Transforms refined exaSPIM neuron reconstructions into CCF space and publishes one AIND derived data asset per neuron.
| Stage | Capsule | Does |
|---|---|---|
| transform | exaspim-swc-transform-capsule | specimen space to CCF space |
| resample | exaspim-swc-resample-capsule | 10 um node spacing, both coordinate spaces |
| packaging | exaspim-swc-packaging-capsule | per-cell layout, data_description.json, processing.json |
Shared logic lives in exaspim-swc-processing.
pipeline/main.nf is generated by the Code Ocean pipeline builder and is overwritten
whenever the pipeline is saved in the UI; it carries a hash:sha256 marker. Do not edit
it by hand. Per-stage CPU and memory are set in the UI and baked into it.
pipeline/nextflow.config is hand-written and survives regeneration. It carries the
PIPELINE_* variables the packaging capsule reads and the cost-monitoring label.
Bump PIPELINE_VERSION in pipeline/nextflow.config and add a CHANGELOG.md entry in
the same commit, then merge to main. The release workflow tags and publishes from
there. Cut a Code Ocean internal release separately; the MAJOR.0 version Code Ocean
assigns is not the semantic version.