hr(s)tem methods @ er-c
news
software

The hrtem methods group of the centre for electron microscopy offers a number free costum software packages also developed for distribution to the microscopy community. The software available at present is listed below and can be downloaded to your local computer.

No guarantees can be made to the accuracy of the code and no responsibility is taken with respect to the usage of the programs. A description of the programs is also given below. Users of the packages are encouraged to e-mail comments and bug reports to the authors of the software.


multi-platform image conversion tool (ImageConverter)::

ImageConverter is a  program to convert and scale in a single run mutliple images with a file format common to electron microscope software applications. The image files can be converted into more widespread pixel image formats or, if information is to be conserved, into a binary file format with a fixed length header. ImageConverter is written in the IDL programming language which supports Apple Mac OS X, LinuX and Windows. A valid installation of the freely distributed IDL virtual machine is required. Visit the IDL website for further information.

Input formats:
  • Gatan Digital Micrograph, version 2.x and 3.x
  • Emispec 3.x 2D image data 
  • Raw Data: raw binary data
  • Tietz (tvips) image format


Output formats:

  • PPM, PNG, TIFF, GIF
  • Tietz (tvips) binary image format with 256 byte fixed header length


click to download the multi-platform binary package (1.1 MB)


author: Lothar Houben, last updated February 2011.


multi-platform tomography suite (tomato)::

tomato is a  is a  program for the three-dimensional object reconstruction from a series of projection images. The program was designed to address specific issues of the refinement of the reconstruction.  It includes common approaches for the reconstruction procedure as well as a graphical user interface. It is therefore useful also in a productive environment. So far, tomato reconstructs from single axis tilt series. tomato is written in the IDL programming language which supports Apple Mac OS X, LinuX and Windows. A valid installation of the freely distributed IDL virtual machine is required. Visit the IDL website for further information.
The free version of tomato includes the following features:
  • import of three-dimensional data stacks in mrc format 
  • export to mrc or animated gif format
  • multiple data stack handling
  • simple data stack manipulations
  • sub-pixel accurate cross-correlation alignment
  • interactive refinement of alignment properties (tilt axis offset, rotation, drift)
  • projection and back projection based on the 2D Radon transform
  • weighted back projection


The licensed version of tomato includes the following features:

  • refinement routines based on grid search algorithms and pseudo-projections
  • simultaneous iterative reconstruction technique


click to see a screenshot of tomato running under Mac OS X

click to download the multi-platform binary package (9 MB)


click to download a demo data package (8 MB)

author: Lothar Houben, last updated February 2011.


general purpose multi-platform image processing tools (iMtools)::

The iMtools software is a binary software collection and graphical user interface developed for digital image processing of electron micrographs. iMtools routines are written in the IDL programming language. A valid installation of the IDL virtual machine is required. Visit the IDL website for further information. IDL supported platforms are Apple Mac OS X 10.x - Compaq Alpha True 64 Unix 5.1 - HP PA RISC HP-UX 11.0 - IBM RS6000 AIX 5.1 - Intel x86 LinuX (glibc2) - SGI Mips Irix 6.5.1 - SUN Sparc Solaris 8 - SUN Ultra (64-bit) Solaris 8 - Microsoft Windows 98, NT, 2000, XP. Tested platforms for iMtools are Mac OS X 10.2 - 10.4, LinuX and Windoze 2000 and XP.

The iMtools free version feature list contains:

  • import of various image formats (CCD images (tvips), Digital Micrograph 2.x and 3.x, FUJI image plate data, tif, gif, png, pict, user specified binary data, support of user defined plug-in filters)
  • export to tvips, tif, png, bmp, ppm, binary and eps format
  • group context: images can be grouped and commands can be performed on these groups
  • supports various data types and arithmetics from integer to complex floating point data
  • measuring and peak fitting operations
  • contrast manipulation
  • FFT operations
  • Fourier mask creation and filtering
  • geometric transformations (image rotation, scaling, cropping, mirroring, recentering)
  • image normalization
  • various complex data type operations
  • unary and binary arithmetic image operations
  • profile extraction in cartesian or polar coordinates
  • region of interest statistics
  • holographic sideband reconstruction
  • geometric distortion imaging based on Fourier space analysis
  • nanodiffraction from complex data type images
  • ... and more


click to see a screenshot of iMtools running under Mac OS X

click to download the (incomplete) html documentation (1.6 MB)

click to download the Mac OS X, Linux and “Windows“ binary package (3.3 MB)

author: Lothar Houben, last updated November 2009.


diffraction contrast image simulation notebook (dcisim)::

This executable notebook for the commercial software "Mathematica" from Wolfram Research Ltd. is to be used for the calculation of diffraction contrast images associated with overpressurized crack-shaped inclusions. The notebook is only intended for use with Mathematica Version 3.x using MAC-OS 8.1 or higher. After downloading the notebook, extract the file dcisim.sit. A brief description of all relevant parameters for the calcualation of two-dimensional images as well as one-dimension intensity line scanns is given at the beginning of the notebook. Adjustable parameters are labelled in red. Default settings assume the excitation of an (004) beam and silicon material properties.

click to download the diffraction contrast image simulation notebook

click to download an associated two-page overview article

author: Karsten Tillmann, last updated June 2002.


chemical mapping package (cmp)::

The package consists of an extension to the commercial software "Digital Micrograph" from Gatan Inc. to be used for the extraction of composition related information from high-resolution micrographs taken under chemically sensitive imaging conditions. The software is only intended for use with Digital Micrograph Version 3.3 using MAC-OS 8.6 or higher. After downloading the software, extract the file jcmp.sit; the folder that is created contains a the package plus a read me file explaining the installation procedure. A brief description of the Package is given in the Manual.

click to download the chemical mapping extension package

click to download an associated full length article

author: Karsten Tillmann, last updated September 2001.


   
© by the er-c | inscreenum & contact | er-c@fz-juelich.de