Table I. Overview of the implemented blocks in an analysis template

+, Processed.

Block (Java Classes)DescriptionVisible Light ImageFluorescence ImageNear-Infrared Image
Preprocessing
 BlRotateAlign rotation+++
 BlAlignAlign orientation+++
 BlDetectBlueMarkersDetect and delete blue markers+
 BlCutFromSideClear images+++
 BlColorBalanceVerticalVisApply vertical color balancing on visible image+
 BlColorBalanceVerticalFluoApply vertical color balancing on fluorescence image+
 BlColorCorrectionNirRemoves shading from near-infrared image+
 BlColorBalanceCircularVisNirApply circular color balancing++
Segmentation
 BlRemoveBackgroundClear background by reference image+++
 BlAdaptiveSegmentationFluoCreate intensity images for red and yellow reflectance+
 BlLabFilterApply filter in L*a*b* color space++
 BlAdaptiveThresholdNirApply adaptive threshold on near-infrared image+
 BlMedianFilterFluoApply median filter+
 BlMorphologicalOperationsApply morphological operations+++
 BlAdaptiveRemoveSmallObjectsVisFluoRemove artifacts++
 BlUseFluoMaskToClearOtherRemove artifacts by image comparison with fluorescence image++
Feature extraction
 BlSkeletonizeVisFluoCalculate the skeleton by thinning++
 BlSkeletonizeNirCalculate the skeleton by thinning+
 BlCalcWidthAndHeightDetermine plant height and width+
 BlCalcMainAxisCalculate the plant main axis growth orientation+
 BlCalcColorHistogramsCalculate overall properties (pixel count, intensities, and plant color indices)+++
 BlCalcConvexHullCalculate convex hull-based shape parameters++
 BlCalcAreasCalculate plant area based on segmentation result+++
 BlCalcVolumesEstimate plant volume (digital biomass)++
 BlDetectLeafTipsDetect leaf tips++
 BlTrackLeafTipsTrack leaf tips++
Postprocessing
 BlRunPostProcessorsDraw analysis results of feature extraction blocks+++
 BlMoveMasksToImageSetTransfer images to result image set+++
 BlHighlightNullResultsMark errors and outliers in result image set+++