Helicon

Tools for cryo-EM analysis of helical structures, such as amyloid filaments and other helical assemblies. Helicon finds the helical parameters (twist, rise, symmetry) from 2D images or 3D maps, relates 2D classes to the filaments they came from, and reconstructs a 3D map from a single 2D image or from a set of 2D classes.

It comes as command-line programs, a file viewer, and a set of web apps that run in your browser, on your own computer or on a cloud server. You can try the web apps online without installing anything.

The Home tab of the web apps. In the app, hover over a box to see what that app does, and click it to open it.

Quick start

Helicon needs Python 3.13 or newer. Use a fresh virtual or conda environment, as it pulls in many packages.

pip install "helicon[shiny]"     # the command-line programs and the web apps
helicon                          # opens the web apps, on their Home tab
helicon --help                   # lists all programs

To get the newest development code instead of the latest release:

pip install "helicon[shiny] @ git+https://github.com/jianglab/helicon"

Choosing what to install

The plain pip install helicon gives the command-line programs. Add what you need in square brackets, separated by commas, e.g. helicon[shiny,gui].

Keeping up to date

helicon --version        # the release and the git commit it was built from
helicon update --check   # is there a newer release?
helicon update           # install it

Only releases count, not the commits between them. helicon update also works for a git checkout (pip install -e): it moves the checkout forward to the newest release tag, and stops if you have uncommitted changes.

What is included

Web apps

Start them with helicon (or helicon webApps). Each tab works on its own.

Command-line programs

Viewer and other apps

Run any of them with -h for its options, for example helicon images2star -h.

Documentation

• Documentation at Read the Docs: for users
• Helicon on DeepWiki: for developers
• Project page

Citation

If Helicon is useful in your work, please cite:

Li, D., Zhang, X., Jiang, W., 2025. Helicon: Helical parameter determination and 3D reconstruction from one image. Journal of Structural Biology 217, 108256. doi:10.1016/j.jsb.2025.108256

@article{li2025helicon,
  author  = {Li, D. and Zhang, X. and Jiang, W.},
  title   = {Helicon: Helical parameter determination and 3D reconstruction from one image},
  journal = {Journal of Structural Biology},
  volume  = {217},
  pages   = {108256},
  year    = {2025},
  doi     = {10.1016/j.jsb.2025.108256}
}

Development

git clone https://github.com/jianglab/helicon.git
cd helicon
pip install -e ".[all,test]"
pytest

The version comes from the release tags (v2026.10), so helicon --version in a checkout shows the commits since the last tag and the commit hash. See AGENTS.md for the code layout and conventions. Bugs and feature requests go to the issue tracker.

License

MIT