| --- |
| license: cc-by-nc-4.0 |
| tags: [vesuvius-challenge, herculaneum, ct, lasagna, lasagnetta, ome-zarr] |
| pretty_name: PHercMANB Lasagnetta field (a preview of villa's lasagna field) |
| --- |
| |
| # PHercMANB Lasagnetta field |
|
|
| A Lasagnetta preview of villa's lasagna field for the whole PHercMANB scan, in villa's own layout, so you can point |
| lasagna or the spiral fit at it without running a model yourself. The open data has no lasagna field for this scroll. |
|
|
|  |
|
|
| ## Get it |
|
|
| ```bash |
| hf download SharpMeow/phercmanb-lasagnetta --repo-type dataset --local-dir phercmanb-lasagnetta |
| cd phercmanb-lasagnetta && sha256sum -c SHA256SUMS |
| for f in parts/*.tar; do tar -xf "$f"; done |
| tar -xf PHercMANB-lasagnetta-meta.tar # last: the whole-scan PHercMANB.lasagna.json and preview.json |
| ``` |
|
|
| You end up with `PHercMANB.lasagna.json` and `PHercMANB_{cos,grad_mag,nx,ny}.ome.zarr`, 33.0 GB in all. |
|
|
| ## Load it |
|
|
| ```python |
| import json |
| import numpy as np |
| import zarr |
| |
| meta = json.load(open("PHercMANB.lasagna.json")) |
| cos = zarr.open(meta["groups"]["cos"]["zarr"], mode="r") # cos, 2x down from the CT level read |
| nx = zarr.open(meta["groups"]["nx"]["zarr"], mode="r") # normals, 4x down; stored as v * 127 + 128 |
| ny = zarr.open(meta["groups"]["ny"]["zarr"], mode="r") |
| z, y, x = 245, 1018, 878 # a voxel on the normals' grid that holds data |
| a, b = (float(nx[z, y, x]) - 128) / 127, (float(ny[z, y, x]) - 128) / 127 |
| c = np.sqrt(max(0.0, 1 - a * a - b * b)) # nz is not stored |
| patch = cos[2 * z, 2 * y:2 * y + 64, 2 * x:2 * x + 64] # the same place on the cos grid |
| print("normal", round(a, 3), round(b, 3), round(c, 3), "cos patch mean", float(np.mean(patch))) |
| ``` |
|
|
| `load_example.py` is this snippet; it was run on an unpacked part before upload. |
|
|
| ## What it is |
|
|
| - Scan: PHercMANB, `20260323091048-2.399um-0.2m-78keV-masked.zarr`, read at level 2 (2.399 um scan, 9.6 um voxels at that level), Vesuvius Challenge open data |
| - Model: [Lasagnetta](https://huggingface.co/SharpMeow/lasagnetta) 0.1.1, weights at revision 0f9ad8cd: the |
| release recipe (three students averaged, cos blur 0.5, cos offset 0.04) |
| - Code: [ChaseHendrick/Scrolls](https://github.com/ChaseHendrick/Scrolls) `scripts/lasagnetta` at a011d5e4, tile 320 x 576 x 576 |
| - Channels: cos at OME-Zarr level 3 to 4 (2x down from the level read); grad_mag, nx, ny at level 4 (4x down) |
| - Run: 26 parts on Hugging Face Jobs (RTX PRO 6000), one x, y, z box each. Every part edge sits on a |
| multiple of 512 scan voxels, so every chunk of every level was written by exactly one part, and the parts together |
| are the whole field. Values are kept only where the masked scan holds CT; everywhere else is fill 0. |
| - Previews: xy at z about 37,664 and xz at y about 13,360 (full-resolution voxels), from OME-Zarr level 4. |
| |
| ## How close to villa |
| |
| Lasagnetta copies villa's lasagna net and runs about 5 times faster. On 30 crops of this scan that no student had |
| trained on, it matched villa's sheet crossings at peak F1 0.870 (crossings matched within one cos voxel; 25 |
| Oct 2026). The [model card](https://huggingface.co/SharpMeow/lasagnetta) has the method and the pooled numbers. The release's self-check, run on this whole volume, kept Lasagnetta here (median peak F1 over its spots 0.82 or more). |
| |
|  |
| |
| ## Notes |
| |
| Model output: a preview of another model's output, not a reading of any text. |
| villa's own field stays the reference where exact values matter. |
| |
| The scan also holds a second, less dense object (the upper one in the xy preview). There the scan shows few layers, cos is nearly flat, and it changes level at some part edges. |
| |
| ## Related |
| |
| The [Lasagnetta guide](https://github.com/ChaseHendrick/Scrolls/blob/main/docs/tools/lasagnetta.md) shows how to run it on your own region, with a self-check that tells you where to |
| use villa's net instead. villa lasagna fields for ten more scans are on the [Lasagna Fields](https://huggingface.co/spaces/SharpMeow/lasagna-fields) page. |
| |
| ## Credit and terms |
| |
| The scan is Vesuvius Challenge open data, CC BY-NC 4.0; this derived field is shared under the same terms. Lasagnetta |
| copies villa's lasagna ([ScrollPrize/villa](https://github.com/ScrollPrize/villa), weights |
| [scrollprize/lasagna](https://huggingface.co/scrollprize/lasagna), MIT); credit to its authors. Shared by Chase Hendrick. |
| |
