Evaluation of automated particle picking for cryogenic electron microscopy using high-precision transmission electron microscope simulation based on a multi-slice method.

This work describes the GRIPS automated particle-picking software for cryogenic electron microscopy and the evaluation of this software using elbis, a high-precision transmission electron microscope (TEM) image simulator. The goal was to develop a method that can pick particles under a small defocus condition where the particles are not clearly visible or under a condition where the particles are exhibiting preferred orientation. The proposed method handles these issues by repeatedly performing three processes, namely extraction, two-dimensional classification and positioning, and by introducing mask processing to exclude areas with particles that have already been picked. TEM images for evaluation were generated with a high-precision TEM image simulator. TEM images containing both particles and amorphous ice were simulated by randomly placing O atoms in the specimen. The experimental results indicate that the proposed method can be used to pick particles correctly under a relatively small defocus condition. Moreover, the results show that the mask processing introduced in the proposed method is valid for particles exhibiting preferred orientation. It is further shown that the proposed method is applicable to data collected from real samples.

Automated specimen search in cryo-TEM observation with DIFF-defocus imaging.

We have developed an automated specimen search algorithm for cryo-electron microscopy imaging of ice-embedded single particles suspended across regularly spaced holes. To maximize the particle visibility under a low electron exposure rate condition, specimen searching is carried out in diffraction mode. However, images in diffraction mode contain significant pincushion distortion, making it difficult to computationally predict the locations of the regularly spaced holes. We have implemented a distortion-correction mechanism to restore the primitive distortion-free image and a correlation-based algorithm to accurately determine the periodicity of the holes. A stage-shift method to optimize positional reproducibility is also implemented. Addition of our algorithms to the JADAS software for automated transmission electron microscopy data acquisition has significantly improved the accuracy of specimen search.

JADAS: a customizable automated data acquisition system and its application to ice-embedded single particles.

The JEOL Automated Data Acquisition System (JADAS) is a software system built for the latest generation of the JEOL Transmission Electron Microscopes. It is designed to partially or fully automate image acquisition for ice-embedded single particles under low dose conditions. Its built-in flexibility permits users to customize the order of various imaging operations. In this paper, we describe how JADAS is used to accurately locate and image suitable specimen areas on a grid of ice-embedded particles. We also demonstrate the utility of JADAS by imaging the epsilon 15 bacteriophage with the JEM3200FSC electron cryo-microscope, showing that sufficient images can be collected in a single 8h session to yield a subnanometer resolution structure which agrees with the previously determined structure.

Assembly of protein complexes restricts diffusion of Wnt3a proteins.

Members of the Wnt protein family play roles in many aspects of embryogenesis and homeostasis. Despite their biological significance, characteristics of Wnt proteins still remain unclear, mainly due to their insolubility after the removal of serum. Here we examine Wnt proteins in serum-containing media by using analytical ultracentrifugation with a fluorescence detection system. This analysis reveals that Wnt3a assembles into high-molecular-weight complexes that become dissociable by interaction with the extracellular domain of the Frizzled8 receptor or secreted Wnt-binding protein sFRP2. Cross-linking and single-particle analyses of Wnt3a fractionated by gel filtration chromatography show the homo-trimer to be the smallest form of the assembled Wnt3a complexes. Fluorescence correlation spectroscopy and immunohistochemistry reveal that the assembly of Wnt3a complexes restricted their diffusion and signaling range in Xenopus laevis embryos. Thus, we propose that the Wnt diffusion range can be controlled by a balance between the assembly of Wnt complexes and their dissociation.

Image transfer with spatial coherence for aberration corrected transmission electron microscopes.

The formula of spatial coherence involving an aberration up to six-fold astigmatism is derived for aberration-corrected transmission electron microscopy. Transfer functions for linear imaging are calculated using the newly derived formula with several residual aberrations. Depending on the symmetry and origin of an aberration, the calculated transfer function shows characteristic symmetries. The aberrations that originate from the field's components, having uniformity along the z direction, namely, the n-fold astigmatism, show rotational symmetric damping of the coherence. The aberrations that originate from the field's derivatives with respect to z, such as coma, star, and three lobe, show non-rotational symmetric damping. It is confirmed that the odd-symmetric wave aberrations have influences on the attenuation of an image via spatial coherence. Examples of image simulations of haemoglobin and Si [211] are shown by using the spatial coherence for an aberration-corrected electron microscope.

Benchmark test of accelerated multi-slice simulation by GPGPU.

A fast multi-slice image simulation by parallelized computation using a graphics processing unit (GPU) has been developed.　The image simulation contains multiple sets of computing steps, such as Fourier transform and pixel-to-pixel operation. The efficiency of GPU varies depending on the type of calculation. In the effective case of utilizing GPU, the calculation speed is conducted hundreds of times faster than a central processing unit (CPU). The benchmark test of parallelized multi-slice was performed, and the results of contents, such as TEM imaging, STEM imaging and CBD calculation are reported. Some features of the simulation software are also introduced.