Metadata-Version: 2.1
Name: blik
Version: 0.2.2
Summary: Python tool for visualising and interacting with cryo-ET and subtomogram averaging data.
Home-page: https://github.com/gutsche-lab/blik
Author: Blik Team
Author-email: blik-team@googlegroups.com
License: GNU General Public License v3 (GPLv3)
Platform: UNKNOWN
Classifier: Development Status :: 2 - Pre-Alpha
Classifier: Environment :: X11 Applications :: Qt
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Programming Language :: Python
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.7
Classifier: Programming Language :: Python :: 3.8
Classifier: Topic :: Scientific/Engineering
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Utilities
Classifier: Operating System :: Microsoft :: Windows
Classifier: Operating System :: POSIX
Classifier: Operating System :: Unix
Classifier: Operating System :: MacOS
Requires-Python: >=3.8
Description-Content-Type: text/markdown
Provides-Extra: dev
License-File: LICENSE

![logo](docs/images/logo.png)

# `blik`

![Codecov branch](https://img.shields.io/codecov/c/github/gutsche-lab/blik/master?label=codecov)
![PyPI](https://img.shields.io/pypi/v/blik)
![PyPI - Python Version](https://img.shields.io/pypi/pyversions/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](https://napari.org) 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

```bash
pip install blik
```

## Basic Usage

From the command line:
```bash
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:
```python
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](https://gutsche-lab.github.io/blik).

## `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](https://napari-hub.org/).

### 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](https://github.com/brisvag/napari-properties-plotter).


