Data from: High-throughput classification and quantification of skinning phenotype in sweet potatoes
Data files
Oct 27, 2025 version files 304.44 MB
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README.md
2.80 KB
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Skinning_ML_Pipeline.zip
304.44 MB
Abstract
Sweetpotatoes (SPs) (Ipomoea batatas) are crops valued for their color, flavor, and nutrition. Harvesting is labor-intensive, requiring hand-picking to maintain skin quality. Mechanical harvesting often causes skin damage, known as “skinning,” where skin is cut, scraped, or torn, leading to lower quality during packing. To manage this, packers may conduct a costly “field-switch” to reduce skinning in the production line. Currently, skinning levels are visually assessed by the packers and stakeholders. Field-switches involve transitioning between multiple fields during harvest to meet specific customer orders (e.g., supermarkets, processing plants, or end users) that require higher-quality SPs. This process aims to minimize skinning and ensure the SPs meet the desired quality standards for those orders. This study introduces a computer vision (CV) pipeline to automate skinning assessment using a ResNet50-based DeepLabV3+ semantic segmentation model. The CV system was trained to identify three classes: skinning, intact skin\textbackslash SP, and background. A machine vision camera, mounted above a conveyor belt, captured images throughout several full production days. The pipeline calculated the percentage of skinning PS as the ratio between the predicted skinning area and the total SP surface area (As + Ap). Using this method, daily production trends and field-switch decisions were studied with image data from six production days, chosen by our grower collaborator. Percent skinning ratings calculated from random sub-samples of imaged SPs—where only a portion of the full image set was analyzed—showed no significant differences compared to those derived from complete image sets. This demonstrates that sub-sampling can reduce computational processing times by 90% while maintaining accuracy. When data was binned in 30-minute intervals, field-switches occurred when there was approximately 1.5 PS. Across 2,417,907 SP instances, the model achieved a root mean square error (RMSE) of 0.55%, R^2 of 0.84, 80.03% recall, 99.99% specificity, 77.44% F1 score, and 99.98% grading accuracy. This offers a promising improvement for automatic skinning detection on a commercial scale.
https://doi.org/10.5061/dryad.v15dv4272
Description of the data and file structure
Data are provided for the machine learning model and pipeline, including the model's coefficients in Matlab, and regions of interest (ROIs) used for training and validation.
Files and variables
File: Skinning_ML_Pipeline.zip
Description: The Skinning_ML_Pipeline.zip archive contains three directories and one MATLAB script:
- Skinning_SP_Training.m: Script for loading training images, running model transfer learning, and converting the raw imagery data used for validation and testing. Certain cells can also be used for inference of new imagery, or inference can be run on the sample data provided.
- Folder Train_and_validate_labels/ contains the labels for the training and validation images used for creating the model. The sub-folder "validate" contains the labels for the validation dataset (2188 images), and the sub-folder "train" contains the corresponding labels used for training (8752 images).
- Folder Train and validate_images/ contains the RGB data for the training and validation images used for creating the model. The sub-folder "validate" contains the RGB images for the validation dataset (2188 images), and the sub-folder "train" contains the corresponding labels used for training (8752 images).
- Folder Test_Images/ contains the data used for testing the model. Sub-folder "validate_test" contains the RGB images for testing, and "train_test" contains the labels for testing.
- Folder Trained_model/ contains the ML model's coefficients for running inference on regions of interest. These coefficients are contained in "Trained_Model.mat." This is in Matlab file format, but it can be viewed or imported into Python using numpy. The file contains 6 cells. Each cell performs the following:
- Cell 1: Transfer learning to a new model to determine new coefficients. If the published coefficients are used, one can start at cell 2 to load the existing coefficients for inference.
- Cell 2: Evaluate the Model with Test Images based on the coefficients located in Trained_Model.
- Cell 3: Implement the network and calculate skinning percentage from results.
- Cell 4: Load masks to verify their uniformity and properties visually.
- Cell 5: Calculate the skinning percentage to generate RMSE plots from the paper.
- Cell 6: Generate confusion matrices and other metrics for the test dataset in units of pixels
Code/software
Shareable_Skinning_SP_Code_by_Zach_Bloom.m: Contains the code needed to train and validate the model, as well as running inference using the model's coefficients.
Data Collection
The data collection process involved reviewing millions of SPs over a two-year period, from late winter 2022 to late winter 2024. Based on discussions with our industry collaborator, we identified specific days when skinning issues were most apparent. SPs for the training dataset were chosen for their fresh skinning marks, which were likely caused by harvesting, rough handling, improper curing, washing, or damage from machinery. These skinning issues typically occurred within one to two weeks of the harvest, guiding the selection of images.
The images collected were stored in .jpg format with a ground sample distance (GSD) of 0.521 mm/pixel. Most images had a size of 866x1599 pixels, though a few were smaller and resized to 866x1599 pixels using MATLAB. The data collection process was ongoing throughout the study, with adjustments made to the dataset after each performance evaluation to ensure that only the most relevant and high-quality images were retained.
Data Curation and Labeling
A dataset of individual SP instances was curated by selecting high-quality images with distinct skinning marks. These images were chosen based on input from our industry collaborator, who helped identify periods when skinning issues were most prevalent. The curated dataset consisted of high-quality images from five distinct days spanning late winter 2022 to late winter 2024. The SPs were selected based on their fresh skinning marks, which were presumed to have occurred within the past one to two weeks due to factors such as harvesting, rough handling, improper curing, washing, and mechanical damage (bumps, scrapes, or falls).
Each image was manually annotated with three categories: skinning, SP, and background. The skinning marks ranged in size from 0.36 mm² to 316.17 mm². The images were taken with a machine vision camera at the eliminator table. Once annotated, the images were processed further for model training. To augment the dataset, each image was randomly partitioned into 20 regions of interest (ROIs). This process increased the dataset size from 547 to 10,940 images. Each ROI was resized to $224\times224$ pixels to match the input size of the ResNet50 model, and labeled images were converted into a single-channel 8-bit format. The resulting dataset was split into an 80/20 ratio for training and validation, with 8,752 images used for training and 2,188 for validation.
Model Pipeline
For our study, a joint model consisting of a DeepLabV3+ model with a ResNet50 backbone was used to enhance feature extraction for semantic segmentation tasks. DeepLabV3+ was chosen due to its strong performance in pixel-level segmentation tasks and its availability in MATLAB's Deep Learning Toolbox, which provided a straightforward implementation path. While newer architectures such as YOLO or SAM/SAM2 have demonstrated superior speed and performance, DeepLabV3+ remains highly effective in various segmentation applications, and it offers a reliable baseline for comparison in this study.
