napari-biomag-annotator

An annotator tool collection by the BIOMAG group.

This plugin allows object annotation on 2/3D images using 4 assisted annotation methods arising from two napari plugins:

• napari-annotatorj
• napari-nD-annotator

This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.

Installation

You can install napari-biomag-annotator via pip:

pip install napari[all]
pip install napari-biomag-annotator

To install latest development version :

pip install git+https://github.com/biomag-lab/napari-biomag-annotator.git

On Linux distributions, the following error may arise upon napari startup after the installation of the plugin: Could not load the Qt platform plugin “xcb” in “” even though it was found. In this case, the manual install of libxcb-xinerama0 for Qt is required:

sudo apt install libxcb-xinerama0

Bundled napari app

The bundled application version of napari allows the pip install of plugins in the .zip distribution. After installation of this release, napari-annotatorj can be installed from the Plugins --> Install/Uninstall plugins... menu by searching for its name and clicking on the Install button next to it.

Script

Single-file install is supported on Windows and Linux (currently). It will create a virtual environment named napariAnnotatorEnv in the parent folder of the cloned repository, install the package via pip and start napari. It requires a valid Python install.

Windows

To start it, run in the Command prompt

git clone https://github.com/biomag-lab/napari-biomag-annotator.git
cd napari-biomag-annotator
install.bat

Or download install.bat and run it from the Command prompt.

After install, you can use startup_napari.bat to activate your installed virtual environment and run napari. Run it from the Command prompt with:

startup_napari.bat

Linux

To start it, run in the Terminal

git clone https://github.com/biomag-lab/napari-biomag-annotator.git
cd napari-annotatorj
install.sh

Or download install.sh and run it from the Terminal.

After install, you can use startup_napari.sh to activate your installed virtual environment and run napari. Run it from the Terminal with:

startup_napari.sh

Contributing

Contributions are very welcome. Tests can be run with tox, please ensure the coverage at least stays the same before you submit a pull request.

License

Distributed under the terms of the BSD-3 license, "napari-biomag-annotator" is free and open source software

Issues

If you encounter any problems, please file an issue along with a detailed description.