Metadata-Version: 2.3
Name: napari-tomoslice
Version: 0.1.1
Summary: Tomogram visualisation and annotation in napari.
Project-URL: homepage, https://github.com/alisterburt/napari-tomoslice
Project-URL: repository, https://github.com/alisterburt/napari-tomoslice
Author-email: Alister Burt <alisterburt@gmail.com>
License: BSD 3-Clause License
License-File: LICENSE
Classifier: Development Status :: 3 - Alpha
Classifier: License :: OSI Approved :: BSD License
Classifier: Natural Language :: English
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Typing :: Typed
Requires-Python: >=3.8
Requires-Dist: mrcfile
Requires-Dist: napari-threedee
Requires-Dist: napari[pyqt5]
Requires-Dist: starfile
Requires-Dist: typer
Provides-Extra: dev
Requires-Dist: black; extra == 'dev'
Requires-Dist: ipython; extra == 'dev'
Requires-Dist: mypy; extra == 'dev'
Requires-Dist: pdbpp; extra == 'dev'
Requires-Dist: pre-commit; extra == 'dev'
Requires-Dist: pytest; extra == 'dev'
Requires-Dist: pytest-cov; extra == 'dev'
Requires-Dist: rich; extra == 'dev'
Requires-Dist: ruff; extra == 'dev'
Provides-Extra: test
Requires-Dist: pytest-cov; extra == 'test'
Requires-Dist: pytest>=6.0; extra == 'test'
Description-Content-Type: text/markdown

# napari-tomoslice

[![License](https://img.shields.io/pypi/l/napari-tomoslice.svg?color=green)](https://github.com/alisterburt/napari-tomoslice/raw/main/LICENSE)
[![PyPI](https://img.shields.io/pypi/v/napari-tomoslice.svg?color=green)](https://pypi.org/project/napari-tomoslice)
[![Python Version](https://img.shields.io/pypi/pyversions/napari-tomoslice.svg?color=green)](https://python.org)
[![CI](https://github.com/alisterburt/napari-tomoslice/actions/workflows/ci.yml/badge.svg)](https://github.com/alisterburt/napari-tomoslice/actions/workflows/ci.yml)
[![codecov](https://codecov.io/gh/alisterburt/napari-tomoslice/branch/main/graph/badge.svg)](https://codecov.io/gh/alisterburt/napari-tomoslice)

*napari-tomoslice* is a tool for tomogram visualisation and annotation in napari.

<p align="center">
  <img src="assets/spheres.gif" alt="Annotating spheres in napari-tomoslice">
  <br>
  <em>annotating spheres in napari-tomoslice</em>
</p>

*napari-tomoslice* is powered by
[*napari*](https://github.com/napari/napari) 
and
[*napari-threedee*](https://github.com/napari-threedee/napari-threedee).

## Features

*napari-tomoslice* allows you to quickly annotate

- points
- paths
- spheres

Annotations are saved in the [STAR file format](https://en.wikipedia.org/wiki/Self-defining_Text_Archive_and_Retrieval)
and can be easily manipulated in Python using [starfile](https://teamtomo.org/starfile/).

## Installation

*napari-tomoslice* is available on PyPI.

```shell
pip install napari-tomoslice
```

We recommend installing into a fresh conda environment.

*napari* does not work well via X forwarding. If you want to use *napari-tomoslice* in a HPC environment
please run via a virtual desktop solution.

## Usage

```sh
 Usage: napari-tomoslice [OPTIONS]                                                                                                                                              
                                                                                                                                                                                
╭─ Options ────────────────────────────────────────────────────────────────────────────────╮
│    --tomogram-directory          PATH                    [default: None]                 │
│    --file-pattern                TEXT                    [default: *.mrc]                │
│    --annotation-directory        PATH                    [default: 2024_05_22_21:16:44]  │
│ *  --mode                        [points|paths|spheres]  [required]                      │
│    --help                                                Show this message and exit.     │
╰──────────────────────────────────────────────────────────────────────────────────────────╯
````

## Inspiration

*napari-tomoslice* is inspired by [*dtmslice* in Dynamo](https://www.dynamo-em.org/w/index.php?title=Dtmslice).

