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:
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
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
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.
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.
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
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
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.
Distributed under the terms of the BSD-3 license, "napari-biomag-annotator" is free and open source software
If you encounter any problems, please file an issue along with a detailed description.