Quantitative dissection of color patterning in the foliar ornamental Coleus reveals underlying features driving aesthetic value

readMe.txt (this file) /Coleus_scans.zip: This directory contains 3 sub-directories:

1. raw_scans: Raw scans of coleus leaves. Data collection described below.

2. binary_leaves: A zip file of individual binary leaves isolated from the raw scans. Data processing described below.

3. colored_leaves: A zip file of individual colored leaves isolated from the raw scans using the binary leaf silhouettes. Data processing described below.

Data collection

Coleus leaf scans were collected from a starting population of 50,000 seedlings that were originally harvested from 133 open-pollinated mother plants in early January in Gainesville, FL. We organized the seedlings into families based on their maternal parents, grew the plants for five weeks and then selected ~2,000 individuals as potential new cultivars based on their foliar color patterning and branching architecture in mid-February. This data represents the youngest fully expanded leaf from each plant between 5-6 weeks of age. Leaves were imaged on Epson Perfection V550 Scanners with Kodak KOCSGS color separation guides included for color calibration. Analysis App Color analysis can be performed using an open-access software program called ColourQuant (Li et al., 2019); available on github: github.com/maoli0923/ColourQuant).

Explanation of isolated binary and colored leaf files

To isolate individual leaves from the raw data scans -  we adjusted the RGB color balance on each scan by a white balance method so that the white swatch in the Kodak KOCSGS color separation guide is pure white, to ensure that scanners were not biasing the color data. Next, we segmented the leaves from the background by converting the RGB matrix into hue-saturation-value (HSV) format. Since most background pixels become grey in HSV, this was used to set a threshold that separates grey values from true leaf values. We then used the binary leaf silhouettes to extract the individual colored leaves by setting the background to pure white, and the foreground to pure black. We manually adjusted the thresholding for leaves that could not be automatically extracted due to shadows in the scan. The binary and colored leaf folder contain outliers, including leaves that were overlapping on the scanner, very small, or broken. These can be manually removed before analysis.  

File ID Key

Files are named with the following code: Year_Family_Scan#. Files containing selected leaves for cultivar development are prepended with an “S” and files containing maternal leaf scans are prepended with an “M.”

For questions regarding released dataset contact: Margaret Frank [e-mail]

Li, M., Frank, M.H., and Migicovsky, Z.. 2019a. ColourQuant: A high throughput technique to extract and quantify colour phenotypes from plant images. arXiv 190301652. http://arxiv.org/abs/1903.01652

本说明文件（readMe.txt）/Coleus_scans.zip：该压缩包包含3个子目录：
1. 原始扫描图像目录（raw_scans）：彩叶草（Coleus）叶片的原始扫描件，数据采集流程详见下文。
2. 二值化叶片文件包（binary_leaves）：从原始扫描图像中分离出的单张二值化叶片的压缩文件，数据处理流程详见下文。
3. 彩色叶片文件包（colored_leaves）：通过二值化叶片轮廓从原始扫描图像中提取出的单张彩色叶片的压缩文件，数据处理流程详见下文。

数据采集
本次采集的彩叶草叶片扫描图像，源自初始群体50000株幼苗。这些幼苗最初于佛罗里达州盖恩斯维尔市，1月初从133株开放授粉的母本植株上收获。研究人员根据母本来源将幼苗划分为不同家系，将植株培育五周后，于2月中旬根据叶片颜色表型与分枝结构，从其中筛选出约2000株作为潜在新品种候选材料。本数据集包含每株植株5至6周龄时，最幼且完全展开的叶片扫描图像。叶片扫描使用爱普生（Epson）Perfection V550扫描仪完成，并搭配柯达（Kodak）KOCSGS色分离标尺进行色彩校准。色彩分析可通过开源软件ColourQuant（Li等，2019）完成，该软件托管于GitHub：github.com/maoli0923/ColourQuant。

二值化与彩色叶片提取文件说明
为从原始扫描图像中提取单张叶片，研究人员采用白平衡方法对每张扫描图的RGB色彩平衡进行调整，使柯达KOCSGS色分离标尺中的白色色块呈现纯白，以避免扫描仪对色彩数据产生偏倚。随后，通过将RGB色彩矩阵转换为色相-饱和度-明度（Hue-Saturation-Value，HSV）色彩空间，实现叶片与背景的分割。由于绝大多数背景像素在HSV空间中呈现灰色，因此可通过设定阈值区分灰色背景与真实叶片区域。随后，利用二值化叶片轮廓，将背景设为纯白、前景设为纯黑，从而提取单张彩色叶片。对于因扫描存在阴影而无法自动分割的叶片，研究人员会手动调整阈值参数进行修正。二值化叶片与彩色叶片文件包中存在异常样本，包括扫描仪上重叠的叶片、尺寸过小或破损的叶片，可在分析前手动剔除这些异常样本。

文件命名规则
文件采用以下编码格式命名：年份_家系_扫描编号。用于品种培育候选叶片的文件前缀加“S”，母本叶片扫描文件的前缀加“M”。

如需对本公开数据集进行咨询，请联系：Margaret Frank，邮箱：[e-mail]

参考文献
Li, M., Frank, M.H. 及 Migicovsky, Z.，2019a。ColourQuant：一种从植物图像中提取并量化色彩表型的高通量技术。arXiv 190301652，http://arxiv.org/abs/1903.01652