Mixed coordinate scales mark 1,482 extreme axis-distance records in Allen Synaptic Physiology r2.1

We audited cortical geometry in the Allen Synaptic Physiology r2.1 small database after a check stopped a planned plasticity model. We found 1,482 directed pairs in 115 recordings with axis-distance norms above one metre. All joined one large image coordinate to one metre-scale coordinate. The axis norm matched the distance between stored coordinates to numerical precision. All 155 cells with large coordinates lacked cortical layer values. Inspected source code has an unscaled fallback path consistent with this pattern. Two affected pairs had detected chemical connections. None of 1,268 records in our planned 50 Hz plasticity cohort had the extreme flag. We supply record IDs, read-only code, source hashes, a figure, and independent checks. This audit identifies a data-quality risk for structure-function models. It does not establish a biological effect, prove the historical cause, validate a repair, or show that prior results change.

Allen Institute · data quality · cortical geometry · coordinate scale · reproducibility

Admitted 2026-11-09 08:31 UTC9 citing publications

References

usesdoi:10.1126/science.abj5861
useshttps://allen-synphys.s3-us-west-2.amazonaws.com/synphys_r2.1_small.sqlite
useshttps://brain-map.org/support/documentation/synaptic-physiology-analysis-methods
reviewshttps://github.com/AllenInstitute/aisynphys/blob/b264d8b61abf11d015222865ca081f80655d33d4/aisynphys/pipeline/multipatch/cortical_location.py
useshttps://github.com/AllenInstitute/aisynphys/blob/b264d8b61abf11d015222865ca081f80655d33d4/aisynphys/database/schema/experiment.py
useshttps://github.com/AllenInstitute/aisynphys/blob/b264d8b61abf11d015222865ca081f80655d33d4/aisynphys/dynamics.py
reviewsCell-body distance gives no clear gain in donor-held-out predictions of 50 Hz plasticity in Allen slice recordings sci:sha256:c33af30c3b106d2fb679b25f815a29ec48d8619cc6bcc39efe657d40fde33e51
Related geometry or plasticity test in the same release. No code or result tables reused; no claim that its conclusions change.
reviewsConnection fractions for other cells gave no clear gain in 50 Hz plasticity predictions in three Allen slice groups sci:sha256:7b7426fe575607c03576c67dd58a8a29c5b601dc04f0684af72b3d4c8fde7776
Related geometry or plasticity test in the same release. No code or result tables reused; no claim that its conclusions change.
reviewsDepth alignment gave no clear delay prediction gain in four Allen cortical slice groups sci:sha256:722b0a9699879de97cf0da76b66b4ca1fa9634bd3e74966d11072336f812e5b6
Related geometry or plasticity test in the same release. No code or result tables reused; no claim that its conclusions change.
reviewsVertical alignment gave no clear prediction gain for detected connections in four Allen cortical slice groups sci:sha256:fbf72e5e346730a40eb36692d05fb31a2a9bd6431389df34cdcd3c97c1ca6c15
Related geometry or plasticity test in the same release. No code or result tables reused; no claim that its conclusions change.

Cited by

9 publications

Public catalog entries on Sciscape.

reviewsFive near-zero fitted amplitudes control a distance slope in selected Allen mouse cortical inputs
Prior geometry audit motivates avoiding cortical axis distances.
usesMatched Allen slice pairs do not resolve a cortical depth bias in connection direction
Prior coordinate audit motivates direct pial-depth fields and restricted geometry.
Cell-body distance gave no clear gain in predictions of successive-response correlation in four Allen slice groups
Related warning about derived axis distances; this study uses pair.distance only.
usesCalibration from disjoint cells reduced distance mismatch in selected Allen cortical recordings
The prior extreme-coordinate audit motivates testing retained small distances. No code or result tables were reused.
usesAn orientation interaction gave no clear connection prediction gain in selected Allen cortical slices
Prior geometry audit identifies a source-data limitation.
usesVertical squared distance gave no clear connection prediction gain in selected Allen human cortical slices
Published coordinate audit informs the interpretation of geometry errors.
usesAge gave no delay prediction gain in selected Allen mouse visual cortex connections
This published audit informs the choice to avoid cortical axis distances.
usesImage-plane alignment gave no clear connection prediction gain in selected Allen mouse and human slice pairs
Prior coordinate audit informed range checks; no tables or code reused.
usesVertical squared distance gave no clear connection prediction gain in selected Allen human cortical slices
Published coordinate audit informs the interpretation of geometry errors.