Monte Carlo softwares are widely used to understand the capabilities of electron microscopes. To study more realistic applications with complex samples, 3D Monte Carlo softwares are needed. In this paper, the development of the 3D version of CASINO is presented. The software feature a graphical user interface, an efficient (in relation to simulation time and memory use) 3D simulation model, accurate physic models for electron microscopy applications, and it is available freely to the scientific community at this website: www.gel.usherbrooke.ca/casino/index.html. It can be used to model backscattered, secondary, and transmitted electron signals as well as absorbed energy. The software features like scan points and shot noise allow the simulation and study of realistic experimental conditions. This software has an improved energy range for scanning electron microscopy and scanning transmission electron microscopy applications.

Scanning transmission electron microscopy (STEM) was used to image gold nanoparticles on top of and below saline water layers of several micrometers thickness. The smallest gold nanoparticles studied had diameters of 1.4 nm and were visible for a liquid thickness of up to 3.3 µm. The imaging of gold nanoparticles below several micrometers of liquid was limited by broadening of the electron probe caused by scattering of the electron beam in the liquid. The experimental data corresponded to analytical models of the resolution and of the electron probe broadening, as function of the liquid thickness. The results were also compared with Monte Carlo simulations of the STEM imaging on modeled specimens of similar geometry and composition as used for the experiments. Applications of STEM imaging in liquid can be found in cell biology, e.g., to study tagged proteins in whole eukaryotic cells in liquid, and in materials science to study the interaction of solid:liquid interfaces at the nanoscale.

We present a three-dimensional (3D) version of the CASINO Monte Carlo software; the current 2D version is widely used in the microscopy community. CASINO is used for the simulation of images and linescans of electron beam instruments. The software has an easy-to-use graphical user interface (GUI). The creation of the sample, setting of the simulation parameters and the viewing of the results are done through this GUI. The software now implements a full 3D sample, allowing users to create realistic geometries for their simulations. Other new features of the software include models for: 1) fast secondary and secondary electrons, 2) annular dark field scanning transmission electron microscopy (ADF STEM) [1], 3) absorbed energy, and 4) elastic cross sections based on the software ELSEPA [2] allowing modeling of the electron scattering in the range up to 500 keV. CASINO is available in 32 and 64-bit version (the latter allowing larger simulations) and uses multi-CPU and multi-core hardware to reduce simulation time [3]. We will present the features of CASINO and examples of its applications.The electron trajectory calculation is based on to the previous version of CASINO [4]. The fast secondary electrons (FSE) are generated using the Möller equation [5] while the slow secondary electrons (SE) are generated from the plasmon theory [6]. Fig. 1 shows backscattered electrons (BSE) and SE images generated with CASINO of tin balls on a carbon substrate sample. These images are used to understand the impact of microscope parameters on image resolution. The difference in contrast between the BSE and SE signal for 1 and 10 keV incident energy is analyzed from these simulations. The largest contrast (2.3) is obtained with the SE signal at 1 keV and is four time larger than the contrast obtained with BSE signal for the same energy.The 3D version of the Monte Carlo software CASINO includes features to analyze the absorbed energy within the sample. These features are the simulation of complex beam scanning pattern and the calculation of the absorbed energy inside a 3D matrix unit volume. Absorbed energy modeling can assist the user in the determination of the exposure parameters and resist thickness when fabricating nanometer-scale semiconductor devices using electron beam lithography (EBL) technique. Fig. 2 shows an example of the impact of incident energy on PMMA resist lines by EBL. Fig. 2B and 2C show a cross section view of the energy summed over 300 nm along the line axis in the PMMA layer. The side view at 3 keV shows that the absorbed energy between the lines is more important at the bottom due to the larger interaction volume. From the first line at the left, we observed that the absorbed energy can occur as far as 50 nm (at the resist/SiO 2 interface) away from the line pattern at 3 keV. At 20 keV, no absorption was observed outside the line pattern, except for a barely visible enlargement at the bottom, which should not cause any problem during the resist development step. From this example, it is clear that such low e...

Scanning transmission electron microscope (STEM) images of three-dimensional (3D) samples were simulated. The samples consisted of a micrometer(s)-thick substrate, and gold nanoparticles at various vertical positions. The atomic number (Z) contrast as obtained via the annular dark field detector was generated. The simulations were carried out using the Monte Carlo metihod in the Casino software (freeware). The software was adapted to include the STEM imaging modality, including the noise characteristics of the electron source, the conical shape of the beam, and 3D scanning. Simulated STEM images of nanoparticles on a carbon substrate revealed the influence of the electron dose on the visibility of the nanoparticles. The 3D datasets obtained by simulating focal-series showed the effect of beam broadening on the spatial resolution, and on the signal-to-noise-ratio. Monte Carlo simulations of STEM imaging of nanoparticles on a thick water layer were compared with experimental data by programming the exact sample geometry. The simulated image corresponded to the experimental image, and the signal-to-noise levels were similar. The Monte Carlo simulation strategy described here can be used to calculate STEM images of objects of an arbitrary geometry and amorphous sample composition. This information can then be used, for example, to optimize the microscope settings for imaging sessions where a low electron dose is crucial, for the design of equipment, or for the analysis of the composition of a certain specimen.

The Monte Carlo software CASINO has been expanded with new modules for the simulation of complex beam scanning patterns, for the simulation of cathodoluminescence (CL), and for the calculation of electron energy deposition in subregions of a three-dimensional (3D) volume. Two examples are presented of the application of these new capabilities of CASINO. First, the CL emission near threading dislocations in gallium nitride (GaN) was modeled. The CL emission simulation of threading dislocations in GaN demonstrated that a better signal-to-noise ratio was obtained with lower incident electron energy than with higher energy. Second, the capability to simulate the distribution of the deposited energy in 3D was used to determine exposure parameters for polymethylmethacrylate resist using electron-beam lithography (EBL). The energy deposition dose in the resist was compared for two different multibeam EBL schemes by changing the incident electron energy.

The scanning transmission electron microscopy (STEM) can be used to image biological and other soft materials with nanometer resolution on nanoparticles in micrometers-thick specimens [1]. For the imaging of thick samples, the spatial resolution is not limited by the optics of STEM, as is the case for ultrathin amorphous substrates, but the interaction of the electron beam with the specimen plays a major role, and the resolution is limited by noise or by beam broadening. It is crucial to have knowledge of the electron beam-specimen interactions, so that the imaging settings can be optimized for maximal resolution, especially when imaging radiation-sensitive samples. Knowledge of the beam broadening can potentially be used to enhance the resolution of 3D datasets by using deconvolution procedures. A precise way to study the interaction between an electron beam and a specific specimen geometry and composition is via the use of Monte Carlo simulations. We present a STEM version of the CASINO Monte Carlo software [2]. The CASINO Monte Carlo software has been modified to include the simulation of STEM with the annular dark-field (ADF) detector [3], exhibiting atomic number (Z) contrast. The electron trajectory calculation is based on to the previous version of CASINO [4]. The electron beam model included the Poisson noise and a conical shape of the electron source, such that realistic STEM images were obtained with these simulations. By using the 3D geometry of the sample and the 3D programming of the electron beam shape and focal point position, various STEM imaging sequences were simulated, including focal series. The electron scattering physical models used in the previous version of CASINO were extended from the energy range of the SEM to energies of up to 300 keV as needed for STEM imaging. For the imaging of radiation sensitive samples, such as biological materials or polymers, it is important to optimize the achievable resolution in terms of the maximal electron dose. This optimization requires the calculation of the resolution and signal-to-noise level obtained for a specific sample and STEM imaging settings. The Monte Carlo simulation of STEM imaging presents a precise method to conduct such calculations. As an example, we have simulated line scans (one-dimensional images) for a sample consisting of gold nanoparticles placed on the top surface-with respect to the electron beam propagation direction-of a 1 mm thick carbon support substrate (see Fig. 1A). Fig. 1C shows an increased noise level compared to Fig. 1B as expected, as the number of electrons has been reduced by a factor of 50. Nanoparticles were assumed to be visible in the noise of the background when the Rose criterion [5] was satisfied, i.e., when SNR 5. In Fig. 1B,C, the dashed horizontal line indicates the signal level for SNR = 5. The smallest nanoparticle (d = 1 nm) is just visible in Fig. 1B, while it vanished in the noise in Fig. 1C. These results demonstrate that the CASINO software can be used to simulate the achievable SNR for specific sa...

The CASINO Monte Carlo software has been modified to include the simulation of a scanning transmission electron microscope (STEM) image acquired with the annular dark-field (ADF) detector. The electron trajectory core calculation models are based on the software CASINO v2 [1]. The software now includes electron-optical parameters, such as the semi-angle of the focused electron beam at the specimen, the opening angle of the ADF detector, the probe current, and the noise characteristics of the electron source. The modified CASINO code also includes the physical models of electron scattering in the energy range up to 300 kV. With the addition of this new electron-optical feature, it is now possible to scan the electron beam to acquire images or linescans at different focal points within the sample according to the depth of field of the simulated STEM. It is thus possible to simulate two-and three-dimensional (3D) datasets of samples of various geometries and chemical composition. A novel STEM technique to characterize cells in a liquid compartment has been developed recently [2], so-called liquid STEM. A liquid specimen, e.g. water, is enclosed in a micro-fluidics chamber with electron-transparent silicon nitride membrane windows. CASINO was used to simulate STEM images of gold nanoparticles on water layers of several micrometers thickness. Fig. 1 shows a qualitative comparison of an experimental and a simulated STEM image of gold nanoparticles marker placed above a water layer of a thickness of 5 µm. A similar spatial resolution and contrast between the simulated and experiments images is observed. These experimental comparisons have been used to improve the simulations models by adding, for example, a more realistic electron source or electron optics. CASINO can thus be used to study the characteristics of STEM imaging of thick (for electron microscopy) specimens. Another second series of simulations involved the recording of 3D datasets via focal-series. Taking advantage of the reduced depth of field of aberration-corrected STEM compared to standard STEM, 3D datasets can be recorded of biological specimens with an axial resolution in the range of several tens of nanometers [3]. Fig. 2a shows three simulated images of such 3D datasets at a focal position of 0 nm (top image), 500 nm (middle image) and 1000 nm (bottom image). The simulated sample consisted of three gold nanoparticles of 10 nm in diameter embedded in a carbon layer of 1 µm in thickness. These nanoparticles were, from left to right, at the top (0 nm), middle (500 nm) and bottom (1000 nm) of the carbon layer. These images have been used to investigate the lateral resolution as a function of particle position within the layer and microscope settings (pixel dwell time, pixel size, focus step size, beam semi-angle, and beam energy). It is also possible to determine the vertical or depth resolution by simulating the detected intensity as a function of the focal position as shown in Fig. 2b. 258

Extended abstract of a paper presented at Microscopy and Microanalysis 2010 in Portland, Oregon, USA, August 1 – August 5, 2010.