How to run an experiment

This page provides a quick guide on how to run an experiment from the EBSD-Image desktop (graphical interface). Please refer to the How to run an experiment from the command line page to run an experiment from a command line prompt.


The first step before running an experiment is to import the diffraction pattern images and/or the EBSD acquisition parameters and results from:


All the parameters and operations of an experiment are setup using a wizard. Once you have EBSD-Image open, click on wizard-button button in the plug-ins toolbar to launch the wizard.


Experiment wizard button in EBSD-Image

The wizard has 11 steps. The first steps are to setup the parameters such as the working directory, phases and calibration. Other information about the EBSD acquisition such as the beam energy, magnification, working distance, etc. can also be specified. All these information are saved with the final results. The latter steps are to select the operations.


The Start page is made to import data from previous experiments or from previous EBSD acquisition. It is therefore optional, but could be very useful to facilitate the creation of a new experiment.


Screenshot of the wizard

By importing the metadata from a previous mapping, the microscope configuration and the size (width and height) of the mapping are loaded.

Previous mappings are derivatives from a EbsdMMap (i.e. they are ZIP files containing the results maps). They can be previous results from an experiment, mapping imported from HKL Channel 5 or TSL OIM.

Operations from a previous experiment can also be imported. The imported operations will appears in the currently selected operations in the latter steps.


This page is to define the name and the working directory of the experiment. The name is used to identify the experiment and the working directory is where all the files created during and after the experiment are automatically saved.


The experiment will automatically overwrite previous files in the working directory.

Microscope configuration

The next step is to input the information about the microscope used for the acquisition of the diffraction patterns. It is not all parameters that are used in an experiment; this will depend on the operations selected by the user. For example, the camera calibration is not required if no indexing operation is selected. It is however beneficial to input all the parameters to keep in reference all the information related to the EBSD acquisition.

The first step is to select the microscope configuration which defines the dimensions and position of the EBSD camera. See Microscope configuration setup for a tutorial on how to create a new microscope configuration.

The other parameters are defined as follows:

  • Column

    • Beam energy: Acceleration voltage of the electron beam used during the EBSD acquisition.
    • Magnification: Magnification of the EBSD acquisition.
    • Working distance: Working distance used for the EBSD acquisition.
  • Sample

    • Tilt angle: Tilt of the sample (typically 70 deg).
    • Sample rotation: Rotation between the sample with respect to the sample frame. It can be used to rotate the sample in a particular direction. For example, to align the rolling direction the sample with the y-axis. The sample rotation is defined using the three Euler angles expressed in the Bunge convention. If the three Euler angles are equal to zero, the rolling direction is aligned with the x-axis, the transverse direction with the y-axis and the normal direction with the z-axis.
  • Camera

    • Pattern center: The position is the pattern center is given as a fraction of the width and height of the diffraction pattern starting from the top-left corner.


      Definition of the pattern center.

      If the x and y position are set to 50%, the pattern center is located in the center of the diffraction pattern.

    • Camera distance: distance between the sample and the camera. It is expressed in unit of length (i.e. mm).



Phases are only required if an indexing operation is selected in the operations.

To facilitate the selection of the phases, it is recommended to save all the user defined phases in a specific directory. This phases directory will contain several XML files defining the phases. The user only needs to define once a phase.

Therefore, the first thing is to select using the Browse button the phases directory. Then using the new phase newphase button the New Phase dialog will appear. Refer to Create a new phase for a tutorial on how to create a new phase. You can also import a phase from a Crystallographic Information File (CIF) [3] by clicking on the Import a phase from a CIF file button cif.

To add a phase to the Current phases list, click on the add add button. The order of the phases in the Current phases list will corresponds to the index of the phases in the PhaseMap.


This page is to select how the diffraction pattern images are loaded. The user has three options:

  • From a SMP file
  • From a folder containing diffraction pattern images
  • From a single diffraction pattern image

For the first two methods, one needs to specify the width and height of the mapping as well as the pixel calibration. The width and height correspond the dimensions of the results maps. The pixel calibration is the actual step size used in the EBSD acquisition - by how much the beam was moved between each pixel. The step size in x and y is usually equal.


The SMP option is preferred since it provides a faster access to the diffraction pattern images.


The next 5 steps are related to the 5 major steps of the experiment’s operations (see What is an experiment?). For each category, a list of available operations are given to the user (list on the right). By clicking the Add add button, the operation is created and added to the current selected operations (list on the left). Some operations requires that the user set-up for parameters while others don’t. A dialog will appear in the former case. Please refer to the List of operations for a description of each operation as well as a detailed explanation of the parameters.


Screenshot of the operations’ wizard page

Depending on the results that the user’s wants, many categories of operations can be left empty without any operation selected. It is however important to realize that the experiment will only execute the operations that are required to obtain the selected results. For example, if a Hough transform operation is selected, but no results operation requires it to be performed, the Hough transform will not be executed. In other words, results operations are an essential part of an experiment.


Finally, the output page is to decided how the experiment will be run. The preview mode allows to check that all the operations are performed correctly. All the operations are executed on diffraction pattern and the resultant map of each operation is temporarily displayed in EBSD-Image. The diffraction pattern is selected by specifying the index of the desired diffraction pattern in the mapping. Please note that the results of operations that do not create a map are not displayed. After verifying the results, the user can either launch the experiment on all the diffraction pattern or return to the wizard to modify some operations. By going back to the wizard, the user can also select another diffraction pattern to preview.


No image analysis routines can be performed in EBSD-Image in the preview mode.

Another output option is to save the experiment to an XML file. This can be used to launch the experiment in a command line prompt or on a computer grid instead than in the graphical interface. It is also useful to archive the operations selected.

Finally, if the run option is selected, the wizard will close and the experiment will be executed in the RML-Image desktop.


When an experiment is being run, the progress bar in the bottom left corner indicates the progress of the experiment. An experiment can be stopped by clicking the Stop button stop. At the moment, no pause function is available.

During the execution, the results maps can be viewed as they are getting filled with new results by selecting a map from the multimap tree (on the left). The maps are refreshed very second.

[1] HKL Channel 5 is a trademark of Oxford Instruments plc.
[2] TSL OIM is a trademark of Ametek Inc.
[3] Data exchange standard file format for crystallographic information maintained by the International Union of Crystallography.