RNA spot enhancement for fluorescent microscopy images.
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
You can install napari-DeepSpot via pip:
pip install napari-DeepSpot
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
Open one or multiple images using Napari GUI :
File > Open > Select your image
(Please note that for now only 256px x 256px images are supported)
The images are then displayed on Napari
Load the Plugin: Plugins > Napari-DeepSpot:Enhance Spot
Click on the right panel Button "Enhance"
Wait a few seconds for the magic to happen :
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.
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}
}
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.
Distributed under the terms of the MIT license, "napari-DeepSpot" is free and open source software
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.
- Use different size of images
- Renaming the enhanced layers
- Possibility to load another model
- Working with large volume of images
- New model from DeepSpot for better enhancement
If you encounter any problems, please file an issue along with a detailed description.