A Vessel Bifurcation Landmark Pair Dataset for Abdominal CT Deformable Image Registration (DIR) Validation.

{"sci_version": "1.0", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39876932", "kind": "science-record", "revision": 2, "content_hash": "sha256:ca78ae6129c1eee7272c0bfbf90b7cfb6e4351dba0d88c16816925eb3b9454d4", "created_at": "2026-11-01T20:30:09Z", "updated_at": "2026-11-01T21:34:44Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "partial", "title": "A Vessel Bifurcation Landmark Pair Dataset for Abdominal CT Deformable Image Registration (DIR) Validation.", "doi": null, "pmid": "39876932", "authors": ["Edward R Criscuolo", "Yao Hao", "Zhendong Zhang", "Trevor McKeown", "Deshan Yang"], "journal": "ArXiv", "year": 2025, "abstract": "Purpose: Deformable image registration (DIR) is an enabling technology in many diagnostic and therapeutic tasks. Despite this, DIR algorithms have limited clinical use, largely due to a lack of benchmark datasets for quality assurance during development. DIRs of intra-patient abdominal CTs are among the most challenging registration scenarios due to significant organ deformations and inconsistent image content. To support future algorithm development, here we introduce our first-of-its-kind abdominal CT DIR benchmark dataset, comprising large numbers of highly accurate landmark pairs on matching blood vessel bifurcations.\nAcquisition and Validation Methods: Abdominal CT image pairs of 30 patients were acquired from several publicly available repositories as well as the authors' institution with IRB approval. The two CTs of each pair were originally acquired for the same patient but on different days. An image processing workflow was developed and applied to each CT image pair: 1) Abdominal organs were segmented with a deep learning model, and image intensity within organ masks was overwritten. 2) Matching image patches were manually identified between two CTs of each image pair. 3) Vessel bifurcation landmarks were labeled on one image of each image patch pair. 4) Image patches were deformably registered, and landmarks were projected onto the second image 5) Landmark pair locations were refined manually or with an automated process. This workflow resulted in 1895 total landmark pairs, or 63 per case on average. Estimates of the landmark pair accuracy using digital phantoms were 0.7mm +/- 1.2 mm.\nData Format and Usage Notes: The data is published in Zenodo at https://doi.org/10.5281/zenodo.14362785. Instructions for use can be found at https://github.com/deshanyang/Abdominal-DIR-QA.\nPotential Applications: This dataset is a first-of-its-kind for abdominal DIR validation. The number, accuracy, and distribution of landmark pairs will allow for robust validation of DIR algorithms with precision beyond what is currently available.", "claims": [{"id": "claim-method", "statement": "Running a paired t-test on this data, we get a strongly significant p value of 1.7e-6.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39876932", "locator": "sections[11] \"Landmark Positions Refined Using Sphere Growing\" paragraph 6", "quote": "Running a paired t-test on this data, we get a strongly significant p value of 1.7e-6."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data is published in Zenodo at https://doi.org/10.5281/zenodo.14362785.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39876932", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "The data is published in Zenodo at https://doi.org/10.5281/zenodo.14362785."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The workflow resulted in 1895 total landmark pairs, or 63 per case on average, with estimated landmark pair accuracy of 0.7mm +/− 1.2 mm.", "kind": "quantitative", "target": {"value": 63.0, "unit": "odds ratio", "tolerance": null, "source": "This workflow resulted in 1895 total landmark pairs, or 63 per case on average."}, "evidence": [{"asset": "source:pmid:39876932", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "This workflow resulted in 1895 total landmark pairs, or 63 per case on average."}, {"asset": "source:pmid:39876932", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Estimates of the landmark pair accuracy using digital phantoms were 0.7mm +/− 1.2 mm."}], "state": "complete"}], "gaps": ["doi"]}, "experiment": {"state": "partial", "objective": "The workflow resulted in 1895 total landmark pairs, or 63 per case on average, with estimated landmark pair accuracy of 0.7mm +/− 1.2 mm.", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:39876932"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "blocked", "blocked_on": "data:accession_absent", "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39876932", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": null, "sha256": "sha256:1d0b0764adca3b0e1ebd2556561b80ecc69303af89709d4816661e633816feb1", "bytes": 45222, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "39876932", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11774459", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": null, "specific": null, "label": "paired t-test", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Running a paired t-test on this data, we get a strongly significant p value of 1.7e-6."}}], "targets": [{"id": "target-published-estimate", "claim_id": "claim-target-result", "operation": null, "expected_value": 63.0, "unit": "odds ratio", "tolerance": null, "state": "complete", "note": "The published estimate as the reader quoted it from the paper. No tolerance is published because the paper states none."}], "gaps": ["method.reader_named_unmapped"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R4", "expressible": false, "required_operations": [], "missing_operations": [], "basis": "The reader quoted the method the paper names (paired t-test), but the corpus's method extractor could not map it onto a DSL operation, so the method is published but not expressible."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": ["The data is published in Zenodo at https://doi.org/10.5281/zenodo.14362785."], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:39876932"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:45:20Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 12126, "completion_tokens": 995, "cached_tokens": 256}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:39876932", "type": "paper", "label": "pmid:39876932"}, {"id": "source:pmid:39876932", "type": "manuscript", "label": "PMID 39876932 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:39876932", "type": "paper", "label": "pmid:39876932"}, {"id": "source:pmid:39876932", "type": "manuscript", "label": "PMID 39876932 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-39876932", "type": "extraction", "used": ["source:pmid:39876932"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:39876932", "parent_hash": "sha256:597b829b760ad8f2a7ef2cd20c1225e72dce1d284f1658f2c93c7f12719b1737", "fork_of": null, "generation": 1}, "gaps": ["doi", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"]}