JEOL 3200 Data Management and Conversion

Overview

From the NCMIR website:

JEM-3200EF IVEM (300 kV). Features custom optics for high-tilt conical illumination for optical sectioning, an energy filter, a piezo-enhanced, high-precision goniometer, three high-resolution digital detectors, and an updated hardware/software control system compatible with the Telescience Portal.

The 3200 is an Intermediate Voltage Electron Microscope capable of shooting, among other things, tilt series for EM tomography.  However, the 3200 saves each tilt image as a Gatan format .dat file and conversion to a .mrc format is necessary before doing any EM tomography processing.

This page highlights the steps that are taken to convert the .dat files to .mrc

3200 Image Saving Format

The 3200 saves each tilt image as a Gatan .dat file.  In addition, the IVEM will save a .log file of various parameter settings that the EM technician used to shoot the series.

During shooting of tilt series, typically the range is shot as follows:

Be aware of this  and make sure the images are in order before stacking the final .mrc file.  Programs such as IMOD and TxBR generally require the tilt series to begin with the lowest tilt degree to the highest i.e. -60 degree tilt, -58 degree tilt, ... +58 degree tilt, +60 degree tilt.

As of August 19, 2009, no software exists to view the .dat files directly

Step by Step Instruction on Converting from .dat to .mrc

Crucial to conversion is to have a "tvips2tif" script.  One has been written by Steve Lamont and should be used for conversion.

1. ssh into shine.ucsd.edu
2. go to directory where .dat data resides
3. copy script to directory
4. using st_mt_tvips2tif: 

   st_mt_tvips2tif [basename]
   

The script command will concatenate all .dat files IN ALPHANUMERIC ORDER into a single .st file.  Confirm that the .dat files are in the proper order (i.e. watch out for negative signs, single vs double digits of angles, etc)

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