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https://github.com/weisongzhao/panelm
Official MATLAB implementation of the "PANEL" -v0.4.5
https://github.com/weisongzhao/panelm
Last synced: 25 days ago
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Official MATLAB implementation of the "PANEL" -v0.4.5
- Host: GitHub
- URL: https://github.com/weisongzhao/panelm
- Owner: WeisongZhao
- License: odbl-1.0
- Created: 2020-11-27T11:49:07.000Z (almost 4 years ago)
- Default Branch: main
- Last Pushed: 2024-02-08T08:39:31.000Z (9 months ago)
- Last Synced: 2024-02-08T09:35:39.624Z (9 months ago)
- Language: MATLAB
- Homepage: https://weisongzhao.github.io/PANELM
- Size: 1.59 MB
- Stars: 3
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
[](https://weisongzhao.github.io/PANELM/)
[](https://github.com/WeisongZhao/PANELM/)
[](https://github.com/WeisongZhao/PANELM/releases/tag/v0.4.5/)
[](https://github.com/WeisongZhao/PANELM/blob/master/LICENSE/)
[](https://doi.org/10.1038/s41377-023-01321-0)
[](https://communities.springernature.com/posts/a-nice-piece-of-the-puzzle-for-super-resolution-microscopy)
[](https://twitter.com/hashtag/rFRCmetric?src=hashtag_click)
[](https://github.com/WeisongZhao/PANELM/)
[](https://github.com/WeisongZhao/PANELM/)
[](https://github.com/WeisongZhao/PANELM/)
PANELM
v0.4.5
rFRC mapping and PANEL pinpointing with Matlab.
rFRC (rolling Fourier ring correlation) mapping and PANEL (Pixel-level ANalysis of Error Locations) pinpointing with Matlab is distributed as accompanying software for publication: [Weisong Zhao et al. Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation, Light: Science & Applications (2023)](https://doi.org/10.1038/s41377-023-01321-0). More details on [Wiki](https://github.com/WeisongZhao/PANELM/wiki/). If it helps your research, please cite our work in your publications.
If you are not a MATLAB user, you can have a try on the ImageJ version: [PANELJ](https://github.com/WeisongZhao/PANELJ), or the Python version: [PANELpy](https://github.com/WeisongZhao/PANELpy).
## Usages of rFRC and PANEL in specific
The `rFRC` is for quantitatively mapping the local image quality (effective resolution, data uncertainty). The lower effective resolution gives a higher probability to the error existence, and thus we can use it to represent the uncertainty revealing the error distribution.
**rFRC is capable of:**
- **Data uncertainty mapping** of reconstructions without Ground-Truth (Reconstruction-1 vs Reconstruction-2) | 3σ curve is recommended;
- **Data uncertainty and leaked model uncertainty mapping** of deep-learning predictions of low-level vision tasks without Ground-Truth (Prediction-1 from input-1 vs Prediction-2 from input-2) | 3σ curve is recommended;
- **Model uncertainty mapping** of deep-learning predictions of low-level vision tasks without Ground-Truth (Prediction-1 from model-1 vs Prediction-2 from model-2) | 3σ curve is recommended;
- **Full error mapping** of reconstructions/predictions with Ground-Truth (Reconstruction/Prediction vs Ground-Truth) | 3σ curve is recommended;
- **Resolution mapping** of raw images (Image-1 vs Image-2) | 1/7 hard threshold or 3σ curve are both feasible;
**When two-frame is not accessible, two alternative strategies for single-frame mapping is also provided (not stable, the two-frame version is recommended).**
**PANEL**
- We also accompany our `filtered rFRC` with `truncated RSM` ([resolution-scaled error map](http://dx.doi.org/10.1038/nmeth.4605)) as a `full PANEL` map, but this `RSM` is an optional feature that can be turn off as the wide-field reference being unavailable. `PANEL` is for biologists to qualitatively pinpoint regions with low reliability as a concise visualization
- Note that our `rFRC` and `PANEL` using two independent captures cannot fully pinpoint the unreliable regions induced by the model bias, which would require more extensive characterization and correction routines based on the underlying theory of the corresponding models.
## PANELM for local quality mapping
## Version
- v0.4.5 Adaptive background threshold & parallel acceleration
- v0.3.0 Single-frame rFRC mapping
- v0.2.0 RSM and PANEL visualization
- v0.1.0 Initial rFRC mapping
## Related links:
- ImageJ version: [PANELJ](https://github.com/WeisongZhao/PANELJ/)
- Python version: [PANELM](https://github.com/WeisongZhao/PANELpy/)
- **Some fancy results and comparisons:** [my website](https://weisongzhao.github.io/home/portfolio-4-col.html#PANEL)
- **Further reading:** [#behind_the_paper](https://communities.springernature.com/posts/a-nice-piece-of-the-puzzle-for-super-resolution-microscopy).
- **Publication:**[Weisong Zhao et al. Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation, Light: Science & Applications (2023)](https://doi.org/10.1038/s41377-023-01321-0).
- **Preprint:** [Weisong Zhao et al., Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation, bioRxiv (2022)](https://doi.org/10.1101/2022.12.01.518675).
## Open source [PANELM](https://github.com/WeisongZhao/PANELM)
- This software and corresponding methods can only be used for **non-commercial** use, and they are under Open Data Commons Open Database License v1.0.
- Feedback, questions, bug reports and patches are welcome and encouraged!