| -replacemaxima 57.5 | Replace maxima above the given threshold with surrounding average. |
| -truncate -0.5,1.2 | Truncate data to minimum and maximum before mass normalization. |
| -rescale 0.5,1.5 | Average and standard deviation for output. |
| -images | Input slices of a single 3D image as 2D images. |
| -slices | Output 2D images as z-slices of a single 3D image. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -type simple | Normalization type: simple, Gaussian (default) or Poisson. |
| -output file.star | Output parameter file. |