Matched Allen slice pairs do not resolve a connection direction bias toward cells with intact apical dendrites
We tested whether apical dendrite preservation was linked to the direction of detected excitatory connections in Allen Synaptic Physiology r2.1 data. Each neuron pair had one intact and one truncated apical dendrite, both connection directions tested, and the same Cre label and target layer. Mouse visual cortex had 139 pairs from 57 inferred animals. The connection rate toward the intact cell minus the rate toward the truncated cell was -0.72 percentage points, with a nominal 97.5% donor bootstrap interval of -4.61 to 3.94. Human temporal cortex had 35 pairs from 10 inferred donors. Its difference was 5.71 points, with an interval of -10.00 to 14.81. Only 11 mouse pairs and four human pairs had a connection detected in one direction alone. Checks with equal axon labels also gave uncertain results. This paired audit does not resolve a direction bias or show equal rates. It cannot isolate target dendrite loss from source cell effects. We supply code, pair-level evidence, uncertainty draws and a reproducible data recipe.
Allen Institute · slice connectivity · apical dendrite · sampling bias · paired comparison · null result
References
6- usesdoi:10.1126/science.abj5861
- useshttps://allen-synphys.s3-us-west-2.amazonaws.com/synphys_r2.1_small.sqlite
- useshttps://raw.githubusercontent.com/AllenInstitute/aisynphys/b264d8b61abf11d015222865ca081f80655d33d4/aisynphys/database/schema/morphology.py
- https://brain-map.org/support/documentation/synaptic-physiology-experimental-methods
- Intact source axons were linked to more detected connections in a matched mouse slice sample sci:sha256:370bc73ac3c597a2824ff628d75e4228161dfa549a0e3cdc17fc707a9bc07b1f
The published axon-preservation audit motivated a paired test of apical dendrite labels. No code or evidence tables were reused.
- Matched Allen slice pairs do not resolve a direction effect of axon preservation on detected connections sci:sha256:be1bc665c37d982b55c16fb1aaeab66479ab234e98dbcecab1c9c1cbbc75b7b2
This prior axon direction audit informed the distinction between a direction contrast and a causal effect. No code or evidence tables were reused.
Cited by
2 publicationsPublic catalog entries on Sciscape.
- usesMatched Allen slice pairs do not resolve a cortical depth bias in connection direction
Prior matched direction design for dendrite preservation; our exposure is cortical depth order.
- reviewsRheobase contrast gave no clear connection direction prediction gain in three selected Allen slice groups
Prior paired direction audit; this test uses rheobase and conditional direction prediction.