The eNanoMapper database for nanomaterial safety information

• Nina Jeliazkova,
• Charalampos Chomenidis,
• Philip Doganis,
• Bengt Fadeel,
• Roland Grafström,
• Barry Hardy,
• Janna Hastings,
• Markus Hegi,
• Vedrin Jeliazkov,
• Nikolay Kochev,
• Pekka Kohonen,
• Cristian R. Munteanu,
• Haralambos Sarimveis,
• Bart Smeets,
• Pantelis Sopasakis,
• Georgia Tsiliki,
• David Vorgrimmler and
• Egon Willighagen

Beilstein J. Nanotechnol. 2015, 6, 1609–1634, doi:10.3762/bjnano.6.165

• support of data integration has recently been described [22]. eNanoMapper supports ontology re-use, for example it re-uses the content of the NPO and BAO, through automated modular import of content subsets into an integrated whole. However, the scope of the ontology goes beyond any of the individually

Possibilities and limitations of advanced transmission electron microscopy for carbon-based nanomaterials

• Xiaoxing Ke,
• Carla Bittencourt and
• Gustaaf Van Tendeloo

Beilstein J. Nanotechnol. 2015, 6, 1541–1557, doi:10.3762/bjnano.6.158

• metal-oxide semiconductor) sensor up to 1600 fps [50]. The high sensitivity and fast acquisition in detecting has made possible the automated and ultra-fast acquisition of a series of under-exposed images from the same region. After drift correction, the images of such a sequence are stacked and can

Using natural language processing techniques to inform research on nanotechnology

• Nastassja A. Lewinski and
• Bridget T. McInnes

Beilstein J. Nanotechnol. 2015, 6, 1439–1449, doi:10.3762/bjnano.6.149

• extractor, or more general NLP systems that provide various NLP tools such as Mallet and Natural Language Toolkit (NLTK) [34][35]. Utilizing and adapting these previously developed NLP tools allows for nanoinformatics researchers to build their automated systems without needing to develop low level NLP

Scalable, high performance, enzymatic cathodes based on nanoimprint lithography

• Dmitry Pankratov,
• Richard Sundberg,
• Javier Sotres,
• Dmitry B. Suyatin,
• Ivan Maximov,
• Sergey Shleev and
• Lars Montelius

Beilstein J. Nanotechnol. 2015, 6, 1377–1384, doi:10.3762/bjnano.6.142

• bio-modification) onto planar Au electrodes (with a roughness factor of about 1.7) was studied in situ by means of null ellipsometry in a similar manner as described in [20]. A thin film, automated ellipsometer (type 43 603-200E, Rudolph Research, Fairfield, NJ, USA) equipped with a xenon arc lamp

Automatic morphological characterization of nanobubbles with a novel image segmentation method and its application in the study of nanobubble coalescence

• Yuliang Wang,
• Huimin Wang,
• Shusheng Bi and
• Bin Guo

Beilstein J. Nanotechnol. 2015, 6, 952–963, doi:10.3762/bjnano.6.98

• threshold method and active contour method were combined to carry out automated image segmentation for all NBs in AFM images. Instead of manually drawing the initial contours for individual NBs, we take the contours detected by the threshold method as the initial guess used further in the implementation of

• . (a) Automated extraction of the NB cross sections after image segmentation. (b) Cross section of the NB indicated by the blue arrow in (a) and a corresponding least squares fit curve by fitting the profile as a circular arc. (c–e) The height, contact angle, and radius of curvature as a function of

Transformation of hydrogen titanate nanoribbons to TiO₂ nanoribbons and the influence of the transformation strategies on the photocatalytic performance

• Melita Rutar,
• Nejc Rozman,
• Matej Pregelj,
• Carla Bittencourt,
• Romana Cerc Korošec,
• Andrijana Sever Škapin,
• Aleš Mrzel,
• Srečo D. Škapin and
• Polona Umek

Beilstein J. Nanotechnol. 2015, 6, 831–844, doi:10.3762/bjnano.6.86

• (EDX) elemental analysis system. The samples for the EDX measurements were prepared by pressing the powder samples into pellets and coating them with a thin carbon layer. The BET specific surface areas of the samples were measured at −196 °C with a TRISTAR 3000 automated gas-adsorption analyzer

Increasing throughput of AFM-based single cell adhesion measurements through multisubstrate surfaces

• Miao Yu,
• Nico Strohmeyer,
• Jinghe Wang,
• Daniel J. Müller and
• Jonne Helenius

Beilstein J. Nanotechnol. 2015, 6, 157–166, doi:10.3762/bjnano.6.15

• , which would increase the accuracy of the profiles. With the help of the PDMS-coated masks, a semi-automated adhesion measurement setup is feasible. Our masks compare favorably to commercially available silicone masks, such as those offered by Ibidi. The production of the mask is easy and commercially

Data-adaptive image-denoising for detecting and quantifying nanoparticle entry in mucosal tissues through intravital 2-photon microscopy

• Torsten Bölke,
• Lisa Krapf,
• Regina Orzekowsky-Schroeder,
• Tobias Vossmeyer,
• Jelena Dimitrijevic,
• Horst Weller,
• Anna Schüth,
• Antje Klinger,
• Gereon Hüttmann and
• Andreas Gebert

Beilstein J. Nanotechnol. 2014, 5, 2016–2025, doi:10.3762/bjnano.5.210

• least in dark image areas, only very few photons are collected per pixel. This unavoidably leads to a low SNR, which not only affects further data interpretation by human observers, but also deteriorates the efficiency of automated processing, segmentation and image analysis [2][3][4]. In our approach

• BM3D algorithm. A further quantitative evaluation was done by calculating the sharpness index (SI) of the reconstructions (see Experimental). While this metric is only rarely applied to evaluations of image reconstructions, it is often used for automated focusing of light microscopes [24]. The SI

• the modified BM3D algorithm considerably facilitates the perception of the nanoparticles by the human observer (compare d to d′) and allows for automated image analysis to be applied to denoised 2PM images. Bar = 5 µm. Intravital 2-photon microscopy of the gut mucosa (lower right corner) and quantum

Real-time monitoring of calcium carbonate and cationic peptide deposition on carboxylate-SAM using a microfluidic SAW biosensor

• Anna Pohl and
• Ingrid M. Weiss

Beilstein J. Nanotechnol. 2014, 5, 1823–1835, doi:10.3762/bjnano.5.193

• , Germany) used in this study combines a four channel microfluidic system with SAW detection and is equipped with an efficient software-driven access for automated sample processing and data analysis. The injection of a glycerol reference is a useful technique to separate the mass signal from the viscosity

• biosensor sam®X. Automated features were used for programming and documentation of the experimental conditions. The software package FitMaster (SAW Instruments, Bonn, Germany) was used to analyze the collected data and to electronically align, for example, the time of injection for comparative analyses of

• indicated in Figure 4. Note that these signals are extremely reproducible. The line in magenta represents the glycerol injection. (A), original phase signal; (B), calculated mass normalized phase signal. The glycerol signal in (A) was used for the software-automated calculation of all signals shown in (B

A reproducible number-based sizing method for pigment-grade titanium dioxide

• Ralf Theissmann,
• Manfred Kluwig and
• Thomas Koch

Beilstein J. Nanotechnol. 2014, 5, 1815–1822, doi:10.3762/bjnano.5.192

• lacking. By using the example of titanium dioxide, this paper shows that both necessities are well met by the sophisticated counting algorithm presented here, which is based on the imaging of polished sections of embedded particles and subsequent automated image analysis. The data presented demonstrate

• minimum of subjective, user-based decisions. The major task to tackle on the way is to prepare a sample suitable for automated particle detection. Since automated detection routines are primarily based on grey-value thresholding, overlapping particles are a serious problem, which is illustrated in Figure

• a problem. The section finally analysed can therefore be reasonably assumed to be representative. The high area density of the pigment in all images ensures that constant conditions for the automated post-processing and detection procedure are assured. Measurement, pigment detection and size

The surface properties of nanoparticles determine the agglomeration state and the size of the particles under physiological conditions

• Christoph Bantz,
• Olga Koshkina,
• Thomas Lang,
• Hans-Joachim Galla,
• C. James Kirkpatrick,
• Roland H. Stauber and
• Michael Maskos

Beilstein J. Nanotechnol. 2014, 5, 1774–1786, doi:10.3762/bjnano.5.188

• sophisticated analysis routines should be applied. Specifically, this should include the analysis of more particles (>500) and, if possible, an automated image analysis to increase reproducibility [76]. The silica particles are found either as single particles or in smaller groups, whereas the siloxane

Different endocytotic uptake mechanisms for nanoparticles in epithelial cells and macrophages

• Dagmar A. Kuhn,
• Dimitri Vanhecke,
• Benjamin Michen,
• Fabian Blank,
• Peter Gehr,
• Alke Petri-Fink and
• Barbara Rothen-Rutishauser

Beilstein J. Nanotechnol. 2014, 5, 1625–1636, doi:10.3762/bjnano.5.174

• an acceleration voltage of 75 kV and equipped with a Morada CCD digital camera (Olympus, Tokyo, Japan). Size distributions of both PS particle types were obtained by image analysis using Fiji software. Thereby, images were converted to binary images by automated thresholding (default threshold) and

The protein corona protects against size- and dose-dependent toxicity of amorphous silica nanoparticles

• Dominic Docter,
• Christoph Bantz,
• Dana Westmeier,
• Hajo J. Galla,
• Qiangbin Wang,
• James C. Kirkpatrick,
• Peter Nielsen,
• Michael Maskos and
• Roland H. Stauber

Beilstein J. Nanotechnol. 2014, 5, 1380–1392, doi:10.3762/bjnano.5.151

• enzymatic/biochemical assays [30], we, here, present an automated high-throughput microscopy based approach, generally applicable to reliably and reproducibly assessing the cell vitality following exposure to nanomaterial. By uUsing the ArrayScan® VTI fluorescence microscopy imaging platform [31], we

• vitality of Caco-2, automated high-throughput microscopy revealed that cell death was almost completely prevented upon treatment in the presence of serum or human plasma proteins (Figure 4, right panel). Similar results were obtained by assessing the cell viability using independent methods, such as the

• (ASP30F and ASP30F-COOH; Table 1). As shown in Figure 7, automated microscopy revealed that in the absence of proteins slightly more ASPs were attached and taken up by the Caco-2 cells compared to the incubation in the presence of proteins after 60 min (Figure 7A/B). By increasing the surface charge by

The study of surface wetting, nanobubbles and boundary slip with an applied voltage: A review

• Yunlu Pan,
• Bharat Bhushan and
• Xuezeng Zhao

Beilstein J. Nanotechnol. 2014, 5, 1042–1065, doi:10.3762/bjnano.5.117

• ellipsometer (model L116C, Gaertner Scientific Corporation) was found to be 66 nm. A DI water droplet was deposited on the spin coated PS surface and the CA of the DI water was measured to be about 94° by using an automated goniometer (Model 290, Rame-Hart Instrument Corporation). The prepared PS surfaces are

• toluene for 24 h. Finally, to remove the unabsorbed molecules from the surface, the wafers were copious rinsed with toluene and dried by compressed air. The CA of DI water on the OTS surface was measured as 106 ± 2° by automated goniometer. The process for applying a voltage to the system was the same as

Methods for rapid frequency-domain characterization of leakage currents in silicon nanowire-based field-effect transistors

• Tomi Roinila,
• Xiao Yu,
• Jarmo Verho,
• Tie Li,
• Pasi Kallio,
• Matti Vilkko,
• Anran Gao and
• Yuelin Wang

Beilstein J. Nanotechnol. 2014, 5, 964–972, doi:10.3762/bjnano.5.110

• , implementing fully automated measurement systems, and designing new frequency-domain-based detection technologies. Conceptual diagram of a SiNW FET. Typical measurement system. Shape of the power spectrum of IRS from 5-bit length shift register. Schematic of the applied SiNW FET device. SEM image of the SiNW

Adsorption and oxidation of formaldehyde on a polycrystalline Pt film electrode: An in situ IR spectroscopy search for adsorbed reaction intermediates

• Zenonas Jusys and
• R. Jürgen Behm

Beilstein J. Nanotechnol. 2014, 5, 747–759, doi:10.3762/bjnano.5.87

• within the sample chamber of a Varian 670i IR-spectrometer, equipped with a liquid nitrogen cooled mercury cadmium telluride (MCT) detector and an automated AutoPro5 polarizer set to 90° angle to transmit only surface-sensitive p-polarized radiation from the light source. The spectral resolution was set

Towards precise defect control in layered oxide structures by using oxide molecular beam epitaxy

• Federico Baiutti,
• Georg Christiani and
• Gennady Logvenov

Beilstein J. Nanotechnol. 2014, 5, 596–602, doi:10.3762/bjnano.5.70

• scattering and recoil spectroscopy (TOF-ISARS), X-ray photoelectron spectroscopy (XPS) or any other, according to demands. Each chamber has a vertical design, which allows for the substrate transfer system to be fully automated. The substrate transfer between the load lock, the storage and each growth

Synthesis of boron nitride nanotubes from unprocessed colemanite

• Saban Kalay,
• Zehra Yilmaz and
• Mustafa Çulha

Beilstein J. Nanotechnol. 2013, 4, 843–851, doi:10.3762/bjnano.4.95

• by a completely automated Renishaw InVia Reflex Raman Microscopy system (Renishaw Plc., New Mills, Wotton-under-Edge, UK) equipped with a 514 nm Ar lasers. The laser power was set at 30 mW, and the exposure time was 10 s. A 50× objective was used. The wavelength of the instrument was automatically

Deformation-induced grain growth and twinning in nanocrystalline palladium thin films

• Aaron Kobler,
• Jochen Lohmiller,
• Jonathan Schäfer,
• Michael Kerber,
• Anna Castrup,
• Ankush Kashiwar,
• Patric A. Gruber,
• Karsten Albe,
• Horst Hahn and
• Christian Kübel

Beilstein J. Nanotechnol. 2013, 4, 554–566, doi:10.3762/bjnano.4.64

• deformation processes in the material, several samples were strained to defined straining states, up to a maximum engineering strain of 10%, and prepared for post-mortem analysis. The nanocrystalline structure was investigated by quantitative automated crystal orientation mapping (ACOM) in a transmission

• active in ncPd films deposited by magnetron sputtering onto compliant substrates. The microstructural analysis is mainly performed by quantitative automated crystal orientation mapping TEM (ACOM-TEM) [23][24] and supplemented with grain size measurement using dark-field TEM (DF-TEM) and conventional X

Plasticity of nanocrystalline alloys with chemical order: on the strength and ductility of nanocrystalline Ni–Fe

• Jonathan Schäfer and
• Karsten Albe

Beilstein J. Nanotechnol. 2013, 4, 542–553, doi:10.3762/bjnano.4.63

• microstructure was done by a novel algorithm, which allows for the extraction and analysis of dislocations from simulation data in a fully automated way [26]. The local atomic volume of each atom was calculated by means of the Voronoi tessellation method [27]. We define the free volume of the GB atoms as the

Large-scale analysis of high-speed atomic force microscopy data sets using adaptive image processing

• Blake W. Erickson,
• Séverine Coquoz,
• Jonathan D. Adams,
• Daniel J. Burns and
• Georg E. Fantner

Beilstein J. Nanotechnol. 2012, 3, 747–758, doi:10.3762/bjnano.3.84

• obtain a true representation of the sample and its changes over time. This paper presents an automated, adaptive algorithm for the required processing of AFM images. The algorithm adaptively corrects for both common one-dimensional distortions as well as the most common two-dimensional distortions. This

• . This amount of data creates a significant increase in the amount of image processing needed to extract the true sample topography, which can no longer be performed by the user on an image-by-image basis [15][17]. In HS-AFM, there is a real need for an automated processing routine that optimizes the

• [30][31]. Automated, AFM quality-control check in semiconductors and other nanotechnologies [32][33][34] also creates large data sets, which would also benefit from reliable automated image processing. In order to automate the image processing, it is important to define a metric by which the success

Friction and durability of virgin and damaged skin with and without skin cream treatment using atomic force microscopy

• Bharat Bhushan,
• Si Chen and
• Shirong Ge

Beilstein J. Nanotechnol. 2012, 3, 731–746, doi:10.3762/bjnano.3.83

• reciprocating tribometer with a velocity 1 mm/s and at a normal load of 50 mN for 3000 cycles. Contact-angle measurements The apparent contact angles were measured for various samples. Measurements were made with a Rame-Hart automated goniometer model 290-F4, where 5 μL water droplets were deposited onto the

Combining nanoscale manipulation with macroscale relocation of single quantum dots

• Francesca Paola Quacquarelli,
• Richard A. J. Woolley,
• Martin Humphry,
• Jasbiner Chauhan,
• Philip J. Moriarty and
• Ashley Cadby

Beilstein J. Nanotechnol. 2012, 3, 324–328, doi:10.3762/bjnano.3.36

• experiments on a single particle. Automated nanoparticle manipulation and imaging routines have been developed so as to facilitate the rapid assembly of specific nanoparticle arrangements. Keywords: automation; nanoscale manipulation; nanotechnology; quantum dots; single molecule spectroscopy; Introduction

• [13]. The gold nanoparticle was shown to dramatically quench the optical lifetime of the QD and to completely suppress its blinking. Experimental In this work, we position a single fluorophore, a CdSe QD, with nanometre precision on a macroscopic registration template, using automated atomic force

Distinction of nucleobases – a tip-enhanced Raman approach

• Regina Treffer,
• Xiumei Lin,
• Elena Bailo,
• Tanja Deckert-Gaudig and
• Volker Deckert

Beilstein J. Nanotechnol. 2011, 2, 628–637, doi:10.3762/bjnano.2.66

• first sequencing methods were published in 1977 by Maxam and Gilbert [1], and Sanger et al. [2]. Since then the sequencing technology has been refined and automated, and current advances show a tendency towards single-molecule sequencing, which eventually results in the development of sequencing systems

Self-organizing bioinspired oligothiophene–oligopeptide hybrids

• Alexey K. Shaytan,
• Eva-Kathrin Schillinger,
• Elena Mena-Osteritz,
• Sylvia Schmid,
• Pavel G. Khalatur,
• Peter Bäuerle and
• Alexei R. Khokhlov

Beilstein J. Nanotechnol. 2011, 2, 525–544, doi:10.3762/bjnano.2.57

• deprotection conditions, the switch ester segment is preserved at low pH. Reestablishment of the native α-amide peptide backbone can be achieved by an increase in the pH to neutral or even slightly basic conditions. The peptide segment was obtained by a semi-automated solid-phase supported peptide synthesis