Individual tree point clouds and tree measurements from multi-platform laser scanning in German forests

Laser scanning from different acquisition platforms enables the collection of 3D point clouds from different perspectives and with varying resolutions. These point clouds allow us to retrieve detailed information on the individual tree and forest structure. We conducted airborne laser scanning (ALS), uncrewed aerial vehicle (UAV)-borne laser scanning (ULS) and terrestrial laser scanning (TLS) in two German mixed forests with species typical of central Europe. We provide the spatially overlapping, georeferenced point clouds for 12 forest plots. As a result of individual tree extraction, we furthermore present a comprehensive database of tree point clouds and corresponding tree metrics. Tree metrics were derived from the point clouds and, for half of the plots, also measured in the field. Our dataset may be used for the creation of 3D tree models for radiative transfer modeling or lidar simulation studies or to fit allometric equations between point cloud metrics and forest inventory variables. It can further serve as a benchmark dataset for different algorithms and machine learning tasks, in particular automated individual tree segmentation, tree species classification or forest inventory metric prediction. The dataset and supplementary metadata are available for download, hosted by the PANGAEA data publisher at https://doi.org/10.1594/PANGAEA.942856 (Weiser et al., 2022a)

Zaznavanje odmrlih stoječih dreves z uporabo laserskega skeniranja v obdobjih rasti in mirovanja

The assessment of forest health is gaining importance with the increasing frequency and severity of drought events. Forest ecosystems are becoming more vulnerable and susceptible to diseases and insect attacks, leading to increased tree mortality and risk of fire. Light Detection and Ranging (LiDAR) allows to obtain valuable 3-dimensional geometrical and spectral information, which is becoming more widely used in forest health assessments. The aim of this study was to examine the potential of bi-temporal UAV-borne laser scanning (ULS) data and voxel-based metrics for predicting the occurrence of standing dead trees without tree delineation. The position of each standing dead tree was measured during field inventory. ULS data was collected under leaf-on and leaf-off conditions. A 2D moving window approach was developed to extract feature sets based on cells, height bins, and columns from leaf-on and leaf-off datasets. The classification was carried out using a random forest classifier, resulting in accuracies of 0.87 and 0.86 for the two tested plots. These results were achieved using the bi-temporal dataset and using a threshold of 2.5 m for the distance of the 2D window position and the location of the field measurement. Among the two voxel-based groups of metrics (height bins and columns), height bins provided more valuable information from vertical vegetation strata, which improved the classification of live and dead trees. Metrics derived from the point cloud divided into columns proved to be prone to noisy points and missing data. The presented approach using a 2D moving window gave satisfactory results, but further analysis would be needed in different forest settings to determine the effects of vegetation structure on classification performance.Ocenjevanje zdravstvenega stanja gozdov postaja vse pomembnejše zaradi pogostejših in daljših sušnih obdobij. Gozdni ekosistemi postajajo bolj ranljivi in dovzetnejši za bolezni in napade žuželk, zaradi česar se povečujeta smrtnost dreves in nevarnost požarov. Z metodo LiDAR (ang. Light Detection and Ranging) lahko pridobimo trirazsežne geometrijske in spektralne podatke, ki se vse pogosteje uporabljajo pri ocenjevanju zdravstvenega stanja gozdov. Namen te študije je bil proučiti potencial bitemporalnih podatkov laserskega skeniranja z uporabo brezpilotnega zrakoplova (ang. UAV-borne laser scanning ali ULS) in atributov na podlagi vokslov za napovedovanje pojavljanja odmrlih stoječih dreves brez njihove predhodne segmentacije. Lokacijo vsakega odmrlega stoječega drevesa smo izmerili na terenu. Podatke laserskega skeniranja smo zajeli v obdobjih rasti in mirovanja. Za pridobivanje atributov na podlagi celic, višinskih slojev in stolpcev iz bitemporalnih podatkov smo uporabili drsno okno. Klasifikacijo smo izvedli z uporabo algoritma naključnih gozdov, pri čemer smo dosegli klasifikacijsko točnost 0,87 za proučevano območje P1 in klasifikacijsko točnost 0,86 za proučevano območje P2. To smo dosegli z bitemporalnimi podatki in z uporabo praga 2,5 m za razdaljo med položajem drsnega okna in najbližjo lokacijo terenske meritve. Med obema skupinama atirbutov, ki temeljita na vokslih (višinski sloji in stolpci) smo z višinskimi sloji pridobili bolj uporabne podatke iz navpičnih slojev vegetacije, kar je izboljšalo klasifikacijo živih in odmrlih dreves. Izkazalo se je, da so atributi, pridobljeni iz oblaka točk razdeljenega v stolpce, dovzetni za šum in manjkajoče vrednosti. Z uporabo drsnega okna smo dobili zadovoljive rezultate, vendar bi bile za ugotavljanje vpliva vegetacijske sestave na uspešnost klasifikacije potrebne nadaljnje analize v različnih gozdnih okoljih

Dejavniki, ki vplivajo na klinično sliko bolnikov s patogeno različico p.G90D gena za rodopsin

Izhodišče: Patogene različice v genu za rodopsin (RHO) največkrat povzročajo različne oblike pigmentne retinopatije (RP), ki je napredujoča degeneracija mrežnice, redkeje pa kongenitalno stacionarno nočno slepoto (CSNB). Do sedaj je bilo predpostavljeno, da posamezna različica povzroča bodisi eno ali drugo klinično sliko (npr. p.G90D CSNB), z redkimi izjemami (npr. p.E113K). V nekaterih raziskavah so pokazali, da lahko jemanje vitamina A upočasni napredovanje RP, vendar zdravljenje z vitaminom A ni sprejeto v klinični praksi. Namen: Ugotoviti ali lahko različica p.G90D poleg CSNB povzroča tudi druge klinične slike in ali obstajajo dejavniki, ki so s tem povezani. Metode: V prospektivni raziskavi smo pregledali vse znane bolnike s potrjeno patogeno različico p.G90D v RHO in vse njihove družinske člane, ki so poročali o nočni slepoti, skupaj 19 bolnikov iz treh družin (13 moških in 6 ženskmediana 41 let, razpon 8 – 71). Opravili so razširjen oftalmološki pregled, ki je vključeval preiskave vidne funkcije (vključno z elektroretinografijo) in slikovne preiskave (avtofluorescenco očesnega ozadja in optično koherentno tomografijo). Bolniki so izpolnili vprašalnik o pridruženih boleznih in življenjskemu sloguiz vzorca venske krvi smo določili serumsko koncentracijo vitamina A. Patogena različica p.G90D je bila potrjena z uporabo sekvenciranja nove generacije ali Sangerjevega sekvenciranja. Rezultati: Bolniki so imeli bodisi nočno slepoto brez strukturne okvare (NBWD) (26 %) klasično RP (48 %), pericentralno RP (5 %) ali sektorsko RP (21 %). Bolniki z NBWD so bili mlajši od ostalih, vendar razlika ni bila statistično značilna. Pridužene bolezni so navajali izključno bolniki s klasično in sektorsko RP (v 75 % in v 56 %), ki pa so bili tudi starejši. Med bolniki starimi 40 let ali več, so imeli tisti z blažjo klinično sliko (NBWD, sektorska RP) statistično značilno višjo koncentracijo vitamina A kot tisti z večjo strukturno okvaro (klasična RP, pericentralna RP) (mediana 3,0 vs. 2,0 μmol/L, Mann-Whitneyev test, p < 0,05). Zaključki: V nasprotju z dosedanjimi raziskavami patogena različica p.G90D poleg disfunkcije paličnic (CSNB oz. NBWD) povzroča tudi različne oblike distrofije mrežnice (klasična RP, pericentralna RP in sektorska RP). Taka fenotipska raznolikost je posebnost med ostalimi več kot 200 različicami v RHO, ki zanje ni značilna. Serumski vitamin A je možen modifikator bolezni vendar je za potrditev potrebna raziskave na večih bolnikih in z daljšim sledenjem.Background: Pathogenic variants in the rhodopsin gene (RHO) most commonly cause various forms of retinitis pigmentosa (RP), which is a progressive retinal degeneration, and less commonly congenital stationary blindness (CSNB). Until now, it has been assumed that a single variant produces either one or the other clinical outcome (e.g. p.G90D CSNB), with rare exceptions (e.g. pE113K). Some studies have shown that taking vitamin A can slow the progression of RP, but vitamin A treatment is not accepted in clinical practice. Aim: To determine whether the p.G90D causes other clinical pictures in addition to CSNB and identify potential modifying factors associated with this. Methods: A prospective study included all known patients harboring p.G90D in RHO and all their family members who reported night blindness, a total of 19 patients from three families (13 male and 6 femalemedian age 41 years, range 8 – 71). They underwent an extended ophthalmologic examination which included examinations of visual function (including electroretinography) and imaging (fundus autofluorescence and optical coherence tomography). Patients completed a questionnare on associated diseases and lifestyle. Serum vitamin A concentration was determined from a venous blood sample. The pathogenic variant p.G90D was confirmed using next-generation sequencing or Sanger sequencing. Results: Patients had either night blindness without degeneration (NBWD) (26%), classic RP (48%), pericentral RP (5%) or sectoral RP (21%). Patients with NBWD were younger than the others, however the diffrence was not significant. Systemic diseases were reported exlusievely by patients with classic and sectoral RP (75 % and 56 %), who were also oldest. In a subgroup of patients aged 40 years or more, patients with a milder clinical signs (NBWD, sectoral RP) had significantly higher vitamin A concentration than patients with greater structural impairment (classic RP, pericentral RP) (median 3.0 vs 2.0 μmol/L, Mann-Whitney test, p < 0.05). Conclusions: Contrary to the previous report, p.G90D also causes various forms of retinal dystrophy (classic RP, sector RP and pericentral RP) in addition to rod dysfunction (CSNB or NBWD). Such phenotypic variability is unusual even among more than 200 variants in RHO, which is not characteristic of them. Serum vitamin A concentration is a possible disease modifier, however studies on larger cohorts and longer follow-up are needed to confirm this

Individual tree point clouds and tree measurements from multi-platform laser scanning in German forests

Laser scanning from different acquisition platforms enables the collection of 3D point clouds from different perspectives and with varying resolutions. These point clouds allow us to retrieve detailed information on the individual tree and forest structure. We conducted airborne laser scanning (ALS), uncrewed aerial vehicle (UAV)-borne laser scanning (ULS) and terrestrial laser scanning (TLS) in two German mixed forests with species typical of central Europe. We provide the spatially overlapping, georeferenced point clouds for 12 forest plots. As a result of individual tree extraction, we furthermore present a comprehensive database of tree point clouds and corresponding tree metrics. Tree metrics were derived from the point clouds and, for half of the plots, also measured in the field. Our dataset may be used for the creation of 3D tree models for radiative transfer modeling or lidar simulation studies or to fit allometric equations between point cloud metrics and forest inventory variables. It can further serve as a benchmark dataset for different algorithms and machine learning tasks, in particular automated individual tree segmentation, tree species classification or forest inventory metric prediction. The dataset and supplementary metadata are available for download, hosted by the PANGAEA data publisher at https://doi.org/10.1594/PANGAEA.942856 (Weiser et al., 2022a)

Correlation between the Serum Concentration of Vitamin A and Disease Severity in Patients Carrying p.G90D in <i>RHO</i>, the Most Frequent Gene Associated with Dominant Retinitis Pigmentosa: Implications for Therapy with Vitamin A

The pathogenic variant p.G90D in RHO is believed to be responsible for a spectrum of phenotypes, including congenital stationary blindness (for the purpose of this study termed night blindness without degeneration; NBWD), Sector RP, Pericentral RP, and Classic RP. We present a correlation between the serum concentration of vitamin A and disease severity in patients with this variant. This prospective study involved 30 patients from 7 families (17 male; median age 46 years, range 8–73). Full ophthalmological examination including visual acuity, Goldmann perimetry, slit-lamp exam, optical coherence tomography, fundus autofluorescence, and electrophysiology was performed to determine the presenting phenotype. The serum concentration of vitamin A was determined from a fasting blood sample taken on the day of the exam, where it was found that 23.3% (7/30) of patients had NBWD, 13.3% (4/30) had Sector RP, 3.3% (1/30) had Pericentral RP, and 60% (18/30) had Classic RP. Multiple logistic regression revealed a significantly higher probability of having a milder phenotype (NBWD or Sector RP) in association with younger age (p p cis-retinal form plays a role in stabilizing the constitutively active p.G90D rhodopsin and its supplementation could be a potential treatment strategy for p.G90D RHO patients

Stationary and Progressive Phenotypes Caused by the p.G90D Mutation in Rhodopsin Gene

Mutations in rhodopsin gene (RHO) are a frequent cause of retinitis pigmentosa (RP) and less often, congenital stationary night blindness (CSNB). Mutation p.G90D has previously been associated with CSNB based on the examination of one family. This study screened 60 patients. Out of these 60 patients, 32 were affected and a full characterization was conducted in 15 patients. We described the clinical characteristics of these 15 patients (12 male, median age 42 years, range 8–71) from three families including visual field (Campus Goldmann), fundus autofluorescence (FAF), optical coherence tomography (OCT) and electrophysiology. Phenotypes were classified into four categories: CSNB (N = 3, 20%) sector RP (N = 3, 20%), pericentral RP (N = 1, 6.7%) and classic RP (N = 8, 53.3% (8/15)). The phenotypes were not associated with family, sex or age (Kruskal–Wallis, p &gt; 0.05), however, cystoid macular edema (CME) was observed only in one family. Among the subjects reporting nyctalopia, 69% (22/32) were male. The clinical characteristics of the largest p.G90D cohort so far showed a large frequency of progressive retinal degeneration with 53.3% developing RP, contrary to the previous report

Terrestrial, UAV-borne, and airborne laser scanning point clouds of central European forest plots, Germany, with extracted individual trees and manual forest inventory measurements

Laser scanning point clouds of forest stands were acquired in southwest Germany in 2019 and 2020 from different platforms: an aircraft, an uncrewed aerial vehicle (UAV) and a ground-based tripod. The UAV-borne and airborne laser scanning campaigns cover twelve forest plots of approximately 1 ha. The plots are located in mixed central European forests close to Bretten and Karlsruhe, in the federal state of Baden-Württemberg, Germany. Terrestrial laser scanning was performed in selected locations within the twelve forest plots. Airborne and terrestrial laser scanning point clouds were acquired under leaf-on conditions, UAV-borne laser scans were acquired both under leaf-on and later under leaf-off conditions. In addition to the laser scanning campaigns, forest inventory tree properties (species, height, diameter at breast height, crown base height, crown diameter) were measured in-situ during summer 2019 in six of the twelve 1-ha plots. Single tree point clouds were extracted from the different laser scanning datasets and matched to the field measurements. For each tree entry, point clouds, tree species, position, and field-measured and point cloud-derived tree metrics are provided. For 249 trees, point clouds from all three platforms are available. The tree models form the basis of a single tree database covering a range of species typical for central European forests which is currently being established in the framework of the SYSSIFOSS project

Terrestrial, UAV-borne, and airborne laser scanning point clouds of central European forest plots, Germany, with extracted individual trees and manual forest inventory measurements

Laser scanning point clouds of forest stands were acquired in southwest Germany in 2019 and 2020 from different platforms: an aircraft, an uncrewed aerial vehicle (UAV) and a ground-based tripod. The UAV-borne and airborne laser scanning campaigns cover twelve forest plots of approximately 1 ha. The plots are located in mixed central European forests close to Bretten and Karlsruhe, in the federal state of Baden-Württemberg, Germany. Terrestrial laser scanning was performed in selected locations within the twelve forest plots. Airborne and terrestrial laser scanning point clouds were acquired under leaf-on conditions, UAV-borne laser scans were acquired both under leaf-on and later under leaf-off conditions. In addition to the laser scanning campaigns, forest inventory tree properties (species, height, diameter at breast height, crown base height, crown diameter) were measured in-situ during summer 2019 in six of the twelve 1-ha plots. Single tree point clouds were extracted from the different laser scanning datasets and matched to the field measurements. For each tree entry, point clouds, tree species, position, and field-measured and point cloud-derived tree metrics are provided. For 249 trees, point clouds from all three platforms are available. The tree models form the basis of a single tree database covering a range of species typical for central European forests which is currently being established in the framework of the SYSSIFOSS project