MTEX_interface userguide

❗ The « user friendly » MTEX_interface has been developed to treat your EBSD data
using the open access Matlab-based MTEX toolbox (https://mtex-toolbox.github.io/). If you
use this interface for any publication, please, do not forget to cite the appropriate
references, including - at least - Hielscher and Schaeben (2008; j. app. crystallogr.) and
Bachmann et al. (2010; Solid state phenom.). The MTEX_interface has been also used
and developed in Précigout et al. (2017; Nat. comm; 2022; Sci. Rep.).❗

The interface can be downloaded at https://www.jacques-precigout.fr

For any problem/feedback, please contact jacques.precigout@univ-orleans.fr

To start using the MTEX_interface:

- Open the downloaded folder « MTEX_interface_#.#.# » in the « current folder » of
Matlab;
- Type « mtex » in the « command window »: the MTEX toolbox which the interface is
based on will be installed on Matlab;
- Click on « import EBSD data », which opens the « import wizard » from MTEX (only for
.ctf or .ang les). If using .mat le (pre-treated EBSD data using the interface), click on
« Load EBSD data » and then click on « Startup treatment » to follow the instructions.
- In the import wizard, click on « + » and select your EBSD data le (.ctf from Oxford/
Bruker or .ang from OIM-TSL);
- Click « next » to skip the step about non-indexed points;
- For each indexed phase, click on « CIF » and select the corresponding .cif le to import
the crystallographic information (if required, any .cif le can be added in the following
folder: mtex-#.#.#/data/cif/).
- Give a color to each phase (the color phase can be modi ed afterward).
- Click « next » to skip the step « specimen reference frame », except whether the EBSD
data treatment will need to be adapted to your SEM reference frame (this can be
modi ed in the script « mtex-#.#.#/Startup_folder/startup_treatment.m » in lines 157 and
158).
- Select « workspace variable » to create the workspace « ebsd » variable, and click on
« nish ».
- Then, click on « Startup treatment » and follow the instructions:

1/ Select the type of EBSD data (map or point dataset)

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2/ Select the extension of your EBSD data le, depending on your EBSD acquisition
system (Orford/Bruker vs. TSL-OIM)

3/ Provide the misorientation angle used to de ne high-angle (grain) » boundaries and

low-angle (inner) boundaries. The values by default are 10° and 2°, respectively for high-
and low-angle boundaries.

4/ Provide the minimum number of pixels used to de ne a grain. According the ISO
standard ISO13067(2011), the value by default is set to 10°; all grains with less than 10
pixels will be removed.
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 5/ De ne twin boundaries to be merged in their parent grains. Either select « all phases »,
so that all (listed) twins will be merged, or click on « selected phase(s) » to de ne twins
you want to be merged. Only the listed twins will be considered. If you need to add some
twin information for a given phase, you will need to edit the script « mtex-#.#.#/
Startup_folder/Twins.m ».

6/ Choose to delete (or not) border grains, i.e., all incomplete grains at the edge of the
map.

7/ Choose to denoise (or not) your dataset. This option uses the halfquadratic lter, as
advised by the MTEX developers, but depending on the size of the EBSD dataset, the
denoising may take a long while.
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 8/ Grains will be calculated and cleaned, and then two menus will appear together with a
phase map con rming (or not) that you are dealing with the good dataset in the right
position. The menu « SETTINGS » is used to de ne the parameters of your map/plot, such
as the phase color, boundary width, color bar or miller indices. Make sure the « OK »
push button at the top right is always green (if red, click on it). This means that all
parameters, upon any modi cation, have been taken into account for plotting. The
second menu « PLOTTING » is used to plot any kind of EBSD data, including map, pole
gure, histogram, etc. The dimensions and font size of the menus can be adapted by
editing and launching the script « BoxSizes.m ».
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SETTINGS Menu

Current phase(s): If one phase is selected, only the data of the current phase will be
plotted. To plot several phases on single plot(s), select « Multiple », click on the OK
button, and then select the phases you want to plot.

⚠ Merge phases: if you want to merge some phases, the EBSD dataset (EBSD variable)
needs to be edited before treating it. To do so, import the EBSD data as usual (using the
import wizard from MTEX), open the script « mergePhases.m » and launch it to select the
phases you want to merge. Then click on « startup treatment » and follow the instructions.

Color bar: Any color bar can be created using the color push buttons from bottom (Bot.) to
top. The percentages below refer to the color position in the color bar. You can create a
color bar with 2, 3, 4 or 5 colors. To produce a color bar with less than 5 colors, enter
« 100 » below the top color. Any created color bar can be recorded in the dropdown menu
using the « R » button (new color bar(s) must be recorded into the « colorbars » folder).
The « R » button can be also used to delete a color bar from the dropdown menu.
PLOTTING Menu

Phase map = Push button to plot a phase map of the current phase(s).

Grain boundaries = Push button to add high-angle (grain) boundaries on the current map
window (for most of map options). If no map window is open, only grain boundaries will be
displayed.

Inner boundaries = Push button to add low-angle (inner) boundaries on the current map
window (for most of the « map » options). If no map window is open, only inner boundaries
will be displayed.

PLOT options:

- Image quality/band contrast = Map of the EBSD pixels based on the kikuchi band
contrast.

- Random color map = Provides a phase map attributing a random color to each grain.
- Inverse pole gure map = Map of the EBSD pixels considering their misorientation
between a given reference axis (X, Y or Z) and their crystal coordinates (displayed in
IPF).

- Grain lattice misorientations = Map of misorientation angles of a pixel orientation with

respect to the mean orientation of a given grain (mis-to-mean).

- Grain orientation spread (GOS) = Provides a map and histogram of the grain
orientation spread for the current phase/selected grains.
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 - Kernel Average Misorientation (KAM) = Provides a map of the mean misorientation
angles between one pixel and its closest neighbor pixels. The order indicates the
number of corona(s) (kernel) considered to de ne the mean orientation of neighbor
pixels.

- Dislocation density = Provides a map of Geometrically Necessary Dislocation (GND)

densities.

- Weighted Burger Vector (WBV) = Provides a map of the WBV magnitude and a IPF of
the mean WBV with respect to crystal coordinates.

- Misorientations along transect = Provides a graph of pixel-to-pixel misorientation

angle along a given transect, as picked on a grain lattice misorientations map. The
transect can be plotted on a full map or a single grain. In the latter case, you rst click
on the grain you want to select, and then click on both ends of the transects. Otherwise,
only click on both ends of the transect. You also have the possibility to access
misorientation axi(e)s by clicking on one or several segments of misorientation (graph),
and then « enter » to plot an IPF of the axi(e)s distribution with respect to crystal
coordinates.

- Pole gure (incl. seismic predictions) = Provides a pole gure (PF) of the current phase
axis/plane (as de ned in the SETTINGS menu) with respect to the reference axes (X, Y
and Z). This option includes several PF options that are automatically considered in
subsequent PF plots using the Quick PF push button. In the PF window, a dropdown
menu also provides information about the dataset/texture. If a dropdown menu
appears in the top left corner, this means that seismic predictions are possible to be
plotted based on the elastic constants (references available in the script
« seismicProperties.m ») and texture of the considered phase.

- Inverse pole gure (IPF) = Provides an inverse pole gure of the main current phase
axes with respect to a given reference axis (X, Y and/or Z).

- Grain size = Provides a grain area color map and a grain size distribution (histogram) of
the current phase(s). The histogram also contains a dropdown menu that includes
statistical information.

- Aspect ratio = Provides a map and histogram of the current phase(s) aspect ratio. The
rose diagram provides the distribution of long axis orientations.

- Shape factor = Provides a map and histogram of the current phase(s) shape factor.
- PARIS factor = Provides a map and histogram of the current phase(s) PARIS factor.
- PAROR/SURFOR = Provides the cumulative projection function of the current grains
and grain boundary segments
(https://mtex-toolbox.github.io/ProjectionBasedParameters.html)

- Low-angle-boundaries axis distribution = Provides an IPF (with and without texture)

and histogram of misorientation axes and angles across inner boundary segments,
respectively.
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 - (Un)correlated Angle Distribution = Provides a misorientation angle (histogram) and
axis (IPF) distribution of either correlated or uncorrelated (only for angle distribution)
grains, considering the mean orientations.
- Twin boundaries = Provides two maps and histogram of misorientation angles at grain
boundaries, including twin boundaries merged into their parent grains.

- Crystal shape = Provides (If available) grain-by-grain 3D representation of the current

phase crystal habit on a phase map.

- Angle between two axes = Calculates the

angle between 2 given axes de ned either by
1/ their Azimuth and Plunge, 2/ pointing on
pole gures or 3/ entering speci c miller
indices (only for axis) and Eigen (E) vector (1
= 1; 2 = 2; 3 = 3). Once all parameters are
entered, click on PLOT. To point on pole
gures, you can either choose a free-of-data
PF or choose any PF with EBSD data by
entering the miller indices and eigen vector
below the push buttons, and then click on « Pointed on PF ». If Miller indices are clear
or partially lled, the PF will be free of any EBSD data. Any angle is calculated using
an equal-area lower-hemisphere PF ⚠ The presence or absence of texture (and
Eigen vector) depends on the current PF parameters, as de ned in the option « Pole
gure ».

- Check for J/M density overestimation = Statistical estimation of density

overestimation for calculating the texture (J) and misorientation (M) indices. This option
estimates the minimum number of grains required to objectively calculate (i.e.,
independent of any calculation artefact) the fabric strength (see Précigout et al., 2022,
Sci. Rep.).

EDIT options:

- Rotate EBSD data = Rotates the EBSD dataset

with respect to the map reference axes (X, Y or Z).
Rotation can be applied either by transferring any
axis into the cardinal axis Z (click on « Rotate into
Z », then « OK » and provides the axis miller
indices) or by providing a rotation angle around X, Y
or Z. The « Check PF » push button may help to
remember how X and Y are oriented. ⚠ Depending
on the EBSD dataset, the rotation is clockwise (map) or anticlockwise (point).

- Remove grain(s) = Opens a phase map of the full EBSD dataset to click on grain(s)
you want to remove. Any « plot » option then do not consider the removed grains/EBSD
pixels anymore.

- Select area(s) = Opens a phase map of the full EBSD dataset to select one or several
areas (up to 4) either by 1) clicking on the top left corner, and then providing the
dimensions (« Fixed » Rectangle) or 2) clicking on vertices. In the latter case, you can
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 choose between rectangle(s) by clicking on the top left and bottom corner (‘On-map’
rectangle), or polygon(s) by clicking on each vertices (‘on-map’ polygon). Only the
selected EBSD dataset is then considered to plot any feature using the « plot » options.

- Select grain(s) = grain(s) can be selected as a function of their

1) grain boundary type (four-grain junctions or triple junctions),
2) size, 3) aspect ratio, 4) shape factor, 5) PARIS factor or 6)
orientation spread (GOS). The last option (Dyn. Recrystal.)
selects a grain dataset according to the de nition of Cross et
al. (2017; GRL) to de ne dynamically recrystallized grains
versus « parent » grains using a threshold value of grain
orientation spread.

- Find twin axis/angle = if applicable, this option allows to

detect any twin boundaries using IPF of misorientation axes for
a given range of misorientation angles.

Quick PF = Push button to plot a pole gure (PF) of the current

dataset using the current PF parameters. To change any parameter, use the Pole gure
« PLOT » option in the dropdown menu. The « D » push button sets the PF (and IPF) back
to its default parameters.

Quick IPF = Push button to plot an inverse pole gure (IPF) of the current dataset using
the current IPF parameters. Refer to the SETTINGS menu to select the reference axi(e)s.

Reset grains = Sets back to the initial dataset for plotting EBSD
data. Depending on the previous selection(s), grains can be
either reset to the original dataset - as imported from the .ctf/.ang
le - or only reset one step back from the last selection (data
rotation, area selection, grain removing or grain selection). One
possibility also exists to set back to the original dataset by
keeping the last area selection.

Record data = Records any imported dataset, modi ed or not,

as a .mat le. After recording, the le can be imported again by
using the weblink « load EBSD data » in the Command window
of any new Matlab/MTEX session. Then, click on « Startup
treatment » again and follow the instructions.
⚠ When treating .mat EBSD data, two new options will appear: « Reset grains » and
« Reset EBSD data ». If you do not want to change anything in the dataset, click « no » in
the rst option and the PLOTTING/SETTINGS menus will appear. Otherwise, you can
either only re-calculate grains of the previously selected dataset (click « yes » on the rst
option and « no » on the second option), or re-calculate grains from the original data,
regardless of any previous selection(s) (click « yes » on the two options). These two
options are also available if you want to re-calculate grains after importing and treating an
EBSD dataset. To do so, click on « startup treatment » and follow the instructions. For
instance, this may be useful to change the entered values of misorientation angles to
de ne grain and inner boundaries. This can be also used to « denoise » a selected area.
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Export dataset = Exports a .txt le with grains information of the selected EBSD dataset,
including the Euler angles, Equivalent diameter, Aspect ratio and Shape preferred
orientation. Other information may be included if necessary (please contact me at
jacques.precigout@univ-orleans.fr).
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