John Lagergren

John Lagergren, Mirko Pavicic, Hari B. Chhetri et al.

Plant phenotyping is typically a time-consuming and expensive endeavor, requiring large groups of researchers to meticulously measure biologically relevant plant traits, and is the main bottleneck in understanding plant adaptation and the genetic architecture underlying complex traits at population scale. In this work, we address these challenges by leveraging few-shot learning with convolutional neural networks (CNNs) to segment the leaf body and visible venation of 2,906 P. trichocarpa leaf images obtained in the field. In contrast to previous methods, our approach (i) does not require experimental or image pre-processing, (ii) uses the raw RGB images at full resolution, and (iii) requires very few samples for training (e.g., just eight images for vein segmentation). Traits relating to leaf morphology and vein topology are extracted from the resulting segmentations using traditional open-source image-processing tools, validated using real-world physical measurements, and used to conduct a genome-wide association study to identify genes controlling the traits. In this way, the current work is designed to provide the plant phenotyping community with (i) methods for fast and accurate image-based feature extraction that require minimal training data, and (ii) a new population-scale data set, including 68 different leaf phenotypes, for domain scientists and machine learning researchers. All of the few-shot learning code, data, and results are made publicly available.

Xi Xiao, Aristeidis Tsaris, Anika Tabassum et al.

Hyperspectral imaging (HSI) captures hundreds of narrow, contiguous wavelength bands, making it a powerful tool in biology, agriculture, and environmental monitoring. However, interpreting Vision Transformers (ViTs) in this setting remains largely unexplored due to two key challenges: (1) existing saliency methods struggle to capture meaningful spectral cues, often collapsing attention onto the class token, and (2) full-spectrum ViTs are computationally prohibitive for interpretability, given the high-dimensional nature of HSI data. We present FOCUS, the first framework that enables reliable and efficient spatial-spectral interpretability for frozen ViTs. FOCUS introduces two core components: class-specific spectral prompts that guide attention toward semantically meaningful wavelength groups, and a learnable [SINK] token trained with an attraction loss to absorb noisy or redundant attention. Together, these designs make it possible to generate stable and interpretable 3D saliency maps and spectral importance curves in a single forward pass, without any gradient backpropagation or backbone modification. FOCUS improves band-level IoU by 15 percent, reduces attention collapse by over 40 percent, and produces saliency results that align closely with expert annotations. With less than 1 percent parameter overhead, our method makes high-resolution ViT interpretability practical for real-world hyperspectral applications, bridging a long-standing gap between black-box modeling and trustworthy HSI decision-making.

John Lagergren, Erica Rutter, Kevin Flores

In this paper we present a methodology that uses convolutional neural networks (CNNs) for segmentation by iteratively growing predicted mask regions in each coordinate direction. The CNN is used to predict class probability scores in a small neighborhood of the center pixel in a tile of an image. We use a threshold on the CNN probability scores to determine whether pixels are added to the region and the iteration continues until no new pixels are added to the region. Our method is able to achieve high segmentation accuracy and preserve biologically realistic morphological features while leveraging small amounts of training data and maintaining computational efficiency. Using retinal blood vessel images from the DRIVE database we found that our method is more accurate than a fully convolutional semantic segmentation CNN for several evaluation metrics.