{"id":17162465,"url":"https://github.com/weisongzhao/sparse-sim","last_synced_at":"2025-04-13T13:26:20.451Z","repository":{"id":152834072,"uuid":"237917135","full_name":"WeisongZhao/Sparse-SIM","owner":"WeisongZhao","description":"Official MATLAB implementation of the \"Sparse deconvolution\" 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\u003cp align='left'\u003e\n    \u003ca href=\"https://weisongzhao.github.io/Sparse-SIM/\"\u003e\u003cimg src='https://img.shields.io/badge/Projects-1.0.3-brightgreen.svg'/\u003e \u003c/a\u003e\n    \u003ca href=\"https://github.com/WeisongZhao/Sparse-SIM/\"\u003e\u003cimg src='https://img.shields.io/badge/code-1.0.3-yellow.svg'/\u003e \u003c/a\u003e\n    \u003ca href=\"https://weisongzhao.github.io/Sparse-SIM/\"\u003e\u003cimg src='https://img.shields.io/badge/website-Up-green.svg' /\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/WeisongZhao/Sparse-SIM/releases/tag/v1.0.3/\"\u003e\u003cimg src='https://img.shields.io/badge/Release-v1.0.3-blue.svg'/\u003e\u003c/a\u003e\n    \u003ca href=\"https://github.com/WeisongZhao/Sparse-SIM/blob/master/LICENSE/\"\u003e\u003cimg src='https://img.shields.io/github/license/WeisongZhao/Sparse-SIM' /\u003e\u003c/a\u003e\n     \u003ca href=\"https://www.nature.com/nbt/\"\u003e\u003cimg src='https://img.shields.io/badge/paper-Nature%20Biotechnology-black.svg' /\u003e\u003c/a\u003e\n \u003c/p\u003e --\u003e\n\n[![code](https://img.shields.io/badge/code-1.0.3-yellow.svg)](https://github.com/WeisongZhao/Sparse-SIM/)\n[![website](https://img.shields.io/badge/website-up-green.svg)](https://weisongzhao.github.io/Sparse-SIM/)\n[![releases](https://img.shields.io/badge/release-v1.0.3-blue.svg)](https://github.com/WeisongZhao/Sparse-SIM/releases/tag/v1.0.3/)\n[![paper](https://img.shields.io/badge/post-behind%20the%20paper-black.svg)](https://bioengineeringcommunity.nature.com/posts/physical-resolution-might-be-meaningless-if-in-the-mathematical-space)\n[![paper](https://img.shields.io/badge/paper-nat.%20biotech.-black.svg)](https://doi.org/10.1038/s41587-021-01092-2)\u003cbr\u003e\n[![Github commit](https://img.shields.io/github/last-commit/WeisongZhao/Sparse-SIM)](https://github.com/WeisongZhao/Sparse-SIM/)\n[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5079743.svg)](https://doi.org/10.5281/zenodo.5079743)\n[![Github All Releases](https://img.shields.io/github/downloads/WeisongZhao/Sparse-SIM/total.svg)](https://github.com/WeisongZhao/Sparse-SIM/releases/tag/v1.0.3/) \n[![License](https://img.shields.io/github/license/WeisongZhao/Sparse-SIM)](https://github.com/WeisongZhao/Sparse-SIM/blob/master/LICENSE/)\u003cbr\u003e\n[![Twitter](https://img.shields.io/twitter/follow/weisong_zhao?label=weisong)](https://twitter.com/hashtag/sparsedeconvolution?src=hashtag_click)\n[![GitHub watchers](https://img.shields.io/github/watchers/WeisongZhao/Sparse-SIM?style=social)](https://github.com/WeisongZhao/Sparse-SIM/) \n[![GitHub stars](https://img.shields.io/github/stars/WeisongZhao/Sparse-SIM?style=social)](https://github.com/WeisongZhao/Sparse-SIM/) \n[![GitHub forks](https://img.shields.io/github/forks/WeisongZhao/Sparse-SIM?style=social)](https://github.com/WeisongZhao/Sparse-SIM/)\n\n\n\u003cp\u003e\n\u003ch1 align=\"center\"\u003eSparse deconvolution\u003csub\u003ev1.0.3\u003c/sub\u003e\u003c/h1\u003e\n\u003c!-- \u003ch6 align=\"center\"\u003e\u003csup\u003ev1.0.3\u003c/sup\u003e\u003c/h6\u003e --\u003e\n\u003c!-- \u003ch4 align=\"center\"\u003eThis repository contains the updating version of Sparse deconvolution.\u003c/h4\u003e --\u003e\n\u003c/p\u003e  \n\n\u003cp align='center'\u003e\n\u003ci\u003eWords written in the front: Physical resolution might be meaningless if in the mathmetical space.\u003c/i\u003e\n\u003c/p\u003e\n\n\nIt 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)\u003chr\u003e\n\n\nThe related Python version can be found at [HERE](https://github.com/WeisongZhao/sparse-deconv-py/)\n\nYou can also find some fancy results and comparisons on my [website](https://weisongzhao.github.io/home/portfolio-4-col.html#Sparse).\n\nIf 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.\n\nHere is also a [blog](https://weisongzhao.github.io/rl_positivity_sim/) about it for further reading.\n\nThis method has been tested on **various types of** `Confocal microscopy \u0026 STED microscopy`, `Wide-field \u0026 TIRF microscopy`, `Light-sheet microscopy`, `Multi-photon microscopy`, and `Structured illumination microscopy`, feasible for single-slice, time-lapse, and volumetric datasets. \n\n\n## Introduction\n\u003cb\u003eThis repository contains the updating version of Sparse deconvolution.\u003c/b\u003e 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. \n\n\u003cp align=\"center\"\u003e\n\u003cimg src='./sources/GUIv2.png' width=750\u003e\n\u003c/p\u003e\n\n\n## Instruction\n- The binary executable files (.exe/.app) can be found in the [release](https://github.com/WeisongZhao/Sparse-SIM/releases)\n- More details on [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/) and [Document](./UserManual.pdf).\n- /src_unix is the source code for Unix-like systems (including MacOS).\n- /src_win is the source code for Windows systems.\n- Clone/download, and run the `Install.m`\n- 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`.\n- Please try help `xxx` to get the API.\n```python\nhelp SparseHessian_core\nhelp background_estimation\nhelp Fourier_Oversample\n```\n\n\n\n### Installation of binary executable file (.exe) for Win10 system.\n\n\n[![](https://res.cloudinary.com/marcomontalbano/image/upload/v1671001722/video_to_markdown/images/youtube--99CoWvTtQwg-c05b58ac6eb4c4700831b2b3070cd403.jpg)](https://www.youtube.com/watch?v=99CoWvTtQwg \"\")\n\n\n### Or directly click the `.\\for Maltab users\\Sparse_SIM.exe` if you are using MATLAB 2017b.\n\n\u003cp align='center'\u003e\n    \u003cimg src='./sources/SSIM.gif' width='800'/\u003e\n\u003c/p\u003e\n\n## Algorithm UI\n\n\u003cp align=\"center\"\u003e\n\u003cimg src='./sources/GUI.png' width=800\u003e\n\u003c/p\u003e\n\n- Details in the [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/) and [Document](./UserManual.pdf).\n\n## Parameters: [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/) and [Document](./UserManual.pdf) \n\n## Tested platform\nThis software has been tested on: \n- MATLAB R2017b on (Win 10: 128 GB and NVIDIA Titan Xp: 12GB; CUDA 9.1); \n- MATLAB R2019b on (Win 10: 128 GB and NVIDIA Titan RTX: 24GB; CUDA 10.0);\n- MATLAB R2019b on (Win 10: 16GB and NVIDIA GTX1050Ti: 4GB, CUDA 10.2);\n- MATLAB R2015b on (CentOS 7: 64GB and Tesla K40 :12GB, CUDA 9.0);\n- MATLAB R2018b on (Ubuntu 18.04: 16GB and NVIDIA TITAN Xp: 12GB, CUDA 10.1);\n- MATLAB R2017b on (MacOS 10: 8GB without GPU acceleration).\n\nMore on [Wiki](https://github.com/WeisongZhao/Sparse-SIM/wiki/).\n\n## Version\n- v1.0.3 Fully open source!\n- v1.0.3 Another type deconvolution, and up-sampling methods, first officially released version!\n- v0.6.3 Reorder the background estimation\n- v0.6.2 Debug mode\n- v0.6.1 Progress bar feature and logo\n- v0.5.1 Up-sampling feature and change input file type from `.mat` to `.tif`\n- v0.4.1 Background estimation feature\n- v0.3.0 Algorithm UI\n- v0.2.0 Full model reconstruction\n- v0.1.0 Sparsity reconstruction core\n\n## Related links: \n- Python version of Sparse deconvolution: [sparse-deconv-py](https://github.com/WeisongZhao/sparse-deconv-py/)\n- A light weight MATLAB library for making exsiting images to videos: [img2vid](https://github.com/WeisongZhao/img2vid/)\n- An adaptive filter to remove isolate hot pixels: [Adaptive filter imagej-plugin](https://github.com/WeisongZhao/AdaptiveMedian.imagej/)\n- A tool for multi-color 2D or 3D imaging: [Merge channels](https://github.com/WeisongZhao/Palette.ui)\n- **Further reading:** [#behind_the_paper](https://bioengineeringcommunity.nature.com/posts/physical-resolution-might-be-meaningless-if-in-the-mathmetical-space) \u0026 [blog](https://weisongzhao.github.io/rl_positivity_sim/)\n- **Some fancy results and comparisons:** [my website](https://weisongzhao.github.io/home/portfolio-4-col.html#Sparse)\n- **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)\n- **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)\n\n\u003cdetails\u003e\n\u003csummary\u003e\u003cb\u003ePlans\u003c/b\u003e\u003c/summary\u003e\n\u003cli\u003e \u003cs\u003eDebug mode for parameter-adjustment;\u003c/s\u003e\u003c/li\u003e\n\u003cli\u003e \u003cs\u003eA Pyhton version of Sparse deconvolution;\u003c/s\u003e\u003c/li\u003e\n\u003cli\u003e A imagej-plugin of Sparse deconvolution;\u003c/li\u003e\n\u003cli\u003e A Headless mode;\u003c/li\u003e\n\u003cli\u003e Reduce the necessary/exposed parameters.\u003c/li\u003e\n\u003c/details\u003e\n\n\n## Open source [Sparse deconvolution](https://github.com/WeisongZhao/Sparse-SIM)\n\n- 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.\n- Feedback, questions, bug reports and patches are welcome and encouraged!\n\n\u003c!-- \u003cp align='center'\u003e\n  \u003cimg src='./sources/HIT.jpg' width='240'/\u003e\n  \u003cimg src='./sources/PKU.jpg' width='240'/\u003e\n\u003c/p\u003e --\u003e\n\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fweisongzhao%2Fsparse-sim","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fweisongzhao%2Fsparse-sim","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fweisongzhao%2Fsparse-sim/lists"}