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.

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.

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.

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.

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.

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.