Fourier analysis and subtomogram averaging of heterogenic cylindrical structures
BSD-3-CLAUSE License
cylindra
is a GUI-integrated cryo-ET image analysis tool for cylindric periodic
structures such as microtubules.
pip
pip install cylindra -U
If you install from the source, you'll need Rust to compile a part of the code.
git clone git+https://github.com/hanjinliu/cylindra
cd cylindra
pip install .
From shell
cylindra
From a Python interpreter
from cylindra import start
# launch a napari viewer with a cylindra dock widget.
ui = start()
cylindra
is implemented with some basic command line interface (CLI).
cylindra --help
dask
, so that you can even run on 8-GB memory PC in many cases. However,If you encountered any bugs or have any requests, feel free to report an issue. (We'll appreciate if you find some methods are over-fitted to microtubules and do not work well on other cylindric structures)
For better reproducibility, please copy your environments from Others > cylindra info
and the recorded macro from Others > Macro > Show macro
.
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