{"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/efficient-connectivity-preserving-instance","title":"Efficient Connectivity-Preserving Instance Segmentation with Supervoxel-Based Loss Function","arxiv_id":"2501.01022","date":"2025-01-02","proceeding":null,"authors":["Anna Grim","Jayaram Chandrashekar","Uygar Sumbul"],"abstract":"Reconstructing the intricate local morphology of neurons and their long-range projecting axons can address many connectivity related questions in neuroscience. The main bottleneck in connectomics pipelines is correcting topological errors, as multiple entangled neuronal arbors is a challenging instance segmentation problem. More broadly, segmentation of curvilinear, filamentous structures continues to pose significant challenges. To address this problem, we extend the notion of simple points from digital topology to connected sets of voxels (i.e. supervoxels) and propose a topology-aware neural network segmentation method with minimal computational overhead. We demonstrate its effectiveness on a new public dataset of 3-d light microscopy images of mouse brains, along with the benchmark datasets DRIVE, ISBI12, and CrackTree.","url_abs":"https://arxiv.org/abs/2501.01022v3","url_pdf":"https://arxiv.org/pdf/2501.01022v3.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":"efficient-connectivity-preserving-instance","repo_url":"https://github.com/allenneuraldynamics/supervoxel-loss","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":1,"framework":"pytorch","reach":null}],"tasks":[{"task_slug":"instance-segmentation","task_name":"Instance Segmentation"},{"task_slug":"segmentation","task_name":"Segmentation"},{"task_slug":"semantic-segmentation","task_name":"Semantic Segmentation"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":"https://app.syntology.ai/?focus=2501.01022","mcp":{"get_harvested_code_for_paper":{"arxiv_id":"2501.01022"}},"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/AllenNeuralDynamics/supervoxel-loss","reach":null}],"summary":{"unverified":1},"by_repo_kind":{"official":{"samples":1,"ran":0,"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":0,"samples":[{"code_sha256_prefix":"df57de53e87d2020","entry":"SuperVoxelLoss","repo":"AllenNeuralDynamics/supervoxel-loss","repo_kind":"official","path":"src/supervoxel_loss/loss.py","file_url":"https://github.com/AllenNeuralDynamics/supervoxel-loss/blob/HEAD/src/supervoxel_loss/loss.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":"df57de53e87d2020"}}]},"arxiv_metadata":null,"syntology_extracted_results":null}