napari-allencell-annotator 1.0.2

A plugin that enables annotations provided by Allen Institute for Cell Science

napari-allencell-annotator

A plugin that enables large image set annotating 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, and spinbox). With napari's multi-dimensional image viewing capabilities and AICSImageIO's image reading and metadata conversion, the plugin seamlessly allows users to view each image in a set and annotate according to the selected template. Annotation templates can be written to a json file for sharing or re-using. After annotating, both annotation template data and the annotations written for the image set are saved to csv file, which can be re-opened for further annotating and conveniently stores annotations.

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

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

Installation

First install the latest version of napari. Find instructions here. If you are unfamiliar with installing Python packages, follow the section titled Install as a bundled app.

Option 1 (recommended):

After you installed napari, you can go to "Plugins" --> "Install/Uninstall Package(s)". Then, you will be able to see all available napari plugins and you can find us by name napari-allencell-annotator. Just click the "install" button to install the Annotator plugin.

Option 2:

You can also install napari-allencell-annotator via pip:

pip install napari-allencell-annotator

Quick Start

In the current version, there are two parts in the plugin: Image List and Annotation Editor. The Annotation Editor allows users to create new annotation templates or upload existing annotation templates from a previous plugin-created csv or json file. Once an annotation template is chosen and approved, annotating can begin on the image set selected in the Image Uploader section of the plugin.

1. Open napari
2. Start the plugin
   • Open napari, go to "Plugins" --> "napari-allencell-annotator".
3. Click create new annotation template or upload existing.
   • Up to 10 new annotations can be created. Each annotation must have a unique name and a type (text, number, checkbox, or dropdown).
   • If the annotation template is uploaded from a csv file, using the image set will open and allow continued editing of all annotations in the csv.
4. Click add images or add files to select images for annotating
   • The plugin is able to support .tiff, .tif. ome.tif, .ome.tiff, .czi, .png, .jpeg, and .jpg files.
   • Once selected, the images can be shuffled and hidden or deleted using the checkbox on the right side.
5. Start Annotating and select or create a .csv file for writing.
   • If the selected file already exists, it will be overwritten.
6. Click Save and Exit at any time and all created image annotations will be written to the .csv file.
   • If the file is opened in the plugin again, annotation will start at the first image with a blank annotation.

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.