| -invert | Invert density in the image before other operations. |
| -rescale -0.1,5.2 | Rescale data to average and standard deviation before other operations. |
| -average 34,1,1 | Moving average window size (voxels). |
| -period 100,32,1 | Periodic frame size (voxels). |
| -width 25 | Window to fit a moving line for estimating the filament width. |
| -density 30,120 | Density with filament width and number of histogram bins. |
| -verbose 7 | Verbosity of output. |
| -datatype u | Force writing of a new data type. |
| -sampling 1.5,1.5,1.5 | Sampling (A/pixel; a single value can be given). |
| -origin 0.8,-10,15.7 | Set the origin (default from input image). |
| -resolution 15.6 | Resolution limit for cross-correlation. |
| -limits 35,57 | Limits on the filament width (default 0 - width of image). |
| -reference file.map | 2D reference for cross-correlation. |
| -Postscript plot.ps | Plot of filament widths. |