VFB domain meshes

Aligned anatomical-region meshes (and filled volume masks) for Virtual Fly Brain painted domains, organised so any template and any source dataset can be added the same way.

Layout

<template_dir>/                         one directory per VFB template (id in the name)
  README.md                             template grid + provenance
  <source>/                             one directory per source dataset
    source.json                         server / space / mesh->template affine
    domains.csv                         per-domain FBbt mapping (curator-checkable)
    obj/                                region meshes in the source's native space
    nrrd/                               filled uint8 masks (255 in / 0 out) on the template grid
templates.csv                           index of templates + their grids
domains.csv                             aggregate of every source's domains.csv
scripts/                                fetch + voxelise helpers (reusable for any source)

Convention: OBJ = source-native coordinates, NRRD = the template's exact voxel grid (same sizes / spacing / origin as the template's volume.nrrd, so masks overlay directly). Each region also carries a proposed FBbt class in domains.csv for curator sign-off.

Adding a new template/source

1. Add a row to templates.csv (read the template's volume.nrrd header for the grid — do not guess).
2. scripts/fetch_catmaid_volumes.py (or your own exporter) -> obj/.
3. scripts/voxelize_to_template.py with that template's grid + the source->template affine -> nrrd/.
4. Write domains.csv with the FBbt mapping; get it curated (curator_* columns).
5. Append to the root domains.csv.

domains.csv columns

template_id, template_label, source, catmaid_vol_id, volume_name, region, side, obj, nrrd, filled_voxels, fbbt_id, fbbt_label, confidence_note, curator_fbbt_ok, curator_notes

Status

Template	Source	Domains	State
L1 larval CNS (VFB_00050000)	CATMAID_L1EM	27	OBJ + NRRD generated; FBbt map pending curator check
JRC2018Unisex adult brain (VFB_00101567)	CATMAID_FAFB	~78	candidate (FAFB14-native Ito neuropils) — not yet generated

See templates.csv for grids and existing painted-domain coverage.