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napari-DeepSpot

napari-DeepSpot

RNA spot enhancement for fluorescent microscopy images

License PyPI Python Version tests codecov napari hub

RNA spot enhancement for fluorescent microscopy images.


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

Installation

You can install napari-DeepSpot via pip:

pip install napari-DeepSpot

Build from source

This plugin is using Tensorflow, make sure your Python environment has Tensorflow, on create a new environment using the following commands:

  • Conda:
    conda env create -f environment.yml
    conda activate deepspot-napari
  • Or pip:
    pip install -r requirements.txt

Usage

Open one or multiple images using Napari GUI : File > Open > Select your image

The images are then displayed on Napari

Load the Plugin: Plugins > Napari-DeepSpot:Enhance Spot

Usage

Click on the right panel Button "Enhance"

Wait a few seconds for the magic to happen :

Usage

You can see the original images and the enhanced version in the left panel in the layer section.

To save the images : File > Save all layers or File > Save selected layers.

Usage

Citation

If you use this plugin please cite the paper:

@article {Bouilhol2021DeepSpot,
author = {Bouilhol, Emmanuel and Lefevre, Edgar and Dartigues, Benjamin and Brackin, Robyn and Savulescu, Anca Flavia and Nikolski, Macha},
title = {DeepSpot: a deep neural network for RNA spot enhancement in smFISH microscopy images},
elocation-id = {2021.11.25.469984},
year = {2021},
doi = {10.1101/2021.11.25.469984},
publisher = {Cold Spring Harbor Laboratory},
URL = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984},
eprint = {https://www.biorxiv.org/content/early/2021/11/25/2021.11.25.469984.full.pdf},
journal = {bioRxiv}
}

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-DeepSpot" is free and open source software

Known Issues

If you have troubles with the Python packages typing extensions, use the command :
pip install typing-extensions --upgrade

When using "Enhance" on multiple images, Napari may freeze. Just wait until it comes to life again, the images will still be enhanced. This is due to Napari memory usage and will be fix one day.

Other Issues

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

Version:

  • 0.0.7

Last updated:

  • 30 November 2021

First released:

  • 29 November 2021

License:

Supported data:

  • Information not submitted

Plugin type:

GitHub activity:

  • Stars: 2
  • Forks: 1
  • Issues + PRs: 0

Python versions supported:

Operating system:

Requirements:

  • napari-plugin-engine (>=0.1.4)
  • numpy
  • pytest
  • pytest-cov
  • pytest-xvfb
  • pytest-qt
  • napari
  • qtpy (==1.9.0)
  • pyqt5
  • tensorflow
  • scikit-image
  • opencv-python

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