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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.

Chromosome higher-order structure has been an enigma for over a century. Proposed models include radial loop model, radial coil model, folded fiber model and helical coiling of radial loops model [1]. These models are based on the assumption that DNA is wrapped around histones and forming nucleosomes, and nucleosome fiber with 11nm is folded into a 30nm basic chromatin fiber. The 30 nm chromatin fibers in chromosomes have been observed by SEM, TEM and TEM tomography. Several results also support existence of 30 nm chromatin fiber structure [2, 3]. On the contrary, the 30 nm chromatin structures in mitotic chromosomes were not found by cryo-EM [2, 3] and small-angle X-ray scattering results. Larger 200-400 nm structures consisted of the 30 nm fibers have also been observed although the structures have not been supported by several results.

We are developing a modular (scanning) transmission electron microscope (S)TEM, referred to as NanoMi, which is released under an open source license by the National Research Council, Canada; see for updates. The electron microscope (EM) is a critical enabling tool in the physical, materials and biological sciences but its impact could be increased by the availability of an easy-to-build, customizable instrument capable of modest resolution and suitable for electron beam lithography, specialized experiments and for training personnel. An instrument that can be built for ~50 k$ and ~1 year of student time would fulfill these requirements in many laboratories around the world. Here we describe an initial design of such an instrument.

Bright field transmission electron microscope (BFTEM) images are often used to measure sample size in two dimensions (2D). Mass thickness (rt) maps of the sample along the electron beam direction, although measurable with a monolayer precision [1,2], are seldom obtained. To measure rt, a calibration sample is needed. We show that calibration can be obtained in-situ using multi wall carbon nanotubes (MWCNTs)., Microscopy & Microanalysis 2019 Meeting

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.

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.

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 β = 3 appear to be a suitable choice for applications in interface roughness measurement.

Parallel nanometer-beam diffraction (NBD) in a scanning transmission electron microscope (STEM) produces vast quantities of potentially useful data. A MATLAB toolbox was developed for automated data collection and analysis and is applied to a sample containing nanoparticles (NPs). The NPs are automatically located in three dimensions (3D) by STEM electron tomography, are automatically tracked between tilts, and then NBD patterns are collected at several sample tilts allowing for the identification of the NP structure., Proceedings of Microscopy & Microanalysis 2018, Aug 5-9, 2018, Baltimore, Maryland

An important observable characteristic of a buried interface between layers or surface of a film is the interface roughness (IR). Here we present a continuous wavelet transform (CWT) description of the interface roughness as an alternative to the traditional root-mean-square (RMS) roughness., Proceedings of Microscopy & Microanalysis 2018, Aug 5-9, 2018, Baltimore, Maryland