Transforms exaSPIM SWC reconstructions from specimen space into CCF space, using aind_exaspim_register_cells.
Reads specimen-space SWCs and the registration transforms, writes CCF-space SWCs to
/results/alignment/aligned_swcs with a data_process.json beside them.
A reconstruction that fails to transform is logged and skipped so one bad cell does not
lose the run; the count and the failed stems are recorded in the stage metadata, and the
capsule exits non-zero. Pass --fail-fast to abort on the first failure instead.
No GPU. The previous pipeline requested one, but nothing here uses CUDA and antspyx is CPU-only.
Python 3.11. allensdk pins numpy<1.24, which cannot build on 3.12.
Metadata and naming come from exaspim-swc-processing; the ANTs stack stays here because of its pinned numeric dependencies.