{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/a-poisson-gaussian-denoising-dataset-with","title":"A Poisson-Gaussian Denoising Dataset with Real Fluorescence Microscopy Images","arxiv_id":"1812.10366","date":"2018-12-26","proceeding":"CVPR 2019 6","authors":["Yide Zhang","Yinhao Zhu","Evan Nichols","Qingfei Wang","Si-Yuan Zhang","Cody Smith","Scott Howard"],"abstract":"Fluorescence microscopy has enabled a dramatic development in modern biology.\nDue to its inherently weak signal, fluorescence microscopy is not only much\nnoisier than photography, but also presented with Poisson-Gaussian noise where\nPoisson noise, or shot noise, is the dominating noise source. To get clean\nfluorescence microscopy images, it is highly desirable to have effective\ndenoising algorithms and datasets that are specifically designed to denoise\nfluorescence microscopy images. While such algorithms exist, no such datasets\nare available. In this paper, we fill this gap by constructing a dataset - the\nFluorescence Microscopy Denoising (FMD) dataset - that is dedicated to\nPoisson-Gaussian denoising. The dataset consists of 12,000 real fluorescence\nmicroscopy images obtained with commercial confocal, two-photon, and wide-field\nmicroscopes and representative biological samples such as cells, zebrafish, and\nmouse brain tissues. We use image averaging to effectively obtain ground truth\nimages and 60,000 noisy images with different noise levels. We use this dataset\nto benchmark 10 representative denoising algorithms and find that deep learning\nmethods have the best performance. To our knowledge, this is the first real\nmicroscopy image dataset for Poisson-Gaussian denoising purposes and it could\nbe an important tool for high-quality, real-time denoising applications in\nbiomedical research.","url_abs":"http://arxiv.org/abs/1812.10366v2","url_pdf":"http://arxiv.org/pdf/1812.10366v2.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"a-poisson-gaussian-denoising-dataset-with","repo_url":"https://github.com/bmmi/denoising-fluorescence","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}},{"paper_slug":"a-poisson-gaussian-denoising-dataset-with","repo_url":"https://github.com/csm9493/FBI-Denoiser","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}},{"paper_slug":"a-poisson-gaussian-denoising-dataset-with","repo_url":"https://github.com/csm9493/GAN2GAN","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok"}},{"paper_slug":"a-poisson-gaussian-denoising-dataset-with","repo_url":"https://github.com/yinhaoz/denoising-fluorescence","is_official":0,"mentioned_in_paper":0,"mentioned_in_github":1,"framework":"pytorch","reach":{"status":"ok","spdx":"MIT"}}],"tasks":[{"task_slug":"denoising","task_name":"Denoising"}],"methods":[],"datasets_introduced":[{"slug":"fmd","name":"FMD","full_name":"Fluorescence Microscopy Denoising"}],"methods_introduced":[],"results":[],"syntology":{"syntology_url":"https://syntology.ai/paper/1812.10366","atlas_url":"https://app.syntology.ai/?focus=1812.10366","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"1812.10366"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-25T09:33:49+00:00","read_at_is":"when the build read Syntology's graph, not when any sample ran","claim":"Per-sample execution status on synthesized fixtures; not a correctness claim about the paper. Samples come from repositories linked to the paper, official or community; repo_kind says which.","repos":[{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/csm9493/FBI-Denoiser","reach":{"status":"ok","spdx":"MIT"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/csm9493/GAN2GAN","reach":{"status":"ok"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/bmmi/denoising-fluorescence","reach":{"status":"ok","spdx":"MIT"}},{"provenance":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/yinhaoz/denoising-fluorescence","reach":{"status":"ok","spdx":"MIT"}}],"summary":{"ran_honours":1,"ran":4,"unverified":17},"by_repo_kind":{"official":{"samples":11,"ran":1,"repositories":1},"listed":{"samples":11,"ran":4,"repositories":2}},"repo_kind_vocabulary":{"official":"The archive marks this repository official for the paper","named_in_paper":"The archive records that the paper mentions this repository; it is not marked official","listed":"In the archive's code links for this paper, not marked official and not recorded as mentioned in the paper","found_in_text":"Syntology found this repository in the paper's own text; whether it is the authors' implementation is not asserted","community":"Not in the archive's code links for this paper; a community repository Syntology harvested"},"n_pointer_only_for_licence":0,"samples":[{"code_sha256_prefix":"14ebf34e2f003912","entry":"adjust_learning_rate","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/practices.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/practices.py","link_basis":"harvester_set","language":"python","status":"ran_honours","verification_level":1,"contract_check":"HONOURS","metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"14ebf34e2f003912"}},{"code_sha256_prefix":"ba05401cbaac305f","entry":"annealing_cos","repo":"yinhaoz/denoising-fluorescence","repo_kind":"listed","path":"denoising/utils/practices.py","file_url":"https://github.com/yinhaoz/denoising-fluorescence/blob/HEAD/denoising/utils/practices.py","link_basis":"plan_row","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":true,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"ba05401cbaac305f"}},{"code_sha256_prefix":"9200656a2a28834f","entry":"conv1x1","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/unet.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/unet.py","link_basis":"harvester_set","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"9200656a2a28834f"}},{"code_sha256_prefix":"fe1bac001ffc64d5","entry":"conv3x3","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/unet.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/unet.py","link_basis":"harvester_set","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"fe1bac001ffc64d5"}},{"code_sha256_prefix":"87dc2e4625e5eb8c","entry":"upconv2x2","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/unet.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/unet.py","link_basis":"harvester_set","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"87dc2e4625e5eb8c"}},{"code_sha256_prefix":"0c73479d03c2508a","entry":"BlindSpotConv","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/dbsn.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/dbsn.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"0c73479d03c2508a"}},{"code_sha256_prefix":"6f5ae543b2665234","entry":"add_noise","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/noise.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/noise.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"6f5ae543b2665234"}},{"code_sha256_prefix":"6ea5c4823811a3e0","entry":"annealing_linear","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/practices.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/practices.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"6ea5c4823811a3e0"}},{"code_sha256_prefix":"08df5d271f487b61","entry":"cal_psnr","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/metrics.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/metrics.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"08df5d271f487b61"}},{"code_sha256_prefix":"8d908c5ef8d3e11d","entry":"conv3x3","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/models/unet.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/models/unet.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"8d908c5ef8d3e11d"}},{"code_sha256_prefix":"a5d2dc2ed601363c","entry":"estimated_bias","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/loss_functions.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/loss_functions.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"a5d2dc2ed601363c"}},{"code_sha256_prefix":"2190c9625267f12c","entry":"fluore_to_tensor","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/data_loader.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/data_loader.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"2190c9625267f12c"}},{"code_sha256_prefix":"f44d660b6ccbeea9","entry":"get_PSNR","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/utils.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/utils.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"f44d660b6ccbeea9"}},{"code_sha256_prefix":"d5f765357da5f38b","entry":"get_SSIM","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/utils.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/utils.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"d5f765357da5f38b"}},{"code_sha256_prefix":"f42a21ac3a36dd53","entry":"im2patch","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/utils.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/utils.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"f42a21ac3a36dd53"}},{"code_sha256_prefix":"3002f15097305815","entry":"is_image_file","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/data_loader.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/data_loader.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"3002f15097305815"}},{"code_sha256_prefix":"8d8b366633b88388","entry":"module_size","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/misc.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/misc.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"8d8b366633b88388"}},{"code_sha256_prefix":"2af64ac313fcf88e","entry":"mse_affine","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/loss_functions.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/loss_functions.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"2af64ac313fcf88e"}},{"code_sha256_prefix":"ba6e70b8f2432f12","entry":"mse_bias","repo":"csm9493/FBI-Denoiser","repo_kind":"listed","path":"core/loss_functions.py","file_url":"https://github.com/csm9493/FBI-Denoiser/blob/HEAD/core/loss_functions.py","link_basis":"harvester_set","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"ba6e70b8f2432f12"}},{"code_sha256_prefix":"b38192a90bf3af95","entry":"pil_loader","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/data_loader.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/data_loader.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"b38192a90bf3af95"}},{"code_sha256_prefix":"d7ed95b364fdca49","entry":"stitch_pathes","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/misc.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/misc.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"d7ed95b364fdca49"}},{"code_sha256_prefix":"c6c52ec834adb730","entry":"to_numpy","repo":"bmmi/denoising-fluorescence","repo_kind":"official","path":"denoising/utils/misc.py","file_url":"https://github.com/bmmi/denoising-fluorescence/blob/HEAD/denoising/utils/misc.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"MIT","inline_ok":true,"mcp_get_code":{"code_sha256":"c6c52ec834adb730"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}