In situ measurement of Scots pine needle PRI

Abstract Background The Photochemical Reflectance Index (PRI) calculated from narrow-band spectral reflectance data is a vegetation index which is increasingly used as an indicator of photosynthetic activity. The leaf-level link between the status of photosynthetic apparatus and PRI has been robustly established under controlled light conditions. However, when a whole canopy is measured instantaneously, the PRI signal is heavily modified by vegetation structure and local variations in incident light conditions. To apply PRI for monitoring the photosynthesis of whole canopies under natural conditions, these large-scale measurements need to be validated against simultaneous leaf PRI. Unfortunately, PRI changes dynamically with incident light and has a large natural variation. No generally accepted procedure exists today for determining the PRI of canopy elements in situ. Results We present a successful procedure for in situ measurements of needle PRI. We describe, characterize and test an optical measurement protocol and demonstrate its applicability in field conditions. The measurement apparatus consisted of a light source, needle clip, spectroradiometer and a controlling computer. The light level inside the clip was approximately two-thirds of that on sunlit needle surfaces at midday. During each measurement the needle was inserted into the clip for approximately 5 s. We found no near-instantaneous changes (sub-second scale jumps) in PRI during the measurements. The time constants for PRI variation in light to full shade acclimations were approximately 10 s. The procedure was successfully applied to monitor the greening-up of Scots pine trees. We detected both facultative (diurnal) PRI changes of 0.02 (unitless) and constitutive (seasonal) variations of 0.1. In order to reliably detect the facultative PRI change of 0.02, 20 needles need to be sampled from both sunlit and shaded locations. Conclusions We established a robust procedure for irradiance-dependent leaf (needle) PRI measurements, facilitating empirical scaling of PRI from leaf (needle) to full canopy level and the application of PRI to monitoring the changes in highly structured vegetation. The measured time constants, and facultative and constitutive PRI variations support the use of an artificial light for in situ PRI measurements at leaf (needle) level

In situ measurement of Scots pine needle PRI

Background: The Photochemical Reflectance Index (PRI) calculated from narrow-band spectral reflectance data is a vegetation index which is increasingly used as an indicator of photosynthetic activity. The leaf-level link between the status of photosynthetic apparatus and PRI has been robustly established under controlled light conditions. However, when a whole canopy is measured instantaneously, the PRI signal is heavily modified by vegetation structure and local variations in incident light conditions. To apply PRI for monitoring the photosynthesis of whole canopies under natural conditions, these large-scale measurements need to be validated against simultaneous leaf PRI. Unfortunately, PRI changes dynamically with incident light and has a large natural variation. No generally accepted procedure exists today for determining the PRI of canopy elements in situ. Results: We present a successful procedure for in situ measurements of needle PRI. We describe, characterize and test an optical measurement protocol and demonstrate its applicability in field conditions. The measurement apparatus consisted of a light source, needle clip, spectroradiometer and a controlling computer. The light level inside the clip was approximately two-thirds of that on sunlit needle surfaces at midday. During each measurement the needle was inserted into the clip for approximately 5 s. We found no near-instantaneous changes (sub-second scale jumps) in PRI during the measurements. The time constants for PRI variation in light to full shade acclimations were approximately 10 s. The procedure was successfully applied to monitor the greening-up of Scots pine trees. We detected both facultative (diurnal) PRI changes of 0.02 (unitless) and constitutive (seasonal) variations of 0.1. In order to reliably detect the facultative PRI change of 0.02, 20 needles need to be sampled from both sunlit and shaded locations. Conclusions: We established a robust procedure for irradiance-dependent leaf (needle) PRI measurements, facilitating empirical scaling of PRI from leaf (needle) to full canopy level and the application of PRI to monitoring the changes in highly structured vegetation. The measured time constants, and facultative and constitutive PRI variations support the use of an artificial light for in situ PRI measurements at leaf (needle) level.Peer reviewe

Making post-glacial uplift visible: A model based high-resolution animation of shore displacement

Glacial isostatic adjustment (GIA) is an ongoing phenomenon that characterizes the landscape of the High Coast (63°04'N, 18°22'E, Sweden) / Kvarken archipelago (63°16'N, 21°10'E, Finland) UNESCO World Heritage site. GIA occurs as the Earth’s crust that was depressed by the continental ice sheet during the last glacial period is slowly rebounding towards isostatic equilibrium. The maximum rate of land uplift in the area is more than eight millimetres per year, which – along with the very different topographical reliefs of the opposite coasts – makes the region an excellent study area for land uplift as a phenomenon. As there is a marine area between the coasts, shore displacement is an essential part of the phenomenon in the study area. The cartographic representation of GIA and shore displacement has classically relied on static maps representing isobases of the uplift rates and of ancient shorelines. However, to dynamically visualize and communicate the continuity and the nature of the phenomena, an animated map is required. To create a visually balanced, seamless animation, we need to create high-resolution image frames that represent digital elevation models (DEMs) together with extracted shorelines of different moments of time. To create these frames, we developed a mathematical model to transform the DEM in a given time for the past ~9300 years. We used the most recent LiDAR-derived DEMs of Finland and Sweden, and a bathymetric model of the Gulf of Bothnia as our initial data, along with a land uplift rate surface derived from geophysical measurements. We compared the current uplift rates with the shoreline observations of the ancient Baltic Sea stages, Litorina Sea and Ancylus Lake, and created a linear model between the elevations of the shorelines and the present-day uplift rates, as there was a near-linear correlation in both cases. Based on the current uplift rates and the elevations and the dating of the ancient shorelines, we derived an exponential model to describe the non-linear correlation between the elapsed time and the occurred land uplift. Near the present time, we adapted the formula proposed by Ekman (2001) to make the model more robust closer to the present day. We assumed that although the uplift rate varies in time, the spatial relation of uplift rates remains the same. Furthermore, as the land uplift is an exponentially decelerating phenomenon occurring with a significantly lower annual rate than shortly after the de-glaciation (Eronen et al. 2001, Nordman et al. 2015), and with most of the total uplift already having occurred (Ekman 1991), we assumed a constant rate of uplift from the present day to the near geological future. We did not consider potential sea level changes caused by human-driven climate change in the predictions, as the geological time scale vastly exceeds the time range of the climate models. Neither did we take into account the historical transgression phases, as they did not appear dominating in the area. The elevation and bathymetry data were harmonized and resampled into 4K (3840 x 2160) pixel dimensions to utilize the best commercially available screen resolutions and to avoid unnecessary sub-pixel level computations. This resulted in a spatial pixel size of about 200 metres. The initial spatial resolution of the DEMs of Finland and Sweden was 2 metres and 1 metre, respectively, while the bathymetric data had a spatial pixel size of 400 metres. This, along with the fact that the bathymetric data was partly modelled and inaccurate near the coastlines, meant that it had to be oversampled to generate plausible coastal bathymetry and to allow any future estimations of shore displacement. All the datasets were resampled to EPSG:3857 Pseudo-Mercator projection to facilitate any future use in web map applications. As the visualized area is only about 430 kilometres in the north-south direction, the use of this projection did not introduce cartographic issues. The rendered frames required by the animation were produced with a programmatic conversion of raster files to RGBimages. The visualization of shore displacement was implemented by a discontinuity in elevation dependent colour scale at sea level. The bathymetry was visualized with a continuous colour scale in shades of blue until the elevation of zero metres. Elevations above zero were visualized with a colour scale starting from green to create an impression of a discrete shoreline (Figure 1). Figure 1. Examples of individual frames for the land uplift animation. Litorina stage 7300 BP (a), 3000 BP (b), current stage (c), and 1000 years after present (d). The imprecision of the predicted shoreline placement compared to the past reconstructions can be observed in the last frame. The whole process from computing the DEMs to rendering the frames was implemented in Python, without the need for traditional GUI operated GIS or image processing software. The raster data was read and processed with GDAL and NumPy libraries, and the visualization was carried out using Matplotlib and Python Imaging Library. Each DEM was given the same elevation based colour scale and an individually created hillshading that was blended with the image by multiplication. The whole process was carried out as an open source solution. The interval between the calculated frames was set to five years as, particularly at the Swedish coast, the shore displacement can appear abrupt with a longer time interval. The frame duration was set to 0.05 seconds, which means a 100-second duration for an animation of 10 000 years. The resulting DEM reconstructions show good agreement with comparable data, such as the Litorina reconstructions by the Geological Survey of Finland (GTK). Also, the mathematical model appears to be in line with previous reconstructions conducted in the area (e.g. Nordman et al. 2015). So far, any continuous series of paleogeographic DEM reconstructions comparable to ours has not been published for this area. The animation provides an understandable way of perceiving the continuous but decelerating nature of the land uplift phenomenon and also highlights the differences in the post-glacial history of Finnish and Swedish coasts. To further improve the visualization, we must consider the removal of post-glacially developed features in the present day DEM, e.g. the various rivers that can both cause bias in the shore displacement and uplift estimations and appear visually distractive. In the very early frames of the animation, the retracting ice sheet must also be present. Also, a balanced addition of other cartographic elements, such as present-day hydrography and place names, can further improve the overall presentation

Animated visualization of post-glacial land uplift and shore displacement from modeled paleotopographic reconstructions

Post-glacial land uplift and shore displacement are dynamic processes that are challenging to present with cartography and geovisualization. To communicate these phenomena, we have created a dynamic visualization in the form of high-quality animation, utilizing automated processes in the computation and rendering of large raster datasets. We have developed a simplified model to assess the past and future elevation models, and applied it to the High Coast/Kvarken Archipelago UNESCO World Heritage Site, which is considered one of the best places in the world to observe land uplift. Additionally, the ice decline in the area has been evaluated and visualized. Based on the model and the present-day topography/bathymetry data, we provide a 40 fps 4K-resolution animation with an 80-s duration of the post-glacial history at the World Heritage Site and its vicinity, extending from 10,500 years ago to 1000 years in the future. Although they do not aim to contain the precision of thorough paleogeographic reconstructions, we have found that the individual frames of the animation are closely aligned with comparable geological data. We also present the computational process flow and the visualization principles used in the automated rendering, and thus aim to contribute to the cartographic presentation of geodynamic processes

Measurement of Diurnal Variation in Needle PRI and Shoot Photosynthesis in a Boreal Forest

This article has an erratum: Remote Sens. 2018. 10, 2030. DOI 10.3390/rs10122030. WOS: 000455637600172Peer reviewe

Assessing chlorophyll fluorescence and light use efficiency in boreal forest canopies using imaging spectroscopy data

The photosynthetic light use efficiency (LUE) is used to estimate the rate of photosynthesis in green vegetation. LUE is generally defined as the carbon uptake divided by absorbed photosynthetically active radiation (PAR). Several proxies for LUE estimation from remotely sensed data have been introduced, while the most promising results have been achieved by the Photochemical Reflectance Index (PRI) and chlorophyll fluorescence (ChlF). Both PRI and ChlF can serve as a proxy for photosynthetic downregulation and photoprotection, and can theoretically be measured and calculated from hyperspectral remote sensing data. Fluorescence and PRI were measured at leaf-level for sample trees of Pinus sylvestris and Betula pendula during two field measurement campaigns at Hyytiälä Forestry Field Station in 2014 and 2015. The spectrometer measurements were performed at crown height, separately for sunlit and shaded foliage. The measurements were taken at different hours of day to observe the diurnal variation of fluorescence and PRI. Along with the spectral measurements, CO2 exchange was constantly measured in shoot chambers attached to the sample trees. The diurnal trend of CO2 assimilation and LUE was then projected against the spectral indicators. An airborne campaign was conducted concurrently with the field measurement campaign in 2015. Hyperspectral data (< 5 nm spectral, 60 cm spatial resolution) was collected over the study area using AISA Eagle II line scanner. ChlF was estimated from the data using Fraunhofer line discrimination (FLD) approach. A change in ChlF between morning and noon acquisitions was estimated using different flight lines covering the same area. The reliability of the estimation was tested in several ways including noise reduction and a change analysis of non-fluorescent targets. Moreover, the non-physiological impact of shadow fraction on apparent fluorescence was estimated. The leaf-level results show a distinctive diurnal trend in fluorescence values measured with the spectrometer. The diurnal variation of PRI appears more unpredictable within the sample trees. Statistically, fluorescence values and PRI were only able to predict CO2 assimilation and LUE during the midday measurements with higher values of PAR, fluorescence performing slightly better. The results obtained at canopy level show an increase in radiance emitted as fluorescence and a decrease in PRI between morning and midday acquisitions. The change was observed in all the canopy types, including low vegetation, broad-leaved forests and coniferous forests. The average change of FLD-derived fluorescence (F763) between different canopy types varied between +24.0 units (14.9 %) and +6.3 units (4.9 %). Furthermore, it was observed that illumination conditions and shadow fraction had a major impact on F763 values, which must be considered when estimating ChlF using the FLD approach.Fotosynteettistä valonkäytön tehokkuutta (LUE) käytetään vihreän kasvillisuuden fotosynteesin arvioinnissa. LUE on yleisesti määritelty hiilen sidonnan ja käytetyn fotosynteettisesti aktiivisen säteilyn (PAR) suhteena. Useita keinoja LUE:n arviointiin kaukokartoitusaineistoista on esitelty, mutta lupaavimpia tuloksia on saavutettu valokemiallisella heijastussuhdeindeksillä (PRI) ja klorofyllin fluoresenssilla (ChlF). Sekä PRI:tä että fluoresenssia voidaan käyttää fotosynteettisen säätelyn ja valostressiltä suojautumisen arvioinnissa, ja niitä voidaan periaatteessa mitata hyperspektraalisesta kaukokartoitusaineistosta. Fluoresenssia ja PRI:tä mitattiin lehtitasolla Pinus sylvestris ja Betula pendula -lajien puissa Hyytiälän metsäasemalla kesinä 2014 ja 2015. Spektrometrimittaukset suoritettiin latvuston korkeudella, erikseen aurinko- ja varjolehdille. Mittauksia otettiin eri vuorokaudenaikoina, jotta fluoresenssin ja PRI:n päivänsisäistä vaihtelua voitiin havainnoida. Lisäksi CO2-vaihtoa mitattiin versokammioissa, ja CO2-sidontaa ja LUE:ta verrattiin spektraalisiin indikaattoreihin. Ilmakuvauskampanja järjestettiin vuoden 2015 kenttämittausjakson yhteydessä. Hyperspektraalista aineistoa (< 5 nm spektraalinen, 60 cm spatiaalinen resoluutio) kerättiin AISA Eagle II -linjaskannerilla. ChlF arviotiin käyttämällä FLD-menetelmää. Aamupäivän ja keskipäivän välisten mittauskuvausten välinen ChlF-tasojen ero laskettiin yhteneviä kuvausalueita hyödyntäen. Havaintojen luotettavuutta parannettiin kohinan vaikutusta vähentämällä ja ei-fluoresoivien kohteiden muutosta tarkastelemalla. Lisäksi varjojen aiheuttamat ei-fysiologiset vaikutukset havaittavaan fluoresenssiin arvioitiin. Lehtimittauksista saadut tulokset näyttivät selkeän päivänsisäisen muutostrendin fluoresenssiarvoissa. PRI:n vuorokausivaihtelu oli tulosten valossa epäselvempi. Tilastollisesti fluoresenssi ja PRI ennustivat CO2-sidontaa ja LUE:ta ainoastaan korkeilla PAR-arvoilla. Tällöin fluoresenssi toimi hieman tarkemmin. Ilmakuvausmittauksien tulokset osoittivat fluoresenssina emittoituvan radianssin lisääntyvän ja PRI-arvojen pienenevän aamu- ja keskipäivän mittausten välillä. Muutosta havaittiin kaikissa luokitelluissa latvustotyypeissä. Keskimääräinen FLD-fluoresenssin (F763) muutos vaihteli +24.0 yksikön (14.9 %) ja +6.3 yksikön (4.9 %) välillä. Lisäksi havaittiin, että valaistusolosuhteilla ja varjoilla oli merkittävä vaikutus F763-arvoihin, mikä pitää huomioida kun ChlF arvioidaan FLD-menetelmää käyttäen

Correction: Mõttus, M. et al. Measurement of Diurnal Variation in Needle PRI and Shoot Photosynthesis in a Boreal Forest. <em>Remote Sens.</em> 2018, <em>10</em>, 1019

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