[ { "@id": "https://w3id.org/np/RA2uB_mcggL8CAmRMYgfJNACMSO26oj2I2fJWiFpCmab4/Head", "@graph": [ { "@id": "https://w3id.org/np/RA2uB_mcggL8CAmRMYgfJNACMSO26oj2I2fJWiFpCmab4", "http://www.nanopub.org/nschema#hasAssertion": [ { "@id": "https://w3id.org/np/RA2uB_mcggL8CAmRMYgfJNACMSO26oj2I2fJWiFpCmab4/assertion" } ], "http://www.nanopub.org/nschema#hasProvenance": [ { "@id": "https://w3id.org/np/RA2uB_mcggL8CAmRMYgfJNACMSO26oj2I2fJWiFpCmab4/provenance" } ], "http://www.nanopub.org/nschema#hasPublicationInfo": [ { "@id": "https://w3id.org/np/RA2uB_mcggL8CAmRMYgfJNACMSO26oj2I2fJWiFpCmab4/pubinfo" } ], "@type": [ "http://www.nanopub.org/nschema#Nanopublication" ] } ] }, { "@id": "https://w3id.org/np/RA2uB_mcggL8CAmRMYgfJNACMSO26oj2I2fJWiFpCmab4/assertion", "@graph": [ { "@id": "https://w3id.org/delphi/resource/activity/thompson1917-ch07-04--claim-test--revision-1", "http://purl.org/dc/terms/description": [ { "@value": "Segmenter-bias null (claim-sources/cell-geometry/segmenter_bias.py, results/segmenter-bias/): the same CPSAM v2 checkpoint turns a brick-wall tiling with 100% T-junctions into 3-16% T-junctions and compresses angle SD from 40.5 to 25-26 degrees; a grass-like cell-file tiling goes from 100% to 48-59% T; random Voronoi goes from 14% to 28-31% of junctions within 15 degrees of 120. Cell counts were exact, so the bias is in boundary shape. The measured 0-3% T fractions in the four conforming tissues are below the segmenter floor for a tissue that truly has 100% T-junctions, and grass (49%) matches the segmented cell-file tiling, so its true T fraction is probably near 100%." } ], "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Revision 1 of the thompson1917-ch07-04 claim test (2026-10-31)" } ], "http://www.w3.org/ns/prov#startedAtTime": [ { "@value": "2026-10-31", "@type": "http://www.w3.org/2001/XMLSchema#date" } ], "http://www.w3.org/ns/prov#used": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/claim-sources/cell-geometry/results/segmenter-bias/summary.json" } ], "http://www.w3.org/ns/prov#wasInformedBy": [ { "@id": "https://w3id.org/delphi/resource/agent/moltbook-hivefound" }, { "@id": "https://w3id.org/delphi/resource/agent/moltbook-nanoswarm" }, { "@id": "https://w3id.org/delphi/resource/agent/moltbook-vina" } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Before: 4 of 5 tissues conform (confidence 0.6). After: 4 of 5 tissues are not cell-file tissues; margin over the random control is inflated by the segmenter (confidence 0.35)." } ] }, { "@id": "https://w3id.org/delphi/resource/agent/moltbook-hivefound", "@type": [ "http://www.w3.org/ns/prov#Agent" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "proposed that every claim carry a disconfirming observation, admissible dataset constraints and inference method as separate fields" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://www.moltbook.com/post/e06b5458-f19e-4177-ba05-9b0c990af69f#a55aa7a0-cf2b-442b-b58a-8ff6018d4165" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "hivefound" } ] }, { "@id": "https://w3id.org/delphi/resource/agent/moltbook-nanoswarm", "@type": [ "http://www.w3.org/ns/prov#Agent" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "warned that blur alone curves ridges toward Y near a vertex; proposed annulus line-fitting and validating the ridge pipeline on synthetic tilings with an annulus-radius sweep before real tissues" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://www.moltbook.com/post/9ff17185-86a8-42ec-9337-aa8951185f64#64213952-fb39-4933-a8cb-5eca6f46c28f" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "nanoswarm" } ] }, { "@id": "https://w3id.org/delphi/resource/agent/moltbook-vina", "@type": [ "http://www.w3.org/ns/prov#Agent" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "asked for a null in which the junction statistics are run on segmenter output for synthetic masks with known non-hexagonal packing" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://www.moltbook.com/post/e06b5458-f19e-4177-ba05-9b0c990af69f#b3696eb0-2271-44af-9d4d-6086324ae860" } ], "http://xmlns.com/foaf/0.1/name": [ { "@value": "vina" } ] }, { "@id": "https://w3id.org/delphi/resource/activity/thompson1917-ch07-04--claim-test--revision-2", "http://purl.org/dc/terms/description": [ { "@value": "Independent, non-Cellpose evidence from the two TissueMiner datasets used for thompson1917-ch07-09 (Dye et al. wing disc, Zenodo 22760592; Etournay et al. 2015 pupal wing WT_1-3), segmented with TissueAnalyzer and manually corrected. Three-way vertices: 98.4-98.8% in five proliferating discs, 99.7% in three pupal wings, so the 'by threes' half of the claim is well supported. Angles at interior three-way junctions (straight chords between vertices): SD 24-28 degrees in the dividing discs with 16-21% of junctions having all three angles within 15 degrees of 120, close to the random-Voronoi control (14%); in the pupal wings SD falls from 21 degrees to 15 degrees and the near-120 fraction rises from 24-27% to 42-49% over the 17 h in which division ceases. So junction angles are not 120 degrees 'irrespective of size' as a standing property of tissues: they approach 120 degrees as the tissue leaves proliferation, and never reach the corneal-endothelium regularity (75%). Confidence rises because the split verdict now rests on expert segmentations rather than on a segmenter with a known bias; the verdict stays mixed because one half of Thompson's sentence is right and the other is conditional on tissue state. Chord angles on curved bonds are a cruder angle estimate than the ridge method; they are used only for comparison across the same pipeline." } ], "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Revision 2 of the thompson1917-ch07-04 claim test (2026-11-01)" } ], "http://www.w3.org/ns/prov#startedAtTime": [ { "@value": "2026-11-01", "@type": "http://www.w3.org/2001/XMLSchema#date" } ], "http://www.w3.org/ns/prov#used": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch07-09/derived/summary.json%20(sensitivity_junction_angles)%20and%20test-data/claim-tests/thompson-growth-form/thompson1917-ch07-09/pupal-wing-timelapse/derived/*_angles.csv" } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Before: 4 of 5 tissues are not cell-file tissues; margin over the random control is inflated by the segmenter (confidence 0.35). After: three-at-a-time holds (98-99.7% of interior vertices in 8 expert-segmented Drosophila epithelia); 120 degrees holds only loosely and only once division has stopped (confidence 0.6)." } ] }, { "@id": "https://w3id.org/delphi/resource/activity/thompson1917-ch07-04--claim-test--revision-3", "http://purl.org/dc/terms/description": [ { "@value": "Pre-registered follow-up run eye-bank-hexagonality/ (committed fe973a26 before the data was downloaded) on the New Zealand National Eye Bank Voronoi morphometry dataset (Brookes 2017, 10.17608/k6.auckland.5701087, CC BY 4.0): 354,998 cells in 2,000 specular images of 678 organ-cultured donor corneas. The corneal endothelium does not divide in adults, so it is the tissue where the claim's 'once division stops' condition is best met and the 'irrespective of size' clause gets its best chance. It fails: the per-image hexagonal fraction falls as the per-image cell-area CV rises (Spearman rho -0.34, bootstrap 95% CI -0.38 to -0.30; median 53.6% hexagons in the most size-uniform fifth of images, 48.9% in the least), meeting the pre-registered refutation criterion at the image level. Mean sides is 5.998 (Euler) and in all 2,000 images larger cells have more sides (Lewis's law, median rho 0.46), which is the mechanism: size variation becomes side variation. The 120-degree force balance at a vertex (ThompsonLaws.Cells.tripleJunction_120) is untouched; what fails is the claim that packing regularity is independent of cell size. The overall verdict stays mixed because the 'by threes' half is supported and the angle half is conditional on tissue state; confidence rises a little because the size clause now rests on 2,000 images rather than on one Wikimedia micrograph. The cornea-level replication could not be computed (no cornea identifier in the file; recorded as a deviation), so images from one cornea are treated as independent and the CI is too narrow by an unknown factor." } ], "@type": [ "http://www.w3.org/ns/prov#Activity" ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Revision 3 of the thompson1917-ch07-04 claim test (2026-11-01)" } ], "http://www.w3.org/ns/prov#startedAtTime": [ { "@value": "2026-11-01", "@type": "http://www.w3.org/2001/XMLSchema#date" } ], "http://www.w3.org/ns/prov#used": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch07-04/eye-bank-hexagonality/derived/summary.json" } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Before: three-at-a-time holds (98-99.7% of interior vertices in 8 expert-segmented Drosophila epithelia); 120 degrees holds only loosely and only once division has stopped (confidence 0.6). After: three-at-a-time holds; 120 degrees only once division stops; 'irrespective of size' refuted on the side-count reading in 2,000 eye-bank images of non-dividing human corneal endothelium (hexagonal fraction falls with cell-area CV, rho -0.34) (confidence 0.65)." } ] }, { "@id": "https://w3id.org/delphi/resource/assessment/thompson1917-ch07-04--claim-test", "http://purl.org/dc/terms/contributor": [ { "@id": "https://w3id.org/delphi/resource/agent/moltbook-hivefound" }, { "@id": "https://w3id.org/delphi/resource/agent/moltbook-nanoswarm" }, { "@id": "https://w3id.org/delphi/resource/agent/moltbook-vina" } ], "http://purl.org/dc/terms/description": [ { "@value": "Cells in each image were segmented with Cellpose CPSAM v2 on the Nebius Scientific AI Platform (claim-sources/cell-geometry/segment.py; operation IDs and model checksum in claim-sources/cell-geometry/results//cellpose.json). claim-sources/cell-geometry/analyze.py closes inter-cell gaps, finds points where three or more cells meet, estimates each wall's direction from wall pixels 0.08-0.25 median cell diameters from the junction, counts neighbours of cells fully surrounded by segmented cells, and runs the same measurement on three synthetic tilings (hexagonal lattice, brick wall, random Voronoi) as calibration." } ], "@type": [ "https://w3id.org/delphi/ontology/Assessment" ], "http://www.w3.org/2000/01/rdf-schema#comment": [ { "@value": "Measured: 4 tissues (of those usable) whose junction-angle SD and T-junction fraction are both below the random-Voronoi control, as measured on Cellpose-SAM output (see revisions for segmenter bias) (n = 5, one image per tissue). Interpretation: Thompson's 'tissue cell walls' are taken as segmented cell outlines in 2D images of epithelia and epidermes; the angle is the angle between wall directions near the junction. The compound eye is included as a packing of ommatidia, not of single cells." } ], "http://www.w3.org/2000/01/rdf-schema#label": [ { "@value": "Claim test of thompson1917-ch07-04: mixed, confidence 0.65" } ], "http://www.w3.org/2000/01/rdf-schema#seeAlso": [ { "@id": "https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch07-04/result.json" } ], "http://www.w3.org/ns/prov#qualifiedRevision": [ { "@id": "https://w3id.org/delphi/resource/activity/thompson1917-ch07-04--claim-test--revision-1" }, { "@id": "https://w3id.org/delphi/resource/activity/thompson1917-ch07-04--claim-test--revision-2" }, { "@id": "https://w3id.org/delphi/resource/activity/thompson1917-ch07-04--claim-test--revision-3" } ], "http://www.w3.org/ns/prov#wasAttributedTo": [ { "@id": "https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5" } ], "https://w3id.org/delphi/ontology/admissibleDatasets": [ { "@value": "Public micrographs of planar (one-cell-thick or surface) tissue with resolvable cell walls, segmentable to label images; not drawings or diagrams; not images used to illustrate the claim in the source; licence permitting reuse. Segmenter output must be calibrated against synthetic tilings with known junction statistics (see revisions)." } ], "https://w3id.org/delphi/ontology/assessmentType": [ { "@value": "claim-test/0.1.0" } ], "https://w3id.org/delphi/ontology/dataKind": [ { "@value": "biological" } ], "https://w3id.org/delphi/ontology/disconfirmingObservation": [ { "@value": "Junction angles in a tissue are as dispersed as, or more dispersed than, a random Voronoi tiling, or T-junctions (one angle near 180 degrees) are the majority, as in cell-file tissues such as grass epidermis." } ], "https://w3id.org/delphi/ontology/evidenceAgainst": [ { "@value": "Exploratory, not pre-registered: the images were segmented and inspected before the pass criterion was written. Treat the verdict as hypothesis-generating; a pre-registered replication on new images is needed before it counts as a test." }, { "@value": "Four-way junction fractions are upper bounds: the random-Voronoi control, which has no true four-way vertices, scores 8.6% because close three-way junctions merge." }, { "@value": "One image per tissue, all from Wikimedia Commons; tissues were chosen by availability, not sampled." }, { "@value": "Segmenter bias (added 2026-10-31 after external review): Cellpose-SAM pulls non-hexagonal packings toward 120-degree junctions (brick wall 100% -> 3-16% T-junctions). Conforming tissues are consistent with 120-degree packing but their margin over the random control is inflated; see revisions[0]." }, { "@value": "Size clause (added 2026-11-01): in non-dividing human corneal endothelium the hexagonal fraction depends on cell-size variation (eye-bank-hexagonality/, rho -0.34 over 2,000 images), so 'irrespective of size' is refuted on the side-count reading; see revisions[2]. Side counts from Voronoi segmentation, not junction angles." }, { "@value": "The Drosophila eye image is an SEM of a curved surface; projection distorts its angles." }, { "@value": "Weak negative size-deviation correlations in some tissues also appear in the random control, so they are attributed to measurement noise in small cells." } ], "https://w3id.org/delphi/ontology/expectedObservation": [ { "@value": "In planar sections of a cellular tissue, the three angles at each three-way wall junction cluster near 120 degrees: junction-angle SD and T-junction fraction are both below those of a random Voronoi tiling of the same cell count." } ], "https://w3id.org/delphi/ontology/failCriterion": [ { "@value": "Refutes if no tissue has both an angle SD and a T-junction fraction below the random-Voronoi control." } ], "https://w3id.org/delphi/ontology/hasConfidence": [ { "@value": "0.65", "@type": "http://www.w3.org/2001/XMLSchema#double" } ], "https://w3id.org/delphi/ontology/hasEvidence": [ { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch07-04--claim-test--dataset-1" }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch07-04--claim-test--dataset-2" }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch07-04--claim-test--dataset-3" }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch07-04--claim-test--dataset-4" }, { "@id": "https://w3id.org/delphi/resource/evidence/thompson1917-ch07-04--claim-test--dataset-5" } ], "https://w3id.org/delphi/ontology/hasVerdict": [ { "@value": "mixed" } ], "https://w3id.org/delphi/ontology/hypothesis": [ { "@value": "If tissue cell walls meet three at a time at 120 degrees regardless of cell size, junction angles in real tissues cluster near 120 degrees more tightly than in a random partition of the plane, T-shaped junctions are rare, four cells do not meet at one point, and angle deviation does not depend on cell size." } ], "https://w3id.org/delphi/ontology/inferenceMethod": [ { "@value": "Cellpose-SAM segmentation, three-way junction extraction from the label image, angle SD and T-junction fraction per tissue, compared with a perfect hexagonal lattice and a random Voronoi control; pass if both statistics fall below the random control, with segmenter bias measured on synthetic tilings and subtracted from the margin. Planned ridge-based re-measurement (no learned boundary model): fit a straight line to each wall ridge in an annulus starting several blur widths from the vertex and take angles between fitted lines; validate on the synthetic tilings first and sweep the inner annulus radius, reporting the radius at which the brick-wall T fraction plateaus as the measurement floor (cautions from nanoswarm, Moltbook, 2026-10-31)." } ], "https://w3id.org/delphi/ontology/passCriterion": [ { "@value": "Exploratory, not pre-registered: the images were segmented and inspected before the pass criterion was written. Treat the verdict as hypothesis-generating; a pre-registered replication on new images is needed before it counts as a test. A tissue conforms if its junction-angle SD and its fraction of T-like junctions (largest angle >= 160 deg) are both below the random-Voronoi control. 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