n License: GNU GPL v3 Data Set Compilation Project name: fip1-dataset Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip1-dataset Operating system(s): Platform independent Programming language: Python License: GNU GPL v3 Data Availability • Data Repository: http://doi.org/20.500.11850/697773 • Hugging Face Data set: https://huggingface.co/datasets/mikeboss/FIP1 • Public GABI marker data repository (also integrated in main Data Repository and Hugging Face Data set): https://doi.org/10.5061/dryad.n02v6wwzc • Private Agroscope marker data repository: Confidential (Con- tact: Boulos Chalhoub, boulos.chalhoub@agroscope.admin.ch). This repository contains marker data (Illumina Infinium
Open resource ↗mikeboss/FIP1 · pdf-raw-page:7 lines:1-110Unverified paper record
The FIP 1.0 Data Set: Highly Resolved Annotated Image Time Series of 4,000 Wheat Plots Grown in Six Years
bioRxiv (Cold Spring Harbor Laboratory) · 5 Oct 2024 · 10.1101/2024.10.04.616624
Abstract
Abstract Background Understanding 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. Findings We 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. Conclusions This 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 phenotyping relevance
高解像度画像時系列と複数の植物形質を含む大規模な公開圃場フェノタイピングデータセットであり、再利用可能なフェノタイピング基盤・ベンチマークとして中心的です。
abstractThis 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.
abstractWe 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.
abstractMeasurement 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.
Code and data availability
This data note directly publishes its own phenotyping measurements and image time series: the FIP 1.0 dataset (images, aligned image sequences, eight wheat traits, environmental and marker data) is publicly available on the ETH Research Collection and Hugging Face, and the authors' analysis/processing code is publicly,
n with FAIR principles [26]: • Findable: This publication and the Hugging Face data set card (https://doi.org/10.57967/hf/3191) provide detailed meta- data and a comprehensive description of the data set’s contents, making it discoverable to researchers. • Accessible: The data is hosted on the Research Collection of ETH Zurich (https://doi.org/20.500.11850/697773), a reliable and openly accessible data storage. • Interoperable: The use of the open-source Hugging Face datasets [27] package makes it easy to use and export to differ- ent formats. The data is fully MIAPPE v1.1 [28] conform. Given the shared genotypes the data set can be used to enhance the data by Gogna et al. [13] by 6 env
Open resource ↗20.500.11850/697773 · pdf-raw-page:2 lines:84-130lly aggregating the derived data into the final data set using the fip1-dataset repository. In addition, the data set can be recreated using the fip1-dataset repository from the derived data that is freely available in the ETH research collection. Trait Data Compilation Project name: FIP 1.0 Data Set - Traits Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip-1.0-data-set-traits Operating system(s): Platform independent Programming language: R, Python License: GNU GPL v3 Image Data Alignment Project name: fip1-alignment Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip1-alignment Operating system(s): Platform independent Programming language: Python License: GNU GPL
Open resource ↗fip-1.0-data-set-traits · pdf-raw-page:7 lines:1-110research collection. Trait Data Compilation Project name: FIP 1.0 Data Set - Traits Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip-1.0-data-set-traits Operating system(s): Platform independent Programming language: R, Python License: GNU GPL v3 Image Data Alignment Project name: fip1-alignment Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip1-alignment Operating system(s): Platform independent Programming language: Python License: GNU GPL v3 Data Set Compilation Project name: fip1-dataset Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip1-dataset Operating system(s): Platform independent Programming language: Python License: GNU GPL v3 Data Availabi
Open resource ↗fip1-alignment · pdf-raw-page:7 lines:1-110ramming language: R, Python License: GNU GPL v3 Image Data Alignment Project name: fip1-alignment Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip1-alignment Operating system(s): Platform independent Programming language: Python License: GNU GPL v3 Data Set Compilation Project name: fip1-dataset Project home page: https://gitlab.ethz.ch/crop_phenotyping/fip1-dataset Operating system(s): Platform independent Programming language: Python License: GNU GPL v3 Data Availability • Data Repository: http://doi.org/20.500.11850/697773 • Hugging Face Data set: https://huggingface.co/datasets/mikeboss/FIP1 • Public GABI marker data repository (also integrated in main Data Repository and H
Open resource ↗fip1-dataset · pdf-raw-page:7 lines:1-110This is an automatically classified, unverified record. Curator approval is required before any resource enters the Catalog.