Supporting information for "Few-Shot Learning Enables Population-Scale Analysis of Leaf Traits in Populus trichocarpa"

Description In this work, we use few-shot learning to segment the body and vein architecture of P. trichocarpa leaves from high-resolution scans obtained in the UC Davis common garden. Leaf and vein segmentation are formulated as separate tasks, in which convolutional neural networks (CNNs) are used to iteratively expand partial segmentations until reaching stopping criteria. Our leaf and vein segmentation approaches use just 50 and 8 manually traced images for training, respectively, and are applied to a set of 2,634 top and bottom leaf scans. We show that both methods achieve high segmentation accuracy and retain biologically realistic features. The leaf and vein segmentations are compared against a U-Net baseline model, and subsequently used to extract 68 morphological traits using traditional open-source image processing tools, which are validated using real-world physical measurements. For a biological perspective, we perform a genome-wide association study using the "vein density" trait to discover novel genetic architectures associated with multiple physiological processes relating to leaf development and function. In addition to sharing all of the few-shot learning code, we are releasing all images, manual segmentations, model predictions, 68 extracted leaf phenotypes, and a new set of SNPs called against the v4 P. trichocarpa genome for 1,419 genotypes. Directories: Few-shot learning for p. trichocarpa leaf traits ├── data │ ├── genomes │ │ ├── Ptri_V4_Nisq1.[...].bed │ │ ├── Ptri_V4_Nisq1.[...].bim │ │ └── Ptri_V4_Nisq1.[...].fam │ ├── images │ │ └── *.jpeg │ ├── leaf_masks │ │ └── *.png │ ├── leaf_preds │ │ └── *.png │ ├── leaf_unet_preds │ │ └── *.png │ ├── results │ │ ├── digital_traits.tsv │ │ ├── gwas_results.csv │ │ ├── manual_traits.tsv │ │ ├── vein_density_blups.tsv │ │ └── vein_density_tps_adj.tsv │ ├── vein_bce_preds │ │ └── *.png │ ├── vein_bce_probs │ │ └── *.png │ ├── vein_fl_preds │ │ └── *.png │ ├── vein_fl_probs │ │ └── *.png │ ├── vein_masks │ │ └── *.png │ ├── vein_unet_bce_preds │ │ └── *.png │ ├── vein_unet_bce_probs │ │ └── *.png │ ├── vein_unet_fl_preds │ │ └── *.png │ ├── vein_unet_fl_probs │ │ └── *.png ├── figures │ └── *.png ├── logs │ ├── leaf_tracer_256.txt │ ├── leaf_unet_256.txt │ ├── vein_grower_bce_128.txt │ ├── vein_grower_fl_128.txt │ ├── vein_unet_bce_128.txt │ └── vein_unet_fl_128.txt ├── models │ ├── BuildCNN.py │ ├── BuildUNet.py │ ├── LeafTracer.py │ └── VeinGrower.py ├── notebooks │ ├── Figures.ipynb │ ├──