The Experts below are selected from a list of 291 Experts worldwide ranked by ideXlab platform
Flavio Monti - One of the best experts on this subject based on the ideXlab platform.
-
genetic connectivity among Osprey populations and consequences for conservation philopatry versus dispersal as key factors
Conservation Genetics, 2018Co-Authors: Flavio Monti, Olivier Duriez, Florie Delfour, Veronique Arnal, Saliha Zenboudji, Claudine MontgelardAbstract:Genetic variability and population structure in Osprey were studied using DNA microsatellite markers. Special emphasis was placed on the subspecies living in the Afro-Palearctic (Pandion haliaetus haliaetus). For comparative purposes, American Osprey subspecies (P. h. carolinensis, P. h. ridgway) and Indo/Australian subspecies (P. h. cristatus) were included in this analysis. Twenty DNA microsatellite loci were analysed across a total of 200 individuals. Cluster analysis of genetic distances generally grouped populations of Osprey in accordance with their subspecific designation and with previous results from mtDNA analysis. Ospreys from America and Australia were clearly separated from P. h. haliaetus suggesting a more ancient isolation which prevented recent gene flow across these groups. Within P. h. haliaetus, significant genetic differentiation was found between populations in northern and southern Europe, suggesting that the Afro-Palearctic group is structured into two interconnected entities (Mediterranean and continental Europe). Population structuring was supported by an assignment test and by analysis of allele-sharing among individuals. At the Mediterranean scale, no significant differences of allelic information were found between populations. Behaviours such as dispersal, migration and philopatry seem to have played simultaneously and in contrary directions in shaping the genetic structure and diversity of populations. Our results provide essential information for reconstructing gene flow and genetic variability among Osprey populations at different scales, which call for caution in the proactive management and conservation of the species, namely in the Mediterranean area.
-
details of environmental covariates analyses from Migrating Ospreys use thermal uplift over the open sea
2018Co-Authors: Olivier Duriez, Andrea Sforzi, Guillaume Peron, David Gremillet, Flavio MontiAbstract:Most large raptors on migration avoid crossing the sea because of the lack of atmospheric convection over temperate seas. The Osprey Pandion haliaetus is an exception among raptors, since it can fly over several hundred km of open water. We equipped five juvenile Ospreys with GPS-Accelerometer-Magnetometer loggers. All birds were able to find and use thermal uplift while crossing the Mediterranean Sea, on average 7.5 times per 100 km, and could reach altitudes of 900 m above the sea surface. Their climb rate was 1.6 time slower than over land, and birds kept flapping most of the time while circling in the thermals, indicating that convections cells were weaker than over land. The frequency of thermal soaring was correlated with the difference between the sea surface and air temperature, indicating that atmospheric convection occurred when surface waters were warmer than the overlaying air. These observations help explaining the transoceanic cosmopolitan distribution of Osprey, and question the widely held assumption that water bodies represent strict barriers for large raptors
-
details of behaviour classification methods from Migrating Ospreys use thermal uplift over the open sea
2018Co-Authors: Olivier Duriez, Andrea Sforzi, Guillaume Peron, David Gremillet, Flavio MontiAbstract:Most large raptors on migration avoid crossing the sea because of the lack of atmospheric convection over temperate seas. The Osprey Pandion haliaetus is an exception among raptors, since it can fly over several hundred km of open water. We equipped five juvenile Ospreys with GPS-Accelerometer-Magnetometer loggers. All birds were able to find and use thermal uplift while crossing the Mediterranean Sea, on average 7.5 times per 100 km, and could reach altitudes of 900 m above the sea surface. Their climb rate was 1.6 time slower than over land, and birds kept flapping most of the time while circling in the thermals, indicating that convections cells were weaker than over land. The frequency of thermal soaring was correlated with the difference between the sea surface and air temperature, indicating that atmospheric convection occurred when surface waters were warmer than the overlaying air. These observations help explaining the transoceanic cosmopolitan distribution of Osprey, and question the widely held assumption that water bodies represent strict barriers for large raptors
-
effects of strong winds on thermal soaring behaviour from Migrating Ospreys use thermal uplift over the open sea
2018Co-Authors: Olivier Duriez, Andrea Sforzi, Guillaume Peron, David Gremillet, Flavio MontiAbstract:Most large raptors on migration avoid crossing the sea because of the lack of atmospheric convection over temperate seas. The Osprey Pandion haliaetus is an exception among raptors, since it can fly over several hundred km of open water. We equipped five juvenile Ospreys with GPS-Accelerometer-Magnetometer loggers. All birds were able to find and use thermal uplift while crossing the Mediterranean Sea, on average 7.5 times per 100 km, and could reach altitudes of 900 m above the sea surface. Their climb rate was 1.6 time slower than over land, and birds kept flapping most of the time while circling in the thermals, indicating that convections cells were weaker than over land. The frequency of thermal soaring was correlated with the difference between the sea surface and air temperature, indicating that atmospheric convection occurred when surface waters were warmer than the overlaying air. These observations help explaining the transoceanic cosmopolitan distribution of Osprey, and question the widely held assumption that water bodies represent strict barriers for large raptors
-
details of behaviour classification methods from Migrating Ospreys use thermal uplift over the open sea
2018Co-Authors: Olivier Duriez, Andrea Sforzi, Guillaume Peron, David Gremillet, Flavio MontiAbstract:Most large raptors on migration avoid crossing the sea because of the lack of atmospheric convection over temperate seas. The Osprey Pandion haliaetus is an exception among raptors, since it can fly over several hundred kilometres of open water. We equipped five juvenile Ospreys with GPS-Accelerometer-Magnetometer loggers. All birds were able to find and use thermal uplift while crossing the Mediterranean Sea, on average 7.5 times per 100 km, and could reach altitudes of 900 m above the sea surface. Their climb rate was 1.6 times slower than over land, and birds kept flapping most of the time while circling in the thermals, indicating that convections cells were weaker than over land. The frequency of thermal soaring was correlated with the difference between the sea surface and air temperature, indicating that atmospheric convection occurred when surface waters were warmer than the overlaying air. These observations help explain the transoceanic cosmopolitan distribution of Osprey, and question the widely held assumption that water bodies represent strict barriers for large raptors
Mary Ann Ottinger - One of the best experts on this subject based on the ideXlab platform.
-
chesapeake bay fish Osprey pandion haliaetus food chain evaluation of contaminant exposure and genetic damage
Environmental Toxicology and Chemistry, 2016Co-Authors: Rebecca S. Lazarus, Barnett A. Rattner, Peter C. Mcgowan, Robert C Hale, Natalie K Karounarenier, Richard A Erickson, Mary Ann OttingerAbstract:From 2011 to 2013, a large-scale ecotoxicological study was conducted in several Chesapeake Bay (USA) tributaries (Susquehanna River and flats, the Back, Baltimore Harbor/Patapsco Rivers, Anacostia/ middle Potomac, Elizabeth and James Rivers) and Poplar Island as a mid-Bay reference site. Osprey (Pandion haliaetus) diet and the transfer of contaminants from fish to Osprey eggs were evaluated. The most bioaccumulative compounds (biomagnification factor > 5) included p,p'-dichlorodiphenyldichloroethylene (DDE), total polychlorinated biphenyls (PCBs), total polybrominated diphenyl ethers (PBDEs), and bromodiphenyl ether (BDE) congeners 47, 99, 100, and 154. This analysis suggested that alternative brominated flame retardants and other compounds (methoxytriclosan) are not appreciably biomagnifying. A multivariate analysis of similarity indicated that major differences in patterns among study sites were driven by PCB congeners 105, 128, 156, 170/190, and 189, and PBDE congeners 99 and 209. An integrative redundancy analysis showed that Osprey eggs from Baltimore Harbor/Patapsco River and the Elizabeth River had high residues of PCBs and p,p'-DDE, with PBDEs making a substantial contribution to overall halogenated contamination on the Susquehanna and Anacostia/middle Potomac Rivers. The redundancy analysis also suggested a potential relation between PBDE residues in Osprey eggs and oxidative DNA damage in nestling blood samples. The results also indicate that there is no longer a discernible relation between halogenated contaminants in Osprey eggs and their reproductive success in Chesapeake Bay. Osprey populations are thriving in much of the Chesapeake, with productivity rates exceeding those required to sustain a stable population. Environ Toxicol Chem 2016;35:1560-1575. Published 2016 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.
-
Exposure and food web transfer of pharmaceuticals in Ospreys (Pandion haliaetus): Predictive model and empirical data.
Integrated environmental assessment and management, 2014Co-Authors: Rebecca S. Lazarus, Barnett A. Rattner, Bryan W. Brooks, Peter C. Mcgowan, Vicki S Blazer, Mary Ann OttingerAbstract:The Osprey (Pandion haliaetus) is a well-known sentinel of environmental contamination, yet no studies have traced pharmaceuticals through the water–fish–Osprey food web. A screening-level exposure assessment was used to evaluate the bioaccumulation potential of 113 pharmaceuticals and metabolites, and an artificial sweetener in this food web. Hypothetical concentrations in water reflecting “wastewater effluent dominated” or “dilution dominated” scenarios were combined with pH-specific bioconcentration factors (BCFs) to predict uptake in fish. Residues in fish and Osprey food intake rate were used to calculate the daily intake (DI) of compounds by an adult female Osprey. Fourteen pharmaceuticals and a drug metabolite with a BCF greater than 100 and a DI greater than 20 µg/kg were identified as being most likely to exceed the adult human therapeutic dose (HTD). These 15 compounds were also evaluated in a 40 day cumulative dose exposure scenario using first-order kinetics to account for uptake and elimination. Assuming comparable absorption to humans, the half-lives (t1/2) for an adult Osprey to reach the HTD within 40 days were calculated. For 3 of these pharmaceuticals, the estimated t1/2 in Ospreys was less than that for humans, and thus an Osprey might theoretically reach or exceed the HTD in 3 to 7 days. To complement the exposure model, 24 compounds were quantified in water, fish plasma, and Osprey nestling plasma from 7 potentially impaired locations in Chesapeake Bay. Of the 18 analytes detected in water, 8 were found in fish plasma, but only 1 in Osprey plasma (the antihypertensive diltiazem). Compared to diltiazem detection rate and concentrations in water (10/12 detects,
-
Evaluation of Osprey Habitat Suitability and Interaction with Contaminant Exposure
Journal of Wildlife Management, 2006Co-Authors: Pamela C. Toschik, Mary C. Christman, Barnett A. Rattner, Mary Ann OttingerAbstract:Abstract Ospreys (Pandion haliaetus) have been the focus of conservation efforts since their dramatic population decline attributed to dichlorodiphenyltrichloroethane and related chemicals in the 1960s. Several recent studies of Ospreys nesting in the United States have indicated improved reproduction. However, the density of breeding Ospreys varies greatly among locations, with some areas seemingly habitable but not occupied. Because of concerns about pollution in the highly industrialized portions of the Delaware River and Bay, USA, we evaluated contaminant exposure and productivity in Ospreys nesting on the Delaware River and Bay in 2002. We characterized habitat in the coastal zone of Delaware, USA, and the area around the river in Pennsylvania, USA, using data we collected as well as extant information provided by state and federal sources. We characterized habitat based on locations of occupied Osprey nests in Delaware and Pennsylvania. We evaluated water clarity, water depth, land use and land cove...
Charles J Henny - One of the best experts on this subject based on the ideXlab platform.
-
Wastewater dilution index partially explains observed polybrominated diphenyl ether flame retardant concentrations in Osprey eggs from Columbia River Basin, 2008–2009
Ecotoxicology, 2011Co-Authors: Charles J Henny, James L Kaiser, Robert A Grove, Branden L. Johnson, Chad V. Furl, Robert J. LetcherAbstract:Several polybrominated biphenyl ether (PBDE) congeners were found in all 175 Osprey ( Pandion haliaetus ) eggs collected from the Columbia River Basin between 2002 and 2009. ΣPBDE concentrations in 2008–2009 were highest in Osprey eggs from the two lowest flow rivers studied; however, each river flowed through relatively large and populous metropolitan areas (Boise, Idaho and Spokane, Washington). We used the volume of Wastewater Treatment Plant (WWTP) discharge, a known source of PBDEs, as a measure of human activity at a location, and combined with river flow (both converted to millions of gallons/day) created a novel approach (an approximate Dilution Index) to relate waterborne contaminants to levels of these contaminants that reach avian eggs. This approach provided a useful understanding of the spatial Osprey egg concentration patterns observed. Individual Osprey egg concentrations along the Upper Willamette River co-varied with the Dilution Index, while combined egg data (geometric means) from rivers or segments of rivers showed a strong, significant relationship to the Dilution Index with one exception, the Boise River. There, we believe Osprey egg concentrations were lower than expected because Boise River Ospreys foraged perhaps 50–75% of the time off the river at ponds and lakes stocked with fish that contained relatively low ΣPBDE concentrations. Our limited temporal data at specific localities (2004–2009) suggests that ΣPBDE concentrations in Osprey eggs peaked between 2005 and 2007, and then decreased, perhaps in response to penta- and octa-PBDE technical mixtures no longer being used in the USA after 2004. Empirical estimates of biomagnification factors (BMFs) from fish to Osprey eggs were 3.76–7.52 on a wet weight (ww) basis or 4.37–11.0 lipid weight. Our earlier Osprey study suggested that ΣPBDE egg concentrations >1,000 ng/g ww may reduce Osprey reproductive success. Only two of the study areas sampled in 2008–2009 contained individual eggs with ΣPBDE concentrations >1,000 ng/g, and non-significant ( P > 0.30) negative relationships were found between ΣPBDEs and reproductive success. Additional monitoring is required to confirm not only the apparent decline in PBDE concentrations in Osprey eggs that occurred during this study, but also to better understand the relationship between PBDEs in eggs and reproductive success.
-
North American Osprey Populations and Contaminants: Historic and Contemporary Perspectives
Journal of toxicology and environmental health. Part B Critical reviews, 2010Co-Authors: Charles J Henny, James L Kaiser, Robert A Grove, Branden L. JohnsonAbstract:Osprey (Pandion haliaetus) populations were adversely affected by DDT and perhaps other contaminants in the United States and elsewhere. Reduced productivity, eggshell thinning, and high DDE concentrations in eggs were the signs associated with declining Osprey populations in the 1950s, 1960s, and 1970s. The species was one of the first studied on a large scale to bring contaminant issues into focus. Although few quantitative population data were available prior to the 1960s, many Osprey populations in North America were studied during the 1960s and 1970s with much learned about basic life history and biology. This article reviews the historical and current effects of contaminants on regional Osprey populations. Breeding populations in many regions of North America showed post-DDT-era (1972) population increases of varying magnitudes, with many populations now appearing to stabilize at much higher numbers than initially reported in the 1970s and 1980s. However, the magnitude of regional population increases in the United States between 1981 (first Nationwide Survey, ∼8,000 pairs), when some recovery had already occurred, 1994 (second survey, ∼14,200), and 2001 (third survey, ∼16,000-19,000), or any other years, is likely not a simple response to the release from earlier contaminant effects, but a response to multi-factorial effects. This indirect "contaminant effects" measurement comparing changes (i.e., recovery) in post-DDT-era population numbers over time is probably confounded by changing human attitudes toward birds of prey (shooting, destroying nests, etc.), changing habitats, changing fish populations, and perhaps competition from other species. The species' adaptation to newly created reservoirs and its increasing use of artificial nesting structures (power poles, nesting platforms, cell towers, channel markers, offshore duck blinds, etc.) are two important factors. The timing of the initial use of artificial nesting structures, which replaced declining numbers of suitable trees at many locations, varied regionally (much later in the western United States and Mexico). Because of the increasing use of artificial nesting structures, there may be more Ospreys nesting in North America now than ever before. Now, with the impact of most legacy organic contaminants (DDT, other organochlorine [OC] pesticides, polychlorinated biphenyls [PCB], polychlorinated dibenzo-p-dioxins [PCDD], polychlorinated dibenzofurans (PCDF]) greatly reduced or eliminated, and some Osprey populations showing evidence of stabilizing, the species was proposed as a Worldwide Sentinel Species for evaluating emerging contaminants. Several emerging contaminants are already being studied, such as polybrominated diphenyl ethers (PBDE) and perfluorinated acids and sulfonate compounds (PFC). The many advantages for continued contaminant investigations using the Osprey include a good understanding of its biology and ecology, its known distribution and abundance, and its ability to habituate to humans and their activities, which permits nesting in some of the potentially most contaminated environments. It is a top predator in most ecosystems, and its nests are relatively easy to locate and study with little researcher impact on reproductive success.
-
Osprey distribution abundance reproductive success and contaminant burdens along lower columbia river 1997 1998 versus 2004
Archives of Environmental Contamination and Toxicology, 2008Co-Authors: Charles J Henny, Robert A Grove, James L KaiserAbstract:The Osprey (Pandion haliaetus) population nesting along the lower portion of the Columbia River (river mile 29 to 286) increased from 94 in 1997 to 103 occupied nests in 1998 (9.6% annual rate of increase) to 225 occupied nests in 2004 (13.9% annual rate of increase). The more recent rate of population increase was associated with higher reproductive rates than in 1997/1998, and significantly lower egg concentrations of most organochlorine (OC) pesticides, polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins (PCDDs) and polychlorinated dibenzofurans (PCDFs). A comparison of observed egg residue concentrations in 2004 with effect-level information for Ospreys indicated that reproduction at few, if any, nests was adversely affected. As recent as 1997/1998, dichlorodiphenyldichloroethylene (DDE) was still adversely affecting reproductive success for a portion of this population. Mercury was the only contaminant evaluated in both 1997/1998 and 2004 that showed a significant increase in eggs over time, but concentrations in 2004 (0.09 μg g−1 ww) remained below established effect levels for birds (generally reported at 0.50 μg g−1 ww or higher). The significant increase in mercury justifies the need for future monitoring. All contaminants mentioned that biomagnify up food chains can be effectively monitored in Osprey eggs. The Osprey has been shown to be an excellent sentinel species for long-term monitoring with their many useful traits described.
-
Interim Summary: Nesting Counts of Ospreys and Brown Pelicans in Northwestern Mexico, 2006
Open-File Report, 2007Co-Authors: Charles J Henny, Daniel W. AndersonAbstract:The distribution and abundance of nesting populations of California brown pelicans (Pelecanus occidentalis californicus) and Ospreys (Pandion haliaetus) were documented in 2006 in northwestern Mexico. For Ospreys only, the 2006 data were compared to population estimates from two previous surveys (one conducted in 1977 and another conducted in the period 1992-1993). Overall, the total Osprey nesting population increased from 1977 to 1992-1993 and then only changed slightly by 2006, but included regions with localized declines, increases, and stable populations. Preliminary population estimates for California brown pelicans suggest a large and apparently healthy breeding population. Problem Statement and Implications California brown pelicans (Pelecanus occidentalis californicus) and Osprey (Pandion haliaetus) nesting along the coast of northwestern Mexico, including the Gulf of California, are an important component of Pacific Coast populations. Surveys of the Osprey nesting population were conducted in 1977 and 1992-93 by Charles Henny (CJH) and Daniel Anderson (DWA), the same observers for this study, which provides a strong basis for comparisons over 29 years. No complete, range-wide survey of nesting California brown pelicans has been conducted in the past, and the subspecies is currently listed as endangered under the Endangered Species Act. The most recent published information for pelicans in the region is from the mid-1970s. Information about the current nesting population size and distribution are a priority need for a delisting analysis. The overall nesting population of Ospreys in northwestern Mexico increased 68% from 810 ± 55 (95% C.I.) pairs in 1977 to 1,362 ± 278 pairs in 1992-93, but the population nesting along the Gulf Coast of Baja California remained stationary (255 versus 236 pairs). This atypical pattern of population recovery warrants additional investigation.
-
biomagnification factors fish to Osprey eggs from willamette river oregon u s a for pcdds pcdfs pcbs and oc pesticides
Environmental Monitoring and Assessment, 2003Co-Authors: Charles J Henny, James L Kaiser, Robert A Grove, Raymond V Bentley, John E ElliottAbstract:A migratory population of 78 pairs of Osprey (Pandion haliaetus) nesting along the Willamette River in westernOregon was studied in 1993. The study was designed to determinecontaminant concentrations in eggs, contaminant concentrationsin fish species predominant in the Ospreys diet, andBiomagnification Factors (BMFs) of contaminants from fish specieseaten to Osprey eggs. Ten Osprey eggs and 25 composite samplesof fish (3 species) were used to evaluate organochlorine (OC)pesticides, polychlorinated biphenyls (PCBs), polychlorinateddibenzo-p-dioxins (PCDDs), and polychlorinated dibenzofurans(PCDFs). Mercury was also analyzed in fish. Geometric meanresidues in Osprey eggs were judged low, e.g., DDE 2.3 μg g-1 wet weight (ww), Σ PCBs 0.69 μg g-1, 2,3,7,8-TCDD 2.3 ng kg-1, and generally well below known threshold values for adverse effects on productivity, and the population was increasing. Osprey egg residue data presentedby River Mile (RM) are discussed, e.g., higher PCDDs were generally found immediately downstream of paper mills and eggsfrom the Willamette River had significantly elevated PCBs and PCDDs compared to reference eggs collected nearby in the CascadeMountains. Prey remains at nest sites indicated that the Largescale Sucker (Catostomus macrocheilus) and NorthernPikeminnow (Ptychocheilus oregonensis) accounted for an estimated 90.1% of the biomass in the Osprey diet, and composite samples of these two species were collected from different sampling sites throughout the study area for contaminant analyses. With the large percentage of the fishbiomass in the Osprey diet sampled for contaminants (and fisheaten by Ospreys similar in size to those chemically analyzed),and fish contaminant concentrations weighted by biomass intake, a mean BMF was estimated from fish to Osprey eggs for the largeseries of contaminants. BMFs ranged from no biomagnification(0.42) for 2,3,7,8-TCDF to 174 for OCDD. Our findings for themigratory Osprey were compared to BMFs for the resident HerringGull (Larus argentatus), and differences are discussed. Webelieve a BMF approach provides some basic understanding ofrelationships between contaminant burdens in prey species offish-eating birds and contaminants incorporated into their eggs,and may prove useful in understanding sources of contaminants inmigratory species although additional studies are needed.
Georg Oeltzschner - One of the best experts on this subject based on the ideXlab platform.
-
Osprey open source processing reconstruction estimation of magnetic resonance spectroscopy data
Journal of Neuroscience Methods, 2020Co-Authors: Georg Oeltzschner, Steve C. N. Hui, Mark Mikkelsen, Muhammad G. Saleh, Sofie Tapper, Helge J Zollner, Richard A.e. EddenAbstract:Abstract Background Processing and quantitative analysis of magnetic resonance spectroscopy (MRS) data are far from standardized and require interfacing with third-party software. Here, we present Osprey, a fully integrated open-source data analysis pipeline for MRS data, with seamless integration of pre-processing, linear-combination modelling, quantification, and data visualization. New Method Osprey loads multiple common MRS data formats, performs phased-array coil combination, frequency-and phase-correction of individual transients, signal averaging and Fourier transformation. Linear combination modelling of the processed spectrum is carried out using simulated basis sets and a spline baseline. The MRS voxel is coregistered to an anatomical image, which is segmented for tissue correction and quantification is performed based upon modelling parameters and tissue segmentation. The results of each analysis step are visualized in the Osprey GUI. The analysis pipeline is demonstrated in 12 PRESS, 11 MEGA-PRESS, and 8 HERMES datasets acquired in healthy subjects. Results Osprey successfully loads, processes, models, and quantifies MRS data acquired with a variety of conventional and spectral editing techniques. Comparison with Existing Method(s) Osprey is the first MRS software to combine uniform pre-processing, linear-combination modelling, tissue correction and quantification into a coherent ecosystem. Compared to existing compiled, often closed-source modelling software, Osprey’s open-source code philosophy allows researchers to integrate state-of-the-art data processing and modelling routines, and potentially converge towards standardization of analysis. Conclusions Osprey combines robust, peer-reviewed data processing methods into a modular workflow that is easily augmented by community developers, allowing the rapid implementation of new methods.
-
Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data
Journal of neuroscience methods, 2020Co-Authors: Georg Oeltzschner, Helge J. Zoellner, Steve C. N. Hui, Mark Mikkelsen, Muhammad G. Saleh, Sofie Tapper, Richard A.e. EddenAbstract:Abstract Background Processing and quantitative analysis of magnetic resonance spectroscopy (MRS) data are far from standardized and require interfacing with third-party software. Here, we present Osprey, a fully integrated open-source data analysis pipeline for MRS data, with seamless integration of pre-processing, linear-combination modelling, quantification, and data visualization. New Method Osprey loads multiple common MRS data formats, performs phased-array coil combination, frequency-and phase-correction of individual transients, signal averaging and Fourier transformation. Linear combination modelling of the processed spectrum is carried out using simulated basis sets and a spline baseline. The MRS voxel is coregistered to an anatomical image, which is segmented for tissue correction and quantification is performed based upon modelling parameters and tissue segmentation. The results of each analysis step are visualized in the Osprey GUI. The analysis pipeline is demonstrated in 12 PRESS, 11 MEGA-PRESS, and 8 HERMES datasets acquired in healthy subjects. Results Osprey successfully loads, processes, models, and quantifies MRS data acquired with a variety of conventional and spectral editing techniques. Comparison with Existing Method(s) Osprey is the first MRS software to combine uniform pre-processing, linear-combination modelling, tissue correction and quantification into a coherent ecosystem. Compared to existing compiled, often closed-source modelling software, Osprey’s open-source code philosophy allows researchers to integrate state-of-the-art data processing and modelling routines, and potentially converge towards standardization of analysis. Conclusions Osprey combines robust, peer-reviewed data processing methods into a modular workflow that is easily augmented by community developers, allowing the rapid implementation of new methods.
Richard A.e. Edden - One of the best experts on this subject based on the ideXlab platform.
-
Osprey open source processing reconstruction estimation of magnetic resonance spectroscopy data
Journal of Neuroscience Methods, 2020Co-Authors: Georg Oeltzschner, Steve C. N. Hui, Mark Mikkelsen, Muhammad G. Saleh, Sofie Tapper, Helge J Zollner, Richard A.e. EddenAbstract:Abstract Background Processing and quantitative analysis of magnetic resonance spectroscopy (MRS) data are far from standardized and require interfacing with third-party software. Here, we present Osprey, a fully integrated open-source data analysis pipeline for MRS data, with seamless integration of pre-processing, linear-combination modelling, quantification, and data visualization. New Method Osprey loads multiple common MRS data formats, performs phased-array coil combination, frequency-and phase-correction of individual transients, signal averaging and Fourier transformation. Linear combination modelling of the processed spectrum is carried out using simulated basis sets and a spline baseline. The MRS voxel is coregistered to an anatomical image, which is segmented for tissue correction and quantification is performed based upon modelling parameters and tissue segmentation. The results of each analysis step are visualized in the Osprey GUI. The analysis pipeline is demonstrated in 12 PRESS, 11 MEGA-PRESS, and 8 HERMES datasets acquired in healthy subjects. Results Osprey successfully loads, processes, models, and quantifies MRS data acquired with a variety of conventional and spectral editing techniques. Comparison with Existing Method(s) Osprey is the first MRS software to combine uniform pre-processing, linear-combination modelling, tissue correction and quantification into a coherent ecosystem. Compared to existing compiled, often closed-source modelling software, Osprey’s open-source code philosophy allows researchers to integrate state-of-the-art data processing and modelling routines, and potentially converge towards standardization of analysis. Conclusions Osprey combines robust, peer-reviewed data processing methods into a modular workflow that is easily augmented by community developers, allowing the rapid implementation of new methods.
-
Osprey: Open-source processing, reconstruction & estimation of magnetic resonance spectroscopy data
Journal of neuroscience methods, 2020Co-Authors: Georg Oeltzschner, Helge J. Zoellner, Steve C. N. Hui, Mark Mikkelsen, Muhammad G. Saleh, Sofie Tapper, Richard A.e. EddenAbstract:Abstract Background Processing and quantitative analysis of magnetic resonance spectroscopy (MRS) data are far from standardized and require interfacing with third-party software. Here, we present Osprey, a fully integrated open-source data analysis pipeline for MRS data, with seamless integration of pre-processing, linear-combination modelling, quantification, and data visualization. New Method Osprey loads multiple common MRS data formats, performs phased-array coil combination, frequency-and phase-correction of individual transients, signal averaging and Fourier transformation. Linear combination modelling of the processed spectrum is carried out using simulated basis sets and a spline baseline. The MRS voxel is coregistered to an anatomical image, which is segmented for tissue correction and quantification is performed based upon modelling parameters and tissue segmentation. The results of each analysis step are visualized in the Osprey GUI. The analysis pipeline is demonstrated in 12 PRESS, 11 MEGA-PRESS, and 8 HERMES datasets acquired in healthy subjects. Results Osprey successfully loads, processes, models, and quantifies MRS data acquired with a variety of conventional and spectral editing techniques. Comparison with Existing Method(s) Osprey is the first MRS software to combine uniform pre-processing, linear-combination modelling, tissue correction and quantification into a coherent ecosystem. Compared to existing compiled, often closed-source modelling software, Osprey’s open-source code philosophy allows researchers to integrate state-of-the-art data processing and modelling routines, and potentially converge towards standardization of analysis. Conclusions Osprey combines robust, peer-reviewed data processing methods into a modular workflow that is easily augmented by community developers, allowing the rapid implementation of new methods.
