Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
Project description
blik
it means glance in Dutch
blik is a python tool for visualising and interacting with cryo-ET and subtomogram averaging data. It leverages the fast, multi-dimensional napari viewer and the scientific python stack.
DISCLAIMER: this package is in early development phase. Expect frequent bugs and crashes. Please, report them on the issue tracker and ask if anything is unclear!
Installation
pip install blik
Basic Usage
From the command line:
blik /path/to.star /path/to/mrc/files/
blik accepts any combination of files and directory, and will try find the right files and display them in napari. blik will also start an ipython shell with the following setup:
import blik
dataset = DataSet([your_data])
viewer = dataset.napari_viewer
For more information, check out the help page with blik -h and head over to the docs.
napari integration
blik is just napari. Particles and images are exposed as simple napari layers, which can be analysed and manipulated with simple python, and most importantly napari plugins.
Property plotting
Particles loaded from a star file or similar format will contain all the additional data that comes in additional columns. To plot this data and select particles based on it, check out napari-property-plotter.
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