Last Modified : 2019/09/20
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Tutorial data for Electron Microsopic Single Particle Analysis

This page is for tutorial data and documents for education of electron microscopy single particle analysis.

A single particle analysis requires a huge amount of 2D image data to reconstruct a high-resolution 3D map. A typical 2D image size ranges from 100GB to 10 TB. These huge data are not good for educational purposes, because they require a long time to be downloaded and computer-processed. For educational purposes, we start to provide small 2D image data by choosing fine images from the EMPIAR database. We also prepare documents describing computer procedures for analyzing these data using the standard software, such as Relion.

These data and documents are free to use. We will be happy if they contribute to educate young EM researchers.

1/100 Tutorial data (apo ferritin)

2D micrographs of apo ferritin taken by JEOL CRYO ARM 300 provides a 3D map with 1.54 angstrom resolution. However, the file size of the original data (EMPIAR-10248) is 145.9 G byte. We made a 1/100 tutorial data (1.7 G byte) [EMPIAR-10248_tutorial_500frames.tar] by choosing fine 2D images from the original images. This tutorial data is easy to be downloaded and to be processed, and quickly yields a 3D map with 2.85 angstrom.
Original data Tutorial data
EMPIAR-10248 Images taken from EMPIAR-10248.
[EMPIAR-10248_tutorial_500frames.tar]
File size 145.9 Gbyte 1.7 Gbyte
Number of micrographs 50 frames x 971 files 25 frames x 20 files
3D map EMD-9865
Resolution (angstrom) 1.54 2.84
The original data EMPIAR-10248 contain 971 TIFF files, each of which has 50 frames. The tutorial data [EMPIAR-10248_tutorial_500frames.tar] was made by chosing 20 TILL files from the 971 files, and only using the first 25 frames from the 50 frames.

Documents to analyze tutorial data (apo ferritin)

Following documents describe how to analysze the tutorial data [EMPIAR-10248_tutorial_500frames.tar] using the program Relion. If you prepare a 2GPU-machine, you can finish these processes within 3-6 hours. The actural computation time will be 90 minutes, however, manual operations, such as pickings takes a longer time.

  • Relion tutorial:preprocessing (apo ferritin)
  • Relion tutorial: Class2D_3D(apo ferritin)
    This project is supported by : Ciclic Innovation for Clinical Empowerment（CiCLE） "Development of equipments for high-throughput protein structure analysis (JEOL)".