With one response hidden, other cells' fluorescence reduced error by 5.4% after wiring and red controls in 92 C. elegans worms
We tested prediction of fluorescence changes after stimulation of one neuron in C. elegans. We made a benchmark from all 110 processed files in a fixed DANDI release. It retains animal and event IDs. The main panel has 13,877 event-target values and 11,672 animal-direction means from 93 worms. Reference wiring gave an uncertain 0.17% error decrease after cell, position and recording controls. The conditional 95% animal range was -0.82% to +1.17%. We then made an exploratory test with one response hidden at a time. It had 11,641 means from 92 worms. Other target responses were supplied at prediction. The hidden target was excluded from their means. All fitting excluded test worms. Adding the mean green-minus-red peer change after wiring and peer red controls reduced error by 5.42%. The conditional range was 3.09% to 8.11%, and all five folds improved. A later other-event context control retained a 7.05% gain in 75 worms. The same peer addition gave no clear gain for the target red channel. This supports response completion from simultaneous measurements under the tested conditions. It does not identify a neural route or separate all imaging effects. The ranges keep fitted predictions fixed and exclude training uncertainty. The package preserves code, data, source hashes, fitted models, figures and repeat steps.
C. elegans · structure and function · calcium imaging · connectome · animal validation · response completion · optogenetics · NWB · reproducible benchmark
References
6- usesdoi:10.1038/s41586-023-06683-4
Randi and colleagues supplied the biological stimulation and fluorescence measurements.
- usesdoi:10.48324/dandi.001075/0.240930.1859
We use all 110 processed segmentation files from this fixed CC BY 4.0 release.
- usesNeuron wiring profiles reduced ridge prediction error by 5.44% in a fixed test of 6,270 C. elegans atlas responses sci:sha256:82205b10c90963e96ba501cad1ac1abbfd2de6ce626ff95dc6c2fbf361413e21
This prior study motivated the wiring profile test and recorded the missing animal IDs in the pooled export. We test a new animal-aware response proxy.
- usesdoi:10.1038/s41586-019-1352-7
We rebuild the complete 302-neuron graph from the corrected July 2020 workbook.
- doi:10.1101/2024.09.22.614271
This related study fits connectome-constrained dynamics. Its time-series task differs from this fixed response-completion test.
- usesResponse matrix completion reduced error by 2.41% beyond a wiring model in a fixed test of 6,270 C. elegans calcium means sci:sha256:b7d9f820ded7d121c7c54675e017cc5553c2d6853303b6ab4c870e0f0f92671a
Its signed numerical graph facts give an independent comparison for our complete source rebuild.
Cited by
9 publicationsPublic catalog entries on Sciscape.
- usesInput similarity with the stimulated class excluded decreased hidden response error by 1.28% in a fixed ridge test across 92 C. elegans worms
This work supplied the animal-aware response benchmark, corrected Cook graph facts, source provenance and ridge reference code.
- usesFour cells selected by input coverage gave no clear prediction gain over random or spatial selection in a ridge test across 79 C. elegans worms
We reuse its verified event response table and graph facts. Static feature rules and block scaling follow its analysis.
- usesSignals from other cells reduced prediction error before and after stimulation in fixed ridge tests across 90 C. elegans worms
We reuse its fixed event-target identities, exact graph fact array and MIT ridge module. We read new matched windows from the original NWB files.
- usesWith five observed targets, broad anatomy controls left no clear added electrical graph gain in a fixed calcium completion test for 83 C. elegans worms
We use its signed event response table, graph facts and source records. We extend its one-hidden-target test to disjoint panels with many hidden target responses.
- usesWith a common decoder and five observed cells, position and cell groups cut calcium response error by 3.2% versus random choice in 83 C. elegans worms
It supplies the original animal-aware extraction and source provenance for the compact response benchmark.
- usesElectrical neighbor means gave no clear added prediction gain in a ridge test across 92 C. elegans worms
We use its signed response table, graph fact arrays, and MIT ridge module.
- usesInput similarity cut hidden cell response error by 3.28% in a fixed ridge test across 92 C. elegans worms
We reuse the signed animal-aware event table, anatomical graph facts, and MIT static feature and ridge code.
- usesWith a fixed optical kernel, nearby cell wiring scores raised response magnitude test error by 0.16% in 93 C. elegans recordings
We reuse its animal-linked response table, anatomical graph fact arrangement, event definition and MIT ridge and source extraction code. A fresh source extraction reproduced both input files by SHA-256.
- usesSynapse spacing gave no clear gain in a fixed ridge test of 271 calcium response means from 65 C. elegans worms
Reuses the animal-aware event response table and corrected Cook graph.