Apart from their effector functions in allergic disorders, tissue-resident mast cells (MC) are gaining recognition as initiators of inflammatory events through their distinctive ability to secrete many bioactive molecules harbored in cytoplasmic granules. Activation triggers mediator release through a regulated exocytosis named degranulation. MC activation is still substantiated by measuring systemic levels of MC-restricted mediators. However, identifying the anatomical location of MC activation is valuable for disease diagnosis. We designed a computer-assisted morphometric method based on image analysis of methylene blue (MB)-stained normal mouse skin tissue sections that quantitates actual in situ MC activation status. We reasoned MC cytoplasm could be viewed as an object featuring unique relative mass values based on activation status. Integrated optical density and area (A) ratios were significantly different between intact and degranulated MC (p<0.001). The examination of fractal characteristics is of translational diagnostic/prognostic value in cancer and readily applied to quantify cytoskeleton morphology and vasculature. Fractal dimension (D), a measure of their comparative space filling capacity and structural density, also differed significantly between intact and degranulated MC (p<0.001). Morphometric analysis provides a reliable and reproducible method for in situ quantification of MC activation status.

Microtubule analysis is of significant value for a better understanding of normal and pathological cellular processes. Although immunofluorescence microscopic techniques have proven useful in the study of microtubules, comparative results commonly rely on a descriptive and subjective visual analysis. We developed an objective and quantitative method based on image processing and analysis of fluorescently labeled microtubular patterns in cultured cells. We used a multi-parameter approach by analyzing four quantifiable characteristics to compose our quantitative feature set. Then we interpreted specific changes in the parameters and revealed the contribution of each feature set using principal component analysis. In addition, we verified that different treatment groups could be clearly discriminated using principal components of the multi-parameter model. High predictive accuracy of four commonly used multi-classification methods confirmed our method. These results demonstrated the effectiveness and efficiency of our method in the analysis of microtubules in fluorescence images. Application of the analytical methods presented here provides information concerning the organization and modification of microtubules, and could aid in the further understanding of structural and functional aspects of microtubules under normal and pathological conditions.

We conducted a comparative study of three widely used algorithms for the detection of fiducial markers in electron microscopy images. The algorithms were applied to four datasets from different sources. For the purpose of obtaining comparable results, we introduced figures of merit and implemented all three algorithms in a unified code base to exclude software-specific differences. The application of the algorithms revealed that none of the three algorithms is superior to the others in all cases. This leads to the conclusion that the choice of a marker detection algorithm highly depends on the properties of the dataset to be analyzed, even within the narrowed domain of electron tomography.

Optical projection tomography (OPT) is a computed tomography technique at optical frequencies for samples of 0.5–15 mm in size, which fills an important “imaging gap” between confocal microscopy (for smaller samples) and large-sample methods such as fluorescence molecular tomography or micro magnetic resonance imaging. OPT operates in either fluorescence or transmission mode. Two-dimensional (2D) projections are taken over 360° with a fixed rotational increment around the vertical axis. Standard 3D reconstruction from 2D OPT uses the filtered backprojection (FBP) algorithm based on the Radon transform. FBP approximates the inverse Radon transform using a ramp filter that spreads reconstructed pixels to neighbor pixels thus producing streak and other types of artifacts, as well as noise. Artifacts increase the variation of grayscale values in the reconstructed images. We present an algorithm that improves the quality of reconstruction even for a low number of projections by simultaneously minimizing the sum of absolute brightness changes in the reconstructed volume (the total variation) and the error between measured and reconstructed data. We demonstrate the efficiency of the method on real biological data acquired on a dedicated OPT device.

On account of its excellent resolution and high throughput, cryoSEM imaging has recently seen resurgence. In this work, we report on the development of cryogenic triple ion gun milling (CryoTIGM™), a broad ion beam milling technique for cryo-planing of vitrified, “frozen-hydrated” specimens. We find that sections prepared with CryoTIGM™ are smooth over exceptionally large areas (~700,000 µm2), and reveal ultrastructural details in similar or better quality than freeze-fractured samples.

In situ environmental transmission electron microscopy (ETEM) experiments require specimen heating holders to study material behavior in gaseous environments at elevated temperatures. In order to extract meaningful kinetic parameters, such as activation energies, it is essential to have a direct and accurate measurement of local sample temperature. This is particularly important if the sample temperature might fluctuate, for example when room temperature gases are introduced to the sample area. Using selected-area diffraction (SAD) in an ETEM, the lattice parameter of Ag nanoparticles was measured as a function of the temperature and pressure of hydrogen gas to provide a calibration of the local sample temperature. SAD permits measurement of temperature to an accuracy of ±30°C using Ag lattice expansion. Gas introduction can cause sample cooling of several hundred degrees celsius for gas pressures achievable in the ETEM.

We demonstrate quantitative core-loss electron energy-loss spectroscopy of iron oxide nanoparticles and imaging resolution of Ag nanoparticles in liquid down to 0.24 nm, in both transmission and scanning transmission modes, in a novel, monolithic liquid cell developed for the transmission electron microscope (TEM). At typical SiN membrane thicknesses of 50 nm the liquid-layer thickness has a maximum change of only 30 nm for the entire TEM viewing area of 200×200 µm.

We demonstrate direct electron beam writing of a nano-scale Cu pattern on a surface with a thin aqueous layer of CuSO4 solution. Electron beams are highly maneuverable down to nano-scales. Aqueous solutions facilitate a plentiful metal ion supply for practical industrial applications, which may require continued reliable writing of sophisticated patterns. A thin aqueous layer on a surface helps to confine the writing on the surface. For this demonstration, liquid sample holder (K-kit) for transmission electron microscope (TEM) was employed to form a sealed space in a TEM. The aqueous CuSO4 solution inside the sample holder was allowed to partially dry until a uniform thin layer was left on the surface. The electron beam thus reduced Cu ions in the solution to form the desired patterns. Furthermore, the influence of e-beam exposure time and CuSO4(aq) concentration on the Cu reduction was studied in this work. Two growth stages of Cu were shown in the plot of Cu thickness versus e-beam exposure time. The measured Cu reduction rate was found to be proportional to the CuSO4(aq) concentration.

In a recent publication by Abou-Ras et al., various techniques for the analysis of elemental distribution in thin films were compared, using the example of a 2-µm thick Cu(In,Ga)Se2 thin film applied as an absorber material in a solar cell. The authors of this work found that similar relative Ga distributions perpendicular to the substrate across the Cu(In,Ga)Se2 thin film were determined by 18 different techniques, applied on samples from the same identical deposition run. Their spatial and depth resolutions, their measuring speeds, their availabilities, as well as their detection limits were discussed. The present work adds two further techniques to this comparison: laser-induced breakdown spectroscopy and grazing-incidence X-ray fluorescence analysis.

An alternative approach for simulating the field evaporation process in atom probe tomography is presented. The model uses the electrostatic Robin’s equation to directly calculate charge distribution over the tip apex conducting surface, without the need for a supporting mesh. The partial ionization state of the surface atoms is at the core of the method. Indeed, each surface atom is considered as a point charge, which is representative of its evaporation probability. The computational efficiency is ensured by an adapted version of the Barnes–Hut N-body problem algorithm. Standard desorption maps for cubic structures are presented in order to demonstrate the effectiveness of the method.