# napari-superres
[](https://github.com/RoccoDAnt/napari-superres/blob/main/LICENSE)
[](https://pypi.org/project/napari-superres)
[](https://python.org)
[](https://github.com/RoccoDAnt/napari-superres/actions)
[](https://codecov.io/gh/RoccoDAnt/napari-superres)
[](https://napari-hub.org/plugins/napari-superres)
A collection of super-resolution microscopy FF-SRM methods.
Open-source implementation of methods for Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM):
Review: [Alva et al., 2022. “Fluorescence Fluctuation-Based Super-Resolution Microscopy: Basic Concepts for an Easy Start.” Journal of Microscopy, August.](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135)
MSSR article: [Torres-García, E., Pinto-Cámara, R., Linares, A. et al. Extending resolution within a single imaging frame. Nat Commun 13, 7452 (2022).](https://doi.org/10.1038/s41467-022-34693-9)
ESI article: [Idir Yahiatene, Simon Hennig, Marcel Müller, Thomas Huser (2015/2016). "Entropy-based Super-resolution Imaging (ESI): From Disorder to Fine Detail" ACS Photonics 8, 2 (2015)](https://doi.org/10.1021/acsphotonics.5b00307)
SOFI article: [T. Dertinger, R. Colyer, G. Iyer, and J. Enderlein. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). PNAS 52, 106 (2009) ](https://doi.org/10.1073/pnas.0907866106)
SRRF article: [Gustafsson, N., Culley, S., Ashdown, G., D. M. Owen, P. Matos Pereira, and R. Henriques. Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations. Nat Commun 7, 12471 (2016)](https://www.nature.com/articles/ncomms12471)
MUSICAL article: [K. Agarwal and R. Machan, Multiple Signal Classification Algorithm for super-resolution fluorescence microscopy, Nature Communications, vol. 7, article id. 13752, (2016)](https://www.nature.com/articles/ncomms13752)
Methods implemented:
- MSSR
- ESI
- SOFI
- SRRF
- MUSICAL
- Split channels
| **Super Resolution Radial Fluctuations (SRRF)** | **Mean-Shift Super Resolution (MSSR)** | **Entropy-based Super-resolution Imaging (ESI)** |
| --- | --- | --- |
|  |  |  |
from Fig. 7 of [Alva et al., 2022](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135) | from Fig. 2 of [García et al., 2021](https://www.biorxiv.org/content/10.1101/2021.10.17.464398v2.full)| from Fig. 6 of [Alva et al., 2022](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135)|
Repositories available:
- [ESI](https://github.com/biophotonics-bielefeld/ESI) GitHub repository
- [PySOFI](https://github.com/xiyuyi-at-LLNL/pysofi) GitHub repository
- [MUSICAL](https://sites.google.com/site/uthkrishth/musical) Google site
----------------------------------
This [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.
<!--
Don't miss the full getting started guide to set up your new package:
https://github.com/napari/cookiecutter-napari-plugin#getting-started
and review the napari docs for plugin developers:
https://napari.org/stable/plugins/index.html
-->
## Installation
First install napari viewer (if you haven't):
conda create -y -n napari-env -c conda-forge python=3.9
conda activate napari-env
pip install "napari[all]"
For details check: https://napari.org/stable/
You can install the plugin [graphically](https://github.com/LIBREhub/napari-LatAm-Workshop-2023/blob/napari-superres/docs/day3/napari-superres/napari-superres_installation_guide.pdf).
or install latest development version :
pip install git+https://github.com/RoccoDAnt/napari-superres.git
You might need to install [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) first.
----------------------------------
Examples of use:
| **Original** | **tMSSR** |
| --- | --- |
| <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/single-frame-good-exposure.png" width=100% height=100%> </p>| <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/tmssr-mean-mag2.png" width=48% height=48%> </p>|
| Parameters: | Amplification: 2, Order: 0, PSF FWHM: 6, <br> Interpolation: Bicubic, Statistical integration: CV*sigma |
| **Original** | **ESI** |
| --- | --- |
| <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/synt.png" width=40% height=40%> </p> | <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/ESI.png" width=50% height=50%> </p> |
| Parameters: | image in output: 2, bins: 2, Order: 2 |
| **Original** | **SOFI** |
| --- | --- |
|<p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/noSOFI.png" width=100% height=100%> </p> | <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/SOFI.png" width=100% height=100%> </p> |
| Parameters: | Amplification factor: 2, Moment Order: 4, lambda parameter: 1.5, No. Iterations: 20, Window size: 100|
| **Original** | **SRRF** |
| --- | --- |
|<p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/synt.png" width=50% height=50%> </p> | <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/SRRF.png" width=50% height=50%> </p>|
| Parameters: | Amplification: 2, Spatial radius: 5, Symmetry Axis: 6, Start frame: 0, End frame: 48|
| **Original** | **MUSICAL** |
| --- | --- |
| <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/musical_mean.png" width=70% height=100%> </p> | <p align="center"> <img src="https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/MUSICAL-CardioMyoblast_Mitochondria.png" width=70% height=100%> </p>|
| Parameters: | Emission [nm]: 510 NA: 1.4, Mag: 100, Pizel size: 8000, Threshold: -0.5, Alpha: 4, Subpixels per pixel: 20|
----------------------------------
## 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-superres" is free and open source software
## Issues
If you encounter any problems, please [file an issue] along with a detailed description.
[napari]: https://github.com/napari/napari
[Cookiecutter]: https://github.com/audreyr/cookiecutter
[@napari]: https://github.com/napari
[MIT]: http://opensource.org/licenses/MIT
[BSD-3]: http://opensource.org/licenses/BSD-3-Clause
[GNU GPL v3.0]: http://www.gnu.org/licenses/gpl-3.0.txt
[GNU LGPL v3.0]: http://www.gnu.org/licenses/lgpl-3.0.txt
[Apache Software License 2.0]: http://www.apache.org/licenses/LICENSE-2.0
[Mozilla Public License 2.0]: https://www.mozilla.org/media/MPL/2.0/index.txt
[cookiecutter-napari-plugin]: https://github.com/napari/cookiecutter-napari-plugin
[file an issue]: https://github.com/RoccoDAnt/napari-superres/issues
[napari]: https://github.com/napari/napari
[tox]: https://tox.readthedocs.io/en/latest/
[pip]: https://pypi.org/project/pip/
[PyPI]: https://pypi.org/
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"author": "\"Rocco D'Antuono, Ad\u00e1n Guerrero, Ra\u00fal Pinto C\u00e1mara, Pa\u00fal Hern\u00e1ndez Herrera, Esley Torres Garcia, Haydee Hern\u00e1ndez, Juli\u00e1n Mej\u00eda\"",
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"description": "# napari-superres\r\n\r\n[](https://github.com/RoccoDAnt/napari-superres/blob/main/LICENSE)\r\n[](https://pypi.org/project/napari-superres)\r\n[](https://python.org)\r\n[](https://github.com/RoccoDAnt/napari-superres/actions)\r\n[](https://codecov.io/gh/RoccoDAnt/napari-superres)\r\n[](https://napari-hub.org/plugins/napari-superres)\r\n\r\n\r\nA collection of super-resolution microscopy FF-SRM methods.\r\n\r\nOpen-source implementation of methods for Fluorescence Fluctuation based Super Resolution Microscopy (FF-SRM):\r\n\r\nReview: [Alva et al., 2022. \u201cFluorescence Fluctuation-Based Super-Resolution Microscopy: Basic Concepts for an Easy Start.\u201d Journal of Microscopy, August.](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135)\r\n\r\nMSSR article: [Torres-Garc\u00eda, E., Pinto-C\u00e1mara, R., Linares, A. et al. Extending resolution within a single imaging frame. Nat Commun 13, 7452 (2022).](https://doi.org/10.1038/s41467-022-34693-9)\r\n\r\nESI article: [Idir Yahiatene, Simon Hennig, Marcel M\u00fcller, Thomas Huser (2015/2016). \"Entropy-based Super-resolution Imaging (ESI): From Disorder to Fine Detail\" ACS Photonics 8, 2 (2015)](https://doi.org/10.1021/acsphotonics.5b00307)\r\n\r\nSOFI article: [T. Dertinger, R. Colyer, G. Iyer, and J. Enderlein. Fast, background-free, 3D super-resolution optical fluctuation imaging (SOFI). PNAS 52, 106 (2009) ](https://doi.org/10.1073/pnas.0907866106)\r\n\r\nSRRF article: [Gustafsson, N., Culley, S., Ashdown, G., D. M. Owen, P. Matos Pereira, and R. Henriques. Fast live-cell conventional fluorophore nanoscopy with ImageJ through super-resolution radial fluctuations. Nat Commun 7, 12471 (2016)](https://www.nature.com/articles/ncomms12471)\r\n\r\nMUSICAL article: [K. Agarwal and R. Machan, Multiple Signal Classification Algorithm for super-resolution fluorescence microscopy, Nature Communications, vol. 7, article id. 13752, (2016)](https://www.nature.com/articles/ncomms13752)\r\n\r\n\r\n\r\nMethods implemented:\r\n- MSSR\r\n- ESI\r\n- SOFI\r\n- SRRF\r\n- MUSICAL\r\n- Split channels\r\n\r\n\r\n| **Super Resolution Radial Fluctuations (SRRF)** | **Mean-Shift Super Resolution (MSSR)** | **Entropy-based Super-resolution Imaging (ESI)** |\r\n| --- | --- | --- |\r\n|  |  |  |\r\nfrom Fig. 7 of [Alva et al., 2022](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135) | from Fig. 2 of [Garc\u00eda et al., 2021](https://www.biorxiv.org/content/10.1101/2021.10.17.464398v2.full)| from Fig. 6 of [Alva et al., 2022](https://onlinelibrary.wiley.com/doi/10.1111/jmi.13135)|\r\n\r\n\r\nRepositories available:\r\n- [ESI](https://github.com/biophotonics-bielefeld/ESI) GitHub repository\r\n- [PySOFI](https://github.com/xiyuyi-at-LLNL/pysofi) GitHub repository\r\n- [MUSICAL](https://sites.google.com/site/uthkrishth/musical) Google site\r\n\r\n----------------------------------\r\n\r\n\r\nThis [napari] plugin was generated with [Cookiecutter] using [@napari]'s [cookiecutter-napari-plugin] template.\r\n\r\n<!--\r\nDon't miss the full getting started guide to set up your new package:\r\nhttps://github.com/napari/cookiecutter-napari-plugin#getting-started\r\n\r\nand review the napari docs for plugin developers:\r\nhttps://napari.org/stable/plugins/index.html\r\n-->\r\n\r\n\r\n## Installation\r\nFirst install napari viewer (if you haven't):\r\n\r\n conda create -y -n napari-env -c conda-forge python=3.9\r\n conda activate napari-env\r\n pip install \"napari[all]\"\r\n\r\nFor details check: https://napari.org/stable/\r\n\r\n\r\n\r\n\r\nYou can install the plugin [graphically](https://github.com/LIBREhub/napari-LatAm-Workshop-2023/blob/napari-superres/docs/day3/napari-superres/napari-superres_installation_guide.pdf).\r\n\r\nor install latest development version :\r\n\r\n pip install git+https://github.com/RoccoDAnt/napari-superres.git\r\n\r\nYou might need to install [git](https://git-scm.com/book/en/v2/Getting-Started-Installing-Git) first.\r\n\r\n----------------------------------\r\nExamples of use:\r\n\r\n| **Original** | **tMSSR** |\r\n| --- | --- |\r\n| <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/single-frame-good-exposure.png\" width=100% height=100%> </p>| <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/tmssr-mean-mag2.png\" width=48% height=48%> </p>|\r\n| Parameters: | Amplification: 2, Order: 0, PSF FWHM: 6, <br> Interpolation: Bicubic, Statistical integration: CV*sigma |\r\n\r\n| **Original** | **ESI** |\r\n| --- | --- |\r\n| <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/synt.png\" width=40% height=40%> </p> | <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/ESI.png\" width=50% height=50%> </p> |\r\n| Parameters: | image in output: 2, bins: 2, Order: 2 |\r\n\r\n| **Original** | **SOFI** |\r\n| --- | --- |\r\n|<p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/noSOFI.png\" width=100% height=100%> </p> | <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/SOFI.png\" width=100% height=100%> </p> |\r\n| Parameters: | Amplification factor: 2, Moment Order: 4, lambda parameter: 1.5, No. Iterations: 20, Window size: 100|\r\n\r\n| **Original** | **SRRF** |\r\n| --- | --- |\r\n|<p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/synt.png\" width=50% height=50%> </p> | <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/SRRF.png\" width=50% height=50%> </p>|\r\n| Parameters: | Amplification: 2, Spatial radius: 5, Symmetry Axis: 6, Start frame: 0, End frame: 48|\r\n\r\n| **Original** | **MUSICAL** |\r\n| --- | --- |\r\n| <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/musical_mean.png\" width=70% height=100%> </p> | <p align=\"center\"> <img src=\"https://raw.githubusercontent.com/RoccoDAnt/napari-superres/main/docs/MUSICAL-CardioMyoblast_Mitochondria.png\" width=70% height=100%> </p>|\r\n| Parameters: | Emission [nm]: 510 NA: 1.4, Mag: 100, Pizel size: 8000, Threshold: -0.5, Alpha: 4, Subpixels per pixel: 20|\r\n----------------------------------\r\n\r\n\r\n\r\n## Contributing\r\n\r\nContributions are very welcome. 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