{"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/multi-stream-cell-segmentation-with-low-level","title":"Multi-stream Cell Segmentation with Low-level Cues for Multi-modality Images","arxiv_id":"2310.14226","date":"2023-10-22","proceeding":null,"authors":["Wei Lou","Xinyi Yu","Chenyu Liu","Xiang Wan","Guanbin Li","SiQi Liu","Haofeng Li"],"abstract":"Cell segmentation for multi-modal microscopy images remains a challenge due to the complex textures, patterns, and cell shapes in these images. To tackle the problem, we first develop an automatic cell classification pipeline to label the microscopy images based on their low-level image characteristics, and then train a classification model based on the category labels. Afterward, we train a separate segmentation model for each category using the images in the corresponding category. Besides, we further deploy two types of segmentation models to segment cells with roundish and irregular shapes respectively. Moreover, an efficient and powerful backbone model is utilized to enhance the efficiency of our segmentation model. Evaluated on the Tuning Set of NeurIPS 2022 Cell Segmentation Challenge, our method achieves an F1-score of 0.8795 and the running time for all cases is within the time tolerance.","url_abs":"https://arxiv.org/abs/2310.14226v1","url_pdf":"https://arxiv.org/pdf/2310.14226v1.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":"multi-stream-cell-segmentation-with-low-level","repo_url":"https://github.com/lhaof/cellseg","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"pytorch","reach":{"status":"ok","spdx":"AGPL-3.0"}}],"tasks":[{"task_slug":"cell-segmentation","task_name":"Cell Segmentation"},{"task_slug":"segmentation","task_name":"Segmentation"}],"methods":[{"method_slug":"set","method_name":"SET"}],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2310.14226","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2310.14226"}},"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":"external:paperswithcode_snapshot_2025-07-28","url":"https://github.com/lhaof/cellseg","reach":{"status":"ok","spdx":"AGPL-3.0"}}],"summary":{"ran":8,"ran_draft_wrong":2,"unverified":1},"by_repo_kind":{"official":{"samples":11,"ran":10,"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":11,"samples":[{"code_sha256_prefix":"81569f8092472c82","entry":"colorize","repo":"lhaof/cellseg","repo_kind":"official","path":"overlay.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/overlay.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"81569f8092472c82"}},{"code_sha256_prefix":"2a80220dabcb742a","entry":"conv1x1","repo":"lhaof/cellseg","repo_kind":"official","path":"classifiers.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/classifiers.py","link_basis":"harvester_set","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"2a80220dabcb742a"}},{"code_sha256_prefix":"600ff2c45e0de056","entry":"conv3x3","repo":"lhaof/cellseg","repo_kind":"official","path":"classifiers.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/classifiers.py","link_basis":"harvester_set","language":"python","status":"ran_draft_wrong","verification_level":1,"contract_check":"OUTPUT_MISDECLARED","metamorphic_tier":"deterministic","behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"600ff2c45e0de056"}},{"code_sha256_prefix":"6d3fc649bf9a6858","entry":"eval_tp_fp_fn","repo":"lhaof/cellseg","repo_kind":"official","path":"compute_metric.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/compute_metric.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"6d3fc649bf9a6858"}},{"code_sha256_prefix":"db85af612797999c","entry":"get_bounding_box","repo":"lhaof/cellseg","repo_kind":"official","path":"overlay.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/overlay.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"db85af612797999c"}},{"code_sha256_prefix":"8fdbd598e86c4817","entry":"normalize_channel","repo":"lhaof/cellseg","repo_kind":"official","path":"predict_unet_convnext.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/predict_unet_convnext.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"8fdbd598e86c4817"}},{"code_sha256_prefix":"99ecbde28fbc0636","entry":"proc_valid_step_output","repo":"lhaof/cellseg","repo_kind":"official","path":"train_convnext_hover..py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/train_convnext_hover..py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"99ecbde28fbc0636"}},{"code_sha256_prefix":"556f4d307b311077","entry":"random_colors","repo":"lhaof/cellseg","repo_kind":"official","path":"overlay.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/overlay.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"556f4d307b311077"}},{"code_sha256_prefix":"1c4662bed43809ce","entry":"remove_boundary_cells","repo":"lhaof/cellseg","repo_kind":"official","path":"compute_metric.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/compute_metric.py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"1c4662bed43809ce"}},{"code_sha256_prefix":"b3e303353660e527","entry":"valid_step","repo":"lhaof/cellseg","repo_kind":"official","path":"train_convnext_hover..py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/train_convnext_hover..py","link_basis":"first_harvest_node","language":"python","status":"ran","verification_level":1,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"b3e303353660e527"}},{"code_sha256_prefix":"a521c4a92cbd4275","entry":"resnet18","repo":"lhaof/cellseg","repo_kind":"official","path":"classifiers.py","file_url":"https://github.com/lhaof/cellseg/blob/HEAD/classifiers.py","link_basis":"first_harvest_node","language":"python","status":"unverified","verification_level":0,"contract_check":null,"metamorphic_tier":null,"behaviour_fingerprint":false,"licence":"AGPL-3.0","inline_ok":false,"mcp_get_code":{"code_sha256":"a521c4a92cbd4275"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}