Site 1 (click me) | Site 2 (click me) | Site 3 (click me) | Site 4 (click me) | Site 5 (click me)
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 the CTF Tutorial below:
Open Source/Development
The source code and all revisions are available on GitHub
You can also embed the Web app into your 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>or a iframe WordPress plugin:
[iframe src="https://ctfsimulation.streamlit.app/?embedded=true" width="100%" height="900" frameborder="0"]
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.