The Particle Orientation Analysis script computes an estimate of the degree of orientation in a particle mixture. This quantity is computed as the area fraction that is covered by oriented domains in EM images using OrientationJ.

1. Install OrientationJ according to the provided instructions
2. Drop Particle_Orientation_Analysis.py into the plugins/ folder of your Fiji installation

1. Open image you want to analyze
2. Convert it to 8-bit grey scale (Image > Type > 8-bit)
3. Set ROIs that you want to discard in the computations
   • Make selection
   • Add selection to overlay (Image > Overlay > Add Selection... or Ctrl+B)
   • When images are saved as TIFF, the overlay (as well as the scaling information) is stored
4. Run Plugins > Particle Orientation Analysis
5. Evaluate output
   • Area fraction of oriented particles in %
   • Histogram of orientations in the areas with a high coherency (currently, this does not discard holes, i.e. regions of the image with a high energy value)

1. Open EM image
2. Make a line selection on the provided scale bar (hold down shift for horizontal line)
3. Open Analyse > Set Scale
4. Provide Known distance from scale bar
5. Set Unit of length

or

1. Open EM image
2. Open Analyse > Set Scale
3. Set Distance in pixels to 1
4. Provide Known distance from "Pixel Size" property in the EM image (in units)
5. Set Unit of length

• map0to180.lut maps values near 180 and 0 degrees to the same grey value. Apply to an open image via Image > Color > Edit LUT... > Open...
• TestWindowSizes.ijm executes OrientationJ with various window sizes (minor changes compared to the one provided by the developers)

Gerigk, M., Bahner, J., Kollek, T., Helfrich, S., Rosenberg, R., Cölfen, H. and Polarz, S. (2016), Order and Defects in Ceramic Semiconductor Nanoparticle Superstructures as a Function of Polydispersity and Aspect Ratio. Part. Part. Syst. Charact.. doi:10.1002/ppsc.201600215