Cylindra

Cylindra is a Python module for image analysis of cylindric structures in cryo-ET. Spectral analysis, simulation and subtomogram averaging of heterogenic cylindrical structures are implemented.

Index

Getting Started

• Installation
• Basics

In-depth Tutorials

• Open an image
• Fit splines
• Measure lattice parameters
• Inspect CFT Results
• Load & Save Projects
• Custom Workflows
• The Plugin System
• Spline
• Molecules
• Subtomogram Alignment and Averaging
• Working with Many Projects
• Working with External Softwares
• Tomogram Simulation
• Process Images
• Case Studies

Others

• API Reference

Major Dependencies

These are the major dependencies of cylindra. You don't have to fully understand them, but knowing them will help you to use cylindra more efficiently.

Show list

• numpy: Most of the basic mathmatical operations, such as trigonometric functions and vector operations are done with this library.
• scipy: Some of the advanced functions, such as Fourier transformation, 3D rotation and spline fitting are done with this library.
• polars: A library for tabular data analysis, with beautifully designed API.
• napari: Multi-dimensional image viewer. Many of the visualization functions in cylindra are based on this library.
• magicgui: A powerful GUI generator for Python. This library "hides" the complexity of GUI programming, making the code very clean.
• magic-class: An extension of magicgui that can convert Python classes into a multi-functional GUI.Multi-threading, macro recording, command palette and undoing are implemented in this library.
• impy: A Python library for image processing.
• acryo: A Python library for parallel cryo-ET data analysis.

Reference

If you find cylindra useful in your work, please consider citing our paper.

Heterogeneous local structures of the microtubule lattice revealed by cryo-ET and non-averaging analysis
Hanjin Liu, Hiroshi Yamaguchi, Masahide Kikkawa, Tomohiro Shima
bioRxiv 2024.04.30.591984; doi: https://doi.org/10.1101/2024.04.30.591984