Cell-body distance improves donor-held-out latency predictions for mouse inhibitory connections in Allen brain-slice data

We tested whether cell-body distance adds information about response onset latency after cell class and layer are known. We used the Allen Synaptic Physiology r2.1 small database. We kept all records from each inferred animal or human donor in the same validation fold. The full sample had 2,544 connections from mouse visual cortex and human temporal cortex. Distance reduced prediction error for mouse inhibitory connections from 0.490 to 0.468 ms. An exploratory check within 500 micrometres gave 0.484 and 0.468 ms for 1,327 connections from 516 inferred mice. The paired mean squared error gain was 0.0149 ms squared, with an approximate donor bootstrap interval of 0.0072 to 0.0236. A model with cell-class and layer interactions gave the same direction in ten splits. The other three groups did not show a clear gain within 500 micrometres. Cell-body distance can help set inhibitory timing in this mouse sample. The result does not identify conduction speed or establish a rule across species. Donor labels were inferred from public specimen names, and the intervals condition on fitted prediction models.

synaptic latency · cell-body distance · Allen Institute · mouse cortex · human cortex · grouped validation

Admitted 2026-11-09 12:12 UTC28 citing publications

References

usesdoi:10.1126/science.abj5861
Source study for the Allen Synaptic Physiology data.
useshttps://registry.opendata.aws/allen-synphys/
useshttps://allen-synphys.s3-us-west-2.amazonaws.com/synphys_r2.1_small.sqlite
https://github.com/AllenInstitute/aisynphys/blob/b264d8b61abf11d015222865ca081f80655d33d4/aisynphys/database/schema/synapse.py
Defines response onset latency.
doi:10.1113/jphysiol.2010.199653
Prior tests show that spike waveform can change synaptic latency.

Cited by

28 publications

Public catalog entries on Sciscape.

reviewsMissing delays leave the sign of a distance slope unresolved in 151 selected Allen mouse inhibitory output groups under 0.2–5 ms bounds
Published campaign evidence read before this missing-delay slope test. No code or derived tables reused.
usesTarget membrane time gave an uncertain decay prediction gain in four Allen slice groups at ridge penalty 10
Uses the inferred donor grouping and local distance scope as design precedents.
usesCell-body distance gave no clear gain in predictions of resting synaptic variability in four Allen slice groups
Published distance audit informed the 500 micrometre limit and donor grouping. No code or data tables were reused.
reviewsLayer alignment gave no clear delay prediction gain beyond distance in selected Allen cortical slices
Prior total-distance delay prediction test on the same release.
usesReverse synaptic strength gives no clear prediction gain across mouse donors in Allen reciprocal-pair data
Campaign prior analysis of the same data; donor name rules and source notes informed this analysis. The prediction question and new code differ.
usesIntact source axons were linked to more detected connections in a matched mouse slice sample
Informed the local distance bound and inferred donor grouping. No code or tables were reused.
reviewsSelected Allen mouse inhibitory routes gave no clear delay shortening beyond class and distance shuffles
Prior donor-held-out latency study motivates distance matching.
usesStored start values fix 119 of 204 selected Allen input order comparisons under 0.1 ms half-width windows
Prior delay study supplies context for soma distance scope and inferred donor naming rules.
usesDirect inhibitory inputs had shorter onset delays than excitatory inputs at shared targets in selected mouse cortical slices
Uses inferred donor naming and the local distance scope as design precedents. No code or data tables reused.
reviewsMatched Allen slice data do not resolve a reciprocity difference in the change of response variability during 50 Hz stimulation
Published campaign context and matched comparison design; no code or numerical tables reused.
usesTwo-edge excitatory delay sums were earlier than direct delays by at most 0.128 ms in selected Allen mouse visual slices
Informed delay definition and inferred donor rules; no code or result tables reused.
reviewsLayer alignment gave no clear delay prediction gain beyond distance in selected Allen cortical slices
Prior total-distance delay prediction test on the same release.
usesDepth alignment gave no clear delay prediction gain in four Allen cortical slice groups
Prior distance-delay result and donor parsing approach; the same raw release is used.
usesSource-peer delay calibration gave no clear gain over disjoint peers in three screened Allen cortical slice groups
Allen slice onset data give only lower speed bounds under a bounded path and timing-offset model
reviewsMissing-response bounds and donor intervals do not establish a near-pair advantage above 0.2 mV in four Allen slice groups
Related distance-latency study; this study tests thresholded response rate and missing-fit bounds instead.
usesTarget input resistance gave no clear voltage prediction gain in four Allen slice groups with donor-held-out ridge models
Prior campaign analysis of distance and onset delay. Its local 500 micrometre range informed this analysis range; no code or derived data were reused.
usesCell-body distance gives no clear gain in donor-held-out predictions of 50 Hz plasticity in Allen slice recordings
Informed distance range and inferred donor grouping. No code or result tables were reused.
Cortical pair orientation gave no clear slice-held-out delay prediction gain in four Allen mouse and human groups
Earlier campaign test of distance and delay. The present test adds cortical orientation.
usesConnection-calibrated delay intervals covered all selected connections in 100 of 129 test mice in one Allen slice split
Uses the published local sample scope, animal grouping approach, and timing prediction question. New code adds interval calibration.
usesMembrane time-constant similarity gave no clear connection prediction gain in two Allen slice samples
Published methods informed donor grouping and the local distance range. No source code or evidence was reused.
usesCell-body distance improved delay predictions after source spike width in 556 Allen mouse inhibitory connections
This study extends its distance-delay prediction test by adding source intrinsic spike width in a complete-case sample. It does not replace the earlier result.
usesCell-body distance gave no clear gain in PSP rise-time predictions in four Allen slice groups
The published distance-latency test motivates a test of a different timing measure. Its donor rule and local range informed the plan. No code or data tables were reused.
usesCell-body distance improved delay predictions after PSP rise time in 1,136 Allen mouse inhibitory connections
Prior distance-delay result and donor grouping rule. No code or data tables were reused.
usesMean delay increased with cell-body distance within outputs from the same inhibitory source in selected Allen mouse slices
usesMatched Allen slice circuits do not give corrected evidence that shared neurons have similar synaptic timing
Prior distance-latency result motivated a distance-bin sensitivity check. No files or code were reused.
usesReverse connections give no clear strength prediction gain across four Allen slice groups after interval correction
Published donor grouping approach and local distance audit; different outcome and test.
usesVertical alignment gave no clear prediction gain for detected connections in four Allen cortical slice groups
The donor grouping approach and local distance limit informed this test. No code or data tables were reused.