napari-allencell-annotator

A plugin that enables image annotation/scoring and writes annotations to a .csv file. Plugin provided by the Allen Institute for Cell Science.

The Allen Cell Image Annotator plugin for napari provides an intuitive graphical user interface to create annotation templates, annotate large image sets using these templates, and save image annotations to a csv file. The Allen Cell Image Annotator is a Python-based open source toolkit developed at the Allen Institute for Cell Science for both blind, unbiased and un-blind microscope image annotating. This toolkit supports easy image set selection from a file finder and creation of annotation templates (text, checkbox, drop-down, spinbox, and point). With napari's multi-dimensional image viewing capabilities, the plugin seamlessly allows users to view each image and write annotations into the custom template. Annotation templates can be written to a json file for sharing or re-using. After annotating, the annotation template, image file list, and the annotation values are conveniently saved to csv file, which can be re-opened for further annotating.

• Supports the following image types:
  • OME-TIFF
  • TIFF
  • CZI
  • PNG
  • JPEG
  • OME-ZARR

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

Installation using Command Line

1. Install the plugin

• Create and activate a virtual environment. We recommend using conda and python 3.10.

  • To create and activate a conda virtual environment, run the following commands one line at a time.

    conda create -n napari_annotator python=3.10
    conda activate napari_annotator

  • To create and activate a venv virtual environment, run the following commands.

  • Windows

    python -m venv venv
    venv\Scripts\activate

  • MacOS/Unix

    python -m venv venv
    source venv/bin/activate

• Install Napari and the annotator plugin by running

  python -m pip install "napari[all]"
  python -m pip install napari-allencell-annotator

• Open Napari by running napari and verify that napari-allencell-annotator is listed in the Plugins tab.

• Not working? Try using conda forge instead of pip.

  • Ex: conda install -c conda-forge napari instead of python -m pip install "napari[all]"

2. Launch the Plugin

• If napari-allencell-annotator is listed in Plugins, click it to launch.
• If it is not listed
  • Install/Uninstall Plugins ⇨ check the box next to napari-allencell-annotator ⇨ close ⇨ Plugins ⇨ napari-allencell-annotator.

Installation from Napari Hub

If you have previously installed Napari on your machine, you can follow these steps to install the plugin from Napari Hub.

1. Install the Plugin

• Open Napari
• Go to Plugins ⇨ Install/Uninstall Plugins...
• Find napari-allencell-annotator in Available Plugins
• Click Install
• Close the window after the installation finishes

2. Launch the Plugin

• Click Plugins ⇨ napari-allencell-annotator
  • You might have to restart Napari for the annotator to appear in the plugin list.
  • If you still can't see the plugin, go to Install/Uninstall Plugins ⇨ check the box next to napari-allencell-annotator.

Quick Start

1. Open napari
2. Start the plugin
   • Open napari, go to Plugins ⇨ napari-allencell-annotator.
3. Create or import annotations and add images to annotate.

For more detailed usage instructions, check out this document

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-allencell-annotator" is free and open source software

Issues

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