Jon Atherton
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View article: A practical guide to long-term field PAM chlorophyll fluorescence measurements: setup, installation, data processing with R package ‘LongTermPAM’ and interpretation
A practical guide to long-term field PAM chlorophyll fluorescence measurements: setup, installation, data processing with R package ‘LongTermPAM’ and interpretation Open
Pulse-amplitude modulated (PAM) chlorophyll fluorescence (ChlF) measurements provide a non-invasive method to study the regulation of the light reactions of photosynthesis in situ. PAM ChlF contributes also to the advancement of the interp…
View article: Connecting optical remote sensing of plant photosynthesis with biogenic volatile organic compound emissions
Connecting optical remote sensing of plant photosynthesis with biogenic volatile organic compound emissions Open
Summary Plant biogenic volatile organic compounds (BVOCs) play a critical role in atmospheric chemistry by forming ozone and secondary organic aerosols, making them key agents in regulating air quality and influencing climate. However, cur…
View article: Introducing the Optical Gas Exchange System (OGES) concept
Introducing the Optical Gas Exchange System (OGES) concept Open
Field and long-term measurements of leaf-level photosynthetic gas exchange have been pivotal to understand and model the environmental regulation of leaf photosynthesis (Hari and Makela 2003). Now, scientists seek for means to understand a…
View article: Behind the Spatio-Temporal Variation in Spectral Chlorophyll Fluorescence of Boreal Species
Behind the Spatio-Temporal Variation in Spectral Chlorophyll Fluorescence of Boreal Species Open
Boreal forests constitute about one-third of all the global forest area (Brandt et al. 2013). Capturing a significant portion of global atmospheric CO2 (Beer et al. 2010, Thurner et al. 2016, Thurner et al. 2013), boreal forests play a key…
View article: Influence of solar zenith angle and neighboring trees on the reflectance of boreal trees in multispectral aerial images (with lidar-derived crown modeling)
Influence of solar zenith angle and neighboring trees on the reflectance of boreal trees in multispectral aerial images (with lidar-derived crown modeling) Open
Information about forest tree species is essential for understanding and managing forest ecosystems. Aerial images and LiDAR are important complementary data sources for species classification in individual tree remote sensing. In Finland,…
View article: Hyperspectral Imaging Reveals Differential Carotenoid and Chlorophyll Temporal Dynamics and Spatial Patterns in Scots Pine Under Water Stress
Hyperspectral Imaging Reveals Differential Carotenoid and Chlorophyll Temporal Dynamics and Spatial Patterns in Scots Pine Under Water Stress Open
Drought‐related die‐off events have been observed throughout Europe in Scots pine ( Pinus sylvestris L.). Such events are exacerbated by carbon starvation that is, an imbalance of photosynthetic productivity and resource usage. Recent evid…
View article: Photosynthetic optical signals studying biogenic volatile organic compound emissions in Scots pine and English oak saplings under drought or warming
Photosynthetic optical signals studying biogenic volatile organic compound emissions in Scots pine and English oak saplings under drought or warming Open
Biogenic volatile organic compounds (BVOCs), primarily emitted into the atmosphere by terrestrial vegetation through biochemical processes, have key ecological functions in protecting vegetation from biotic or abiotic stresses. However, ac…
View article: Investigating Foliar Macro- and Micronutrient Variation with Chlorophyll Fluorescence and Reflectance Measurements at the Leaf and Canopy Scales in Potato
Investigating Foliar Macro- and Micronutrient Variation with Chlorophyll Fluorescence and Reflectance Measurements at the Leaf and Canopy Scales in Potato Open
Vegetation indices (VIs) related to plant greenness have been studied extensively for the remote detection of foliar nitrogen content. Yet, the potential of chlorophyll fluorescence (ChlF) and photoprotection-based indices such as the phot…
View article: The photosynthetic response of spectral chlorophyll fluorescence differs across species and light environments in a boreal forest ecosystem
The photosynthetic response of spectral chlorophyll fluorescence differs across species and light environments in a boreal forest ecosystem Open
Chlorophyll fluorescence can serve as a proxy of photosynthesis in boreal forests. When sustained non-photochemical quenching (NPQS) relaxes towards summer, leaf chlorophyll fluorescence (ChlF) emission increases along with photosynthesis.…
View article: Uncrewed aircraft system spherical photography for the vertical characterization of canopy structural traits
Uncrewed aircraft system spherical photography for the vertical characterization of canopy structural traits Open
Summary The plant area index (PAI) is a structural trait that succinctly parametrizes the foliage distribution of a canopy and is usually estimated using indirect optical techniques such as digital hemispherical photography. Critically, on…
View article: UAS spherical photography for the vertical characterisation of canopy structural traits
UAS spherical photography for the vertical characterisation of canopy structural traits Open
Data and scripts for New Phytologist manuscript: UAS spherical photography for the vertical characterisation of canopy structural traits Vicent Agustí Ribas Costa, Maxime Durand, T Matthew Robson, Albert Porcar-Castell, Ilkka Korpela, Jon…
View article: UAS spherical photography for the vertical characterisation of canopy structural traits
UAS spherical photography for the vertical characterisation of canopy structural traits Open
Data and scripts for New Phytologist manuscript: UAS spherical photography for the vertical characterisation of canopy structural traits Vicent Agustí Ribas Costa, Maxime Durand, T Matthew Robson, Albert Porcar-Castell, Ilkka Korpela, Jon…
View article: UAS spherical photography for the characterisation of canopy structural traits
UAS spherical photography for the characterisation of canopy structural traits Open
Data and Python scripts for manuscript: UAS spherical photography for the characterisation of canopy structural traits Vicent Agustí Ribas Costa1, Maxime Durand2, T Matthew Robson2 Albert Porcar-Castell1, Ilkka Korpela3, Jon Atherton1* No…
View article: Measuring Solar-Induced Fluorescence from Unmanned Aircraft Systems for Operational Use in Plant Phenotyping and Precision Farming
Measuring Solar-Induced Fluorescence from Unmanned Aircraft Systems for Operational Use in Plant Phenotyping and Precision Farming Open
Demand for high spatial and temporal resolution measurements has triggered a rapid development of unmanned aircraft systems (UAS) for plant phenotyping and precision farming purposes. Similarly, recent progress in low-altitude remote sensi…
View article: Structural and photosynthetic dynamics mediate the response of SIF to water stress in a potato crop
Structural and photosynthetic dynamics mediate the response of SIF to water stress in a potato crop Open
Solar-induced Fluorescence (SIF) has an advantage over greenness-based Vegetation Indices in detecting drought. This advantage is the mechanistic coupling between SIF and Gross Primary Productivity (GPP). Under water stress, SIF tends to d…
View article: Structural and photosynthetic dynamics mediate the response of SIF to water stress in a potato crop
Structural and photosynthetic dynamics mediate the response of SIF to water stress in a potato crop Open
Publication is now online and open access at: https://www.sciencedirect.com/science/article/pii/S0034425721002753 1. Introduction We provide data and processing code associated with Xu et al. (2021) study investigating the structural and p…
View article: Structural and photosynthetic dynamics mediate the response of SIF to water stress in a potato crop
Structural and photosynthetic dynamics mediate the response of SIF to water stress in a potato crop Open
Publication is now online and open access at: https://www.sciencedirect.com/science/article/pii/S0034425721002753 1. Introduction We provide data and processing code associated with Xu et al. (2021) study investigating the structural and p…
View article: Simulation-Based Evaluation of the Estimation Methods of Far-Red Solar-Induced Chlorophyll Fluorescence Escape Probability in Discontinuous Forest Canopies
Simulation-Based Evaluation of the Estimation Methods of Far-Red Solar-Induced Chlorophyll Fluorescence Escape Probability in Discontinuous Forest Canopies Open
The escape probability of Solar-induced chlorophyll fluorescence (SIF) can be remotely estimated using reflectance measurements based on spectral invariants theory. This can then be used to correct the effects of canopy structure on canopy…
View article: On the Estimation of the Leaf Angle Distribution from Drone Based Photogrammetry
On the Estimation of the Leaf Angle Distribution from Drone Based Photogrammetry Open
Leaf angle distribution (LAD) is a key canopy structural parameter, playing an important role in light transfer. LAD can be estimated from fixed point of view photography, however this is time consuming and spatially limited. Recently, Ter…
View article: What does the NDVI really tell us about crops? Insight from proximal spectral field sensors
What does the NDVI really tell us about crops? Insight from proximal spectral field sensors Open
The use of remote sensing in agriculture is expanding due to innovation in sensors and platforms. Drones, high resolution instruments on CubeSats, and robot mounted proximal phenotyping sensors all feature in this drive. Common threads inc…
View article: Seasonal dynamics of spectral vegetation indices at leaf, ecosystem and satellite scales for a boreal evergreen coniferous forest
Seasonal dynamics of spectral vegetation indices at leaf, ecosystem and satellite scales for a boreal evergreen coniferous forest Open
<div> <p>The spectral vegetation indices (VIs) are widely used in ecology and ecosystem modelling to study carbon uptake and plant responses to climate change. VIs can potentially be used the learn about ecosystem processes at …
View article: Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage?
Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage? Open
Chlorophyll a fluorescence (ChlF) is closely related to photosynthesis and can be measured remotely using multiple spectral features as solar‐induced fluorescence (SIF). In boreal regions, SIF shows particular promise as an indicator of ph…
View article: Data for: Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage?
Data for: Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage? Open
This dataset includes all the data for producing the figures and support materials of " Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage?", published in Plant, C…
View article: Data for: Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage?
Data for: Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage? Open
This dataset includes all the data for producing the figures and support materials of " Do all chlorophyll fluorescence emission wavelengths capture the spring recovery of photosynthesis in boreal evergreen foliage?", published in Plant, C…
View article: Simulating solar-induced chlorophyll fluorescence in a boreal forest stand reconstructed from terrestrial laser scanning measurements
Simulating solar-induced chlorophyll fluorescence in a boreal forest stand reconstructed from terrestrial laser scanning measurements Open
Solar-induced chlorophyll fluorescence (SIF) has been shown to be a suitable remote sensing proxy of photosynthesis at multiple scales. However, the relationship between fluorescence and photosynthesis observed at the leaf level cannot be …
View article: Nocturnal Light Emitting Diode Induced Fluorescence (LEDIF): A new technique to measure the chlorophyll a fluorescence emission spectral distribution of plant canopies in situ
Nocturnal Light Emitting Diode Induced Fluorescence (LEDIF): A new technique to measure the chlorophyll a fluorescence emission spectral distribution of plant canopies in situ Open
This repository contains data reported in the below study: Atherton, J., Liu, W. and Porcar-Castell, A., 2019. Nocturnal Light Emitting Diode Induced Fluorescence (LEDIF): A new technique to measure the chlorophyll a fluorescence emission …