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https://github.com/weisongzhao/sparse-sim
Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3
https://github.com/weisongzhao/sparse-sim
deconvolution fluorescence-microscopy-imaging image-processing image-restoration matlab-gui microscopy super-resolution
Last synced: about 22 hours ago
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Official MATLAB implementation of the "Sparse deconvolution" -v1.0.3
- Host: GitHub
- URL: https://github.com/weisongzhao/sparse-sim
- Owner: WeisongZhao
- License: odbl-1.0
- Created: 2020-02-03T08:22:44.000Z (almost 5 years ago)
- Default Branch: master
- Last Pushed: 2024-02-08T08:21:20.000Z (9 months ago)
- Last Synced: 2024-02-08T09:27:10.904Z (9 months ago)
- Topics: deconvolution, fluorescence-microscopy-imaging, image-processing, image-restoration, matlab-gui, microscopy, super-resolution
- Language: MATLAB
- Homepage: https://weisongzhao.github.io/Sparse-SIM/
- Size: 15.1 MB
- Stars: 61
- Watchers: 4
- Forks: 14
- Open Issues: 3
-
Metadata Files:
- Readme: README.md
- License: LICENSE.txt
Awesome Lists containing this project
README
[](https://github.com/WeisongZhao/Sparse-SIM/)
[](https://weisongzhao.github.io/Sparse-SIM/)
[](https://github.com/WeisongZhao/Sparse-SIM/releases/tag/v1.0.3/)
[](https://bioengineeringcommunity.nature.com/posts/physical-resolution-might-be-meaningless-if-in-the-mathematical-space)
[](https://doi.org/10.1038/s41587-021-01092-2)
[](https://github.com/WeisongZhao/Sparse-SIM/)
[](https://doi.org/10.5281/zenodo.5079743)
[](https://github.com/WeisongZhao/Sparse-SIM/releases/tag/v1.0.3/)
[](https://github.com/WeisongZhao/Sparse-SIM/blob/master/LICENSE/)
[](https://twitter.com/hashtag/sparsedeconvolution?src=hashtag_click)
[](https://github.com/WeisongZhao/Sparse-SIM/)
[](https://github.com/WeisongZhao/Sparse-SIM/)
[](https://github.com/WeisongZhao/Sparse-SIM/)
Sparse deconvolutionv1.0.3
Words written in the front: Physical resolution might be meaningless if in the mathmetical space.
It is a part of publication. For details, please refer to: [Weisong Zhao et al. Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy, Nature Biotechnology 40, 606–617 (2022).](https://doi.org/10.1038/s41587-021-01092-2)
The related Python version can be found at [HERE](https://github.com/WeisongZhao/sparse-deconv-py/)
You can also find some fancy results and comparisons on my [website](https://weisongzhao.github.io/home/portfolio-4-col.html#Sparse).
If you are interested in our work, I wrote a [#behind_the_paper](https://bioengineeringcommunity.nature.com/posts/physical-resolution-might-be-meaningless-if-in-the-mathmetical-space) post for further reading.
Here is also a [blog](https://weisongzhao.github.io/rl_positivity_sim/) about it for further reading.
This method has been tested on **various types of** `Confocal microscopy & STED microscopy`, `Wide-field & TIRF microscopy`, `Light-sheet microscopy`, `Multi-photon microscopy`, and `Structured illumination microscopy`, feasible for single-slice, time-lapse, and volumetric datasets.
## Introduction
This repository contains the updating version of Sparse deconvolution. The Sparse deconvolution is an universal post-processing framework for fluorescence (or intensity-based) image restoration, including xy (2D), xy-t (2D along t axis), and xy-z (3D) images. It is based on the natural priori knowledge of forward fluorescence imaging model: sparsity and continuity along xy-t (z) axes.
## Instruction
- The binary executable files (.exe/.app) can be found in the [release](https://github.com/WeisongZhao/Sparse-SIM/releases)
- More details on [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/) and [Document](./UserManual.pdf).
- /src_unix is the source code for Unix-like systems (including MacOS).
- /src_win is the source code for Windows systems.
- Clone/download, and run the `Install.m`
- The input `Effective NA` should be given according to the sum of `illumination NA` and `detection NA`. For instances: wide-field is the `objective NA` (e.g., 1.49); SIM is the `illumination NA + objective NA` (e.g., 1.3 + 1.7); SD-SIM is `~1.8 * objective NA`.
- Please try help `xxx` to get the API.
```python
help SparseHessian_core
help background_estimation
help Fourier_Oversample
```
### Installation of binary executable file (.exe) for Win10 system.
[](https://www.youtube.com/watch?v=99CoWvTtQwg "")
### Or directly click the `.\for Maltab users\Sparse_SIM.exe` if you are using MATLAB 2017b.
## Algorithm UI
- Details in the [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/) and [Document](./UserManual.pdf).
## Parameters: [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/) and [Document](./UserManual.pdf)
## Tested platform
This software has been tested on:
- MATLAB R2017b on (Win 10: 128 GB and NVIDIA Titan Xp: 12GB; CUDA 9.1);
- MATLAB R2019b on (Win 10: 128 GB and NVIDIA Titan RTX: 24GB; CUDA 10.0);
- MATLAB R2019b on (Win 10: 16GB and NVIDIA GTX1050Ti: 4GB, CUDA 10.2);
- MATLAB R2015b on (CentOS 7: 64GB and Tesla K40 :12GB, CUDA 9.0);
- MATLAB R2018b on (Ubuntu 18.04: 16GB and NVIDIA TITAN Xp: 12GB, CUDA 10.1);
- MATLAB R2017b on (MacOS 10: 8GB without GPU acceleration).
More on [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/).
## Version
- v1.0.3 Fully open source!
- v1.0.3 Another type deconvolution, and up-sampling methods, first officially released version!
- v0.6.3 Reorder the background estimation
- v0.6.2 Debug mode
- v0.6.1 Progress bar feature and logo
- v0.5.1 Up-sampling feature and change input file type from `.mat` to `.tif`
- v0.4.1 Background estimation feature
- v0.3.0 Algorithm UI
- v0.2.0 Full model reconstruction
- v0.1.0 Sparsity reconstruction core
## Related links:
- Python version of Sparse deconvolution: [sparse-deconv-py](https://github.com/WeisongZhao/sparse-deconv-py/)
- A light weight MATLAB library for making exsiting images to videos: [img2vid](https://github.com/WeisongZhao/img2vid/)
- An adaptive filter to remove isolate hot pixels: [Adaptive filter imagej-plugin](https://github.com/WeisongZhao/AdaptiveMedian.imagej/)
- A tool for multi-color 2D or 3D imaging: [Merge channels](https://github.com/WeisongZhao/Palette.ui)
- **Further reading:** [#behind_the_paper](https://bioengineeringcommunity.nature.com/posts/physical-resolution-might-be-meaningless-if-in-the-mathmetical-space) & [blog](https://weisongzhao.github.io/rl_positivity_sim/)
- **Some fancy results and comparisons:** [my website](https://weisongzhao.github.io/home/portfolio-4-col.html#Sparse)
- **Preprint:** [Weisong Zhao et al., Extending resolution of structured illumination microscopy with sparse deconvolution, Research Square (2021).](https://doi.org/10.21203/rs.3.rs-279271/v1)
- **Reference:** [Weisong Zhao et al. Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy, Nature Biotechnology 40, 606–617 (2022).](https://doi.org/10.1038/s41587-021-01092-2)
Plans
## Open source [Sparse deconvolution](https://github.com/WeisongZhao/Sparse-SIM)
- 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!