Phantom_simulate_microscope_v31

!xmipp_phantom_simulate_microscope (v3.1)

Usage

Simulate the effect of the microscope on ideal projections.

Parameters

$``: Input file: metadata, stack, volume or image. $--mode <modeoverwrite> where <mode> can be:

• • $--label <image_labelimage> $-o, --output <output_file> $--oroot <root> $--save_metadata_stack <output_md> $: Store the original image filename in the output metadata in column imageOriginal. $: Preserve the columns from the input metadata. Some of the column values can be changed by the program.

CTF options $--ctf <CTFdescr> $``: apply noise after CTF $--defocus_change <v0>

Noise options $--noise <stddev> <w0.5> $ or: the necessary noise power for a specified SNR is estimated $ or: do not add any noise, only simulate the CTF $--downsampling <D1>

Examples and notes

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

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

Generate a set of images with a target SNR

xmipp_phantom_simulate_microscope -i g0ta.sel --oroot g2ta --ctf untilt_ARMAavg.ctfparam --targetSNR 0.2 --after_ctf_noise

Generate a set of images with the CTF applied and noise before and after CTF

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

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