After two index repairs, site label tests found synapse direction separation on both neurites in three of 72 two-way neuron pairs in one adult C. elegans map
We checked a spatial test of chemical synapse directions in the released adult C. elegans neurite data of Ruach et al. Two index operations read distances from unintended rows or from a single matrix column. Only 12 of 1,024 selected local row numbers read the intended full row. All 1,670,431 stored distance entries matched the supplied neurite graphs. Both index repairs changed every separation score in a common panel of 67 pairs. The repaired scores stayed fixed in 1,460 row shuffles. Tests that exchanged complete site labels retained three of 73 pairs after Holm adjustment. A later test that required separation on both neurites retained the same three of 72 eligible pairs: RMDDL–RMDVR, RIAR–SMDDL, and RMDDR–RMDVL. The result also held when site identifiers had to match across both neurons. These tests assume exchangeable labels at fixed positions. They do not control whole-neuron polarity or establish local electrical function. We provide code, source checks, numerical results, figures, and repeat instructions. Original inputs remain external.
connectome · Caenorhabditis elegans · neurite · synapse position · reciprocal connection · index audit · permutation test · reproducibility
References
7- challengesdoi:10.1073/pnas.2201699120
We audit two index operations in its released direction script. We repair them and test the saved cable distances. This challenges the released quantification, not all evidence of synapse clustering.
- usesdoi:10.1038/s41586-019-1352-7
This study supplied the anatomical reconstruction from which the compiled N2U neurite data were made.
- usesNormal distance rank tests gave 1.9–4.5 percent false calls at a 1 percent cutoff with random labels and fixed counts in eight C. elegans brain maps sci:sha256:49e2675b2aaaaa8db46586fb0472293e080e22f84d5d9954496187eff1d48621
We extend its complete site-label reference to the original released cable-distance matrices, with a separate audit of row identities.
- supportsTests of synapse distances rejected 7.7 to 9.2 percent of random label controls at a 5 percent cutoff in two C. elegans maps sci:sha256:6a0837ec9fa0234935c1c7b650569234c623d16dc447bfeff15511bb4263e31e
The result agrees that shared distances need a reference that moves complete site labels. Our data and index audit are different.
- usesdoi:10.2202/1544-6115.1585
Sampled site probabilities include the observed assignment through the added-one rule.
- usesdoi:10.2307/4615733
Holm adjustment controls the family of pair tests without an independence assumption.
- doi:10.1186/s12915-026-02539-1
This later study gives context for spatial synapse organization across development.
Cited by
1 publicationPublic catalog entries on Sciscape.
- usesWith input and output layouts fixed, a mean distance test retained no corrected call in 72 reciprocal pairs from one adult C. elegans map
We reuse its MIT source extraction and retrieval code, source checks, pair eligibility rule, and known three-pair comparison. We test its stated limitation about whole-neuron input and output layout.