to the plugins folder,
or subfolder, restart ImageJ, and there will be a new “Asymmetry”
command in the Plugins menu or submenu.
This plugin allows an automated analysis of variations in
imaging conditions across the field of view in high-resolution TEM
images (see http://arxiv.org/abs/1006.0712, section XIV).
Open the HRTEM image of choice. For the hexagonal structure,
hexagons should be dark, the center of the hexagon white (maximum
intensity). Multiply by -1 if your contrast is reversed. Try with
the example image:
Convert to 32bit. Up-scale by a factor of 4 to minimize pixelation
spacing should be at least 12 pixel in our experience). Cut away the
high-frequency information in a Fourier filter to reduce pixel noise
(FFT, draw circular mask, Edit-> clear outside, Inverse FFT). Here
we cut just outside the first lattice reflection:
Measure atomic spacing and angle (of course, measure a multiple of this
length and divide, for better accuracy). For our example of
Single-layer hexagonal boron nitride (hBN), we
chose to define the vector from the center of the hexagon to the
which forms stable mono-vacancies. In this way, the sign of the
asymmetry is defined. Run the asymmetry plugin. Enter angle
and atom spacing as displayed in ImageJ when you draw a line as for the
yellow arrow of the following image (all defaults should work for the
after above steps). Click OK. Input box “Hexagon radius” should usually
be the same as atomic spacing (default).
Now, from each image point, the plugin will search for the nearest
intensity maximum (within the given mask). It will then measure
intensity at this maximum point (center of the hexagon) and on
sub-lattices A and B (away from the center by +- the given
vector, arrow and dashed line in above illustration). If “use
mean value of 3 neighbored atoms” is activated,
it will use the average of the three neighbours for each sublattice
(red and green circles above).
Note that, in this case, the result from neighbouring unit cells is not
statistically independent. The result shows variations in imaging
conditions across the field of view. The “Rainbow RGB” color map
* Activate “show images with min and max” displays images with
intensities for each sublattice. An image generated as 2*Max
-Min1-Min2 (e.g.) can be used to asses layer thickness (total
* Separate images can be used for location of intensity maxima and
actual measurement. In particular for noisy data, it is useful to
generate a Fourier filtered copy of the image with enhanced periodic
and select this image for “maxima positions”.
* A stack of images can be used as input, e.g. to monitor variations
with time in image sequences.
* Arbitrary user-generated images can be used as unit cell mask (e.g.
for non-hexagonal structures). The mask must consist of values 0
and 1 only.
Author: Paul Baggethun (Paul.Baggethun at ALCOA.COM) Date: 2002/06/10 Source: Microscope_Scale.java Installation: Download Microscope_Scale.class to the plugins folder and restart ImageJ. Description: This plugin lets you
Author: Karl Schmidt (firstname.lastname@example.org) Date: 2002/06/19 Source: Included in the ZIP archive Installation: Download MRI_CALC_PLUGIN.zip and unzip the files to a temporary folder. Once unzipped,
Author: Wayne Rasband (email@example.com) History: 2000/11/28: First version 2003/01/28: Uses the image or selection min and max; works correctly with signed images Source: SixteenBit_Histogram.java Installation:
Author: Wayne Rasband (wsr at nih.gov) History: 2001/08/17: First version 2004/07/13: Works with stacks Source: Batch_Statistics.java Installation: Download Batch_Statistics.class to the plugins folder and restart