seg_synapse_nri — EMPROOF `wiring` op

• Data kinds: labels2d × labels2d × table → table

• Call: import fullseye as fs; fs.ledger.seg_synapse_nri(a, b, synapses, spacing=None, background=0) (to call the implementation directly, import segcompare; segcompare.seg_synapse_nri(a, b, synapses, spacing=None, background=0); from the registry, opsemproof.get("seg_synapse_nri"))

Usage

Neural reconstruction integrity (Reilly et al. 2018) of candidate `b against truth a`.

NRI scores the pairs of synapse ends that a reconstruction keeps together. Over the

`2n ends (synapses as in :func:seg_synapse_partners; ends on background` in

the truth are dropped, ends on background in the candidate are singletons), a pair of

ends that lies in one truth neuron and one candidate object is a true positive; a

pair in one truth neuron but different candidate objects is a false negative (a split);

a pair in one candidate object but different truth neurons is a false positive (a

merge). `nri = 2TP / (2TP + FP + FN) with the pair precision and recall`.

Identity (checked inside, fail-closed): with `n_ij` the contingency table of the ends,

`TP = sum C(n_ij, 2), TP + FN = sum C(s_i, 2), TP + FP = sum C(t_j, 2)`, so NRI

is exactly `1 - adapted_rand_error of :func:seg_rand` taken over the ends (the

`- N form of the pair counts is 2 C(n, 2)`). Both are computed and must agree to

1e-12. Returns `nri, precision, recall, tp, fp, fn, n_ends`.

Raises `ValueError: as :func:seg_wiring_variation`; fewer than 2 ends.

Detailed usage guide

• emproof family guide

References (sample data, literature)

• Sample-data catalog (download URLs / licences) — 2-D uses skimage.data (BSD/public domain) plus synthetic images; 3-D lists download URLs for real data sources (Stanford, PDS, …).

• Operator provenance and references — the sources of the research/methods this op family came from.

• The canonical algorithm (author, year) and its uses are named in the family usage guide above.

Runnable examples (verified samples that actually call this op)

• poc_em_wiring_errors — py -3.11 examples/poc_em_wiring_errors.py

Ops the type connects to (they accept `table` as input)

seg_synapse_partners · seg_wiring_variation · seg_wiring_exposure

Same category (`wiring`)

seg_synapse_partners · seg_wiring_variation · seg_wiring_exposure

*Provenance: segcompare.py — EMPROOF operator registry. This per-op note is generated by tools/opdocs.py md (do not hand-edit).*

seg_synapse_nri — EMPROOF wiring op