Fluorescence Imaging Spectrometer Research Articles

Spectral Background Calibration of Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) Spectrometer Onboard the Perseverance Rover Enables Identification of a Ubiquitous Martian Spectral Component.

The Perseverance rover landed at Jezero crater, Mars, on 18 February 2021, with a payload of scientific instruments to examine Mars' past habitability, look for signs of past life, and process samples for future return to Earth. The instrument payload includes the Scanning Habitable Environments with Raman and Luminescence for Organics and Chemicals (SHERLOC) deep ultraviolet Raman and fluorescence imaging spectrometer designed to detect, characterize, and map the presence of organics and minerals on the Martian surface. Operation and engineering constraints sometimes result in the acquisition of spectra with features near the detection limit. It is therefore important to separate instrumental (background) spectral components and spectral components inherent to Martian surface materials. For SHERLOC, the instrumental background is assessed by collecting spectra in the stowed-arm configuration where the instrument is pointed at the Martian nighttime sky with no surface sample present in its optical path. These measurements reveal weak Raman and fluorescence background spectral signatures as well as charged-coupled device pixels prone to erroneous intensity spikes separate from cosmic rays. We quantitatively describe these features and provide a subtraction procedure to remove the spectral background from surface spectra. By identifying and accounting for the SHERLOC Raman background features within the median Raman spectra of Martian target scans, we find that the undefined silicate spectral feature interpreted to be either amorphous silicate or plagioclase feldspar is ubiquitously found in every Mars target Raman scan collected through Sol 751.

Identification of an optimal ground-based validation site for FLEX and quantification of uncertainties using airborne HyPlant data - A case study in Italy

The Fluorescence Explorer (FLEX) satellite will carry the high-resolution Fluorescence Imaging Spectrometer (FLORIS) that measures the complete fluorescence spectrum emitted by chlorophyll of terrestrial vegetation. This small signal must be validated. One validation approach is comparing the fluorescence signal retrieved from satellite-based measurements with ground based measurements. However, the difference in spatial resolution of the satellite and ground-based instruments and a geolocation mismatch will result in differences in the detected signal and thus, in uncertainties of the validation strategy. In a case study, we identify a representative ground site for validating the fluorescence signal by analyzing surface reflectance measurements from an aeroplane.We define requirements of representativeness for a validation ground site in vegetated areas. Based on those requirements, we identify a suitable position within a case study in central Italy using surface reflectance data from the airborne High-Performance Airborne Imaging Spectrometer (HyPlant) measured in summer 2018. The representativeness is quantified by the relative difference between the single HyPlant pixel representing a ground-based measurement and the averaged signal of several HyPlant pixels that mimics a FLORIS pixel. With this measure, we quantify the validation uncertainty due to spatial resolution and geolocation mismatch. The effect of the temporal evolution of the surface properties on the validation uncertainty due to spatial resolution is investigated.We select the ground site position by minimizing the validation uncertainty due to spatial resolution. Especially for wavelengths larger than 700 nm, this uncertainty is smaller than 2 % for all different reference areas. The largest differences between ground-based like measurement and satellite-like measurement of the surface reflectance is due to geolocation mismatch. The uncertainty due the geolocation mismatch is very large for wavelengths smaller than 720 nm and moderate for wavelengths larger than 720 nm. Thus, the surface reflectance at the chosen position for the validation site is not homogeneous enough for validation purpose. Considering a reference area of 13.5 × 13.5 m2, we quantify temporal stable and small uncertainties for the spectral range between 720 and 800 nm. For an all-embracing validation of the surface reflectance of vegetated areas, the chosen site is not appropriate.

Solar-induced chlorophyll fluorescence imaging spectrometer: design, manufacture, and evaluation.

A scientific imaging spectrometer has been presented for the observation of solar-induced chlorophyll fluorescence of vegetation in NIR waveband, which may provide a new method to scale SIF application from leaf to canopy for the research of terrestrial vegetation photosynthesis. The SIF imaging spectrometer accommodates a telescope with a medium spatial resolution (1 mrad) over a field of view of 20°, a high spectral resolution (0.3nm) to measure the fluorescence spectrum within two oxygen absorption bands (O2A and O2B), and a high numerical aperture (0.25) for high SNR. Both of transmission optical systems, with high etendue and dispersive prism-VPH grating (P-G) with high diffraction efficiency, have been utilized for the optical design of imaging spectrometer. The design and prototype present excellent optical performances as demonstrated by the latest simulation and calibration. The in-situ observation proves that the advanced SIF imaging spectrometer could provide precise fluorescence data. The instrument will highlight SIF signal retrieval strategies, techniques for field and airborne and satellite sensing, and applications of these capabilities in evaluation of photosynthesis and stress effects for fluorescence science.

A Light-Sheet-Based Imaaging Spectrometer to Characterize Acridine Orange Fluorescence within Leukocytes.

Low-cost imaging systems that utilize exogenous fluorescent dyes, such as acridine orange (AO), have recently been developed for use as point-of-care (POC) blood analyzers. AO-based fluorescence imaging exploits variations in emission wavelength within different cell types to enumerate and classify leukocyte subpopulations from whole blood specimens. This approach to leukocyte classification relies on accurate and reproducible colorimetric features, which have previously been demonstrated to be highly dependent on the cell staining protocols (such as specific AO concentration, timing, and pH). We have developed a light-sheet-based fluorescence imaging spectrometer, featuring a spectral resolution of 9 nm, with an automated spectral extraction algorithm as an investigative tool to study the spectral features from AO-stained leukocytes. Whole blood specimens were collected from human subjects, stained with AO using POC methods, and leukocyte spectra were acquired on a cell-by-cell basis. The post-processing method involves three steps: image segmentation to isolate individual cells in each spectral image; image quality control to exclude cells with low emission intensity, out-of-focus cells, and cellular debris; and the extraction of spectra for each cell. An increase in AO concentration was determined to contribute to the red-shift in AO-fluorescence, while varied pH values did not cause a change in fluorescence. In relation to the spectra of AO-stained leukocytes, there were corresponding red-shift trends associated with dye accumulation within acidic vesicles and at increasing incubation periods. The system presented here could guide future development of POC systems reliant on AO fluorescence and colorimetric features to identify leukocyte subpopulations in whole blood specimens.

The potential of satellite FPAR product for GPP estimation: An indirect evaluation using solar-induced chlorophyll fluorescence

Satellite remotely sensed fraction of photosynthetically active radiation (FPAR) products are widely used in land-surface monitoring and modeling, especially for estimating global terrestrial photosynthetic activity through light use efficiency (LUE) models. PAR absorbed by active chlorophyll (APARchl) is directly linked to vegetation photosynthesis and can be used to estimate ecosystem gross primary production (GPP). Previous studies have demonstrated that solar induced chlorophyll fluorescence has very tight relationship with APARchl at various ecosystems. Therefore, the solar angle normalized SIF (nSIF) is directly related to the fraction of PAR absorbed by chlorophyll (FPARchl). This paper intercompared six space FPAR products from Moderate Resolution Imaging Spectroradiometer (MODIS), Visible Infrared Imaging Radiometer Suite (VIIRS), Copernicus Global Land Service (CGLS), Multi-angle Imaging SpectroRadiometer (MISR), Earth Polychromatic Imaging Camera (EPIC) and Ocean and Land Colour Instrument (OLCI). Their potential relationships with FPARchl were indirectly evaluated with both spaceborne (Orbiting Carbon Observatory-2, OCO-2 and TROPOspheric Monitoring Instrument, TROPOMI) and airborne (Chlorophyll Fluorescence Imaging Spectrometer, CFIS) nSIF data as well as in situ GPP measurements. Our results show that these FPAR products are different in terms of amplitudes and seasonal variations across biomes. Among six FPAR products, OLCI FPAR shows the best relationships with TROPOMI nSIF740, OCO-2 nSIF757, and CFIS nSIF755. The coefficient of determination (R2) for the relationship between OLCI FPAR and TROPOMI nSIF740 is 0.79 ± 0.17 on a global average. APAR calculated from OLCI also exhibits the best relationship (R2 = 0.79) with in situ GPP over 25 flux towers.

A framework for harmonizing multiple satellite instruments to generate a long-term global high spatial-resolution solar-induced chlorophyll fluorescence (SIF)

Several decade-long satellite retrievals of solar-induced chlorophyll fluorescence (SIF) have become available during the past few years, but understanding the long-term dynamics of SIF and elucidating its co-variation with historical gross primary production (GPP) remains a challenge. Part of the challenge is due to the lack of direct comparability among these SIF products as they are derived from various satellite platforms with different retrieval methods, instruments characteristics, overpass time, and viewing-illumination geometries. This study presents a framework that circumvents these discrepancies and allows the harmonization of SIF products from multiple instruments to achieve long-term coverage. We demonstrate this framework by fusing SIF retrievals from SCanning Imaging Absorption spectroMeter for Atmospheric CHartographY (SCIAMACHY) and Global Ozone Monitoring Experiment 2 (GOME-2) onboard MetOp-A developed at German Research Center for Geosciences (GFZ). We first downscale both original SIF datasets from their native resolutions to 0.05° (SIF¯GOME2_005 and SIF¯SCIA_005 respectively) using machine learning (ML) algorithms imposed with regionalization constraints to account for the varying relationships between predictors and SIF in space and time. We then apply the cumulative distribution function (CDF) matching technique to correct the offset between SIF¯GOME2_005 and SIF¯SCIA_005 inherited from the original instrumental discrepancies to generate a harmonized SIF time series from 2002 to present (SIF¯005). Finally, we quantify the uncertainty of SIF¯005. SIF¯005 is validated with 1) the original retrievals to ensure the spatial and temporal variabilities are preserved, 2) airborne SIF derived from the Chlorophyll Fluorescence Imaging Spectrometer (CFIS, R2 = 0.73), and 3) ground-based SIF measurements at a subalpine coniferous forest (R2 = 0.91). The SIFyield derived from SIF¯005 has high seasonal consistency with the ground measurements (R2 = 0.93), suggesting that the harmonized product SIF¯005 carries physiological information beyond the absorbed photosynthetically active radiation. Additionally, SIF¯005 has a good capability for large-scale stress monitoring as demonstrated with several major historical drought and heatwave events. The framework developed in this study sets the stage for future development of even more advanced SIF products from all SIF-capable satellite platforms once issues related to inter-sensor calibration are resolved and SIF physiology is better understood.

Instrument predevelopment activities for FLEX mission

The fluorescence imaging spectrometer (FLORIS) is the payload of the fluorescence explorer mission (FLEX) of the European Space Agency. The mission objective is to perform quantitative measurements of the solar-induced vegetation fluorescence aiming at monitoring photosynthetic activity. FLORIS works in a push-broom configuration, and it is designed to acquire data in the 500 to 780 nm spectral range with a sampling of 0.1 nm in the oxygen bands (759 to 769 nm and 686 to 697 nm) and 0.5 to 2.0 nm in the red edge, chlorophyll absorption, and photochemical reflectance index bands. FLEX will fly in formation with Sentinel-3 to benefit from the measurements made by Sentinel-3 instruments, OLCI, and SLSTR, particularly concerning the cloud screening, the proper characterization of the atmospheric state, and the determination of the surface temperature. The instrument concept is based on a common telescope and two modified Offner spectrometers with reflective concave gratings both for the high resolution (HR) and low resolution (LR) spectrometers. In the frame of the instrument predevelopment, Leonardo Company (Italy) has built and tested an elegant breadboard of the instrument consisting of the telescope and the HR spectrometer. OHB System AG (Germany) is in charge of the development of the LR spectrometer. The main objectives of the activity are to anticipate the development of the instrument and provide early risk retirement of the critical components; evaluate the system performances such as imaging quality parameters, straylight, ghost, polarization sensitivity, and environmental influences; verify the adequacy of critical tests such as spectral characterization and straylight; and define and optimize instrument alignment procedures. Following a brief overview of the FLEX mission, we will cover the design and the development of the optics breadboard with emphasis on the results obtained during the tests and the lessons learned for the flight unit.

Evaluation of full‐field energy dispersive X‐ray fluorescence imaging apparatus and super resolution analysis with compressed sensing technique

A full‐field energy dispersive X‐ray fluorescence (FF‐EDXRF) imaging spectrometer that utilizes single‐photon counting analysis with a charge‐coupled device was developed in our laboratory.We evaluated the developed spectrometer with respect to its energy resolution, spatial resolution, quantitative performance, and elemental imaging and compared it with the corresponding characteristics of scanning‐type EDXRF spectrometers. In addition, we demonstrate that the limit of detection and sensitivity deteriorate as the analytical area decreases. Finally, compressed sensing, which is a widely used information‐processing technique, was applied for clearing XRF images.

High‐Resolution Global Contiguous SIF of OCO‐2

AbstractThe Orbiting Carbon Observatory‐2 (OCO‐2) collects solar‐induced chlorophyll fluorescence (SIF) at high spatial resolution along orbits (oco2_orbit), but its discontinuous spatial coverage precludes its full potential for understanding the mechanistic SIF‐photosynthesis relationship. This study developed a spatially contiguous global OCO‐2 SIF product at 0.05° and 16‐day resolutions (oco2_005) using machine learning constrained by physiological understandings. This was achieved by stratifying biomes and times for training and predictions, which accounts for varying plant physiological properties in space and time.oco2_005accurately preserved the spatiotemporal variations ofoco2_orbitacross the globe. Validation ofoco2_005with Chlorophyll Fluorescence Imaging Spectrometer airborne measurements revealed striking consistency (R2 = 0.72; regression slope = 0.96). Further, without time and biome stratification, (1)oco2_005of croplands, deciduous temperate, and needleleaf forests would be underestimated during the peak season, (2)oco2_005of needleleaf forests would be overestimated during autumn, and (3) the capability ofoco2_005to detect drought would be diminished.

The Chlorophyll Fluorescence Imaging Spectrometer (CFIS), mapping far red fluorescence from aircraft

The Chlorophyll Fluorescence Imaging Spectrometer (CFIS) is an airborne high resolution imaging spectrometer built at NASA's Jet Propulsion Laboratory (JPL) for evaluating solar-induced fluorescence (SIF) from the Orbiting Carbon Observatory-2 (OCO-2). OCO-2 is a NASA mission designed to measure atmospheric CO2 but one of the novel data products is SIF, retrieved using reductions in the optical depth of Fraunhofer lines in OCO-2’s O2 A-band, covering 757–775 nm at 0.042 nm spectral resolution. CFIS was specifically designed to retrieve SIF within the wavelength range of OCO-2, but extends further down to 737 nm, nearly maintaining the high spectral resolution of the OCO-2 instrument (0.07 vs. 0.042 nm). Here, we provide an overview of the instrument calibration and performance as well as the retrieval strategy based on non-linear weighted least-squares. To illustrate the retrieval performance using actual flight data, we focus on data acquired over agricultural fields in Mead, Nebraska from an unpressurized Twin Otter (DHC-6) aircraft at a flight altitude of 3000 m above ground level (AGL). Spectral residuals are consistent with expected detector noise, which enables us to compute realistic 1-σ precision errors of 0.5–0.7 W/m2/sr/μm for typical SIF retrievals, which can be reduced to <0.2 W/m2/sr/μm when individual data is gridded at 30 m spatial resolution. The 30 m resolution also enabled direct comparison with the Crop Data Layer from the National Agricultural Statistics Service as well as Landsat imagery (NDVI, EVI, Tskin), taken just a day prior to the CFIS overflights. Results show consistently higher vegetation indices and SIF values over soy fields compared to corn, likely due to the respective phenological stage, which might already have affected chlorophyll content and canopy structure (August 15, 2016). While this work is intended to highlight the technical capabilities and performance of CFIS, the comparisons against Landsat and crop types provide insights into how CFIS can be used to study mechanisms related to photosynthesis at fine spatial scales, with the fidelity needed to obtain un-biased SIF retrievals void of atmospheric correction.

Design of a Generic 3-D Scene Generator for Passive Optical Missions and Its Implementation for the ESA’s FLEX/Sentinel-3 Tandem Mission

During the design phase of a satellite mission, end-to-end mission performance simulator (E2ES) tools allow scientists and engineers evaluating the mission concept, consolidating system technical requirements and analyzing the suitability of the implemented technical solutions and data processing algorithms. The generation of synthetic scenes is one of the core parts of an E2ES, providing scenes (ground truth) as would be observed by satellite instruments and used as reference against simulated retrieved mission products. An appropriate generation of the scene also allows assessing the performance of the ground data processing chain replacing real instrument data before the mission is in orbit, for which the fidelity of the scene generation is critical. This paper describes the design of a generic scene generator (GSG) with capabilities to generate complex 3-D synthetic scenes that combine the effects of surface, heterogeneity, topography and atmosphere, and viewing/illumination geometry. The proposed design allows generating consistent high spatial and spectral resolution top-of-atmosphere radiance scenes for multiple instruments based on the use of thematic maps, radiative transfer models, and reflectance databases. The described GSG was implemented within the FLuorescence EXplorer (FLEX) E2ES software tool and showed its capabilities to generate compatible scenes for the fluorescence imaging spectrometer, ocean and land color instrument, and sea and land surface temperature radiometer instruments of ESA’s FLEX/Sentinel-3 tandem mission and to validate the fulfillment of the FLEX mission requirements.

OCO-2 advances photosynthesis observation from space via solar-induced chlorophyll fluorescence

Quantifying gross primary production (GPP) remains a major challenge in global carbon cycle research. Spaceborne monitoring of solar-induced chlorophyll fluorescence (SIF), an integrative photosynthetic signal of molecular origin, can assist in terrestrial GPP monitoring. However, the extent to which SIF tracks spatiotemporal variations in GPP remains unresolved. Orbiting Carbon Observatory-2 (OCO-2)'s SIF data acquisition and fine spatial resolution permit direct validation against ground and airborne observations. Empirical orthogonal function analysis shows consistent spatiotemporal correspondence between OCO-2 SIF and GPP globally. A linear SIF-GPP relationship is also obtained at eddy-flux sites covering diverse biomes, setting the stage for future investigations of the robustness of such a relationship across more biomes. Our findings support the central importance of high-quality satellite SIF for studying terrestrial carbon cycle dynamics.

The FLuorescence EXplorer Mission Concept—ESA’s Earth Explorer 8

In November 2015, the FLuorescence EXplorer (FLEX) was selected as the eighth Earth Explorer mission of the European Space Agency. The tandem mission concept will provide measurements at a spectral and spatial resolution enabling the retrieval and interpretation of the full chlorophyll fluorescence spectrum emitted by the terrestrial vegetation. This paper provides a mission concept overview of the scientific goals, the key objectives related to fluorescence, and the requirements guaranteeing the fitness for purpose of the resulting scientific data set. We present the mission design at the time of selection, i.e., at the end of project phase Phase A/B1, as developed by two independent industrial consortia. The mission concepts both rely on a single payload Fluorescence Imaging Spectrometer, covering the spectral range from 500 to 780 nm. In the oxygen absorption bands, its spectral resolution will be 0.3 nm with a spectral sampling interval of 0.1 nm. The swath width of the spectrometer is 150 km and the spatial resolution will be $300 \times 300~\text{m}^{2}$ . The satellite will fly in tandem with Sentinel-3 providing different and complementary measurements with a temporal collocation of 6 to 15 s. The FLEX launch is scheduled for 2022.

Retrieval of sun-induced fluorescence using advanced spectral fitting methods

Abstract The FLuorescence EXplorer (FLEX) satellite mission, candidate of ESA's 8th Earth Explorer program, is explicitly optimized for detecting the sun-induced fluorescence emitted by plants. It will allow consistent measurements around the O2-B (687 nm) and O2-A (760 nm) bands, related to the red and far-red fluorescence emission peaks respectively, the photochemical reflectance index, and the structural-chemical state variables of the canopy. The sun-induced fluorescence signal, overlapped to the surface reflected radiance, can be accurately retrieved by employing the powerful spectral fitting technique. In this framework, a set of fluorescence retrieval algorithms optimized for FLEX are proposed in this study. Two main retrieval approaches were investigated: i) the optimization of the spectral fitting for retrieving fluorescence at the oxygen absorption bands; ii) the extension of the spectral fitting to a broader spectral window to retrieve the full fluorescence spectrum in the range from 670 to 780 nm. The accuracy of the retrieval algorithms is assessed by employing atmosphere-surface radiative transfer simulations obtained by coupling SCOPE and MODTRAN5 codes. The simulated dataset considers more realistic conditions because it includes directional effects, and the top-of-atmosphere radiance spectra are resampled to the current specifications of the FLuORescence Imaging Spectrometer (FLORIS) planned to serve as the primary instrument aboard FLEX. The retrieval accuracy obtained at the O2-A band is strongly affected by directional effects, and better performance is found in cases where directional effects are lower. However, the best performing algorithms tested provided similar performance, the RMSE (RRMSE) is 0.044 mW m− 2 sr− 1 nm− 1 (6.2%) at the O2-A band, 0.018 mW m− 2 sr− 1 nm− 1 (2.9%) at the O2-B band, and 6.225 mW m− 2 sr− 1 (6.4%) for the spectrally integrated fluorescence emission. The promising results achieved open new perspectives extending fluorescence studies not only in limited absorption bands, but its spectral behavior in relation to different plant species, photosynthetic rates and stress occurrences.

Misión FLEX (Fluorescence Explorer): Observación de la fluorescencia por teledetección como nueva técnica de estudio del estado de la vegetación terrestre a escala global

FLEX (Fluorescence EXplorer) is a candidate for the 8th ESA’s Earth Explorer mission. Is the first space mission specifically designed for the estimation of vegetation fluorescence on a global scale. The mission is proposed to fly in tandem with the future ESA´s Sentinel-3 satellite. It is foreseen that the information obtained by Sentinel-3 will be supplemented with that provided by FLORIS (Fluorescence Imaging Spectrometer) onboard FLEX. FLORIS will measure the radiance between 500 and 800 nm with a bandwidth between 0.1 nm and 2 nm, providing images with a 150 km swath and 300 m pixel size. This information will allow a detailed monitoring of vegetation dynamics, by improving the methods for the estimation of classical biophysical parameters, and by introducing a new one: fluorescence. This paper presents the current status of FLEX mission in A/B1 phase and the different ongoing studies, campaigns and projects carried out in support of the FLEX mission.

Wavelength dispersive X-ray fluorescence imaging using a high-sensitivity imaging sensor

A new wavelength-dispersive X-ray fluorescence (WD-XRF) imaging spectrometer equipped with a high-sensitivity imaging sensor was developed in our laboratory. In this instrument, a straight polycapillary optic was applied instead of a Soller slit as well as a 2D imaging X-ray detector instead of X-ray counters, which are used in conventional WD-XRF spectrometers. Therefore, images of elemental distribution were available after a short exposure time. Ni Kα images and Cu Kα images were clearly obtained at corresponding diffraction angles for a short exposure time of 10s. By optimizing the spectrometer, the time required for imaging is reduced, leading to XRF image movies. It is difficult to distinguish two peaks (Ti Kα (4.508keV) and Ba Lα (4.465keV)) due to the poor energy resolution of EDXRS. However, Ti and Ba images could be successfully observed by the WD-XRF imaging spectrometer. The energy resolution of the developed spectrometer was 25eV at the Ti Kα peak.

Wavelength Dispersive X-ray Fluorescence Imaging

A new wavelength-dispersive X-ray fluorescence (WD-XRF) imaging spectrometer equipped with a two-dimensional X-ray detector was developed in the laboratory. Straight polycapillary optics was applied instead of a soller slit, which is used in conventional WD-XRF spectrometers. X-rays were guided through the straight polycapillary to the exit of the optics by X-ray external total reflections. X-ray fluorescence was dispersed by an analyzing crystal (LiF(200)), keeping the information of elemental distribution on the surface of the sample. The energy resolution of the developed spectrometer was 130-152 eV at the Zn Kα peak. X-ray elemental images of Cu Kα and Ni Kα were successfully obtained by an X-ray CCD detector at the corresponding diffraction angles. The analytical performance of this technique, and further improvements are discussed.