edge: draft BIL sheets from OME-Zarr stores and voxel manifests

README.md

@@ -225,6 +225,8 @@ $ scigantic-bil submission-draft ./ctx            # one draft per acquisition di
 
 The prior is the same base64 capsule the edge's own `-export-prior` writes; its card holds one `bil-image` context record per Image row of the BIL record, with the Instrument sheet folded in. The draft uses BIL's own column names, so a row pastes into the submission spreadsheet. Measured on 2026-10-17: of 1,004 light-sheet records on BIL, 849 have an Instrument block and about half of those name an objective, detector or wavelength; 808 are LifeCanvas SmartSPIM, whose `metadata.txt` carries every one of those values.
 
+OME-Zarr stores are drafted from the edge's `ome-zarr` records: step sizes from the level-0 scale transform (converted to micrometres from whatever unit the axes name), channels, slices and array size from the shape, `dimensionorder` from the axes names (`CZYX`, `TCZYX`). An acquisition written by the Allen Institute's `voxel` engine is one store per volume and channel under `<root>/volumes/NNNNNN/<profile>/<channel>.ome.zarr` beside a `manifest.json`; those stores collapse into one draft per manifest (matched through the store's sidecar, the manifest's store paths, or the `/volumes/` prefix), with `channels` counted as the distinct `<channel>.ome.zarr` names across volumes. The manifest's `voxel-manifest` record fills the Instrument sheet (instrument name, objective, laser lines, emission bands, camera) and the draft's `acquisition` block carries what the sheets have no column for: store and volume counts, channel names, status, revision and timestamps. The microscope type is set to light-sheet only when the instrument's name says so; voxel's template instrument is a simulator. `fixtures/edge/voxel_run1_index.jsonl` is the edge decoder's own `index.jsonl` over one such run (2 tiles x 2 channels, 10 frames of 128 x 192 uint16), `exaspim_public_index.jsonl` holds hand-written records for two public exaSPIM tiles, and `tests/test_edge.py` reads both.
+
 ## Caching
 
 On by default. Metadata responses, directory listings and manifests are cached to `~/.cache/scigantic-bil` (macOS: `~/Library/Caches/scigantic-bil`; override with `SCIGANTIC_BIL_CACHE` or `enable_cache(cache_dir=...)`) and expire after 7 days, since BIL republishes its inventory every few days. Inventory snapshots are immutable once published and are kept as plain TSV files without expiry. Image bytes are never cached.

fixtures/edge/exaspim_public_index.jsonl

@@ -0,0 +1,2 @@
+{"source": "exaSPIM_851474_2026-07-10_15-23-22/SPIM.ome.zarr/tile_000000_ch_488.zarr", "sizeBytes": 7759, "mtime": 1784108793, "decoded": {"format": "ome-zarr", "summary": "OME-Zarr v2 (NGFF 0.4) multiscales, 7 levels, tczyx 1x1x2560x1330x1774 uint16, 8 x 5.984 x 5.984 micrometer, blosc/zstd", "fields": {"zarrFormat": 2, "ngffVersion": "0.4", "layout": "multiscales", "axes": [{"name": "t", "type": "time", "unit": "millisecond"}, {"name": "c", "type": "channel"}, {"name": "z", "type": "space", "unit": "micrometer"}, {"name": "y", "type": "space", "unit": "micrometer"}, {"name": "x", "type": "space", "unit": "micrometer"}], "levels": 7, "datasetPaths": ["0", "1", "2", "3", "4", "5", "6"], "sizeT": 1, "sizeC": 1, "sizeZ": 2560, "sizeY": 1330, "sizeX": 1774, "dtype": "uint16", "fillValue": 0, "chunkShape": [1, 1, 128, 256, 256], "shardShape": null, "codecs": ["blosc"], "compressor": "blosc/zstd", "compressionLevel": 1, "voxelSizeX": 5.984, "voxelSizeY": 5.984, "voxelSizeZ": 8.0, "voxelSizeUnit": "micrometer", "channelNames": ["Channel:tile_000000_ch_488.zarr:0"], "omeroPresent": true, "presentChunks": 0, "presentChunksIsLowerBound": true, "metadataFiles": [".zgroup", ".zattrs", "0/.zarray", "6/.zarray"], "arrayMetadataMissing": ["1/.zarray", "2/.zarray", "3/.zarray", "4/.zarray", "5/.zarray"], "sidecars": []}}}
+{"source": "exaSPIM_2026-08-04_10-27-41/SPIM/tile_000000_ch_488.ome.zarr/zarr.json", "sizeBytes": 1849, "mtime": 1789153861, "decoded": {"format": "ome-zarr", "summary": "OME-Zarr v3 (NGFF 0.5) multiscales, 6 levels, tczyx 1x1x1024x2660x3548 uint16, 20 x 15.04 x 15.04 micrometer, sharded, zstd", "fields": {"zarrFormat": 3, "ngffVersion": "0.5", "layout": "multiscales", "axes": [{"name": "t", "type": "time", "unit": "millisecond"}, {"name": "c", "type": "channel"}, {"name": "z", "type": "space", "unit": "micrometer"}, {"name": "y", "type": "space", "unit": "micrometer"}, {"name": "x", "type": "space", "unit": "micrometer"}], "levels": 6, "datasetPaths": ["0", "1", "2", "3", "4", "5"], "sizeT": 1, "sizeC": 1, "sizeZ": 1024, "sizeY": 2660, "sizeX": 3548, "dtype": "uint16", "fillValue": 0, "chunkShape": [1, 1, 128, 256, 256], "shardShape": [1, 1, 512, 512, 512], "codecs": ["sharding_indexed", "transpose", "bytes", "zstd"], "compressor": "zstd", "compressionLevel": 3, "voxelSizeX": 15.039999977980552, "voxelSizeY": 15.040000146851504, "voxelSizeZ": 20.0, "voxelSizeUnit": "micrometer", "channelNames": ["tile_000000_ch_488"], "omeroPresent": true, "presentChunks": 0, "presentChunksIsLowerBound": true, "metadataFiles": ["zarr.json", "0/zarr.json", "1/zarr.json", "2/zarr.json", "3/zarr.json", "4/zarr.json", "5/zarr.json"], "arrayMetadataMissing": [], "sidecars": []}}}