{"id":17162455,"url":"https://github.com/weisongzhao/sparse-deconv-py","last_synced_at":"2025-04-13T13:30:44.836Z","repository":{"id":45828430,"uuid":"428170602","full_name":"WeisongZhao/sparse-deconv-py","owner":"WeisongZhao","description":"Official Python implementation of the 'Sparse deconvolution'-v0.3.0","archived":false,"fork":false,"pushed_at":"2024-02-08T08:33:52.000Z","size":69,"stargazers_count":51,"open_issues_count":5,"forks_count":18,"subscribers_count":4,"default_branch":"main","last_synced_at":"2025-03-27T04:33:22.639Z","etag":null,"topics":["fluorescence-microscopy-imaging","image-processing","image-restoration","microscopy","python3","super-resolution"],"latest_commit_sha":null,"homepage":"","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"odbl-1.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/WeisongZhao.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null}},"created_at":"2021-11-15T07:53:56.000Z","updated_at":"2025-02-11T07:38:36.000Z","dependencies_parsed_at":"2024-02-04T11:49:52.768Z","dependency_job_id":null,"html_url":"https://github.com/WeisongZhao/sparse-deconv-py","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WeisongZhao%2Fsparse-deconv-py","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WeisongZhao%2Fsparse-deconv-py/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WeisongZhao%2Fsparse-deconv-py/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/WeisongZhao%2Fsparse-deconv-py/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/WeisongZhao","download_url":"https://codeload.github.com/WeisongZhao/sparse-deconv-py/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248720953,"owners_count":21151018,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["fluorescence-microscopy-imaging","image-processing","image-restoration","microscopy","python3","super-resolution"],"created_at":"2024-10-14T22:45:44.238Z","updated_at":"2025-04-13T13:30:44.814Z","avatar_url":"https://github.com/WeisongZhao.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![paper](https://img.shields.io/badge/paper-nat.%20biotech.-black.svg)](https://doi.org/10.1038/s41587-021-01092-2)\n[![Github commit](https://img.shields.io/github/last-commit/WeisongZhao/sparse-deconv-py)](https://github.com/WeisongZhao/sparse-deconv-py/)\n[![License](https://img.shields.io/github/license/WeisongZhao/sparse-deconv-py)](https://github.com/WeisongZhao/sparse-deconv-py/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-deconv-py?style=social)](https://github.com/WeisongZhao/sparse-deconv-py/) \n[![GitHub stars](https://img.shields.io/github/stars/WeisongZhao/sparse-deconv-py?style=social)](https://github.com/WeisongZhao/sparse-deconv-py/) \n[![GitHub forks](https://img.shields.io/github/forks/WeisongZhao/sparse-deconv-py?style=social)](https://github.com/WeisongZhao/sparse-deconv-py/)\n\n\n\u003cp\u003e\n\u003ch2 align=\"center\"\u003eSparse deconvolution\u003csub\u003e Python v0.3.0\u003c/sub\u003e\u003c/h2\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\nOfficial **Python** implementation of the '**Sparse deconvolution**', and the `CPU (NumPy)` and `GPU (CuPy)` calculation backend will be automatically selected. \n\nWe haven’t tested it thoroughly, and the development is work in progress, so expect rough edges. As a result, feedback, questions, bug reports, and patches are welcome and encouraged!\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 (2021)](https://doi.org/10.1038/s41587-021-01092-2)\".\n\n\n## Instruction\n\n- NOTE: The MATLAB version and detailed information can be found at https://github.com/WeisongZhao/Sparse-SIM.\n- NOTE: The GPU acceleration feature using CuPy requires a CUDA-based NVIDIA GPU. It could provide a ~30 times faster reconstruction speed for a `512 × 512 × 5` image stack.\n- Clone/download, and run the `demo.py`\n\n```python\nfrom sparse_recon.sparse_deconv import sparse_deconv\n\nim = io.imread('test.tif')\nplt.imshow(im,cmap = 'gray')\nplt.show()\n\npixelsize = 65 #(nm)\nresolution = 280 #(nm)\n\nimg_recon = sparse_deconv(im, resolution / pixelsize)\nplt.imshow(img_recon / img_recon.max() * 255,cmap = 'gray')\nplt.show()\n```\n\n## Tested dependency \n\n- Python 3.7\n- NumPy 1.21.4\n- CuPy 9.6.0 (CUDA 11.5)\n- PyWavelets 1.1.1\n\n## Version\n\n- v0.3.0 full Sparse deconvolution features\n- v0.2.0 iterative deconvolution\n- v0.1.0 initialized and started from [dzh929](https://github.com/dzh929/Sparse-SIM-python)\n\n## Related links: \n- MATLAB version of Sparse deconvolution: [MATLAB version](https://github.com/WeisongZhao/Sparse-SIM)\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 (2021).](https://doi.org/10.1038/s41587-021-01092-2)\n\n\n\n## Open source [Sparse deconvolution](https://github.com/WeisongZhao/Sparse-deconv-py)\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\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fweisongzhao%2Fsparse-deconv-py","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fweisongzhao%2Fsparse-deconv-py","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fweisongzhao%2Fsparse-deconv-py/lists"}