SharpMeow/pherc0139-afv-fibers

PHerc0139 papyrus fibers (AFV V2)

Every papyrus fiber that Qual's AFV V2 model finds in the whole PHerc0139 scan, traced into curves with his AVF_SPLINE_GENERATOR: 6,812,631 fibers (6,590 m of fiber in all), 1,105,762 of them 1 mm or longer. Horizontal fibers run along the wraps; vertical fibers cross them. Same model, same recipe and the same .afv format as Qual's own published sets, run here on a scan he had not done.

Zoom on dense wraps: horizontal fibers (cyan) follow each sheet, vertical fibers (orange) cross the slice as short marks.	Every fiber in a 256-voxel cube, turning.
Sweeping through 60 slices of the zoom box.	A vertical section through the same place: here the vertical fibers show as long lines.

What is here

File	What	Size
PHerc0139_afv_v2_1mm.afv	fibers 1 mm and longer, the set most people want: 1,105,762 fibers, 322,111,205 points	10.50 GB
PHerc0139_afv_v2.afv	every traced fiber: 6,812,631 fibers, 447,564,177 points	17.44 GB
tiles/	one small .afv per 1024-voxel cell of the model's grid (471 cells with fibers); tiles/index.json gives each cell's level-0 box. Read a box without the whole file.	37.74 GB
stream/	the same fibers as 905 Parquet shards on a spatial grid, every fiber in exactly one, with stream/index.json: stream any box without the whole file (below)	5.13 GB
previews/	the pictures on this card and their views (index.json)
load_example.py	read the fibers in any box with Python's sqlite3 and NumPy
villa-check.jsonl	villa's own AFV reader run over every file here
stats.json	the counts on this card

	Fibers	Fiber length	Median	90th percentile	Longest
All, horizontal	2,942,255	3,171 m
All, vertical	3,870,376	3,419 m
All	6,812,631	6,590 m	0.28 mm	1.77 mm	204.1 mm
1 mm and longer, horizontal	539,078	2,393 m
1 mm and longer, vertical	566,684	2,404 m
1 mm and longer	1,105,762	4,797 m	2.25 mm	9.52 mm	204.1 mm

Get it

hf download SharpMeow/pherc0139-afv-fibers PHerc0139_afv_v2_1mm.afv --repo-type dataset --local-dir pherc0139-afv-fibers
python3 load_example.py pherc0139-afv-fibers/PHerc0139_afv_v2_1mm.afv        # or: X Y Z [HALF] in level-0 voxels

Or explore any box, see it over the CT and download just that box as .afv, on the AFV Fibers page.

Stream a box

Read just the fibers in one box, without downloading the whole file, with the Scrolls kit (pip install numpy pyarrow, then from a clone):

python -m kit fibers stream --scan PHerc0139 --box 384 640 1408 1664 3456 3712 --out box.afv

The box is Z0 Z1 Y0 Y1 X0 X1 in level-0 voxels. This one holds 1,587 fibers and read 3.5 MB of the 17.44 GB whole-scan file (measured 28 Oct 2026). The result is exactly what filtering PHerc0139_afv_v2.afv gives: the same fibers, and a byte-identical box.afv that villa's importer opens. Add --family H or V, or --min-len 1 for the 1 mm set. Every fiber as rows, streamed with the datasets library:

from datasets import load_dataset
ds = load_dataset("SharpMeow/pherc0139-afv-fibers", "stream", streaming=True, split="train")
for row in ds.take(3):
    print(row["id"], row["family"], row["length_mm"], len(row["points"]) // 3)

Each row is one fiber: its .afv columns, bounding box (bmin_x to bmax_z), blocks and points (flat x, y, z, float64). Before upload, every test box, a control box outside the scan (no fibers) and the whole scan were streamed back from here and matched the whole-scan file; the format and checks are on the tool page.

Open in VC3D

PYTHONPATH=build/python python3 vc_object_store/scripts/import_afv.py PHerc0139_afv_v2_1mm.afv pherc0139-fibers.vcobj \
    --volume-id 20250728140407

Then attach pherc0139-fibers.vcobj from VC3D's File → Object Store menu, with the 20250728140407-9.362um-1.2m-113keV-masked.zarr volume open (its catalog id must be 20250728140407; see the script's notes for a local cache). villa's import_afv.py takes native level-0 coordinates; every file here is in level-0 voxels of 20250728140407-9.362um-1.2m-113keV-masked.zarr with scale factor 1, and that script's own reader accepted every file before upload (villa-check.jsonl).

How it was made

• Scan: PHerc0139, 20250728140407-9.362um-1.2m-113keV-masked.zarr, Vesuvius Challenge open data. The model ran on level 0 (9.362 um voxels).
• Fiber maps: Qualzz20/afv_fiber_9um_v2 (nnU-Net, checkpoint sha256 b8519a4c...), Qual's recipe: 128-voxel windows at stride 64 on one global lattice, Gaussian blending, bf16, per-window normalization, no mirroring. 467 blocks of 1024 voxels on Hugging Face Jobs (RTX PRO 6000).
• Curves: AVF_SPLINE_GENERATOR at commit 3c8b7362, run per 1024-voxel region with a 128-voxel halo and seeds only inside the region, on Hugging Face CPU Jobs.
• Stitching: each region's curves cut at its own faces and joined across faces where ends meet within 1.5 voxels (913,390 joins); then the CT exterior cleaning Qual uses (curves touching air connected to the scan's outside are dropped). No region missing.
• Checks: on a test cube of Qual's own published V2 set, this pipeline's fibers match his to 98% within one voxel (recall and precision), with lengths within 1%. Region stitching matches one unsplit run to 99.75 to 99.99% within one voxel.

Notes

Model output, nobody has checked it fiber by fiber. Fibers are geometry, a map of papyrus structure: not a reading of any text.

Related

The AFV Fibers page has all six scans and a catalog of every public fiber set, including Qual's own.

Credit and terms

Fiber model, spline generator and .afv format: Qual, Apache 2.0. Scan: Vesuvius Challenge open data, CC BY-NC 4.0; these fibers are derived from it and shared under the same terms. Runs, stitching and this dataset: Chase Hendrick.