This Web app provides an interactive online simulation of the contrast transfer function (CTF) of transmission electron microscopes. Click one of the links above to explore the CTF function!
Features
- CTF as Fourier space transfer function of the TEM electron optical system
- Inverse Fourier transform of CTF (PSF, point spread function) in real space demonstrating the delocalization effect
- 1D and 2D CTF/PSF
- Display modes: CTF, |CTF| (phase-corrected CTF), and CTF^2 (power spectra)
- Astigmatism: shows the additional beats in the 1D rotational average
- Simulate the bad CTF phase correction using an inaccurate defocus value
- Scherzer defocus: maximize the pass-band
- Phase shifts: see how well a 90° phase shift in-focus CTF preserves the image
- Envelope functions: B-factor, spatial coherence, energy spread, lens current instability, sample motion in XY and Z-directions
- Shows how over-sampling can improve the sampling of CTFs especially at high resolutions and at large defocuses
- CTF effects on 2D images: geometric patterns (Delta function, Lens Focus Test Chart, TV Test Signal, Spiral Rainbow Squares), cover images of EMDB entries, or an arbitrary image on the Internet
- Multiple 1D/2D CTFs with unique parameters, pixel size, image size, oversampling rate, etc. for you to compare different CTFs
- The average of multiple CTFs
- The meaning of RELION option “Ignore CTFs until first peak?”
- Tooltips for the input variables display the CTF equation with the input variable highlighted in red
- CTF raw data export
- Sharable/bookmarkable URL with parameters that can reproduce your simulations: https://ctfsimulation.streamlitapp.com/?show_psf=1&show_2d=1&simulate_ctf_effect=1&defocus=1.0&bfactor=50.0&imagesize=300&share_url=1
- Displays QR code on the screen to facilitate sharing/reproduction of the exact simulations
CTF Tutorial: These features are also demonstrated in this CTF Tutorial
Open Source/Development: The source code and all revisions are available on GitHub
You can also embed the Web app into your own Website using an iframe, for example using the following code:
<iframe src="https://ctfsimulation.streamlit.app/?embedded=true" style='width: 1000px; height: 900px; overflow: visible; margin: 0px; resize: both; border-style:none;'></iframe>
Reference/Citation
The Web app was developed originally using Java Applet and reported in this paper:
Jiang, W., & Chiu, W. (2001). Web-based Simulation for Contrast Transfer Function and Envelope Functions. Microscopy and Microanalysis. 7(4), 329–334
The original Java-based Web app is now obsolete due to the removal of Java support by current Web browsers. The new Web app is a rewrite with numerous enhancements. If you have found it useful for your research/teaching/learning, please consider citing the 2001 paper.
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