Xmipp

xmipp_phantom_simulate_microscope (v3.0)

Usage

Simulate the effect of the microscope on ideal projections.

Parameters

-i, --input <input_file>
Input file: metadata, stack, volume or image.
--mode <mode=overwrite>
Metadata writing mode.
where <mode> can be:
  • overwrite Replace the content of the file with the Metadata
  • append Write the Metadata as a new block, removing the old one
-o, --output <output_file=>
Output file: metadata, stack, volume or image.
--oroot <root=>
Rootname of output individual images. Output image format can be set adding extension after rootname as ":ext".

CTF options

--ctf <CTFdescr>
a CTF description, if this param is not supplied it should come in metadata
--after_ctf_noise
apply noise after CTF
--defocus_change <v=0>
change in the defocus value (percentage)

Noise options

--noise <stddev> <w=0.5>
noise to be added, this noise is filtered at the frequency specified (<0.5).
or --targetSNR <snr>
the necessary noise power for a specified SNR is estimated
or --noNoise
do not add any noise, only simulate the CTF

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

User's comments

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