Biology subjects

Volpi, M.

Publications and source records attributed to Volpi, M..

5 recordsLinked to original sources

bioRxiv2026

OneGrow: Unified Temporal Plant Image and Mask Generation

Image-based crop phenotyping benefits from image series that capture plant development together with organ-level labels. Such paired data are limited because organ annotation is expensive, and following the same plants over time requires repeated, registered imaging. Existing generative models for plants either synthesize temporal imagery without structural labels or generate labeled images without a temporal dimension. We introduce OneGrow, a latent flow-matching model that jointly models wheat images and their organ-segmentation masks over time. Images and masks share a single frozen image autoencoder. A reveal specifies which content is observed context, so the same model covers tasks such as mask-to-image synthesis, image-to-mask segmentation, and temporal forecasting. For sequences longer than the training window, a sliding-window roll-out generates each new image from the preceding frames, keeping long sequences temporally consistent. We train jointly on a large single-frame wheat dataset and a multi-year temporal dataset, using pseudo-labels from a pretrained segmentation model. We evaluate segmentation and image quality against held-out references and assess the multi-task and temporal behavior qualitatively.

plant biology↗

bioRxiv2026

Neural Processes with Normalizing Flows for Wheat Height Estimation

In this work, we investigate modeling plant traits over time using neural processes, a class of machine learning models that learn distributions over functions. Plant growth is an inherently stochastic process with complex dynamics measured mostly at irregular times throughout the growing seasons. While individual trait trajectories may be simple, their distributions are shaped by complex interactions between genotype, environment, and other factors. In particular, we focus on plant height in wheat, a deceptively simple-looking trait with complex dynamics. To model these trajectory distributions, we evaluate neural processes and in particular extensions using normalizing flows, with different combinations of genotype and environmental covariates. For controlled evaluations, we generate synthetic wheat height trajectories calibrated against Swiss weather station records and the FIP1 dataset. To fully evaluate these trajectory distributions, we use signatures, vector representations of sequential data, together with Sig-MMD and the recently introduced CSig-MMD. Sig-MMD enables direct pathwise comparison of predicted and simulator trajectory distributions, while CSig-MMD focuses this comparison on the tail, including lodged trajectories. Together, these metrics allow us to assess whether the models capture the full distribution of growth trajectories, including rare outcomes.

Plant Biology↗

bioRxiv2026

Modular biofabrication of a vascularized skeletal muscle model through endothelialized microvascular seeds

The clinical translation of engineered skeletal muscle (eSM) for volumetric muscle regeneration is hindered by the challenge of establishing a functional vascular network capable of sustaining its high metabolic demand and ensuring graft survival. Here, we present a bottom-up biofabrication strategy to generate a pre-vascularized in vitro eSM model through the modular assembly of independently matured muscle and vascular compartments. C2C12 myoblasts were encapsulated within core-shell fibers using rotary wet-spinning (RoWS), yielding anisotropically aligned, multinucleated, and contractile myofibers expressing myosin heavy chain and sarcomeric -actinin. In parallel, gelatin methacryloyl (GelMA)-based microvascular seeds ({micro}VS), pre-endothelialized with human umbilical vein endothelial cells, were engineered to guide rapid and structurally stable vascular formation while preventing uncontrolled capillary self-organization. Fully endothelialized {micro}VS were incorporated into a pro-angiogenic bioink and processed via RoWS to generate tubular vascular fibers with physiological diameters (100-200 m) and continuous CD31-positive lumens. After independent maturation, muscle and vascular constructs were bioassembled into a hierarchically organized tissue and co-cultured. By decoupling myogenic and angiogenic differentiation, this strategy overcomes medium incompatibility typical of conventional co-cultures, preserving compartment-specific architecture and function and establishing a versatile platform for muscle-vascular modeling and translational muscle repair.

bioengineering↗

bioRxiv2025

The plant-time-bender model: predicting yield through wheat's perception of time

To address challenges in food security, a better understanding of crop performance under varying and changing environmental conditions is required. Plant Time Warping (PTW) is a deep learning model that integrates high-throughput field phenotyping data with genomic and environmental information to predict wheat yield. PTW leverages image time series, genetic markers, and environmental covariates to learn genotype-specific physiological responses to temperature and vapor pressure deficit. Compared to mere genomic prediction models, PTW demonstrates superior performance when predicting yield in unseen environments across 48 year-locations in Europe. The PTW model captures non-linear growth responses varying with phenological stages and identifies distinct patterns associated with yield performance and stability. Specifically, varieties with higher yield stability exhibit reduced sensitivity to vapor pressure deficit around 1.5 kPa and distinctive temperature responses during emergence and senescence. The learned response pattern enable retrospective and prospective yield predictions, providing a foundation for location-specific variety recommendations and targeted breeding strategies. The integration of phenomic, genomic, and enviromic data has the potential to substantially advance research in climate adaptation strategies for crop production by addressing generalization challenges of predictions to novel environmental conditions. HighlightWe present a novel deep learning model that seamlessly combines high-throughput image data, genomic data, and weather data, enabling better crop predictions for future climates.

genomics↗

bioRxiv2024

The FIP 1.0 Data Set: Highly Resolved Annotated Image Time Series of 4,000 Wheat Plots Grown in Six Years

BackgroundUnderstanding genotype-environment interactions of plants is crucial for crop improvement, yet limited by the scarcity of quality phenotyping data. This data note presents the Field Phenotyping Platform 1.0 data set, a comprehensive resource for winter wheat research that combines imaging, trait, environmental, and genetic data. FindingsWe provide time series data for more than 4,000 wheat plots, including aligned high-resolution image sequences totaling more than 153,000 aligned images across six years. Measurement data for eight key wheat traits is included, namely canopy cover values, plant heights, wheat head counts, senescence ratings, heading date, final plant height, grain yield, and protein content. Genetic marker information and environmental data complement the time series. Data quality is demonstrated through heritability analyses and genomic prediction models, achieving accuracies aligned with previous research. ConclusionsThis extensive data set offers opportunities for advancing crop modeling and phenotyping techniques, enabling researchers to develop novel approaches for understanding genotype-environment interactions, analyzing growth dynamics, and predicting crop performance. By making this resource publicly available, we aim to accelerate research in climate-adaptive agriculture and foster collaboration between plant science and machine learning communities.

plant biology↗