DM3_Reader plugin

DM3_Reader plugin for ImageJ

Author: Gregory Jefferis (jefferis AT gmail DOT com)

Date(s):

- 23 June 2003 (Version 1.2.7 Beta) First version posted

- 24 June 2003 (Version 1.2.8 Beta) Fixed setting of min/max brightness according to info in DM3 file

- 25 June 2003 (Version 1.2.9 Beta) Fixed handling of unsigned 16-bit images

- 25 June 2003 (Version 1.3.0 Beta) Removed calls to functions absent from Java versions <1.2. Should now run on MacOS 9 machines with Apple MRJ >=2.1.4 (Java v1.1.7)

- 25 June 2003 (Version 1.3.1 Beta) Fixed Unicode conversion problem on MacOS9/MRJ. Tested fine with ImageJ 1.30 and MRJ 2.2.3

- 8 August 2003 (Version 1.3.2 Beta) Fixed a bug which meant that the last image contained in a DM3 file was always selected for opening, regardless of whether this was appropriate. Also fixed a bug handling calibration units - nm didn't work properly.

- 25 August 2003 (Version 1.3.3) Public version - fixed one remaining bug with image choice uncovered by 8th August changes.

- 7 May 2004 (Version 1.3.4) Fixed a bug preventing reading of unsigned 16 bit integer images.

- 13 December 2005 (Version 1.3.5) - Adding handling of DIFFRACTION mode images (ie reciprocal space). .

- 4 September 2006 (Version 1.3.6) Added storing of struct fields to tag list; this means that Digital Micrograph selection rectangles can be seen in Show Info.

- 31 August 2007 (Version 1.3.7) Can now open data type 23 (RGBA_UINT8_3_DATA) images. Can also get a debug log by turning on Edit ... Options ... Misc ... Debug Mode. reading of unsigned 16 bit integer images.

- 27 March 2008 (Version 1.3.8) Fixed a bug in which tag hashes were not cleared when reading a new file. Also small speed improvement by converting tags to String via StringBuffer.

Source: DM3_Reader.java

Requires: ImageJ version >=1.29

Installation: Download DM3_Reader.class to the plugins folder and restart ImageJ.

Description: The DM3_Reader plugin allows ImageJ to open files produced by Gatan's Digital Micrograph software, which is commonly used with Transmission Electron Microscopes. It is restricted to version 3 of this file format (the most recent version). It correctly reads in images that I have tested, setting the XY spatial scale. The minimum and maximum brightness thresholds are also set according to information in the DM3 file. All the data in DM3 format images is saved in the form of tags, which must be parsed by the reader. After extracting all of these tags they are copied to the "Info" property which can be accessed in ImageJ by the Image/Show Info menu command. Some of these tags may be useful eg sample name, magnification, exposure time etc.

Documentation: None although the source code is quite well commented. The format of the DM3 file is succinctly described here.

Limitations: The DM3 reader has now been tested with at least the following kinds of data: 16 bit signed and unsigned integer, 32 bit float.
Limited to the following DM3 data types: UNSIGNED_INT8_DATA, SIGNED_INT16_DATA, UNSIGNED_INT16_DATA, SIGNED_INT32_DATA, UNSIGNED_INT32_DATA, REAL4_DATA, RGB_DATA, BINARY_DATA, RGBA_UINT8_3_DATA

Limited to single images since I do not have any stacks to test.

I welcome any feedback on bugs