JANAS

Joint ANAlysis of Stacks for CryoEM

Installation • Documentation •

JANAS is a command-line toolkit for particle ranking, subset selection and class reassignment in single-particle cryo-EM workflows.

It uses the per-particle Structural Cross-correlation Index (SCI) to rank particles by their contribution to local map quality.

Quick access

• Install from PyPI — install JANAS with pip install janas.
• Source code — main GitLab repository.
• Documentation — installation, workflows, command reference and utilities.
• Quick start — minimal commands to start using JANAS.
• Particle selection workflow — SCI-based ranking and subset selection.
• 3D class reassignment workflow — reassignment of particles across predefined 3D classes.
• Demo bundle — self-contained software-testing bundle with example inputs, scripts, expected outputs, run-time information and documentation for particle selection and 3D class reassignment.
• JANAS application datasets and analysis outputs — deposited particle selections, class reassignments, refined maps, models, metadata and SCI characterisation files.

The demo package contains small example inputs, scripts, expected outputs and run-time information for testing the two core workflows. These examples are intended for installation checks and end-to-end command validation. The simulated examples are provided to test installation and command execution; the scientific analyses are based on experimental cryo-EM datasets. The Zenodo record contains datasets associated with the application of JANAS, including particle selections, class reassignments, refined maps, models, metadata, local-resolution analyses and SCI characterisation files. Raw particle stacks from public EMPIAR entries are not duplicated there and should be obtained from the corresponding EMPIAR records.

Core workflows

Monitoring a running session

JANAS records the outcome of every selection iteration in overview.txt and the timing of every individual processing step in runtime/step_timings.csv. While the session runs it also keeps an HTML dashboard, progress.html, in sync with the latest state. See Monitoring a running session for how to view it locally or over SSH from a remote browser.

Interoperability workflows

Accessory utils

Installation

Requires Python 3.8+, a C++ compiler, and CMake 3.10+.

pip install janas

We recommend installing in an isolated environment:

python3 -m venv ~/.janas_env
source ~/.janas_env/bin/activate
pip install janas

Verify:

janas --version

See the Installation Guide for conda, pipx, troubleshooting, and building from source.

Documentation

• Documentation index
• Installation
• Quick start
• Iterative particle selection
• 3D class reassignment
• CryoSPARC integration
• CLI command reference
• Accessory utilities
  • sigma_estimate
• STAR file operations
• Computational requirements
• Tutorial: EMPIAR-10308
• Troubleshooting

Contact

For questions or issues: mauro.maiorca@cssb-hamburg.de