https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08/Head https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08 http://www.nanopub.org/nschema#hasAssertion https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08/assertion https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08 http://www.nanopub.org/nschema#hasProvenance https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08/provenance https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08 http://www.nanopub.org/nschema#hasPublicationInfo https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08/pubinfo https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08 http://www.w3.org/1999/02/22-rdf-syntax-ns#type http://www.nanopub.org/nschema#Nanopublication https://w3id.org/np/RA2vjHVr0316OGuerKSwlKl_TJpgrvZ3Pe_oOjqYJ6x08/assertion https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test http://purl.org/dc/terms/description analysis.py range-extracts the five members per archive and, for each wall flagged new whose two flanking cells are >= 40 um^3 and whose bounding boxes do not touch the image border, takes the mother as the union of the two cells. The wall normal is the smallest principal axis of the midpoints of the voxel faces shared by the two cells (um coordinates); the mother's longest axis and elongation sqrt(lambda1/lambda2) come from the covariance of its voxel coordinates. theta is the folded angle between them. Part 2 searches for cells X sharing a new wall with both cells of another new wall Y1|Y2. As a control that was not pre-registered, 1000 randomly sampled walls per apex that are not flagged new are analysed identically. Secondary: the eLife table is read and fractions are computed by division type. Per-wall rows are written to data/part1.csv (regenerated, not committed); derived/part1_theta_histogram.csv has theta counts by wall kind and elongation bin. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test http://www.w3.org/1999/02/22-rdf-syntax-ns#type https://w3id.org/delphi/ontology/Assessment https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test http://www.w3.org/2000/01/rdf-schema#comment Measured: 35.85 median angle (deg) between the new wall's normal and the mother cell's longest principal axis, elongated mothers (axis ratio >= 1.2) (n = 22810, IQR 20.3-58.4 deg; random-orientation median 59.8 deg; per-apex medians 27.2-52.9 deg across the 8 apices). Interpretation: Thompson derives the rule for an ideal rectangular parallelepiped bisected by a least-area plane: the plane is perpendicular to the longest edge, and successive bisections alternate at right angles. Real meristem cells are not rectangular, so 'longest axis' is the largest principal axis of the cell volume and the test is restricted to mothers that are measurably elongated (principal-axis ratio >= 1.2), where the axis is defined. Successive divisions are identified only where both walls are still flagged as recent in one snapshot, so Part 2 samples rapid successive divisions. Division orientation in the shoot apex is also influenced by tissue stress, which can mimic or mask the geometric rule; the test measures the outcome, not the cause. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test http://www.w3.org/2000/01/rdf-schema#label Claim test of thompson1917-ch08-01: mixed, confidence 0.5 https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test http://www.w3.org/2000/01/rdf-schema#seeAlso https://github.com/fractastical/delphisci/blob/bf2af6ee0a84e23ffa6414ad7a0a50a8c276506e/test-data/claim-tests/thompson-growth-form/thompson1917-ch08-01/result.json https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test http://www.w3.org/ns/prov#wasAttributedTo https://w3id.org/delphi/resource/agent/delphisci-claim-tester-claude-opus-5-5 https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/admissibleDatasets 3D segmentations of dividing plant cells with identifiable sister pairs and known voxel size; independent of Thompson; public licence. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/assessmentType claim-test/0.1.0 https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/dataKind biological https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/disconfirmingObservation New-wall normals are oriented no better than random relative to the longest axis (median angle >= 50 deg), and successive walls are no closer to perpendicular than random (median <= 60 deg). https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst A control that was not pre-registered weakens the support from Part 1. Walls not flagged as new, between arbitrary neighbouring cells, score better (median 26.5 deg, 59% within 30 deg) than new walls do. The union of any two adjacent cells is elongated across their shared wall, so this measure favours the rule by construction. New walls lining up less well than that geometric baseline suggests that the observed alignment is not evidence for a division rule beyond geometry. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Part 1 is between the pre-registered pass and fail bands. New walls are better aligned with the mother's long axis than random planes (median 35.9 deg against 59.8 deg), but short of the 30 deg median and 60%-within-30-deg needed to pass (41%). Alignment increases with elongation: median 26.7 deg for mothers with axis ratio >= 2, and 42-48 deg for nearly isodiametric ones, as the rule predicts if 'longest axis' only matters when one is clearly longest. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Part 2 could not be tested. The dataset's new-wall detection pairs each cell with at most one sister (no cell lies on two new walls in any of the 8 apices), so no successive-division triples exist. Under the pre-registered rule the verdict is Part 1's outcome (mixed), with confidence capped at 0.6. The alternation half of the claim is untested. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Secondary (eLife 79224, embryo apical cells at 16C, not part of the verdict): 136 of 140 longitudinal divisions are in cells whose radial length exceeds their longitudinal length, as the rule predicts. All 9 transverse divisions are also in such cells, against the rule. Nearly all these cells are radially longer (median ratio 0.73), so the table cannot show cells choosing their division by length. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Shoot-apex division orientation is also influenced by mechanical stress and growth direction, which this test does not separate from geometry. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst Sister identification relies on the dataset's own new-wall filter, which flags 4,365 walls in the first apex (8,730 of 12,499 cells), more than a single recent round of division would give. It probably includes older walls, which this test cannot separate from recent ones. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst The 'cell crosses image border' field in *_cell_data.csv is 0 for every cell, so border contact was judged from each cell's bounding box touching the image edge. Mothers whose sister volumes the segmentation already limits to >= 40 um^3 all pass the volume filter. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/evidenceAgainst preregistered_at is the time of the pre-registration commit (9e0ec83d); the committed pre-registration carried an estimated time (21:40Z) written before committing. Data were first fetched after that commit; criteria are unchanged. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/expectedObservation New-wall normals cluster near the mother's longest axis (median angle <= 30 deg, versus 60 deg for random planes), and successive recent walls meet near 90 deg. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/failCriterion Pre-registered. Part 1 fails if median theta >= 50 deg; Part 2 fails if median phi <= 60 deg. REFUTES if both parts fail. MIXED for any other combination of pass/fail/neither. If Part 2 has fewer than 15 triples it is underpowered; the verdict is then Part 1's outcome (supports if it passes, refutes if it fails, mixed otherwise) with that limitation noted and confidence capped at 0.6. If Part 1 has fewer than 30 elongated mothers: inconclusive (underpowered). Secondary, reported but not used for the verdict: in eLife 79224 Figure 8 source data 2 (Laruelle et al. 2022, Arabidopsis embryo apical cells at 16C), the fraction of horizontally dividing cells whose longitudinal length exceeds their maximal radial length, and of longitudinally dividing cells whose longitudinal length is below it. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/hasConfidence 0.5 https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/thompson1917-ch08-01--claim-test--dataset-1 https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/hasEvidence https://w3id.org/delphi/resource/evidence/thompson1917-ch08-01--claim-test--dataset-2 https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/hasVerdict mixed https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/hypothesis In dividing plant cells, the new wall cuts across the mother cell's longest axis (its normal is near-parallel to that axis), and when two successive divisions are both recent, the second wall is near-perpendicular to the first. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/inferenceMethod Principal axes of the reconstructed mother and of the interface; angle statistics compared with the random-orientation expectation and the pre-registered thresholds. https://w3id.org/delphi/resource/assessment/thompson1917-ch08-01--claim-test https://w3id.org/delphi/ontology/passCriterion Pre-registered. Data: the same 8 Arabidopsis shoot-apex archives as thompson1917-ch08-02 (first 8 archive names, alphabetical, of Zenodo record 18711581). Sister pairs = the two cells separated by a wall in *_new_walls.tif; mother = their union; sisters >= 40 um^3, not touching the border. Part 1 (longest axis): theta = angle between the new wall's normal (smallest principal axis of the shared-interface voxel coordinates, in um) and the mother's longest principal axis (largest-variance axis of its voxel coordinates, in um); analysed for elongated mothers (sqrt(lambda1/lambda2) >= 1.2), all mothers reported too. Under random orientation the median theta is 60 deg. Part 1 passes if median theta <= 30 deg and >= 60% of elongated mothers have theta <= 30 deg. Part 2 (alternation): triples X, Y1, Y2 where Y1|Y2 is a new wall and Y1 and Y2 each also share a new wall with the same cell X (so Y divided after X|Y formed); phi = angle between the normals of wall Y1|Y2 and wall X|(Y1 u Y2), folded to [0, 90]. Part 2 passes if median phi >= 75 deg and >= 50% of triples have phi >= 70 deg. 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