janas 2.1.6

Pipeline for per-particle selection and 3D class reassignment in single-particle cryo-EM.

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

Workflow	Purpose
Iterative particle selection	Score, rank and select particle subsets that maximise local resolution.
Custom selected stacks	Extract an ad-hoc top-N best-ranked subset from a converged selection, e.g. as input for JANAS-based repicking.
3D class reassignment	Assign particles to pre-computed classes using per-map SCI scores.

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

Workflow	Purpose
CryoSPARC particle STAR recovery	Convert CryoSPARC .cs particle metadata to RELION/JANAS STAR format, adjust stack references, and restore original source particle image names after stack-based processing.

Accessory utils

Utility	Purpose
sigma_estimate	Estimate a Gaussian sigma for SCI scoring from a pair of half-maps.
compare_maps	Compare two 3D maps using cross-correlation and related similarity measures.
csparc2star-stack	Convert a CryoSPARC .cs file to a RELION STAR and assemble a consolidated .mrcs stack.
clip blur	Gaussian-blur a 3D volume (sigma in Ångström).
clip bfac	B-factor weighting (sharpening) of a 3D volume, automatic or user-driven.
fsc	Compute Fourier Shell Correlation (FSC) between half-map pairs.
locres	Compute a local-resolution map from a pair of half-maps.
project_map	Project a 3D reference map at each particle pose, writing 2D reprojections.
janas_reconstructor	Internal 3D reconstruction from scored particles (GPU or CPU).

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: [e-mail]