napari PRAM

Plugin for PRAM data annotation and processing.

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

Usage

Open napari-pram toolbox:

On the toolbar, select [Plugins] > napari-pram: Open PRAM's toolbox

Load PRAM image and annotations:

Press Command/Control + O:

• Select *.json files for annotations (from either VGG Annotator or napari-pram)
• Select *.png files for PRAM image

Annotate

• Press Annotate
• Click the plus-in-circle icon on the top-left panel and start editing

Run PRAM particles detector

• Select a proper threshold between 1 (ultra sensitive) - 10 (less sensitive)
• Press Run Detector

Evaluate

• Press Evaluate
• Hide/Unhide true positive/ false postive/false negative layers

Load new image

• Press Clear All to remove all layers

Export to JSON

• Press Save to File to export all annotations, predictions from the algorithm to a JSON file

Installation

Following this tutorial to install napari.

Alternatively, you can follow my instructions as follows:

You will need a python environment. I recommend Conda. Create a new environment, for example:

conda create --name napari-env python=3.7 pip 

Activate the new environment:

conda activate napari-env 

Install napari via pip:

pip install napari[all]

Then you can finally install our plugin napari-pram via pip:

pip install napari-pram

Alternatively, the plugin can be installed using napari-GUI

[Plugins] > Install/Uninstall Plugins and search for napari-pram

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 MIT license, "napari-pram" is free and open source software

Issues

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