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Features - Download - User Manual

This user guide contains the information on how to install, configure and run the Absolute Integrator STEM analysis code. Absolute integrator is continually being improved based on user feedback so please check the support page for update notifications and changelogs.

User Manual Quick Links:

Installation    -    Configuration    -    Running    -    Results


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Absolute Integrator Componant Files

As Absolute Integrator is being activley developed and improved small updates may be distributed frequently. To facilitate this it is built from several modules each of which can be updated seperatly. The table below outlines the files that you should have in your installation, their purpose and the most current version. Before running Absolute Integrator for the first time users should check all these files are present in the same folder along with the image file to be processed.

File Purpose Current Version Release Date
AbsoluteIntegrator_Core_1_2 Performs the majority of the analysis and communicates to the other modules. 1.2 1st October 2013
AbsoluteIntegrator_Wrapper_1_2 User interface for variable set-up of the analysis variables. 1.2 1st October 2013
Integrator_license_check Checks the current license state. 1.0 12th September 2013
convolve2* Performs a fast 2D convolution used in the background subtraction step. - 11th April 2011
File_Opener_1_5_3 Opens image files of various types and passes image data to "AbsoluteIntegrator_Core". 1.5.3 12th September 2013
Ranger_Core_2_2 Performs the peak-finding. 2.2 13th September 2013
Ranger_license_check Checks the current license state. 1.0 12th September 2013
ReadDM3* Allows "File_Opener" to handle Gatan .dm3 files. - 19th March 2010
serReader* Allows "File_Opener" to handle Titan .ser files. - 6th August 2009
weightedEllipticalGaussianFit Perfomrs the experimental eccentricity fitting calculation - 20th March 2013

In addition to the above the Matlab Image-processing, Statistics and Curve-fitting Toolboxes are required to use Absolute Integrator.

Example Installation

The image below shows a typical installation of Absolute Integrator (ordered alphabetically). All the componant files as well as the image to be processed must be in the same folder as each other.

Typical Jitterbug Installation


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Setting the Analysis Variables

The Absolute Integrator wrapper file sets up all the input variables needed to process the image to the user’s specification. Before running the code each of the variables should be verified. Once verified however these will only need modifying rather than entireley resetting each time.

The following table defines the action of each input variable.

Show / hide variablesShow / hide variable definitions

Running Absolute Integrator

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Once the above parameters have been selected in the Absolute Integrator Wrapper file simply press run (or F5).

The restoration then proceeds in the folloing stages which are described in turn below:

  1. The detector image is read in to the workspace by the'File_Opener' module.
  2. The detector sensitivity histogram will be displayed for vacuum and active-area threshold selection.
  3. The HAADF image is read in to the workspace.
  4. Diffractogram Calibration of the HAADF image.

1 - Detector File Reading

If a .dm3 or .ser file was selected the greyscale image will be extracted from the file by the appropriate file converter.

2 - Sensitivity Threshold Selection

The annular detector will be displayed, along with a histogram of the recorded counts at every pixel. The user must select two thresholds using the crosshairs mouse cursor; first the upper limit (right edge) of the first histogram peak corresponding to the image vacuum pixels, and second the lower limit (left edge) of the second histogram peak corresponding to the active region of the detector. Incorrect clicks can be undone by pressing the 'Backspace' button; once happy press 'Enter' to accept.

Typical Absolute Integrator Installation

After pressign 'Enter' the histogram will be updated with two solid black lines that represent the threshold vlaues that were selected, as well as with two dashed black lines that represent the average intensities of the vacuum and detector respectively. The three histogram segments will be colour coded to reflect this division as will the detector map image. The detector sensitivity is now calibrated.

3 - HAADF Image File Reading

4 - Diffractogram Image-Magnification Calibration

For the magnification calibration the experimental image will be displayed alongside the central part of its Fourier transform.

Using the crosshair mouse cursor the user must select two diffractogram spots that correspond to the indices configured in the Wrapper file. If two unique spots cannot be reliably identified then it is acceptable, but not preffered, to accept a spot and its conjugate. Incorrect clicks can be undone by pressing the 'Backspace' button; once happy press 'Enter' to accept the selections.

Absolute Integrator Diffractogram Calibration

After pressing 'Enter' the lengths selected on the diffractogram will be highlighted and a scale marker will be added to the experimental image. Magnification calibration is then complete.

5 - HAADF Image Peak-finding

Peak Finding Results

Peak-finding is performed on the experimental image to determine the locations of the atomic columns. The user can modify the suggested results by manually clicking any missing peaks or removing any surplus ones. A full description of the peak-finding module can be found here.

6 - HAADF Image Segmentation and Integration

Peak Finding Results

The peak-finding results are used to determine the appropriate regions for integration. Following integration the scattering cross-sections are calcualted and illustrated back in the same areas as the integration regions.

Additionally two histograms are shown illustrating the areas (in square pixels) of the integration regions used (to inspect for consistency), and also showing the spread of the calcualted scattering cross-sections.

Absolute Integrator Results

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After completion the workspace will be cleared.

* MatLab function files available from MatLab Central.

  • "convolve2.m" was developed by David Young.
  • "ReadDM3" was developed by Fred Sigworth and Liguo Wang at Yale University.
  • "serReader.m" was developed by Peter Ercius at the National Center for Electron Microscopy (NCEM).

  • Content © 2012 Lewys Jones - layout & design by Vincent Chan