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https://github.com/hanjinliu/cylindra
Fourier analysis and subtomogram averaging of heterogenic cylindrical structures
https://github.com/hanjinliu/cylindra
gui microtubule python tomography
Last synced: 2 months ago
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Fourier analysis and subtomogram averaging of heterogenic cylindrical structures
- Host: GitHub
- URL: https://github.com/hanjinliu/cylindra
- Owner: hanjinliu
- License: bsd-3-clause
- Created: 2021-08-30T11:27:58.000Z (over 3 years ago)
- Default Branch: main
- Last Pushed: 2024-09-27T07:35:52.000Z (3 months ago)
- Last Synced: 2024-10-19T02:47:07.950Z (3 months ago)
- Topics: gui, microtubule, python, tomography
- Language: Python
- Homepage: https://hanjinliu.github.io/cylindra/
- Size: 32 MB
- Stars: 9
- Watchers: 1
- Forks: 0
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
[](https://github.com/hanjinliu/cylindra/blob/main/LICENSE)
[](https://pypistats.org/packages/cylindra)
[](https://badge.fury.io/py/cylindra)
[](https://codecov.io/gh/hanjinliu/cylindra)
[](https://napari-hub.org/plugins/cylindra)
# cylindra
`cylindra` is a GUI-integrated cryo-ET image analysis tool for cylindric periodic
structures such as microtubules.
### [→ Documentation](https://hanjinliu.github.io/cylindra/)
## Installation
- Use `pip`
```shell
pip install cylindra -U
```
- From source
If you install from the source, you'll need Rust to compile a part of the code.
```shell
git clone git+https://github.com/hanjinliu/cylindra
cd cylindra
pip install .
```
## Usage
#### Launch GUI
- From shell
```shell
cylindra
```
- From a Python interpreter
```python
from cylindra import start
# launch a napari viewer with a cylindra dock widget.
ui = start()
```
#### Command line interface
`cylindra` is implemented with some basic command line interface (CLI).
```shell
cylindra --help
```
## Implemented Functions
- Automatic/manual fitting of splines to cylindrical structures in 3D.
- Analyze lattice structures (such as lattice spacing and skew angle) using Cylindric
Fourier transformation.
- Automatic determination of polarity, protofilament number etc.
- Monomer mapping along splines for subtomogram averaging and alignment.
- Microtubule seam search with or without binding proteins.
- Subtomogram alignment with 2D constraint.
- Tomogram simulation of cylindric structure.
## Prerequisite and Recommendations
- **Python ≥ 3.10**. This project follows [spec-0000](https://scientific-python.org/specs/spec-0000/).
- **Sufficient memory size**. Most of the intense calculations are done out-of-core
using `dask`, so that you can even run on 8-GB memory PC in many cases. However,
larger memory size will make parallel processing more efficient. ≥32 GB is
recommended.
- **Images should be loaded from SSD**. Raw image stacks are loaded lazily in most of
the processes. Loading from HDD will slow down many analyses as well.
## Issues
If you encountered any bugs or have any requests, feel free to
[report an issue](https://github.com/hanjinliu/cylindra/issues/new).
(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`.
## Citation
If you find `cylindra` useful in your work, please consider citing [our paper](https://www.biorxiv.org/content/10.1101/2024.04.30.591984v1).
```
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
```