Microscope

phantom_simulate_microscope

Purpose

This program simulates the effect of the microscope on ideal projections. This program is usually used with phantom data.

Usage

$ phantom_simulate_microscope ...

Parameters I/O:

• `` Set of ideal projections
• `` If an input image is provided (instead of a selfile), use this option to produce an output image with a different name. By default, the input image will be overwritten.
• `` If a selfile is provided, use this option to change the rootname of the output images. Otherwise, the input images will be rewritten. Alternatively, use the -oext option.
• `` If a selfile is provided, use this option to change the extension of the output images. Otherwise, the input images will be rewritten.
• `` Do not produce on screen information

Microscope description:

• `` The CTF description file is produced byAdjust_CTFOrAssign_CTF
• -defocus_change [v0= Use this option to simulate random defoci around the nominal value
• -low_pass [w0] = Low pass filter the noise before the CTF. w is the frequency cutoff normalized to 0.5
• `` Standard deviation of the noise to be added to the ideal projection images. The amount of noise to be added can be calculated using this trickEstimatingNoisePowerForAGivenSNR
• `` The CTF description file is produced byAdjust_CTFOrAssign_CTF
• `` By default, noise after CTF is not added. Use this option to force the program to add it.

Examples and notes

Generate a set of images with the CTF applied without any noise

phantom_simulate_microscope -i g0ta.sel -oroot g1ta -ctf untilt_ARMAavg.ctfparam

Generate a set of images with the CTF applied and noise before and after CTF. The standard deviation of the noise has been estimated as described inEstimatingNoisePowerForAGivenSNR

phantom_simulate_microscope -i g0ta.sel -oroot g2ta -ctf untilt_ARMAavg.ctfparam -noise 4.15773 -after_ctf_noise

The following images show the effect of each of the previous commands

Original	CTF affected	CTF and noise affected
/g0ta00001.gif	/g1ta00001.gif	/g2ta00001.gif

--Main.CoSS - 05 Feb 2007