (Area/ConvexArea). Values near 1 indicate compact, solid colonies with minimal indentations. Lower values (< 0.9) may indicate invasive growth, colony spreading, or the presence of clearing zones around colonies. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` - - * - ``Shape_Extent`` - Ratio of colony area to its bounding box area (ObjectArea/BboxArea). Measures how efficiently the colony fills its allocated space. Compact colonies have higher extent values, while spread-out or irregular colonies have lower values. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` - - * - ``Shape_BboxArea`` - Area of the smallest rectangle that completely contains the colony. Represents the total spatial shape of the colony including any empty space. In high-throughput assays, this helps assess colony positioning and potential interference with neighboring colonies. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_MajorAxisLength`` - Length of the longest axis of the ellipse that best fits the colony shape. Represents the maximum colony dimension. In arrayed microbial growth, this measurement helps identify colonies that have grown beyond their intended grid positions. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_MinorAxisLength`` - Length of the shortest axis of the ellipse that best fits the colony shape. Represents the minimum colony dimension. Together with major axis length, this helps characterize colony aspect ratio and growth anisotropy. - :bdg-ref-success:`Tier 1 · Direct phenotype ` - - * - ``Shape_Compactness`` - Calculated as :math:`\frac{\text{Perimeter}^2}{4\pi*\text{Area}}`. Inverse of circularity (ranges from 1 for perfect circles to higher values for irregular shapes). Measures colony shape complexity - compact, circular colonies have values near 1, while irregular or filamentous colonies have much higher values. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` - - * - ``Shape_Orientation`` - Angle (in radians) between the colony's major axis and the horizontal axis. Measures colony alignment and growth directionality. Random orientations are typical for most bacterial colonies, while consistent orientations may indicate environmental gradients or mechanical stresses during plating. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` - - .. _measurement-info-size: :doc:`SIZE ` ------------------------------------------------------- .. list-table:: Category: **Size** :header-rows: 1 * - Column label - Description - Type * - ``Size_Area`` - Total number of pixels occupied by the microbial colony.Larger areas typically indicate more robust growth or longer incubation times. - :bdg-ref-success:`Tier 1 · Direct phenotype ` * - ``Size_IntegratedIntensity`` - The sum of the object's grayscale pixels. Calculated as :math:`\sum{\text{pixel values}} \times \text{area}`. - :bdg-ref-success:`Tier 1 · Direct phenotype ` .. _measurement-info-orientation-zone-diagnostic: :doc:`ORIENTATION_ZONE_DIAGNOSTIC ` ----------------------------------------------------------------------------------------------------- .. list-table:: Category: **OrientZones** :header-rows: 1 * - Column label - Description - Type * - ``OrientZones_OutwardRotationRawPeak-Mask-Overall`` - Largest absolute cumulative literal skeleton-ring rotation from the inferred inoculum boundary through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. This raw maximum is outlier-sensitive and should be compared with the primary sustained peak. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRawPeak-Mask-Dense`` - Largest absolute cumulative literal skeleton-ring rotation from the inferred inoculum boundary to dense_end. Reported in degrees, nonnegative with no fixed upper bound. This raw maximum is outlier-sensitive and should be compared with the primary sustained peak. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRawPeak-Mask-Sparse`` - Largest absolute cumulative literal skeleton-ring rotation from dense_end through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. This raw maximum is outlier-sensitive. Cumulative rotation is not rebased at dense_end, so this Sparse magnitude may include rotation accumulated while the profile was in Dense. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationP90-Mask-Overall`` - 90th percentile of absolute cumulative literal skeleton-ring rotation over supported rings from the inferred inoculum boundary through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. This validation comparator ignores radial order. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationP90-Mask-Dense`` - 90th percentile of absolute cumulative literal skeleton-ring rotation over supported rings from the inferred inoculum boundary to dense_end. Reported in degrees, nonnegative with no fixed upper bound. This validation comparator ignores radial order. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationP90-Mask-Sparse`` - 90th percentile of absolute cumulative literal skeleton-ring rotation over supported rings from dense_end through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. This comparator ignores radial order. Cumulative rotation is not rebased at dense_end, so this Sparse magnitude may include rotation accumulated while the profile was in Dense. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationP95-Mask-Overall`` - 95th percentile of absolute cumulative literal skeleton-ring rotation over supported rings from the inferred inoculum boundary through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. With few supported rings it remains close to the raw maximum and is not the primary robust metric. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationP95-Mask-Dense`` - 95th percentile of absolute cumulative literal skeleton-ring rotation over supported rings from the inferred inoculum boundary to dense_end. Reported in degrees, nonnegative with no fixed upper bound. With few supported rings it remains close to the raw maximum. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationP95-Mask-Sparse`` - 95th percentile of absolute cumulative literal skeleton-ring rotation over supported rings from dense_end through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. Cumulative rotation is not rebased at dense_end, so this Sparse magnitude may include rotation accumulated while the profile was in Dense. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationMedianMagnitude-Mask-Overall`` - Median absolute cumulative literal skeleton-ring rotation over supported rings from the inferred inoculum boundary through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. This validation comparator describes typical magnitude but ignores radial order and localized outer turns. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationMedianMagnitude-Mask-Dense`` - Median absolute cumulative literal skeleton-ring rotation over supported rings from the inferred inoculum boundary to dense_end. Reported in degrees, nonnegative with no fixed upper bound. This validation comparator describes typical magnitude but ignores radial order. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationMedianMagnitude-Mask-Sparse`` - Median absolute cumulative literal skeleton-ring rotation over supported rings from dense_end through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. Cumulative rotation is not rebased at dense_end, so this Sparse magnitude may include rotation accumulated while the profile was in Dense. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationAbsoluteArea-Mask-Overall`` - Trapezoidal area under absolute cumulative rotation within supported runs from the inferred inoculum boundary through the full detected object extent, divided by their total supported radial span. Reported in degrees, nonnegative with no fixed upper bound. It describes radially persistent rotation but can remain high after one early step. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationAbsoluteArea-Mask-Dense`` - Trapezoidal area under absolute cumulative rotation within supported runs from the inferred inoculum boundary to dense_end, divided by their total supported radial span. Reported in degrees, nonnegative with no fixed upper bound. It describes radially persistent rotation but can remain high after one early step. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationAbsoluteArea-Mask-Sparse`` - Trapezoidal area under absolute cumulative rotation within supported runs from dense_end through the full detected object extent, divided by their total supported radial span. Reported in degrees, nonnegative with no fixed upper bound. Cumulative rotation is not rebased at dense_end, so this Sparse magnitude may include rotation accumulated while the profile was in Dense. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationTotalVariation-Mask-Overall`` - Sum of absolute adjacent cumulative-rotation changes within supported runs from the inferred inoculum boundary through the full detected object extent, without bridging gaps. Reported in degrees, nonnegative with no fixed upper bound. It is sensitive to oscillation, profile length, and noise and is diagnostic only. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationTotalVariation-Mask-Dense`` - Sum of absolute adjacent cumulative-rotation changes within supported runs from the inferred inoculum boundary to dense_end, without bridging gaps. Reported in degrees, nonnegative with no fixed upper bound. It is sensitive to oscillation, profile length, and noise and is diagnostic only. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationTotalVariation-Mask-Sparse`` - Sum of absolute adjacent cumulative-rotation changes within supported runs from dense_end through the full detected object extent, without bridging gaps. Reported in degrees, nonnegative with no fixed upper bound. It is sensitive to oscillation, profile length, and noise and is diagnostic only. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRateGradient-Mask-Overall`` - Outer-half robust rotation rate minus inner-half robust rotation rate, divided by the separation of their median radii, along the longest supported run from the inferred inoculum boundary through the full detected object extent. Reported in signed degrees per pixel squared. This is a spatial rate gradient, not temporal acceleration, and is NaN unless the run meets both the configured minimum and eight rings. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRateGradient-Mask-Dense`` - Outer-half robust rotation rate minus inner-half robust rotation rate, divided by the separation of their median radii, along the longest supported run from the inferred inoculum boundary to dense_end. Reported in signed degrees per pixel squared. This is a spatial rate gradient, not temporal acceleration, and is NaN unless the run meets both the configured minimum and eight rings. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRateGradient-Mask-Sparse`` - Outer-half robust rotation rate minus inner-half robust rotation rate, divided by the separation of their median radii, along the longest supported run from dense_end through the full detected object extent. Reported in signed degrees per pixel squared. This is a spatial rate gradient, not temporal acceleration, and is NaN for runs shorter than the larger of eight rings and the configured minimum. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRingSupport-Mask-Overall`` - Fraction of candidate literal sampling rings from the inferred inoculum boundary through the full detected object extent with a finite cumulative-rotation state. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRingSupport-Mask-Dense`` - Fraction of candidate literal sampling rings from the inferred inoculum boundary to dense_end with a finite cumulative-rotation state. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRingSupport-Mask-Sparse`` - Fraction of candidate literal sampling rings from dense_end through the full detected object extent with a finite cumulative-rotation state. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRunSpanSupport-Mask-Overall`` - Radial span of the longest contiguous supported literal-crossing run divided by the full candidate span from the inferred inoculum boundary through the full detected object extent. Dimensionless in [0, 1]. This reports continuity of usable evidence, not orientation. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRunSpanSupport-Mask-Dense`` - Radial span of the longest contiguous supported literal-crossing run divided by the full candidate span from the inferred inoculum boundary to dense_end. Dimensionless in [0, 1]. This reports continuity of usable evidence, not orientation. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationRunSpanSupport-Mask-Sparse`` - Radial span of the longest contiguous supported literal-crossing run divided by the full candidate span from dense_end through the full detected object extent. Dimensionless in [0, 1]. This reports continuity of usable evidence, not orientation. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationMedianResultant-Mask-Overall`` - Median doubled-angle resultant of crossing orientations among eligible literal rings from the inferred inoculum boundary through the full detected object extent. Dimensionless in [0, 1]; larger values mean stronger within-ring axial agreement. This is an orientation-reliability diagnostic, not a rotation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationMedianResultant-Mask-Dense`` - Median doubled-angle resultant of crossing orientations among eligible literal rings from the inferred inoculum boundary to dense_end. Dimensionless in [0, 1]; larger values mean stronger within-ring axial agreement. This is an orientation-reliability diagnostic, not a rotation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardRotationMedianResultant-Mask-Sparse`` - Median doubled-angle resultant of crossing orientations among eligible literal rings from dense_end through the full detected object extent. Dimensionless in [0, 1]; larger values mean stronger within-ring axial agreement. This is an orientation-reliability diagnostic, not a rotation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Concentration-Radial-Overall`` - Coherence-weighted resultant length R of the doubled-angle orientation field over all tile pixels in the full symmetric disk (0 .. symmetric_radius) region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = isotropic. NaN when the summed coherence over the selector is ~0 or the zone has zero width. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Concentration-Radial-Dense`` - Coherence-weighted resultant length R of the doubled-angle orientation field over all tile pixels in the dense ring (core_end .. dense_end radii) region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = isotropic. NaN when the summed coherence over the selector is ~0 or the zone has zero width. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Concentration-Radial-Sparse`` - Coherence-weighted resultant length R of the doubled-angle orientation field over all tile pixels in the sparse ring (dense_end .. sparse_end radii) region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = isotropic. NaN when the summed coherence over the selector is ~0 or the zone has zero width. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Concentration-Mask-Overall`` - Coherence-weighted resultant length R of the doubled-angle orientation field over detected-object pixels in the full symmetric disk (0 .. symmetric_radius) region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = isotropic. NaN when the summed coherence over the selector is ~0 or the zone has zero width. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Concentration-Mask-Dense`` - Coherence-weighted resultant length R of the doubled-angle orientation field over detected-object pixels in the dense ring (core_end .. dense_end radii) region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = isotropic. NaN when the summed coherence over the selector is ~0 or the zone has zero width. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Concentration-Mask-Sparse`` - Coherence-weighted resultant length R of the doubled-angle orientation field over detected-object pixels in the sparse ring (dense_end .. sparse_end radii) region. Dimensionless in [0, 1]; 1 = perfectly aligned hyphae, 0 = isotropic. NaN when the summed coherence over the selector is ~0 or the zone has zero width. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Turning-Radial-Overall`` - Coherence-weighted mean orientation-gradient magnitude <\|grad phi\|> over all tile pixels in the full symmetric disk (0 .. symmetric_radius) region, in degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 indicates straight parallel growth. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Turning-Radial-Dense`` - Coherence-weighted mean orientation-gradient magnitude <\|grad phi\|> over all tile pixels in the dense ring (core_end .. dense_end radii) region, in degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 indicates straight parallel growth. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Turning-Radial-Sparse`` - Coherence-weighted mean orientation-gradient magnitude <\|grad phi\|> over all tile pixels in the sparse ring (dense_end .. sparse_end radii) region, in degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 indicates straight parallel growth. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Turning-Mask-Overall`` - Coherence-weighted mean orientation-gradient magnitude <\|grad phi\|> over detected-object pixels in the full symmetric disk (0 .. symmetric_radius) region, in degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 indicates straight parallel growth. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Turning-Mask-Dense`` - Coherence-weighted mean orientation-gradient magnitude <\|grad phi\|> over detected-object pixels in the dense ring (core_end .. dense_end radii) region, in degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 indicates straight parallel growth. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Turning-Mask-Sparse`` - Coherence-weighted mean orientation-gradient magnitude <\|grad phi\|> over detected-object pixels in the sparse ring (dense_end .. sparse_end radii) region, in degrees per pixel. Higher values indicate curving/fanning hyphae; ~0 indicates straight parallel growth. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Coherence-Radial-Overall`` - Mean structure-tensor coherence C over all tile pixels in the full symmetric disk (0 .. symmetric_radius) region. Dimensionless in [0, 1]; a confidence/QC readout for how well orientation is defined there (low where texture is isotropic). - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Coherence-Radial-Dense`` - Mean structure-tensor coherence C over all tile pixels in the dense ring (core_end .. dense_end radii) region. Dimensionless in [0, 1]; a confidence/QC readout for how well orientation is defined there (low where texture is isotropic). - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Coherence-Radial-Sparse`` - Mean structure-tensor coherence C over all tile pixels in the sparse ring (dense_end .. sparse_end radii) region. Dimensionless in [0, 1]; a confidence/QC readout for how well orientation is defined there (low where texture is isotropic). - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Coherence-Mask-Overall`` - Mean structure-tensor coherence C over detected-object pixels in the full symmetric disk (0 .. symmetric_radius) region. Dimensionless in [0, 1]; a confidence/QC readout for how well orientation is defined there (low where texture is isotropic). - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Coherence-Mask-Dense`` - Mean structure-tensor coherence C over detected-object pixels in the dense ring (core_end .. dense_end radii) region. Dimensionless in [0, 1]; a confidence/QC readout for how well orientation is defined there (low where texture is isotropic). - :bdg-ref-secondary:`Quality ` * - ``OrientZones_Coherence-Mask-Sparse`` - Mean structure-tensor coherence C over detected-object pixels in the sparse ring (dense_end .. sparse_end radii) region. Dimensionless in [0, 1]; a confidence/QC readout for how well orientation is defined there (low where texture is isotropic). - :bdg-ref-secondary:`Quality ` * - ``OrientZones_RadialTilt-Mask-Overall`` - Equal-angular-sector mean of the coherence-weighted absolute axial difference between the local fiber axis and the outward radial spoke at the same pixel, over detected-object pixels in the full symmetric disk (0 .. symmetric_radius) region. Reported in degrees in [0, 90]; 0 = locally radial and 90 = locally tangential. Each occupied 10-degree angular sector contributes equally. For a fixed set of reliable sectors, multiplying branch evidence without changing within-sector tilt distributions leaves the result unchanged. A support-threshold crossing can add a newly reliable sector and change the estimate; mixed orientations within one sector remain pixel-weighted. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_RadialTilt-Mask-Dense`` - Equal-angular-sector mean of the coherence-weighted absolute axial difference between the local fiber axis and the outward radial spoke at the same pixel, over detected-object pixels in the dense ring (core_end .. dense_end radii) region. Reported in degrees in [0, 90]; 0 = locally radial and 90 = locally tangential. Each occupied 10-degree angular sector contributes equally. For a fixed set of reliable sectors, multiplying branch evidence without changing within-sector tilt distributions leaves the result unchanged. A support-threshold crossing can add a newly reliable sector and change the estimate; mixed orientations within one sector remain pixel-weighted. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_RadialTilt-Mask-Sparse`` - Equal-angular-sector mean of the coherence-weighted absolute axial difference between the local fiber axis and the outward radial spoke at the same pixel, over detected-object pixels in the sparse ring (dense_end .. sparse_end radii) region. Reported in degrees in [0, 90]; 0 = locally radial and 90 = locally tangential. Each occupied 10-degree angular sector contributes equally. For a fixed set of reliable sectors, multiplying branch evidence without changing within-sector tilt distributions leaves the result unchanged. A support-threshold crossing can add a newly reliable sector and change the estimate; mixed orientations within one sector remain pixel-weighted. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardTurning-Mask-Overall`` - Equal-angular-sector mean radial derivative magnitude of the radial-relative fiber tilt, over detected-object pixels in the full symmetric disk (0 .. symmetric_radius) region. Reported in degrees per pixel. 0 means the tilt stays constant while moving outward; larger values mean the local fiber field rotates relative to its radial spoke. The aggregation gives each occupied 10-degree angular sector equal weight. This is a field-level curvature measure, not parent-to-daughter branch tracking. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardTurning-Mask-Dense`` - Equal-angular-sector mean radial derivative magnitude of the radial-relative fiber tilt, over detected-object pixels in the dense ring (core_end .. dense_end radii) region. Reported in degrees per pixel. 0 means the tilt stays constant while moving outward; larger values mean the local fiber field rotates relative to its radial spoke. The aggregation gives each occupied 10-degree angular sector equal weight. This is a field-level curvature measure, not parent-to-daughter branch tracking. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_OutwardTurning-Mask-Sparse`` - Equal-angular-sector mean radial derivative magnitude of the radial-relative fiber tilt, over detected-object pixels in the sparse ring (dense_end .. sparse_end radii) region. Reported in degrees per pixel. 0 means the tilt stays constant while moving outward; larger values mean the local fiber field rotates relative to its radial spoke. The aggregation gives each occupied 10-degree angular sector equal weight. This is a field-level curvature measure, not parent-to-daughter branch tracking. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_RadialSectorSupport-Mask-Overall`` - Fraction of the 36 fixed 10-degree sectors in the full symmetric disk (0 .. symmetric_radius) region that contain at least three detected-structure pixels with structure-tensor coherence C >= 0.15. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic for interpreting radial tilt and outward turning, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_RadialSectorSupport-Mask-Dense`` - Fraction of the 36 fixed 10-degree sectors in the dense ring (core_end .. dense_end radii) region that contain at least three detected-structure pixels with structure-tensor coherence C >= 0.15. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic for interpreting radial tilt and outward turning, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_RadialSectorSupport-Mask-Sparse`` - Fraction of the 36 fixed 10-degree sectors in the sparse ring (dense_end .. sparse_end radii) region that contain at least three detected-structure pixels with structure-tensor coherence C >= 0.15. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic for interpreting radial tilt and outward turning, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotation-Mask-Overall`` - Equal-cell mean absolute seam-safe axial change between matching 10-degree sectors in configured-width Sholl-style annular bands (8 pixels by default) whose centres are separated by the configured long-range lag (16 pixels by default). Ring pairs are assigned to the core-excluded symmetric region (core_end .. min(sparse_end, symmetric_radius)) region by their midpoint. Reported in degrees in [0, 90]. Annular bands begin outside the inferred inoculum core. Each reliable ring-sector comparison contributes equally, so multiplying same-orientation branch evidence within an already reliable cell does not change its contribution. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotation-Mask-Dense`` - Equal-cell mean absolute seam-safe axial change between matching 10-degree sectors in configured-width Sholl-style annular bands (8 pixels by default) whose centres are separated by the configured long-range lag (16 pixels by default). Ring pairs are assigned to the dense ring (core_end .. dense_end radii) region by their midpoint. Reported in degrees in [0, 90]. Annular bands begin outside the inferred inoculum core. Each reliable ring-sector comparison contributes equally, so multiplying same-orientation branch evidence within an already reliable cell does not change its contribution. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotation-Mask-Sparse`` - Equal-cell mean absolute seam-safe axial change between matching 10-degree sectors in configured-width Sholl-style annular bands (8 pixels by default) whose centres are separated by the configured long-range lag (16 pixels by default). Ring pairs are assigned to the sparse ring (dense_end .. sparse_end radii) region by their midpoint. Reported in degrees in [0, 90]. Annular bands begin outside the inferred inoculum core. Each reliable ring-sector comparison contributes equally, so multiplying same-orientation branch evidence within an already reliable cell does not change its contribution. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_SignedLongRangeRotation-Mask-Overall`` - Signed counterpart of LongRangeRotation over the core-excluded symmetric region (core_end .. min(sparse_end, symmetric_radius)) region, in degrees in [-90, 90]. Positive means the radial-relative fiber axis rotates clockwise and negative means counterclockwise while moving outward in image coordinates. Opposing reliable ring-sector changes cancel in this directional summary; inspect the absolute metric and support alongside it. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_SignedLongRangeRotation-Mask-Dense`` - Signed counterpart of LongRangeRotation over the dense ring (core_end .. dense_end radii) region, in degrees in [-90, 90]. Positive means the radial-relative fiber axis rotates clockwise and negative means counterclockwise while moving outward in image coordinates. Opposing reliable ring-sector changes cancel in this directional summary; inspect the absolute metric and support alongside it. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_SignedLongRangeRotation-Mask-Sparse`` - Signed counterpart of LongRangeRotation over the sparse ring (dense_end .. sparse_end radii) region, in degrees in [-90, 90]. Positive means the radial-relative fiber axis rotates clockwise and negative means counterclockwise while moving outward in image coordinates. Opposing reliable ring-sector changes cancel in this directional summary; inspect the absolute metric and support alongside it. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotationSupport-Mask-Overall`` - Fraction of fixed-lag ring-sector comparison cells assigned to the core-excluded symmetric region (core_end .. min(sparse_end, symmetric_radius)) region that have reliable orientation estimates at both radii. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotationSupport-Mask-Dense`` - Fraction of fixed-lag ring-sector comparison cells assigned to the dense ring (core_end .. dense_end radii) region that have reliable orientation estimates at both radii. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotationSupport-Mask-Sparse`` - Fraction of fixed-lag ring-sector comparison cells assigned to the sparse ring (dense_end .. sparse_end radii) region that have reliable orientation estimates at both radii. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotation-Mask-DenseToSparse`` - Equal-sector mean absolute seam-safe axial difference between the broad Dense-zone and Sparse-zone radial-relative fiber means. Reported in degrees in [0, 90]. Only 10-degree sectors reliable in both zones contribute, and each paired sector receives equal weight. This measures accumulated zone-to-zone rotation without detecting individual branches. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_SignedLongRangeRotation-Mask-DenseToSparse`` - Signed mean Dense-to-Sparse axial change over paired reliable 10-degree sectors, in degrees in [-90, 90]. Positive means clockwise and negative means counterclockwise radial-relative rotation while moving outward in image coordinates. Opposing sector rotations cancel. - :bdg-ref-secondary:`Quality ` * - ``OrientZones_LongRangeRotationSupport-Mask-DenseToSparse`` - Fraction of the 36 fixed 10-degree sectors with reliable radial-relative orientation estimates in both the Dense and Sparse zones. Dimensionless in [0, 1]. This is a density-sensitive quality diagnostic, not an orientation phenotype. - :bdg-ref-secondary:`Quality ` .. _measurement-info-orientation-zone-primary: :doc:`ORIENTATION_ZONE_PRIMARY ` ----------------------------------------------------------------------------------------------- .. list-table:: Category: **OrientZones** :header-rows: 1 * - Column label - Description - Type * - ``OrientZones_OutwardRotationSustainedPeak-Mask-Overall`` - Largest rolling-median absolute cumulative rotation across consecutive supported literal skeleton-ring crossings from the inferred inoculum boundary through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. The default three-ring window rejects a one-ring spike; NaN means no complete supported window. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationSustainedPeak-Mask-Dense`` - Largest rolling-median absolute cumulative rotation across consecutive supported literal skeleton-ring crossings from the inferred inoculum boundary to dense_end. Reported in degrees, nonnegative with no fixed upper bound. The default three-ring window rejects a one-ring spike; NaN means no complete supported window. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationSustainedPeak-Mask-Sparse`` - Largest rolling-median absolute cumulative rotation across consecutive supported literal skeleton-ring crossings from dense_end through the full detected object extent. Reported in degrees, nonnegative with no fixed upper bound. The default three-ring window rejects a one-ring spike; NaN means no complete supported window. Cumulative rotation is not rebased at dense_end, so this Sparse magnitude may include rotation accumulated while the profile was in Dense. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationNet-Mask-Overall`` - Outer endpoint median minus inner endpoint median of cumulative literal skeleton-ring rotation along the longest supported run from the inferred inoculum boundary through the full detected object extent. Reported in signed degrees with no fixed bounds; positive is clockwise and negative is counterclockwise while moving outward in image coordinates. NaN means the run is shorter than the configured minimum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationNet-Mask-Dense`` - Outer endpoint median minus inner endpoint median of cumulative literal skeleton-ring rotation along the longest supported run from the inferred inoculum boundary to dense_end. Reported in signed degrees with no fixed bounds; positive is clockwise and negative is counterclockwise while moving outward in image coordinates. NaN means the run is shorter than the configured minimum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationNet-Mask-Sparse`` - Outer endpoint median minus inner endpoint median of cumulative literal skeleton-ring rotation along the longest supported run from dense_end through the full detected object extent. Reported in signed degrees with no fixed bounds; positive is clockwise and negative is counterclockwise while moving outward in image coordinates. NaN means the run is shorter than the configured minimum. Because this is a difference, cumulative rotation carried into Sparse cancels from the result. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationRate-Mask-Overall`` - Median of all pairwise cumulative-rotation slopes along the longest supported literal skeleton-ring run from the inferred inoculum boundary through the full detected object extent. Reported in signed degrees per pixel; positive is clockwise and negative is counterclockwise while moving outward in image coordinates. NaN means the run is shorter than the configured minimum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationRate-Mask-Dense`` - Median of all pairwise cumulative-rotation slopes along the longest supported literal skeleton-ring run from the inferred inoculum boundary to dense_end. Reported in signed degrees per pixel; positive is clockwise and negative is counterclockwise while moving outward in image coordinates. NaN means the run is shorter than the configured minimum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationRate-Mask-Sparse`` - Median of all pairwise cumulative-rotation slopes along the longest supported literal skeleton-ring run from dense_end through the full detected object extent. Reported in signed degrees per pixel; positive is clockwise and negative is counterclockwise while moving outward in image coordinates. NaN means the run is shorter than the configured minimum. The slope is unchanged by cumulative rotation carried into Sparse. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationConsistency-Mask-Overall`` - Absolute Kendall tau-b association between radius and cumulative literal skeleton-ring rotation along the longest supported run from the inferred inoculum boundary through the full detected object extent. Dimensionless in [0, 1]; 1 is fully monotonic and values near 0 indicate reversals, plateaus, or no ordered trend. Direction is carried by the rotation rate. NaN means the run is shorter than the configured minimum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationConsistency-Mask-Dense`` - Absolute Kendall tau-b association between radius and cumulative literal skeleton-ring rotation along the longest supported run from the inferred inoculum boundary to dense_end. Dimensionless in [0, 1]; 1 is fully monotonic and values near 0 indicate reversals, plateaus, or no ordered trend. Direction is carried by the rotation rate. NaN means the run is shorter than the configured minimum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``OrientZones_OutwardRotationConsistency-Mask-Sparse`` - Absolute Kendall tau-b association between radius and cumulative literal skeleton-ring rotation along the longest supported run from dense_end through the full detected object extent. Dimensionless in [0, 1]; 1 is fully monotonic and values near 0 indicate reversals, plateaus, or no ordered trend. Direction is carried by the rotation rate, and the rank association is unchanged by rotation carried into Sparse. NaN means the run is shorter than the configured minimum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` .. _measurement-info-symmetric-zones: :doc:`SYMMETRIC_ZONES ` ----------------------------------------------------------------------------- .. list-table:: Category: **SymZones** :header-rows: 1 * - Column label - Description - Type * - ``SymZones_CoreRadius`` - Radius of the dense inoculum core, determined by PELT changepoint detection on the radial mask-density profile centered on the inoculum. Growth measurements are reported relative to this boundary. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_SymmetricRadius`` - Radial distance from the inoculum centroid at which colony growth ceases to be angularly uniform. Computed as the first radius past the core where the smoothed per-annulus circular mean resultant length of mask-boundary pixels exceeds the symmetry threshold. Equals the colony outer envelope when growth remains symmetric throughout. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_MeanExpansion`` - Mean distance of mask-boundary pixels from the inoculum centroid, measured from the core boundary outward. Captures the typical radial extent of growth past the inoculum, averaged over all angular directions. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_MaxExpansion`` - Maximum distance of any mask pixel from the inoculum centroid, measured from the core boundary outward. Captures the farthest extent of growth past the inoculum. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_CoreEndRadius`` - Mean radius of the inoculum core boundary derived from the per-angle bright/background ratio walk. Each of 360 1° angular sectors finds the outer edge of the contiguous core run (bright fraction >= tau_core); the reported value is the mean across sectors. Compare with CoreRadius (the global PELT changepoint) — close agreement indicates a well-formed core. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_DenseEndRadius`` - Mean outer radius of the dense branching zone, where mask-bright pixels dominate (bright fraction >= tau_sparse). Per-angle radii are capped at the SymmetricRadius and angularly median-smoothed before averaging. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_SparseEndRadius`` - Mean outer radius of the sparse branching zone (= colony envelope inside the symmetric growth front). Equals min(objmask outer envelope, SymmetricRadius) per angle, averaged across 360 sectors. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_CoreArea`` - Pixel^2 area of the inoculum core zone, integrated across the 360-sector polar polygon defined by the per-angle core radii. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_DenseArea`` - Pixel^2 area of the dense branching zone, the annular region between the per-angle core boundary and dense-branching boundary. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` * - ``SymZones_SparseArea`` - Pixel^2 area of the sparse branching zone, the annular region between the per-angle dense boundary and the symmetric-envelope outer boundary. - :bdg-ref-primary:`Tier 2 · Descriptive trait ` .. _measurement-info-texture: :doc:`TEXTURE ` ------------------------------------------------------------- .. list-table:: Category: **Texture** :header-rows: 1 * - Column label - Description - Type * - ``Texture_AngularSecondMoment`` - Angular second moment (energy / uniformity). Measures the degree of local homogeneity (Σ p(i,j)²). High values → uniform texture (e.g., smooth, yeast-like colonies with consistent mycelial density). Low values → heterogeneous surfaces (e.g., sectored, wrinkled, or mixed sporulation zones). Reflects colony surface regularity rather than brightness. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_Contrast`` - Contrast (local intensity variation; Σ (i–j)² p(i,j)). High values indicate strong gray-level differences (e.g., sharply defined rings, radial sectors, raised or folded regions). Low values indicate gradual tonal changes or uniformly pigmented colonies. Quantifies visual roughness and zonation amplitude. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_Correlation`` - Linear gray-level correlation between neighboring pixels. Positive, high values suggest structured spatial dependence (e.g., oriented radial hyphae or concentric patterns); near-zero values indicate uncorrelated, disordered growth (e.g., diffuse cottony mycelium). Sensitive to illumination gradients and directional GLCM computation. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_HaralickVariance`` - GLCM variance (Σ (i–μ)² p(i,j)). Captures spread of co-occurring gray-level pairs, distinct from raw intensity variance. High values → complex, multi-zone textures with variable hyphal/spore densities. Low values → consistent gray-level relationships and simpler colony surfaces. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_InverseDifferenceMoment`` - Homogeneity (Σ p(i,j) / (1 + (i–j)²)). High values → smooth, locally uniform textures (e.g., glabrous colonies, uniform aerial mycelium). Low values → abrupt gray-level changes (e.g., granular sporulation, wrinkled surfaces). Typically inversely correlated with Contrast. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_SumAverage`` - Mean of gray-level sums (Σ k·p_{x+y}(k)). Reflects the average intensity combination of neighboring pixels. In fungal colonies, can loosely parallel mean colony brightness when illumination and exposure are controlled, but remains a second-order rather than first-order intensity metric. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_SumVariance`` - Variance of gray-level sum distribution. High values → heterogeneous brightness zones (e.g., alternating dense/sparse or pigmented/non-pigmented regions). Low values → uniform tone across the colony. Often correlated with Contrast; use comparatively within one setup. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_SumEntropy`` - Entropy of the gray-level sum distribution. High values → diverse brightness combinations and irregular zonation. Low values → repetitive or periodic brightness patterns (e.g., evenly spaced rings). Indicates spatial unpredictability of summed intensities. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_Entropy`` - Global GLCM entropy (–Σ p(i,j)·log p(i,j)). Measures total texture disorder and information content. High values → complex, irregular colony surfaces (powdery, fuzzy, or sectored growth). Low values → simple, smooth, predictable patterns (glabrous or uniform colonies). Sensitive to gray-level quantization and image dynamic range. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_DiffVariance`` - Variance of gray-level difference distribution. High values → mixture of smooth and textured regions (e.g., smooth margins with wrinkled centers). Low values → consistent edge content. Highlights heterogeneity in edge magnitude across the colony. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_DiffEntropy`` - Entropy of gray-level difference distribution. High values → irregular, unpredictable intensity transitions (e.g., random sporulation or uneven mycelial networks). Low values → regular periodic transitions (e.g., concentric zonation). Reflects randomness of local contrast rather than its magnitude. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_InfoCorrelation1`` - Information measure of correlation 1. Compares joint vs marginal entropies to quantify mutual dependence between gray levels. Positive values → structured, predictable textures (e.g., organized radial growth); near-zero → independence between adjacent regions. Direction of sign varies with implementation. - :bdg-ref-warning:`Tier 3 · Discriminative feature ` * - ``Texture_InfoCorrelation2`` - Information measure of correlation 2 (√[1 – exp(–2 (H_xy2–H_xy))]). Always ≥ 0. Values approaching 1 → strong spatial dependence and organized architecture (e.g., symmetric rings, radial structure). Values near 0 → random, independent patterns. Captures nonlinear organization missed by linear correlation. - :bdg-ref-warning:`Tier 3 · Discriminative feature `