| -invert | Invert density in the image. |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation after filtering. |
| -minmax -0.5,1.2 | Rescale data to minimum and maximum. |
| -average 7,5,3 | Averaging/smoothing filter: kernel size. |
| -gaussian 11,2.6 | Gaussian smoothing filter: kernel size and sigma. |
| -median 3 | Median filter: kernel edge size. |
| -peak 5 | Peak filter: kernel edge size. |
| -gradient | Gradient filter (3x3x3). |
| -laplacian | Laplacian filter (3x3x3). |
| -LoG 2.5 | Laplacian-of-Gaussian filter. |
| -DoG 1.5,3.1 | Difference-of-Gaussians filter. |
| -denoise 2,0.4 | Denoising filter: distance and density difference sigmas. |
| -rollingball 5,4.3 | Rolling ball filter: radius and density scaling (default scaling=1). |
| -variance 11,1 | Calculate a local variance image using the given size kernel, |
| with a flag to indicate standard deviation rather than variance. |
| -extremes his | Filter image extremes: his=histogram-based, mg=for micrograph. |
| -replacemaxima 1.5 | Replace maxima above the given threshold with surrounding average. |
| -bandpass 25.3,200,0.02 | Bandpass filter: resolution limits (angstrom) and band edge width (1/angstrom). |
| -amplitude 8.3 | Amplitude filter: setting all amplitudes below the threshold to zero. |
| -phasesonly | Set all amplitudes to one. |
| -Bfactor 44,25.3 | B-factor application: B-factor (A^2), high resolution limit (A,optional) |
| Multiplied in reciprocal space by exp(-B-factor/4 * s^2). |
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