Natsuko Nakamura

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.

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.

A Programmable TEM Image Collection System

There have been many efforts to develop computerized methods to acquire data using TEM. These methods increase the rate at which researchers can acquire data. For example, automated acquisition of tilted images have freed TEM users who are working on tomography from repetitive operations [1,2,3,4,5]; automatic specimen search and acquisition on ice-embedded specimens have helped researchers study single particles in a high throughput manner [6,7]; and automatic sample screening has reduced a need to sit in front of a TEM for hours to screen for potential crystalline specimens [8].