HTP

Archive the big folder

In the PhenoCopter platform, I have to deal with the limited space in the storage of our data center. The practical solution is to archive old flights into tape and current flights in the active storage.

From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize G×E Over Time

Genotype by environment interaction (G×E) for the target trait, e.g. yield, is an emerging property of agricultural systems and results from the interplay between a hierarchy of secondary traits involving the capture and allocation of environmental …

Combining Crop Growth Modeling and Statistical Genetic Modeling to Evaluate Phenotyping Strategies

Genomic prediction of complex traits, say yield, benefits from including information on correlated component traits. Statistical criteria to decide which yield components to consider in the prediction model include the heritability of the component …

Extraction of phenotypic traits using unmanned aerial vehicle for field experiments in the agronomy and crop breeding

With advances in camera and robotic technologies, unmanned aerial vehicles (UAV) provide the means to capture images at sufficiently large scale to extract crop phenotypic traits. The current challenges are to efficiently manage the meta information …

Estimation of plot variability using unmanned aerial vehicle (UAV) for the wheat breeding trials

Gaps in breeders’ plots (spatial variability) are caused by multiple biotic and abiotic stresses (i.e. poor seed gemination, frost, heat, drought, and/or disease). The gaps are either ignored or visually scored by human inspection. However, this …

A Weakly Supervised Deep Learning Framework for Sorghum Head Detection and Counting

The yield of cereal crops such as sorghum (Sorghum bicolor L. Moench) depends on the distribution of crop-heads in varying branching arrangements. Therefore, counting the head number per unit area is critical for plant breeders to correlate with the …

Pixel size of aerial imagery constrains the applications of unmanned aerial vehicle in crop breeding

Image analysis using proximal sensors can help accelerate the selection process in plant breeding and improve the breeding efficiency. However, the accuracies of extracted phenotypic traits, especially those that require image classification, are …

Accuracy assessment of plant height using an unmanned aerial vehicle for quantitative genomic analysis in bread wheat

Background: Plant height is an important selection target since it is associated with yield potential, stability and particularly with lodging resistance in various environments. Rapid and cost-effective estimation of plant height from airborne …

A new probabilistic forecasting model for canopy temperature with consideration of periodicity and parameter variation

Continuous measurement of canopy temperature is an important indicator of plant water status of crops and the ability to predict canopy temperature will assist in the implementation of this technology for guiding crop irrigation scheduling. By noting …

Characterization of peach tree crown by using high-resolution images from an unmanned aerial vehicle

In orchards, measuring crown characteristics is essential for monitoring the dynamics of tree growth and optimizing farm management. However, it lacks a rapid and reliable method of extracting the features of trees with an irregular crown shape such …

Efficient characterization of orchard tree using high resolution images from unmanned aerial vehicle An effective method for crown characteristics analysis in orchard using UAV images

[Background] In orchard, phenotyping the crown related characteristics (e.g. crown diameter and area) is important for monitoring the dynamic of crown growth during growing season and optimizing farming management (e.g. precision spraying and machine …

Estimation of aboveground biomass and leaf area for a wheat trial index using unmanned aerial vehicle

Aboveground biomass (AGB) and leaf area index (LAI) are very important in plant breeding and precision agriculture, as major indicators of crop growth status and grain yield. However, the traditional destructive sampling method is impractical and …

PhenoCopter: An cloud based solution for image processing captured by unmanned aerial vehicle in high throughput phenotyping

As the advances of technologies, unmanned aerial vehicles (UAV) are more convenient to capture images in large scale to extract crop phenotypes. However, the key challenge is how to efficiently manage all meta information, process huge amount of …

Estimation of plant height using a high throughput phenotyping platform based on unmanned aerial vehicle and self-calibration: Example for sorghum breeding

Plant height is an essential trait to evaluate in grain sorghum, being positively associated with potential grain yield. Standard manual measures of plant height for large breeding trials are labour-intensive and time-consuming. Due to potential …

Phenotyping with light interception

Quantification and evaluation of the phenotyping parameters and light interception function of the crop canopy based on rotor unmanned aerial vehicle (UAV) platform

PhenoCopter: An cloud based platform to manage, process and visualize images captured by unmanned aerial vehicle for high throughput phenotyping

As the advances of technologies, unmanned aerial vehicles (UAV) are more convenient to capture images in large scale to extract crop phenotypes. However, the key challenge is how to efficiently manage all meta information, process huge amount of …

The big impacts of image resolution on the estimation of ground coverage for wheat in UAV survey

Ground coverage (GC) is a simple and important trait to monitor crop growth and development, which can be easily captured by visual camera attached on the ground and aerial based platform. However, the accuracy of GC is determined by pixel size …

Estimation of canopy height using an unmanned aerial vehicle in the field during wheat growth season

Canopy height is a simple trait to represent status of plant growth and development and potentially biomass production, as well as having an influence on lodging susceptibility. Measurement is labour-intensive and time consuming, especially in the …

A faster way to trim a raster file

In the plot segmentation of image-based HTP platforms (e.g. UAV, ground-vehicle), we always need to trim a plot to remove the edge effect, then extracts the pixel values we are interesting.

Dynamic monitoring of NDVI in wheat agronomy and breeding trials using an unmanned aerial vehicle

While new technologies can capture high-resolution normalized difference vegetation index (NDVI), a surrogate for biomass and leaf greenness, it is a challenge to efficiently apply this technology in a large breeding program. Here we validate a …

EasyPCC: Benchmark Datasets and Tools for High-Throughput Measurement of the Plant Canopy Coverage Ratio under Field Conditions

Understanding interactions of genotype, environment, and management under field conditions is vital for selecting new cultivars and farming systems. Image analysis is considered a robust technique in high-throughput phenotyping with non-destructive …

Comparison of ground cover estimates from experiment plots in cotton, sorghum and sugarcane based on images and ortho-mosaics captured by UAV

Ground cover is an important physiological trait affecting crop radiation capture, water-use efficiency and grain yield. It is challenging to efficiently measure ground cover with reasonable precision for large numbers of plots, especially in tall …

Phenomics

Improving APSIM to deliver solutions in GxExM and Phenomics

Pheno-Copter: a low-altitude, autonomous remote-sensing robotic helicopter for high-throughput field-based phenotyping

Plant breeding trials are extensive (100s to 1000s of plots) and are difficult and expensive to monitor by conventional means, especially where measurements are time-sensitive. For example, in a land-based measure of canopy temperature (hand-held …

National adaptation

National adaptation Assessment: Adaptation Value in Wheat & Grazing farm systems

Aerial Imaging

Transformational Biology Aerial Imaging Project - scoping field phenotyping 'stick'