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.
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].
| Extra | Adds |
|---|
shiny | the web apps (helicon webApps, or just helicon) |
gui | the display file viewer (napari, PySide6, pyqtgraph) |
streamlit | the Streamlit apps (ctfSimulation, map2seq, procart) |
all | shiny, streamlit, gui and the curvelet extras |
test | what the test suite needs, for developers |
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.
| Tab | What it does |
|---|
| AbInitio3D | Reconstruct a 3D map from a set of 2D classes, with the twist found by a phase fit |
| Denovo3D | De novo helical indexing and 3D reconstruction from a single 2D image |
| HelicalPitch | Determine the helical pitch and twist from 2D classification results |
| HILL | Helical indexing with Fourier-Bessel layer lines (power spectra and phase differences) |
| HI3D | Helical indexing by cylindrical projection of a 3D map |
| HelicalProjection | Compare 2D images with projections of helical structures from the EMDB |
| HelicalLattice | Convert between a 2D lattice and a helical lattice |
| WhereIsMyClass | Map 2D classes back to the helical tube/filament images they contain |
Command-line programs
| Program | What it does |
|---|
cryosparc | Talk to a CryoSPARC server and run image analysis tasks |
images2star | Analyze and transform datasets and save them as a RELION star file |
proc3d | Analyze and transform 3D maps |
trueFSC | Compute the True FSC curve with an optimal mask and phase randomization |
update | Update Helicon to the newest release |
Viewer and other apps
| Program | Needs | What it does |
|---|
display | gui | A file browser for images, maps, star, bild, eps, pdf, html and text files |
ctfSimulation | streamlit | Simulate 1D and 2D TEM contrast transfer functions |
map2seq | streamlit | Find the protein sequence that best explains a 3D density map |
procart | streamlit | Plot cartoon illustrations of residue properties of amyloid atomic models |
Run any of them with -h for its options, for example helicon images2star -h.
Documentation
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
