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
In-depth Tutorials
- Open an Image
- Fit Splines
- Measure Lattice Parameters
- Inspect CFT Results
- Load & Save Projects
- Custom Workflows
- Spline
- Molecules
- Subtomogram Alignment and Averaging
- Working with Many Projects
- Working with External Softwares
- Tomogram Simulation
- Case Studies
Developers Guide
Others
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
cylindraare 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
magicguithat 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