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):
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 | from Fig. 2 of García et al., 2021 | from Fig. 6 of Alva et al., 2022 |
Repositories available:
This napari plugin was generated with Cookiecutter using @napari's cookiecutter-napari-plugin template.
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.
or install latest development version :
pip install git+https://github.com/RoccoDAnt/napari-superres.git
You might need to install git first.
Examples of use:
| Original | tMSSR |
|---|---|
|
|
| Parameters: | Amplification: 2, Order: 0, PSF FWHM: 6, Interpolation: Bicubic, Statistical integration: CV*sigma |
| Original | ESI |
|---|---|
|
|
| Parameters: | image in output: 2, bins: 2, Order: 2 |
| Original | SOFI |
|---|---|
|
|
| Parameters: | Amplification factor: 2, Moment Order: 4, lambda parameter: 1.5, No. Iterations: 20, Window size: 100 |
| Original | SRRF |
|---|---|
|
|
| Parameters: | Amplification: 2, Spatial radius: 5, Symmetry Axis: 6, Start frame: 0, End frame: 48 |
| Original | MUSICAL |
|---|---|
|
|
| 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.
1 maintainer
Metadata
1 maintainer
Release files for napari-superres 0.1.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | Provenance | Actions |
|---|---|---|---|---|
| napari-superres-0.1.1.tar.gz | 4.7 MB | Without provenance | Details for napari-superres-0.1.1.tar.gz |
Release files / napari-superres-0.1.1.tar.gz
| Download URL | napari-superres-0.1.1.tar.gz |
|---|---|
| Size | 4.7 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
d38f98572daac58331ac2dedd4a3e0cd0ad2c4743ac036fd9a9ab12c79f6d2ab
|
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BLAKE2b-256 checksum How to use checksums |
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| Upload date | |
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Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/4.0.2 CPython/3.9.16
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Security for napari-superres 0.1.1
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