Table I. Phenotype calculations in PANorama.
The following phenotypes are written to a .csv file after running ExtractMeasures.py using the PANorama phenotype designation. For simplicity, we refer to rice phenotypes in subsequent tables using the QTL abbreviations given here. All parameters described within the table are controlled by the iftPANorama.h file.
| PANorama Phenotype Designation | Calculation | QTL Abbreviation |
|---|---|---|
| LengthOfExsertion (cm) | The distance between the EP and the IMAP. In rice, we select these points at the flag leaf ligule attachment point and the panicle notch, respectively. | EL |
| LengthOfMainAxis (cm) | The distance between the IMAP and the FMAP. In rice, we select these points at the panicle notch and inflorescence abortion point, respectively. | RL |
| InflorescenceLength (cm) | The distance between the IMAP and the tip of the longest terminal branch. In rice, the IMAP is selected at the panicle notch. | PL |
| NumberOfPrimaryBranches | A primary branch is any distinct skeleton segment that attaches (i.e. shares a neighboring pixel with the main axis) between the IMAP and the FMAP. The MINBRANCSZ parameter defines the minimum length requirement of a primary branch. | PBN |
| MeanLengthOfPrimaryBranches (cm) | The distance from the first pixel in a primary branch that borders the rachis skeleton, to the eight-neighbor pixel at the tip of a terminal seed. PBL is the average of all primary branches within a panicle. | PBL |
| MaxLengthOfPrimaryBranches (cm) | The maximum length of a primary branch within a panicle. | xPBL |
| MinLengthOfPrimaryBranches (cm) | The minimum length of a primary branch within a panicle. | nPBL |
| StdevLengthOfPrimaryBranches (cm) | The sd of the mean length of primary branches. | |
| NumberOfNodesOnMainAxis | Nodes are defined as anywhere a meristem transition has occurred. The pixels at which primary branches attach are considered nodes. If a branch forms at the IMAP and FMAP, they are also treated as nodes. Branches that attach within a specified distance of one another are automatically collapsed into a single internode point using the MINJCTDIST parameter, and the pixel closest to the geometric center of the cluster is considered the true internode point. NN is defined is as the total number of nodes in an image. | NN |
| MeanNumberOfBranchesPerNode | The average number of branches per node for all nodes within a panicle. Branches are collapsed into single nodes using the MINJCTDIST parameter, and the pixel closest to the geometric center of the cluster is considered the true node. | BpN |
| MaxNumberOfBranchesPerNode | The maximum number of branches to occur at a single node within a panicle. | xBpN |
| StdevNumberOfBranchesPerNode | The sd when calculating the number of branches per node. | |
| MeanLengthBetweenNodes (cm) | The distance between two nodes, after collapsing of primary branches. NL is the average length of all internodes in an image. | NL |
| MaxLengthBetweenNodes (cm) | The maximum distance between two nodes. | xNL |
| MinLengthBetweenNodes (cm) | The minimum distance between two nodes. | nNL |
| StdevLengthBetweenNodes (cm) | The sd of the mean length between nodes. | |
| MeanThicknessOfMainAxis (cm) | Thickness is calculated as 2× the distance between a skeleton point and its closest pixel on the image contour. Distances are obtained directly from the Euclidean distance map of the panicle mask during the skeletonization step. MeanThicknessOfMainAxis is the average of all thickness measures between the IMAP and the FMAP. | TR |
| MaxThicknessOfMainAxis (cm) | The maximum thickness between the IMAP and the FMAP. | xTR |
| StdevThicknessOfMainAxis (cm) | The sd of the mean thickness of the main axis. | |
| MeanThicknessOfExsertion (cm) | Thickness is calculated as 2× the distance between a skeleton point and its closest pixel on the image contour. Distances are obtained directly from the Euclidean distance map of the panicle mask during the skeletonization step. MeanThicknessOfExsertion is the average of all thickness measures between the EP and the IMAP. | TE |
| MaxThicknessOfExsertion (cm) | The maximum of all thickness measures between the EP and the IMAP. | xTE |
| MinThicknessOfExsertion (cm) | The minimum thickness measurement between the EP and the IMAP. | nTE |
| StdevThicknessOfExsertion (cm) | The sd of the mean thickness of exsertion. |