GSECARS Tomography Processing Software

Mark Rivers

University of Chicago

October 14, 2015

This document describes the IDL software used for reconstructing and viewing tomography data at CARS. All of these IDL routines are available in tar and zip files. The reconstruction is normally done using the tomoRecon reconstruction code, which is written in C++. The idl_tomography.tar file contains the required tomoRecon DLLs (Windows) and shareable libraries (Linux, Mac) to run the IDL software without compiling any code. The tomoRecon source code is also available through the tomoRecon home page. tomoRecon is based on the Gridrec reconstruction algorithm, but with multi-threading to utilize multiple cores on modern workstations.

The normal user interface for this software is through the IDL GUI routine tomo_display. The following screen shot shows the tomo_display interface.

IDL tomo_display GUI


The following screen shot shows the screen that provides control for the preproccessing and reconstruction options.

IDL tomo_display Options screen


We have broken the tomography data processing down into 3 steps:


The preprocessing routine performs the following steps:


The reconstruction routine performs the following steps when using tomoRecon. (When using filtered backprojection similar steps are used, but all of the code is in IDL itself.)


The standard IDL procedures TV and TVSCL are very useful for displaying 2-D data. IDL's SLICER3 procedure is good for displaying 3-D data. In addition there is set of GSECARS-developed routines for visualizing 2-D and 3-D tomography (or other) data.

The reconstructed data are written as 16-bit integer netCDF files. These can be read into ImageJ using the ( ImageJ netCDF plugin jar file) and a small ImageJ script called GSETomo_.ijm that is also in the idl_tomography.tar file. Put both the netCDF_.jar and GSETomo_.ijm files in the ImageJ/Plugins folder. Plugins/GSETomo can then be used to read the reconstructed files.

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