NanoMi: An open source electron microscope hardware and software platform.

We outline a public license (open source) electron microscopy platform, referred to as NanoMi. NanoMi offers a modular, flexible electron microscope platform that can be utilized for a variety of applications, such as microscopy education and development of proof-of-principle experiments, and can be used to complement an existing experimental apparatus. All components are ultra-high vacuum compatible and the electron optics elements are independent from the vacuum envelope. The individual optical components are mounted on a 127 mm (5-inch) diameter half-pipe, allowing customizing of electron optics for a variety of purposes. The target capabilities include SEM, TEM, scanning TEM (STEM), and electron diffraction (ED) at up to 50 keV incident electron energy. The intended image resolution in SEM, TEM and STEM modes is ≈ 10 nm. We describe the existing components and the interfaces among components that ensure their compatibility and interchangeability. The paper provides a resource for those who consider building or utilizing their own NanoMi.

Toward the quantitative the interpretation of hole-free phase plate images in a transmission electron microscope.

We present progress toward the quantitative interpretation of phase contrast images obtained using a hole-free phase plate (HFPP) in a transmission electron microscope (TEM). We consider a sinusoidal phase grating test object composed of ~5 nm deep groves in a ~13 nm thick amorphous silicon membrane. The periodic grating splits the beam current into direct beam and diffracted side beams in the focal plane of the imaging lens, where the HFPP is located. The physical separation between the beams allows for a detailed study of the HFPP phase shift evolution and its effect on image contrast. The residual phase shift of the electron beam footprint on the phase plate was measured by electron holography and used as input to image simulations that were compared to experimental data. Our results confirm that phase contrast is established by the phase difference between the direct and side beams, which we can estimate by fitting the image contrast evolution in time with an analytical formula describing the image intensity of a sinusoidal strong phase object. We also observed contrast reversal and frequency doubling of the grating image with time, which we interpret as the phase contrast arising from the interference between side beams becoming dominant. Another observation is the lateral displacement of the image fringes, which can be accounted for by a phase difference between the side beams.

3D observation of chromosome scaffold structure using a 360° electron tomography sample holder.

The chromosome scaffold is considered to be a key structure of the mitotic chromosome. It plays a vital role in chromosome condensation, shaping the X-shaped structure of the mitotic chromosome, and also provides flexibility for chromosome movement during cell division. However, it remains to be elucidated how the chromosome scaffold organizes the mitotic chromosome and how it supports shaping the structure of the chromosome during metaphase. Here we present a new technique that enables the observation of the chromosome scaffold structure in metaphase chromosomes from any direction, by transferring an isolated chromosome to a 360° rotational holder for electron tomography (ET). The chromosome was stained with immunogold-labeled condensin complex, one of the major chromosome scaffold proteins and then observed in three dimensions using ET. Using the locations of gold nanoparticles to visualize the underlying structure, the tomograms we obtained reveal the patterns of chromosome scaffold organization, which appears to consist of a helical structure that serves to organize chromatin loops into the metaphase chromosome.

Parameters affecting the accuracy of nanoparticle shape and size measurement in 3D.

While electron tomography can be used to visualize objects at nanoscale, it is difficult to perform reproducible quantitative measurements. Here we measure the shape and size of nanoparticles (NPs) in three dimensions (3D) using electron tomography. We evaluated the accuracy of maximum Feret diameter (Feretmax), minimum Feret diameter (Feretmini) and volume of NPs measurements from reconstructed 3D images which were obtained from data acquired with varied electron dose. We perform both simulations and experiment to clarify what factors effect on the accuracy of the NP shape measurement. Based on the results, suitable reconstruction methods and threshold for binarization were evaluated. We also report comparison results obtained on exactly the same samples in two different laboratories.

Wavelet transform-based electron tomography measurement of buried interface roughness.

Interface roughness is a critical parameter determining the performance of semiconductor devices. We show that a continuous wavelet transform is useful to describe not only the magnitude of the interface roughness, but also the spatial frequencies that describe the interface. We propose a simple presentation of the results that makes it convenient to compare between interfaces. In particular, an average and maximum value wavelet profile that is obtained from a series of one dimensional wavelet transforms provides a traceable and quick survey of the results. We demonstrate the wavelet transform method using both computer simulations and by applying it to experimental data obtained by electron tomography of a test sample and to a molecular layer interface. Wavelet descriptions of the interface roughness suffers less from the presence of shot noise in the experimental data than the traditional root mean square error description of interface roughness. An increase in lateral dimensions of an interface that has large features increases the content of low spatial frequencies in wavelet transforms. In comparison, the value of root mean square error increases in an untraceable manner with the same increase in lateral dimensions on the same interface. Morse wavelets with γ = 9 and ß = 3 appear to be a suitable choice for applications in interface roughness measurement.

Measurement of orthodontic bracket tie wing elastic and plastic deformation by arch wire torque expression utilizing an optical image correlation technique.

Orthodontic lingual root movement (torque) is an important aspect of treatment biomechanics and is typically achieved by torsion of a rectangular wire within the orthodontic bracket slot which introduces a force couple. The magnitude of the force moment achieved by wire torsion may be influenced by deformation of the orthodontic bracket. A device utilizing an optical image correlation technique has been developed to accurately quantify bracket slot dimensional changes during application of wire torsion. Simultaneous torque moment magnitude, degrees of wire twist, and bracket slot dimension data can be gathered. Bracket tie wing elastic deformation when loaded was demonstrated and plastic deformation was also observed with a single rotation of the wire.