napari-tomoslice's Introduction

napari-tomoslice

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

annotating spheres in napari-tomoslice

napari-tomoslice is powered by napari and napari-threedee.

Features

napari-tomoslice allows you to quickly annotate

points
paths
spheres

Annotations are saved in the STAR file format and can be easily manipulated in Python using starfile.

Installation

napari-tomoslice is available on PyPI.

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

 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.     │
╰──────────────────────────────────────────────────────────────────────────────────────────╯