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Calc dSpace

1,526 bytes added, 17:24, 16 November 2019
How it works
== '''Overview ''' ==
This plugin can be used to quickly calculate the interplanar spacing values ''(d)'' directly within imageJ without copying the results table to another program like Excel to then convert measurements into d-values, which saves you time. It is also remarkably easy to use, accurate, and robust for both spot and ring electron diffraction patterns.
== '''How it works ''' ==
Use imageJ’s circle tool (shift + oval tool) to measure the spot/ring patterns concentric to the (000) direct beam. From the area measurement, the radius (G) is found. From G = 1/d in reciprocal space, the d-spacing is calculated for each measurement made. The calculated values for G and d are added to the imageJ Results window This plugin has three different modes in new columnswhich it can operate.
== Image Requirements ==[[File:Modes.jpeg|300px|center]]
The first, and most basic mode, is '''calculate''' where the calculated values for G and d are added to the imageJ Results window in new columns. G is in nanometers and d is in Angstroms. There is also a 2% error column, which is just 2 % of d in angstroms. '''Overlay''' is the second mode, which draws the positions of the measurements made back onto the diffraction pattern image, and displays an inset with the calculated d-spacing values for each ring. It also labels the rings and d-spacing measurements in the inset so that there is traceability between the calculated values and the measurements made using the circle tool. This visual correlation between d spacing and measured rings is useful for indexing diffraction patterns, because the TEM operator can subjectively take ring intensity into account. For example, you may be deciding between two phases that have similar d-spacing lists, but different ring intensities. This helps determine which rings are the most intense in the patterns adding a data component that is sometimes lost in SAD analysis. The final mode is '''Overlay & Crop''', which is more of a publication-ready mode that actually crops the diffraction pattern down to the size of the measured region. This is more suitable for publication, as it zooms to the measured region and makes the image square. This image is best saved as a jpeg first and then saved as a tiff if that is the preferred format. [[File:CropExample.jpeg|400px|center]] == '''Image Requirements''' == You need to have a properly calibrated diffraction pattern for the calculations to work. Most TEM operators TEMs use Gatan’s Digital Micrograph software for image collection. If you are using DM, then it is likely that this plugin will work right away, or will work with the help of your TEM technician.
The preferred image is a .dm3 file (Gatan’s format) that is properly calibrated in reciprocal space (see Gatan’s documentation). The easiest way to check this is that the scale bar in your images is displayed in DM with 1/nm units.
== '''Strontium Titanate Example ''' ==
The example below is from a single crystalline STO (strontium titanate) sample. It illustrates how the measurements should be made in order to ensure the plugin is calculating the d-spacing values accurately. Make your measurements working from the inner most spots/rings outwards.
[[File:New_Fig_1.jpg|800px|center]]
There are 3 new columns in the Results window: G, d, 2% error. The scalar component of the G vector in reciprocal space is found and measured in 1/nm since these are the image units. The d-spacing is listed in Angstroms, and the 2% error is just 2% of the d-spacing. While it is ''not'' an actual uncertainty measurement, it can help you index your sample.
== '''Tips ''' ==
# If you hold down both control and shift while clicking on one of the white squares on the circle and dragging, the circle expands and contracts concentrically.
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