Changelog

Source: NEWS.md

yakuba (development version)

yakuba 0.2.0

Behaviour change to yakuba <-> MANC transforms:

• Points are now shifted by about (-6.5, -7.1, -8.0) µm before the 1000 point TPS registrations are applied, because those registrations were computed in a frame offset from current yakuba coordinates. As a result, xform_brain(x, sample = "yakuba", reference = "MANC") gives different (more accurate) results than in 0.1.0. Mean distance between matched yakuba/MANC DNs drops from 8.9 to 5.6 µm. The old behaviour is available as xform_dyak2manc(x, method = "tps1000_unshifted").

New features:

• New xform_dyak2manc() maps yakuba neurons or points to MANC space (or back). It offers alternative registrations via method: "tps1000" (default, same as xform_brain()), "manual" (Hiroshi Shiozaki’s landmarks), "ngscene" (Clio neuroglancer landmarks via malecns) and "tps1000_unshifted".
• Left-right mirroring based on Sebastian Cachero’s registration to a symmetrised yakuba template:
  • mirror_dyak() and symmetric_dyak(), analogous to malevnc::mirror_manc() and malevnc::symmetric_manc().
  • dyak_lr_position(), analogous to malevnc::manc_lr_position().
  • New yakubasym template brain; yakubaum -> yakubasym is registered for nat.templatebrains::xform_brain().
• New datasets yakuba_neuropil_shell and yakuba_vnc_shell (surface meshes).
• New article “Transforms between yakuba and MANC” documents the registrations and the coordinate offset.

Full Changelog: https://github.com/flyconnectome/yakuba/compare/v0.1.0…v0.2.0

yakuba 0.1.0

• First tagged release. Thin wrapper around malevnc for the D. yakuba male VNC neuprint and Clio datasets: dyak_neuprint(), dyak_neuprint_meta(), dyak_connection_table(), read_dyak_neurons(), dyak_ids(), dyak_xyz2bodyid(), dyak_islatest(), dyak_body_annotations(), yakuba_annotate_body(), choose_dyak(), choose_dyak_dataset() and with_dyak().
• Bridging registration from yakuba to MANC for nat.templatebrains::xform_brain().
• yakuba_annotate_body() follows malevnc::manc_annotate_body() 0.4.0 defaults: test = FALSE and new dry_run = TRUE, so a bare call previews the POST body rather than writing. Requires malevnc (>= 0.4.0).