Helpful Tools

Direct Electron is passionate about science and proud to be a contributing member of the scientific community. In pursuit of our own research and development, we have developed several tools that may be useful to you. Please feel free to use the following tools to advance your own research, for teaching, and/or for publications. If you use any of these tools in your publications, posters, or talks, please acknowledge us by name (Direct Electron LP, San Diego, CA USA) and/or Web address (

We will continue adding to this repository as we develop new tools. If you have ideas for further improving or adding to these tools, please contact us (you may the form at the bottom of this page).

Contrast Transfer Function (CTF) Simulator

Microsoft Excel spreadsheet for simulating TEM contrast transfer functions, including many input parameters and output values not typically included in other online CTF simulators.

Input values include: Accelerating Voltage, Electron Source Angle, Electron Source Spread, Accelerating Voltage Stability, Objective Lens Current Stability, Spherical Aberration, Chromatic Aberration, Phase Shift (e.g., from a Phase Plate), Defocus, Amplitude Contrast, Angstroms per Pixel Sampling, Detector DQE.

Output values include: Electron Wavelength, Focus Spread, First CTF Zero, Information Limit, Estimated B-Factor, Scherzer Defocus, Point Resolution, Phase-Shift Scherzer Defocus, Phase-Shift Point Resolution, Total Contrast to 1st Zero.

The output plot includes: Temporal Envelope, Spatial Envelope, Detector Envelope, Total Envelope, Microscope CTF, Detected Power, Nyquist Frequency.

B-Factor Estimator

Microsoft Excel spreadsheet for estimating the B-factor (also called temperature factor) for single particle cryo-EM reconstructions as described in Rosenthal & Henderson, 2003. The B-factor describes the relationship between the number of particles used to generate a 3D reconstruction with the final resolution of that 3D reconstruction. This is helpful for understanding the quality of your data and image processing, as well as for predicting the number of particles necessary to reach a higher resolution.

To use the spreadsheet, first input the number of symmetric units in the 3D reconstruction (e.g., 1 for an asymmetric specimen or 60 for an icosahedral specimen), and then input the number of particles and corresponding resolution for multiple 3D reconstructions. The spreadsheet will generate a plot showing the data points and the fit with the estimated B-factor. You may also enter a desired target resolution and the spreadsheet will estimate the number of particles needed to reach that resolution.