README.md

---
license: apache-2.0
size_categories:
- 1K<n<10K
dataset_info:
  features:
  - name: plot_uid
    dtype: string
  - name: yearsite_uid
    dtype: string
  - name: crop_type
    dtype: string
  - name: experiment_number
    dtype: uint8
  - name: plot_number
    dtype: int16
  - name: sowing_date
    dtype: date32
  - name: harvest_date
    dtype: date32
  - name: harvest_year
    dtype: uint16
  - name: images
    sequence: string
  - name: image_dates
    sequence: date32
  - name: image_times
    sequence: time32[s]
  - name: alignment_plot_soil_polygons
    sequence:
      sequence:
        sequence: float16
  - name: alignment_num_steps
    sequence: uint8
  - name: alignment_dates
    sequence: date32
  - name: alignment_times
    sequence: time32[s]
  - name: alignment_initial_date
    dtype: date32
  - name: alignment_inner_plot_transform
    sequence:
      sequence: float16
  - name: inner_plot_images
    sequence: string
  - name: image_inner_plot_transforms
    sequence:
      sequence:
        sequence: float16
  - name: genotype_id
    dtype: string
  - name: marker_biallelic_codes
    sequence: uint8
  - name: marker_metadata_strings
    sequence: string
  - name: canopy_cover_values
    sequence: float16
  - name: canopy_cover_dates
    sequence: date32
  - name: canopy_cover_trait_ids
    sequence: uint8
  - name: canopy_cover_method_ids
    sequence: uint16
  - name: height_values
    sequence: float16
  - name: height_dates
    sequence: date32
  - name: height_trait_ids
    sequence: uint8
  - name: height_method_ids
    sequence: uint16
  - name: spike_count_values
    sequence: float16
  - name: spike_count_dates
    sequence: date32
  - name: spike_count_trait_ids
    sequence: uint8
  - name: spike_count_method_ids
    sequence: uint16
  - name: senescence_values
    sequence: float16
  - name: senescence_dates
    sequence: date32
  - name: senescence_trait_ids
    sequence: uint8
  - name: senescence_method_ids
    sequence: uint16
  - name: heading_date_value
    dtype: float16
  - name: heading_date_date
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  - name: heading_date_blue
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  - name: heading_date_heritability
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  - name: heading_date_trait_id
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  - name: heading_date_method_id
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  - name: height_final_value
    dtype: float16
  - name: height_final_date
    dtype: date32
  - name: height_final_blue
    dtype: float16
  - name: height_final_heritability
    dtype: float16
  - name: height_final_trait_id
    dtype: uint8
  - name: height_final_method_id
    dtype: uint16
  - name: yield_value
    dtype: float16
  - name: yield_date
    dtype: date32
  - name: yield_blue
    dtype: float16
  - name: yield_heritability
    dtype: float16
  - name: yield_trait_id
    dtype: uint8
  - name: yield_method_id
    dtype: uint16
  - name: protein_value
    dtype: float16
  - name: protein_date
    dtype: date32
  - name: protein_blue
    dtype: float16
  - name: protein_heritability
    dtype: float16
  - name: protein_trait_id
    dtype: uint8
  - name: protein_method_id
    dtype: uint16
  - name: temperature_air_10cm_values
    sequence: float16
  - name: temperature_air_10cm_dates
    sequence: date32
  - name: temperature_air_10cm_times
    sequence: time32[s]
  - name: temperature_air_200cm_values
    sequence: float16
  - name: temperature_air_200cm_dates
    sequence: date32
  - name: temperature_air_200cm_times
    sequence: time32[s]
  - name: temperature_soil_5cm_values
    sequence: float16
  - name: temperature_soil_5cm_dates
    sequence: date32
  - name: temperature_soil_5cm_times
    sequence: time32[s]
  - name: humidity_air_10cm_values
    sequence: float16
  - name: humidity_air_10cm_dates
    sequence: date32
  - name: humidity_air_10cm_times
    sequence: time32[s]
  - name: humidity_air_200cm_values
    sequence: float16
  - name: humidity_air_200cm_dates
    sequence: date32
  - name: humidity_air_200cm_times
    sequence: time32[s]
  - name: precipitation_200cm_values
    sequence: float16
  - name: precipitation_200cm_dates
    sequence: date32
  - name: precipitation_200cm_times
    sequence: time32[s]
  - name: irradiance_solar_200cm_values
    sequence: float16
  - name: irradiance_solar_200cm_dates
    sequence: date32
  - name: irradiance_solar_200cm_times
    sequence: time32[s]
  splits:
  - name: train
    num_bytes: 3203900670
    num_examples: 2930
  - name: validation
    num_bytes: 676408828
    num_examples: 380
  - name: test_plot
    num_bytes: 444994130
    num_examples: 250
  - name: test_genotype
    num_bytes: 438095034
    num_examples: 246
  - name: test_environment
    num_bytes: 162273287
    num_examples: 190
  - name: test_genotype_environment
    num_bytes: 110272291
    num_examples: 62
  download_size: 1388423768
  dataset_size: 5035944240
configs:
- config_name: default
  data_files:
  - split: train
    path: data/train-*
  - split: validation
    path: data/validation-*
  - split: test_plot
    path: data/test_plot-*
  - split: test_genotype
    path: data/test_genotype-*
  - split: test_environment
    path: data/test_environment-*
  - split: test_genotype_environment
    path: data/test_genotype_environment-*
tags:
- phenotyping
- wheat
- plant
- regression
- trait
- pheno
---
!**The image data is currently being uploaded and will be available soon.**!

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

## Dataset Details

### Dataset Description

We provide time series data for more than 4,000 wheat plots, including aligned high-resolution image sequences totaling more than 151,000 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.


- **Curated by:** Mike Boss, Lukas Roth, Norbert Kirchgessner
- **License:** CC-BY

### Dataset Sources

<!-- Provide the basic links for the dataset. -->

- **Data:** [doi.org/20.500.11850/697773](doi.org/20.500.11850/697773)
  > Note that the image data is not included in this repository, instead image paths point to */data* either */data/image* or */data/inner_plot_image*.
  > You will need to place these folders in */data* or change the image path.
  >
  > This is due to some limitations with *datasets* that will hopefully soon be resolved, we will update the dataset accordingly.
- **Paper:** Coming soon!

## Uses

We see the largest re-use potential of the presented data set for the development and evaluation of new modelling and prediction approaches in crop genomics and phenomics.
The multi-faceted data set allows modelling approaches on various levels:
- Genomic prediction approaches that include genotype-environment interactions: The presented data enhance the data by Gogna et al. by 6 environments, totalling to 14 environments that are characterized by environmental covariates. The presented benchmark of a genomic prediction with random regressions to environmental covariates  provides a baseline that novel approaches can challenge.
- Modelling plant growth and development with longitudinal modelling approaches: The four low-level traits canopy cover, plant height, wheat head count and senescence cover the full growing season of winter wheat in 6 environments that are characterized by environmental covariates. Baseline approaches for plant height growth modelling, canopy cover growth modelling and senescence dynamics modelling for subsets of the presented data exist.
- Image-based phenomic predictions and combined phenomic and genomic prediction approaches: The dense time series of images allow training and analysing end-to-end modelling approaches (e.g., deep learning based) that predict target traits such as yield based on images.

## Dataset Structure

The data is structured such that each row contains all data for a plot in a given year.
The plot can be identified by it's *plot_uid* which is also available in parts as *yearsite_uid*, *crop_type*, etc.
If data does not exist for a certain plot it is *None*, while if time series data does not exist for a certain date it is simply not present.

The image data is in the *images* and *inner_plot_images* colums.
*images* are the original images while *inner_plot_images* are aligned cutouts of the inner wheat plot.
Trait data is included as the values in *trait_value(s)* and the dates *trait_date(s)*.
Marker data includes an anyomized *genotype_id* string, biallelic codes and corresponding metadata strings.
Enviroment variables are also included as *_value(s)*, *_date(s)* and in addition *_time(s)*.

The sowing date, harvest date and harvest_year are included.
The data set includes additional data used for the creation of the data set itself such as the alignments.

## Dataset Creation

### Curation Rationale

Winter wheat provides a crucial share of calories for human nutrition, with global demand steadily increasing. 
However, crop production faces challenges due to limited resources like water, agrochemicals, and land. 
Climate change further threatens crop yields, necessitating responsible and efficient resource use.

Crop yields are substantially driven by complex interactions between plant genetics and environmental factors.
For instance, genes involved in fruit formation interact with temperatures at flowering, influencing growth and yield potential. 
Limited phenotyping data is seen as the major reason for the incomplete understanding of such genotype-environment interactions.

HTFP was developed to address this data gap.
Imaging HTFP platforms allow researchers to monitor crop canopy development over time, generating dense time series data of plant growth. 
There are many approaches to process such data ranging from extracting traits at critical time points to modeling growth dynamics and finally using end-to-end methods that directly analyze image time series.

This data set aims to provide a comprehensive foundation for these diverse approaches. 
Our goal is to foster collaboration between plant physiology, biometrics, and computer vision research, ultimately improving the ability to predict genotype-environment interactions for current and future climates.

### Source Data

The FIP at ETH was established in 2015 to collect image time series of crops growing under realistic field conditions.
The FIP's cable carrying system is capable of carrying a 90 kg sensor head.
The original sensor head, hereafter referred to as the FIP 1.0 head, was equipped with a red, green, and blue (RGB) camera and a TLS, among other sensors.
Wheat field experiments were observed using FIP 1.0 over an eight-year period from 2015 to 2022, yielding six years of data collection, with 2015 and 2020 excluded due to incomplete measuring seasons .
Up to three times a week, RGB images of all experimental units (so-called `plots') were collected, and plant heights were measured simultaneously using either the TLS (2016, 2017) or drones (2018--2022) .
In 2023, the FIP 1.0 sensor head was replaced with a new, multi-view RGB sensor head.
The described data set includes all RGB and height data collected in winter wheat experiments up to this replacement.

The area of approximately one ha that the FIP can monitor is divided into six smaller parts (so-called `lots') that are integrated into a crop rotation. 
The two FIP lots dedicated to winter wheat provide space for ~350 genotypes, replicated once per lot.
For the first three years (2016--2018), the GABI-WHEAT panel was grown as the genotype set.
From 2019--2022, a subset of the GABI-WHEAT panel was grown in addition to other genotypes .
The GABI-WHEAT panel consists of registered genotypes from different climatic regions of Europe .
Genetic marker data and MET data from eight year-locations for GABI-WHEAT are publicly available.

The GABI-WHEAT panel was largely superseded by the Swiss breeding set in 2021 . 
This new set primarily consists of eighth-generation (F8) breeding genotypes.
For the Swiss breeding set, genetic marker data exists but remains confidential.
The remaining genotypes, linked to specific projects such as INVITE, were present throughout all years but were generally only grown in a single year each . 
These genotypes currently lack available marker data.

Regular measurements with the FIP 1.0 head were accompanied by reference measurement campaigns as part of several projects.
The heading date and senescence ratings were performed to investigate the relationships of senescence dynamics and diseases .
Yield measurements taken on the FIP field were combined with data from other locations to train phenomic prediction models .
The plant height measurements served as a basis to quantify the temperature response of wheat genotypes in the stem elongation phase .
The extracted plant height values demonstrated their usefulness in improving trait extraction methods from longitudinal data .

The images collected were used to quantify canopy covers and examine their relationship to frost damage events using CNNs.
Using a combination of drone data and the high-resolution images the rows in the individual plots were identified .
In a small subset (375 images), the wheat heads were annotated and the data was integrated into the public global wheat head detection data set .
The image-based canopy cover values served as a test data set to evaluate the cultivar-specific extensions of the thermal time concept .


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## Dataset Card Authors

Mike Boss, Lukas Roth, Norbert Kirchgessner

## Dataset Card Contact

Mike Boss ([email protected])