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| # Connect your tool: Fiber Checker | |
| The Space reads open-data meshes and CT by URL and keeps none of it; here are the same sources for your own tools, and the page's API and MCP server, which checks any segment with the free judge. | |
| Checked 2026-10-26. Generated from `connect.json` by `kit spaceconnect` in [ChaseHendrick/Scrolls](https://github.com/ChaseHendrick/Scrolls). | |
| ## A traced segment's mesh: PHerc0500P2 z_dbg_gen_00440 on the 2.215 um scan | |
| `https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/segments/20250611171318-z_dbg_gen_00440_inp_hr/mesh/20250611171318-on-20250526151718-2.215um.tifxyz/` | |
| License: CC BY-NC 4.0 (Vesuvius Challenge open data). x.tif, y.tif and z.tif in the scan's level-0 voxels. fiber.tif from a check has the same grid, so it lines up vertex for vertex. | |
| ### Python (numpy, tifffile) (tested 2026-10-24) | |
| ```python | |
| # pip install numpy tifffile | |
| import io, json, urllib.request | |
| import numpy as np, tifffile | |
| T = "https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/segments/20250611171318-z_dbg_gen_00440_inp_hr/mesh/20250611171318-on-20250526151718-2.215um.tifxyz" | |
| meta = json.load(urllib.request.urlopen(T + "/meta.json")) # scale, bbox, format | |
| get = lambda c: tifffile.imread(io.BytesIO(urllib.request.urlopen(f"{T}/{c}.tif").read())) | |
| xyz = np.stack([get(c) for c in "xyz"], -1) # xyz[i, j] = (x, y, z) in scan voxels; -1 = no surface | |
| ``` | |
| ## The CT that mesh is on, PHerc0500P2 2.215 um | |
| `https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/volumes/20250526151718-2.215um-0.4m-111keV-masked.zarr` | |
| License: CC BY-NC 4.0 (Vesuvius Challenge open data). Read live from the open-data bucket, never copied here. The free judge reads level 2 of the 2.2 to 2.4 um scans (about 9 um). | |
| ### Python (zarr) (tested 2026-10-24) | |
| ```python | |
| # pip install "zarr>=3" fsspec aiohttp | |
| import zarr | |
| root = zarr.open_group("https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/volumes/20250526151718-2.215um-0.4m-111keV-masked.zarr", mode="r") # OME-Zarr, zarr v2 | |
| a = root["2"] # level 0 is full resolution; level L is 2**L times coarser | |
| print(a.shape, a.dtype, a.chunks) | |
| block = a[1500:1564, 2000:2064, 3000:3064] # (z, y, x); reads only the chunks it touches | |
| ``` | |
| ### villa's vesuvius package (tested 2026-10-24) | |
| ```python | |
| # pip install "vesuvius[volume-only]" | |
| from vesuvius import Volume | |
| v = Volume(type="zarr", path="https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/volumes/20250526151718-2.215um-0.4m-111keV-masked.zarr/2") # one pyramid level | |
| block = v[1500:1564, 2000:2064, 3000:3064] | |
| ``` | |
| ### VC3D (from villa's source) | |
| ```text | |
| In VC3D (villa's volume-cartographer), open or create a project, then | |
| File > Attach Remote Zarr... and paste: | |
| https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/volumes/20250526151718-2.215um-0.4m-111keV-masked.zarr | |
| It accepts http, https and s3 OME-Zarr roots. | |
| ``` | |
| ### neuroglancer (tested 2026-10-24) | |
| ```text | |
| https://neuroglancer-demo.appspot.com/#!%7B%22layers%22%3A%5B%7B%22type%22%3A%22image%22%2C%22source%22%3A%22zarr%3A%2F%2Fhttps%3A%2F%2Fvesuvius-challenge-open-data.s3.us-east-1.amazonaws.com%2FPHerc0500P2%2Fvolumes%2F20250526151718-2.215um-0.4m-111keV-masked.zarr%2F%22%2C%22name%22%3A%22The%20CT%20that%20mesh%20is%20on%2C%20PHerc0500P2%202.215%20um%22%7D%5D%2C%22layout%22%3A%224panel%22%7D | |
| ``` | |
| ### curl (tested 2026-10-24) | |
| ```bash | |
| curl -s https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/volumes/20250526151718-2.215um-0.4m-111keV-masked.zarr/.zattrs # OME multiscales metadata | |
| curl -s https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0500P2/volumes/20250526151718-2.215um-0.4m-111keV-masked.zarr/2/.zarray # one level: shape, chunks, dtype, codec | |
| ``` | |
| ## Check any segment, from code or an agent | |
| `https://huggingface.co/spaces/SharpMeow/fiber-checker` | |
| License: Code and weights Apache 2.0; scans and meshes CC BY-NC 4.0. check_segment (sample, segment, volume, patches) runs the free judge on the Space's CPU, about two minutes for 60 patches. Model output, not a reading. | |
| ### Python /list_scrolls (tested 2026-10-24) | |
| ```python | |
| # pip install gradio_client | |
| from gradio_client import Client | |
| client = Client("SharpMeow/fiber-checker") | |
| result = client.predict(api_name="/list_scrolls") | |
| ``` | |
| ### Python /example_segments (tested 2026-10-24) | |
| ```python | |
| # pip install gradio_client | |
| from gradio_client import Client | |
| client = Client("SharpMeow/fiber-checker") | |
| result = client.predict(api_name="/example_segments") | |
| ``` | |
| ### Python /list_segments (tested 2026-10-24) | |
| ```python | |
| # pip install gradio_client | |
| from gradio_client import Client | |
| client = Client("SharpMeow/fiber-checker") | |
| result = client.predict(sample="PHerc0343P", api_name="/list_segments") | |
| ``` | |
| ### curl /list_scrolls (tested 2026-10-24) | |
| ```bash | |
| URL=https://sharpmeow-fiber-checker.hf.space | |
| EVENT=$(curl -s -X POST $URL/gradio_api/call/list_scrolls -H 'Content-Type: application/json' \ | |
| -d '{"data": []}' | python3 -c 'import json,sys; print(json.load(sys.stdin)["event_id"])') | |
| curl -sN $URL/gradio_api/call/list_scrolls/$EVENT | |
| ``` | |
| ### MCP (Claude, Cursor and other agents) (tested 2026-10-24) | |
| ```json | |
| { | |
| "mcpServers": { | |
| "fiber-checker": { | |
| "url": "https://sharpmeow-fiber-checker.hf.space/gradio_api/mcp/sse" | |
| } | |
| } | |
| } | |
| Tool list: https://sharpmeow-fiber-checker.hf.space/gradio_api/mcp/schema | |
| ``` | |