Dataset DOI: 10.5061/dryad.kwh70rzm9

Description of the data and file structure

These Excel sheets contain raw phenotyping data for leaf pavement cell shape and size features measured in natural and transgenic lines of European aspen (Populus tremula) and hybrid aspen (P. tremula x tremuloides) clone T89.

Materials and methods for plant growth, leaf sampling and imaging and pavement cell shape and size analysis using the ImageJ plugin PaCeQuant are detailed in the manuscript:

Liu S, Doyle SM, Robinson KM, Rahneshan Z, Street NR and Robert S, 2026, New Phytologist

The features included in the manuscript are:

• circularity (measure of deviation from a perfect circle; 0 to 1, with 1 being a perfect circle)
• branch count (number of branches in the cell skeleton)
• lobe number (number of cell outgrowths)
• solidity (ratio of cell area to area of the cell’s convex hull, a convex polygon fitting around the cell)
• non-lobe area (µm² or pixels²; cell area excluding lobes)
• total cell area (µm² or pixels²)
• perimeter (µm or pixels)
• length and width (lengths of the major and minor axes, respectively, of an ellipse fitting around the cell) and convex hull perimeter (µm or pixels).

Lobeyness was then calculated as the convex hull perimeter divided by the cell perimeter.

In the raw data generated by PaCeQuant, most of the following features are also automatically included, depending on the version used:

• eccentricity (measure of elongation, or deviation from a circle, with 0 being circular and higher values being elongated)
• margin roughness (deviation of averaged local curvature for each contour pixel from the expected averaged angle of a perfect circle sampled the same number of times as the number of contour points measured)
• average branch length (µm or pixels; average length of branches in the cell skeleton)
• average endpoint distance (µm or pixels; average cell lobe radius at branch endpoints)
• longest path length (µm or pixels; length of the longest path connecting two endpoints in the cell skeleton)
• minimum core width (µm or pixels; estimate of the minimal width, given by twice the first quartile value of sorted measurements, of the cell's core, represented by the parts of the cell in which the skeleton is not branched)
• maximum core width (µm or pixels; estimate of the maximal width, given by twice the third quartile value of sorted measurements, of the cell's core)
• largest empty circle (pixels; size of the largest circle fitting inside the cell)
• average concavity (average of angles between tangents of neighboring points along the cell contour)
• standard deviation of concavity (standard deviation of angles between tangents of neighboring points along the cell contour)
• convex hull area (µm² or pixels²; area of the cell’s convex hull, a convex polygon fitting around the cell)
• convex hull convexity (ratio of the convex hull perimeter and the cell perimeter)
• convex hull roundness (circularity, or deviation from a perfect circle, of the cell’s convex hull)
• average lobe length (µm or pixels; average length from the baseline to the maximal tip of all lobes in the cell)
• average apical lobe length (µm or pixels; average length from the maximal tip to the equator, or line connecting the two inflection points where the sign of the curvature changes, of all lobes in the cell)
• average basal lobe length (µm or pixels; average length from the baseline to the equator of all lobes in the cell)
• average basal lobe width (µm or pixels; average baseline length of all lobes in the cell)
• average equator lobe width (µm or pixels; average equator length of all lobes in the cell)
• average length of indentations (pixels; average length from the maximal indentation point to the baseline, at the cell convex hull, of all indentations, or spacings between lobes, in the cell)
• average length of apical indentations (pixels; average length from the maximal indentation point to the equator, or line connecting the two inflection points where the sign of the curvature changes, of all indentations in the cell)
• average length of basal indentations (pixels; average length from the baseline to the equator of all indentations in the cell)
• average length of baseline indentations (pixels; average baseline length of all indentations in the cell)
• average length of equator indentations (pixels; average equator length of all indentations in the cell)

See Möller et al. (2017) Plant Physiology 175: 998-1017 for further details on the features measured by PaCeQuant.

Files and variables

File: Figures_1__S1__S2.zip

Description: Data from Figures 1, S1a-c and S2a-d in the manuscript submitted to New Phytologist. The file names are xxx_y.yyLzz, where xxx = the SwAsp line number, y.yy = the tree number and Lzz = the leaf number.

File: Figure_3.zip

Description: Data from Figure 3a-d in the manuscript submitted to New Phytologist. The file names are InVxxx_LyyM, where InVxxx = the in vitro SwAsp line number, Lyy = the leaf number and M means the middle of the leaf blade.

File: Figure_5.zip

Description: Data from Figure 5a-d in the manuscript submitted to New Phytologist. The file names are T89, myb305a-Lxx or p35S-MYB305a-Lxx, where Lxx = the genotype line number.

File: Figure_6.zip

Description: Data from Figure 6b-d in the manuscript submitted to New Phytologist. The file names are pMYB305a-GFP-Lxx, where Lxx = the leaf number.

File: Figure_7.zip

Description: Data from Figure 7a-c in the manuscript submitted to New Phytologist. The file names are T89, myb305a-Lxx or p35S-MYB305a-Lxx, where Lxx = the genotype line number.

File: Figure_S8.zip

Description: Data from Figure S8 in the manuscript submitted to New Phytologist. The file names are T89_Lxx, where Lxx = the leaf number.

File: Figure_S12.zip

Description: Data from Figure S12 in the manuscript submitted to New Phytologist. The file names are T89 or myb305ab-Lxx, where Lxx = the genotype line number.

Code/software

Microsoft Excel may be used to open the data files.