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napari PRAM

napari-pram

plugin for PRAM data annotation and processing

License PyPI Python Version tests codecov napari hub

Plugin for PRAM data annotation and processing.

PRAM Demo


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.

Version:

  • 0.1.3

Last updated:

  • 03 May 2022

First released:

  • 29 April 2022

License:

Supported data:

  • Information not submitted

Open extension:

Save extension:

Save layers:

GitHub activity:

  • Stars: 0
  • Forks: 0
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • numpy
  • magicgui
  • qtpy
  • opencv-python
  • scipy

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