{"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/deepliif-an-online-platform-for","title":"DeepLIIF: An Online Platform for Quantification of Clinical Pathology Slides","arxiv_id":"2204.04494","date":"2022-04-09","proceeding":"CVPR 2022 1","authors":["Parmida Ghahremani","Joseph Marino","Ricardo Dodds","Saad Nadeem"],"abstract":"In the clinic, resected tissue samples are stained with Hematoxylin-and-Eosin (H&E) and/or Immunhistochemistry (IHC) stains and presented to the pathologists on glass slides or as digital scans for diagnosis and assessment of disease progression. Cell-level quantification, e.g. in IHC protein expression scoring, can be extremely inefficient and subjective. We present DeepLIIF (https://deepliif.org), a first free online platform for efficient and reproducible IHC scoring. DeepLIIF outperforms current state-of-the-art approaches (relying on manual error-prone annotations) by virtually restaining clinical IHC slides with more informative multiplex immunofluorescence staining. Our DeepLIIF cloud-native platform supports (1) more than 150 proprietary/non-proprietary input formats via the Bio-Formats standard, (2) interactive adjustment, visualization, and downloading of the IHC quantification results and the accompanying restained images, (3) consumption of an exposed workflow API programmatically or through interactive plugins for open source whole slide image viewers such as QuPath/ImageJ, and (4) auto scaling to efficiently scale GPU resources based on user demand.","url_abs":"https://arxiv.org/abs/2204.04494v1","url_pdf":"https://arxiv.org/pdf/2204.04494v1.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":"deepliif-an-online-platform-for","repo_url":"https://github.com/nadeemlab/deepliif","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":null,"task_name":"GPU"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2204.04494","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2204.04494"}},"developers":"https://syntology.ai/developers","read_at":"2026-09-24T18:15:14+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":"deterministic:regex_extraction","url":"https://github.com/nadeemlab/DeepLIIF","reach":null}],"summary":{"ran":3,"ran_draft_wrong":3,"unverified":2},"by_repo_kind":{"official":{"samples":8,"ran":6,"repositories":1}},"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":8,"samples":[{"code_sha256_prefix":"f09f55325496f95c","entry":"disable_batchnorm_tracking_stats","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"f09f55325496f95c"}},{"code_sha256_prefix":"f4d6b0c4dd2bac4a","entry":"enable_batchnorm_tracking_stats","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"f4d6b0c4dd2bac4a"}},{"code_sha256_prefix":"57284dc76621f840","entry":"get_input_id","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"57284dc76621f840"}},{"code_sha256_prefix":"20c27055a2f3e1e4","entry":"get_mod_id_seg","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"20c27055a2f3e1e4"}},{"code_sha256_prefix":"d8965540a77e8f46","entry":"get_optimizer","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"d8965540a77e8f46"}},{"code_sha256_prefix":"f69061f7cd076d6e","entry":"init_input_and_mod_id","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"f69061f7cd076d6e"}},{"code_sha256_prefix":"0308fc8e2104b1f8","entry":"BaseModel","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"0308fc8e2104b1f8"}},{"code_sha256_prefix":"22280afe93ca7e37","entry":"DeepLIIFModel","repo":"nadeemlab/DeepLIIF","repo_kind":"official","path":"deepliif/models/DeepLIIF_model.py","file_url":"https://github.com/nadeemlab/DeepLIIF/blob/HEAD/deepliif/models/DeepLIIF_model.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"NOASSERTION","inline_ok":false,"mcp_get_code":{"code_sha256":"22280afe93ca7e37"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}