Open Forest Data: Digitalizing and building an online repository

Academy Of Sciences

Poland is characterised by a relatively high variety of living organisms attributed to terrestrial and water environments. Currently, close to 57.000 species of living organisms are described that occur in Poland (Symonides 2008), including lowland and mountain species, those attributed to oceanic and continental areas, as well as species from forested and open habitats. Poland comprehensively represents biodiversity of living organisms on a continental scale and thus, is considered to have an important role for biodiversity maintenance. The Mammal Research Institute of Polish Academy of Sciences (MRI PAS), located in Białowieża Forest, a UNESCO Heritage Site, has been collecting biodiversity data for 90 years. However, a great amount of data gathered over the years, especially old data, is gradually being forgotten and hard to access. Old catalogues and databases have never been digitalized or publicly shared, and not many Polish scientists are aware of the existence of such resources, not to mention the rest of the scientific world. Recognizing the need for an online, interoperable platform, following FAIR data principles (findable, accessible, interoperable, reusable), where biodiversity and scientific data can be shared, MRI PAS took a lead in creation of an Open Forest Data (OFD) repository. OpenForestData.pl (Fig. 1) is a newly created (2020) digital repository, designed to provide access to natural sciences data and provide scientists with an infrastructure for storing, sharing and archiving their research outcomes. Creating such a platform is a part of an ongoing development of life sciences in Poland, aiming for an open, modern science, where data are published as free-access. OFD also allows for the consolidation of natural science data, enabling the use and processing of shared data, including API (Application Programming Interface) tools. OFD is indexed by the Directory of Open Repositories (OpenDOAR) and Registry of Research Data Repositories (re3data). The OFD platform is based entirely on reliable, globally recognized open source software: DATAVERSE, an interactive database app which supports sharing, storing, exploration, citation and analysis of scientific data; GEONODE, a content management geospatial system used for storing, publicly sharing and visualising vector and raster layers, GRAFANA, a system meant for storing and analysis of metrics and large scale measurement data, as well as visualisation of historical graphs at any time range and analysis for trends; and external tools for database storage (Orthanc) and data visualisation (Orthanc plugin Osimis Web Viewer and Online 3D Viewer (https://3dviewer.net/), which were integrated with the system mechanism of Dataverse. Furthermore, according to the need for specimen description, Darwin Core (Wieczorek et al. 2012) metadata schema was decided to be the most suitable for specimen and collections description and mapped into a Dataverse additional metadata block. The use of Darwin Core is based on the same file format, the Darwin Core Archive (DwC-A) which allows for sharing data using common terminology and provides the possibility for easy evaluation and comparison of biodiversity datasets. It allows the contributors to OFD to optionally choose Darwin Core for object descriptions making it possible to share biodiversity datasets in a standardized way for users to download, analyse and compare. Currently, OFD stores more than 10.000 datasets and objects from the collections of Mammal Research Institute of Polish Academy of Sciences and Forest Science Institute of Białystok University of Technology. The objects from natural collections were digitalized, described, catalogued and made public in free-access. OFD manages seven types of collection materials: 3D and 2D scans of specimen in Herbarium, Fungarium, Insect and Mammal Collections, images from microscopes (including stereoscopic and scanning electron microscopes), morphometric measurements, computed tomography and microtomography scans in Mammal Collection, mammal telemetry data, satellite imagery, geospatial climatic and environmental data, georeferenced historical maps. 3D and 2D scans of specimen in Herbarium, Fungarium, Insect and Mammal Collections, images from microscopes (including stereoscopic and scanning electron microscopes), morphometric measurements, computed tomography and microtomography scans in Mammal Collection, mammal telemetry data, satellite imagery, geospatial climatic and environmental data, georeferenced historical maps. In the OFD repository, researchers have the possibility to share data in standardized way, which nowadays is often a requirement during the publishing process of a scientific article. Beside scientists, OFD is designed to be open and free for students and specialists in nature protection, but also for officials, foresters and nature enthusiasts. Creation of the OFD repository supports the development of citizen science in Poland, increases visibility and access to published data, improves scientific collaboration, exchange and reuse of data within and across borders.

Toward High-Resolution Low-Voltage SEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100103152 ◽

1988 ◽

Vol 46 ◽

pp. 218-219

Author(s):

Zhifeng Shao

Keyword(s):

Low Voltage ◽

Spherical Aberration ◽

Chromatic Aberration ◽

Limiting Factor ◽

Operating Voltage ◽

Probe Radius ◽

Non Local ◽

Electron Microscopes ◽

Image Position ◽

Recently, low voltage (≤5kV) scanning electron microscopes have become popular because of their unprecedented advantages, such as minimized charging effects and smaller specimen damage, etc. Perhaps the most important advantage of LVSEM is that they may be able to provide ultrahigh resolution since the interaction volume decreases when electron energy is reduced. It is obvious that no matter how low the operating voltage is, the resolution is always poorer than the probe radius. To achieve 10Å resolution at 5kV (including non-local effects), we would require a probe radius of 5∽6 Å. At low voltages, we can no longer ignore the effects of chromatic aberration because of the increased ratio δV/V. The 3rd order spherical aberration is another major limiting factor. The optimized aperture should be calculated as

Current State of Biological High-Resolution Scanning Electron Microscopy

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100102985 ◽

1988 ◽

Vol 46 ◽

pp. 180-181 ◽

Cited By ~ 1

Author(s):

Klaus-Ruediger Peters

Keyword(s):

High Performance ◽

Low Voltage ◽

Backscattered Electrons ◽

Lens Position ◽

Low Voltage Operation ◽

Signal Collection ◽

Probe Size ◽

Electron Microscopes ◽

Scanning Electron

A new generation of high performance field emission scanning electron microscopes (FSEM) is now commercially available (JEOL 890, Hitachi S 900, ISI OS 130-F) characterized by an "in lens" position of the specimen where probe diameters are reduced and signal collection improved. Additionally, low voltage operation is extended to 1 kV. Compared to the first generation of FSEM (JE0L JSM 30, Hitachi S 800), which utilized a specimen position below the final lens, specimen size had to be reduced but useful magnification could be impressively increased in both low (1-4 kV) and high (5-40 kV) voltage operation, i.e. from 50,000 to 200,000 and 250,000 to 1,000,000 x respectively.At high accelerating voltage and magnification, contrasts on biological specimens are well characterized1 and are produced by the entering probe electrons in the outmost surface layer within -vl nm depth. Backscattered electrons produce only a background signal. Under these conditions (FIG. 1) image quality is similar to conventional TEM (FIG. 2) and only limited at magnifications >1,000,000 x by probe size (0.5 nm) or non-localization effects (%0.5 nm).

Chromatic aberration and low-voltage SEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100127293 ◽

1987 ◽

Vol 45 ◽

pp. 546-547

Author(s):

Zhifeng Shao ◽

A.V. Crewe

Keyword(s):

Electron Energy ◽

Low Voltage ◽

Spherical Aberration ◽

Chromatic Aberration ◽

Primary Electron ◽

Probe Size ◽

Non Local ◽

Optical Treatment ◽

Electron Microscopes ◽

For scanning electron microscopes, it is plausible that by lowering the primary electron energy, one can decrease the volume of interaction and improve resolution. As shown by Crewe /1/, at V0 =5kV a 10Å resolution (including non-local effects) is possible. To achieve this, we would need a probe size about 5Å. However, at low voltages, the chromatic aberration becomes the major concern even for field emission sources. In this case, δV/V = 0.1 V/5kV = 2x10-5. As a rough estimate, it has been shown that /2/ the chromatic aberration δC should be less than ⅓ of δ0 the probe size determined by diffraction and spherical aberration in order to neglect its effect. But this did not take into account the distribution of electron energy. We will show that by using a wave optical treatment, the tolerance on the chromatic aberration is much larger than we expected.

High-resolution observation of sintered alumina (Al2O3) using the specimen-heated and electron-beam-induced conductivity method in a UHR-SEM

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100172966 ◽

1994 ◽

Vol 52 ◽

pp. 1046-1047

Author(s):

K. Ogura ◽

T. Suzuki ◽

C. Nielsen

Keyword(s):

Electron Beam ◽

High Resolution ◽

Specimen Preparation ◽

Conductivity Method ◽

Fine Grain ◽

Grain Structures ◽

Resolution Observation ◽

Electron Microscopes ◽

Charging Effect

In spite of the complicated specimen preparation, Transmission Electron Microscopes (TEM) have traditionally been used for the investigation of the fine grain structures of sintered ceramics. Scanning Electron Microscopes (SEM) have not been used much for the same purpose as TEM because of poor results caused by the specimen charging effect, and also the lack of sufficient resolution. Here, we are presenting a successful result of high resolution imaging of sintered alumina (pure Al2O3) using the Specimen Heated and Electron Beam Induced Conductivity (SHEBIC) method, which we recently reported, in an ultrahigh resolution SEM (UHR-SEM). The JSM-6000F, equipped with a Field Emission Gun (FEG) and an in-lens specimen position, was used for this application.After sintered Al2O3 was sliced into a piece approximately 0.5 mm in thickness, one side was mechanically polished to get a shiny plane for the observation. When the observation was started at 20 kV, an enormous charging effect occured, and it was impossible to obtain a clear Secondary Electron (SE) image (Fig.1).

High resolution at low voltage: A new approach

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152355 ◽

1989 ◽

Vol 47 ◽

pp. 76-77

Author(s):

Arthur V. Jones

Keyword(s):

Low Voltage ◽

Emission Sources ◽

New Approach ◽

Design Concepts ◽

Probe Diameter ◽

Low Voltage Operation ◽

Sufficient Intensity ◽

Electron Microscopes ◽

Immersion Type

With the introduction of field-emission sources and “immersion-type” objective lenses, the resolution obtainable with modern scanning electron microscopes is approaching that obtainable in STEM and TEM-but only with specific types of specimens. Bulk specimens still suffer from the restrictions imposed by internal scattering and the need to be conducting. Advances in coating techniques have largely overcome these problems but for a sizeable body of specimens, the restrictions imposed by coating are unacceptable.For such specimens, low voltage operation, with its low beam penetration and freedom from charging artifacts, is the method of choice.Unfortunately the technical dificulties in producing an electron beam sufficiently small and of sufficient intensity are considerably greater at low beam energies — so much so that a radical reevaluation of convential design concepts is needed.The probe diameter is usually given by

Observation of GaAs/AlAs Superlattice Structures in both Secondary and Backscattcred Electron Imaging Modes with an Ultrahigh Resolution Scanning Electron Microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010018077x ◽

1990 ◽

Vol 48 (1) ◽

pp. 404-405

Author(s):

K. Ogura ◽

A. Ono ◽

S. Franchi ◽

P.G. Merli ◽

A. Migliori

Keyword(s):

Gaas Layer ◽

Objective Lens ◽

Superlattice Structure ◽

Backscattered Electron ◽

Instrumental Resolution ◽

Electron Microscopes ◽

Superlattice Structures ◽

Electron Imaging ◽

Scanning Electron

In the last few years the development of Scanning Electron Microscopes (SEM), equipped with a Field Emission Gun (FEG) and using in-lens specimen position, has allowed a significant improvement of the instrumental resolution . This is a result of the fine and bright probe provided by the FEG and by the reduced aberration coefficients of the strongly excited objective lens. The smaller specimen size required by in-lens instruments (about 1 cm, in comparison to 15 or 20 cm of a conventional SEM) doesn’t represent a serious limitation in the evaluation of semiconductor process techniques, where the demand of high resolution is continuosly increasing. In this field one of the more interesting applications, already described (1), is the observation of superlattice structures.In this note we report a comparison between secondary electron (SE) and backscattered electron (BSE) images of a GaAs / AlAs superlattice structure, whose cross section is reported in fig. 1. The structure consist of a 3 nm GaAs layer and 10 pairs of 7 nm GaAs / 15 nm AlAs layers grown on GaAs substrate. Fig. 2, 3 and 4 are SE images of this structure made with a JEOL JSM 890 SEM operating at an accelerating voltage of 3, 15 and 25 kV respectively. Fig. 5 is a 25 kV BSE image of the same specimen. It can be noticed that the 3nm layer is always visible and that the 3 kV SE image, in spite of the poorer resolution, shows the same contrast of the BSE image. In the SE mode, an increase of the accelerating voltage produces a contrast inversion. On the contrary, when observed with BSE, the layers of GaAs are always brighter than the AlAs ones , independently of the beam energy.

Pollen morphology of some Tamarix (Tamaricaceae) species of Iran

Acta Botanica Hungarica ◽

10.1556/034.62.2020.1-2.9 ◽

2020 ◽

Vol 62 (1-2) ◽

pp. 151-161

Author(s):

T. Shagholi ◽

M. Keshavarzi ◽

M. Sheidai

Keyword(s):

North Africa ◽

Pollen Grains ◽

Ecological Niches ◽

Multivariate Statistical Methods ◽

Multivariate Statistical ◽

Qualitative And Quantitative ◽

Petal Length ◽

Electron Microscopes ◽

High Level ◽

Tamarix L. (Tamaricaceae) is a halophytic shrub in different parts of Asia and North Africa. Taxonomy and species limitation of Tamarix is very complex. This genus has three sections as Tamarix, Oligadenia, and Polyadenia, which are mainly separated by petal length, the number of stamens, the shape of androecial disk and attachment of filament on the androecial disk. As there was no palynological data on pollen features of Tamarix species of Iran, in the present study 12 qualitative and quantitative pollen features were evaluated to find diagnostic ones. Pollen grains of 8 Tamarix species were collected from nature. Pollen grains were studied without any treatment. Measurements were based on at least 50 pollen grains per specimen. Light and scanning electron microscopes were used. Multivariate statistical methods were applied to clarify the species relationships based on pollen data. All species studied showed monad and tricolpate (except some individuals of T. androssowii). Some Tamarix species show a high level of variability, in response to ecological niches and phenotypic plasticity, which make Tamarix species separation much more difficult. Based on the results of the present study, pollen grains features are not in agreement with previous morphological and molecular genetics about the sectional distinction.

Characteristics of Lightweight Cellular Concrete and Effects on Mechanical Properties

Materials ◽

10.3390/ma13122678 ◽

2020 ◽

Vol 13 (12) ◽

pp. 2678 ◽

Cited By ~ 1

Author(s):

Wei Yu ◽

Xu Liang ◽

Frank Mi-Way Ni ◽

Abimbola Grace Oyeyi ◽

Susan Tighe

Keyword(s):

Mechanical Properties ◽

Pore Structure ◽

High Definition ◽

Pore Characteristics ◽

Software Applications ◽

Solid Part ◽

Electron Microscopes ◽

Lab Test ◽

Cellular Concrete

This study investigated the pore structure and its effects on mechanical properties of lightweight cellular concrete (LCC) in order to understand more and detailed characteristics of such structure. As part of investigation, environment scanning electron microscopes (ESEM) and industrial high-definition (HD) macro photography camera were separately used to capture and compare images of specimens. Physical properties of the pore structure, including pore area, size, perimeter, fit ellipse, and shape descriptors, were studied based on the image processing technology and software applications. Specimens with three different densities (400, 475, and 600 kg/m3) were prepared in the laboratory. Firstly, the effects of density on the characteristics of pore structure were investigated; furthermore, mechanical properties (compressive strength, modulus of elasticity and Poisson’s ratio, flexural strength and splitting tensile strength of LCC) were tested. The relationships among pore characteristics, density, and mechanical properties were analyzed. Based on the results obtained from the lab test—comparisons made between specimens with high-densities and those with low-densities—it was found significant variability in bubble size, thickness, and irregularity of pores. Furthermore, the increase of density is accompanied by better mechanical properties, and the main influencing factors are the thickness of the solid part and the shape of the bubble. The thicker of solid part and more regular pores of LCC has, the better mechanical properties are.

Discoasters of the Blue Clay (Middle Miocene) of Malta and Gozo

Geological Magazine ◽

10.1017/s0016756800040942 ◽

1978 ◽

Vol 115 (1) ◽

pp. 1-19 ◽

Cited By ~ 3

Author(s):

Minoo Hojjatzadeh

Keyword(s):

Middle Miocene ◽

The Family ◽

Electron Microscopes ◽

Scanning Electron

SummaryTwenty-three species of the Family Discoasteraceae Vekshina, 1959 recovered from 18 samples of the Blue Clay at Fort Chambray, Gozo, and 31 samples from Fomm-Ir-Rih Bay, Malta, have been studied under light and scanning electron microscopes. Fourteen Middle Miocene species are reviewed, their stratigraphical ranges and importance as marker species discussed. Nine species are described as new. On the basis of the discoaster species present, a Middle Miocene age (NN.6 Discoaster exilis Zone – NN.7 Discoaster kugleri Zone) for the Blue Clay in Malta and Gozo is suggested.

Analysis on Microstructure of Laser Brazing Diamond Grits with a Ni-Based Filler Alloy

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.97-101.3879 ◽

2010 ◽

Vol 97-101 ◽

pp. 3879-3883 ◽

Cited By ~ 1

Author(s):

Zhi Bo Yang ◽

Jiu Hua Xu ◽

Ai Ju Liu

Keyword(s):

Active Element ◽

Steel Substrate ◽

Parameters Optimization ◽

Interfacial Region ◽

Filler Alloy ◽

X Ray Diffraction ◽

X Ray ◽

Cross Diffusion ◽

Electron Microscopes ◽

Brazing diamond grits onto steel substrate using a Ni-based filler alloy was carried out via laser beam in an argon atmosphere. The microstructure of the interfacial region among the Diamond grits and the filler layer were investigated by means of scanning electron microscopes (SEM), X-ray diffraction (XRD) and energy dispersive X-ray spectroscopy (EDS). Meanwhile, the formation mechanism of carbide layers was discussed. All the results indicated that the active element chromium in the Ni-based alloy concentrated preferentially to the surface of the grits to form a chromium-rich layer, and the hard joint between the alloy and the steel substrate is established through a cross-diffusion of iron and Ni-based alloy through parameters optimization.