Spaces:

SharpMeow
/

umbilici

Running

App Files Files Community

umbilici / CONNECT.md

SharpMeow

Umbilici 1.10.0 from Scrolls main 50020b3a452eb431f739185e7e725c57f5987671, lines from center lines v2.6.1 (51603382)

3def64b verified 8 days ago

preview code

Raw History Blame Contribute Delete

6.42 kB

# Connect your tool: Umbilici

Every center line, CT scan and lasagna field on this page reads straight from these URLs, with no account and no download step. Each scan card also has its own OME-Zarr URL and an Open in neuroglancer link.

Checked 2026-10-24. Generated from `connect.json` by `kit spaceconnect` in [ChaseHendrick/Scrolls](https://github.com/ChaseHendrick/Scrolls).

## Center lines (every line, every scan)

`https://huggingface.co/datasets/SharpMeow/vesuvius-center-lines`

License: CC BY-NC 4.0 bundle; each file keeps its own license (MIT, CC BY 4.0 or CC BY-NC 4.0, listed in index.json). Files under lines/ are in VC3D's umbilicus JSON format, level-0 voxels (x, y, z).

### Python (huggingface_hub) (tested 2026-10-24)
```python
# pip install huggingface_hub
from huggingface_hub import hf_hub_download, snapshot_download

path = hf_hub_download("SharpMeow/vesuvius-center-lines", "index.json", repo_type="dataset")  # one file, cached
folder = snapshot_download("SharpMeow/vesuvius-center-lines", repo_type="dataset")
```
### Python (datasets) (tested 2026-10-24)
```python
# pip install datasets
from datasets import load_dataset

lines = load_dataset("SharpMeow/vesuvius-center-lines", "lines", split="train")
points = load_dataset("SharpMeow/vesuvius-center-lines", "points", split="train")
```
### pandas (tested 2026-10-24)
```python
# pip install pandas huggingface_hub
import pandas as pd
df = pd.read_json("hf://datasets/SharpMeow/vesuvius-center-lines/tables/points.jsonl", lines=True)
```
### Command line (hf) (tested 2026-10-24)
```bash
pip install -U huggingface_hub
hf download SharpMeow/vesuvius-center-lines index.json --repo-type dataset --local-dir vesuvius-center-lines
```
### curl (tested 2026-10-24)
```bash
curl -L -O https://huggingface.co/datasets/SharpMeow/vesuvius-center-lines/resolve/main/index.json
```
## X-ray CT, example PHerc0125 (each scan card has its own URL)
`https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr`
License: CC BY-NC 4.0 (Vesuvius Challenge open data). Read live from the open-data bucket, never copied here. uint8, 128^3 chunks, no compressor, 6 levels.
### 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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-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[2600:2664, 1000:1064, 1000:1064]  # (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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr/2")  # one pyramid level
block = v[2600:2664, 1000:1064, 1000:1064]
```
### 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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-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%2FPHerc0125%2Fvolumes%2F20250821151825-9.362um-1.2m-113keV-masked.zarr%2F%22%2C%22name%22%3A%22X-ray%20CT%2C%20example%20PHerc0125%20%28each%20scan%20card%20has%20its%20own%20URL%29%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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr/.zattrs            # OME multiscales metadata
curl -s https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr/2/.zarray     # one level: shape, chunks, dtype, codec
```
## Lasagna field, PHerc0175A
`https://huggingface.co/datasets/SharpMeow/pherc0175a-lasagna`
License: CC BY-NC 4.0. villa lasagna predict3d output (scrollprize/lasagna); model output, not checked by eye.
### Python (huggingface_hub) (tested 2026-10-24)
```python
# pip install huggingface_hub
from huggingface_hub import hf_hub_download, snapshot_download
path = hf_hub_download("SharpMeow/pherc0175a-lasagna", "README.md", repo_type="dataset")  # one file, cached
folder = snapshot_download("SharpMeow/pherc0175a-lasagna", repo_type="dataset")  # large; allow_patterns=[...] fetches part of it
```
### Command line (hf) (tested 2026-10-24)
```bash
pip install -U huggingface_hub
hf download SharpMeow/pherc0175a-lasagna README.md --repo-type dataset --local-dir pherc0175a-lasagna
```
### curl (tested 2026-10-24)
```bash
curl -L -O https://huggingface.co/datasets/SharpMeow/pherc0175a-lasagna/resolve/main/README.md
```
## Lasagna fields, ten scans
`https://huggingface.co/spaces/SharpMeow/lasagna-fields`
License: CC BY-NC 4.0. villa lasagna predict3d output (model output) for ten scans, public and read live: each scan's cos, grad_mag, nx and ny fields as OME-Zarr plus a SCAN.lasagna.json for VC3D's Attach Remote Lasagna Manifest. That Space has its own Connect your tool section.
### Links and embed (tested 2026-10-24)
```text
Lasagna Fields: every field's OME-Zarr URL, VC3D manifest and tested snippets: https://huggingface.co/spaces/SharpMeow/lasagna-fields
```
## This page's own data and API
`https://sharpmeow-umbilici.static.hf.space/`
License: Page code Apache 2.0; data as above. In a browser or headless Chromium, window.umbilici has scans(), lines(scroll), at(scroll, z), csv(...) and more (Guide, For researchers).
### Links and embed (tested 2026-10-24)
```text
Every line, scan and CT pyramid as one JSON: https://huggingface.co/spaces/SharpMeow/umbilici/resolve/main/data/lines.json
Open a scan in a given mode and height: https://sharpmeow-umbilici.static.hf.space/?mode=scan&scan=PHerc0191&z=10400
Page source and build scripts: https://huggingface.co/spaces/SharpMeow/umbilici/tree/main
```

	# Connect your tool: Umbilici

	Every center line, CT scan and lasagna field on this page reads straight from these URLs, with no account and no download step. Each scan card also has its own OME-Zarr URL and an Open in neuroglancer link.

	Checked 2026-10-24. Generated from `connect.json` by `kit spaceconnect` in [ChaseHendrick/Scrolls](https://github.com/ChaseHendrick/Scrolls).

	## Center lines (every line, every scan)

	`https://huggingface.co/datasets/SharpMeow/vesuvius-center-lines`

	License: CC BY-NC 4.0 bundle; each file keeps its own license (MIT, CC BY 4.0 or CC BY-NC 4.0, listed in index.json). Files under lines/ are in VC3D's umbilicus JSON format, level-0 voxels (x, y, z).

	### Python (huggingface_hub) (tested 2026-10-24)

	```python
	# pip install huggingface_hub
	from huggingface_hub import hf_hub_download, snapshot_download

	path = hf_hub_download("SharpMeow/vesuvius-center-lines", "index.json", repo_type="dataset") # one file, cached
	folder = snapshot_download("SharpMeow/vesuvius-center-lines", repo_type="dataset")
	```

	### Python (datasets) (tested 2026-10-24)

	```python
	# pip install datasets
	from datasets import load_dataset

	lines = load_dataset("SharpMeow/vesuvius-center-lines", "lines", split="train")
	points = load_dataset("SharpMeow/vesuvius-center-lines", "points", split="train")
	```

	### pandas (tested 2026-10-24)

	```python
	# pip install pandas huggingface_hub
	import pandas as pd

	df = pd.read_json("hf://datasets/SharpMeow/vesuvius-center-lines/tables/points.jsonl", lines=True)
	```

	### Command line (hf) (tested 2026-10-24)

	```bash
	pip install -U huggingface_hub
	hf download SharpMeow/vesuvius-center-lines index.json --repo-type dataset --local-dir vesuvius-center-lines
	```

	### curl (tested 2026-10-24)

	```bash
	curl -L -O https://huggingface.co/datasets/SharpMeow/vesuvius-center-lines/resolve/main/index.json
	```

	## X-ray CT, example PHerc0125 (each scan card has its own URL)

	`https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr`

	License: CC BY-NC 4.0 (Vesuvius Challenge open data). Read live from the open-data bucket, never copied here. uint8, 128^3 chunks, no compressor, 6 levels.

	### 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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-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[2600:2664, 1000:1064, 1000:1064] # (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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr/2") # one pyramid level
	block = v[2600:2664, 1000:1064, 1000:1064]
	```

	### 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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-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%2FPHerc0125%2Fvolumes%2F20250821151825-9.362um-1.2m-113keV-masked.zarr%2F%22%2C%22name%22%3A%22X-ray%20CT%2C%20example%20PHerc0125%20%28each%20scan%20card%20has%20its%20own%20URL%29%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/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr/.zattrs # OME multiscales metadata
	curl -s https://vesuvius-challenge-open-data.s3.us-east-1.amazonaws.com/PHerc0125/volumes/20250821151825-9.362um-1.2m-113keV-masked.zarr/2/.zarray # one level: shape, chunks, dtype, codec
	```

	## Lasagna field, PHerc0175A

	`https://huggingface.co/datasets/SharpMeow/pherc0175a-lasagna`

	License: CC BY-NC 4.0. villa lasagna predict3d output (scrollprize/lasagna); model output, not checked by eye.

	### Python (huggingface_hub) (tested 2026-10-24)

	```python
	# pip install huggingface_hub
	from huggingface_hub import hf_hub_download, snapshot_download

	path = hf_hub_download("SharpMeow/pherc0175a-lasagna", "README.md", repo_type="dataset") # one file, cached
	folder = snapshot_download("SharpMeow/pherc0175a-lasagna", repo_type="dataset") # large; allow_patterns=[...] fetches part of it
	```

	### Command line (hf) (tested 2026-10-24)

	```bash
	pip install -U huggingface_hub
	hf download SharpMeow/pherc0175a-lasagna README.md --repo-type dataset --local-dir pherc0175a-lasagna
	```

	### curl (tested 2026-10-24)

	```bash
	curl -L -O https://huggingface.co/datasets/SharpMeow/pherc0175a-lasagna/resolve/main/README.md
	```

	## Lasagna fields, ten scans

	`https://huggingface.co/spaces/SharpMeow/lasagna-fields`

	License: CC BY-NC 4.0. villa lasagna predict3d output (model output) for ten scans, public and read live: each scan's cos, grad_mag, nx and ny fields as OME-Zarr plus a SCAN.lasagna.json for VC3D's Attach Remote Lasagna Manifest. That Space has its own Connect your tool section.

	### Links and embed (tested 2026-10-24)

	```text
	Lasagna Fields: every field's OME-Zarr URL, VC3D manifest and tested snippets: https://huggingface.co/spaces/SharpMeow/lasagna-fields
	```

	## This page's own data and API

	`https://sharpmeow-umbilici.static.hf.space/`

	License: Page code Apache 2.0; data as above. In a browser or headless Chromium, window.umbilici has scans(), lines(scroll), at(scroll, z), csv(...) and more (Guide, For researchers).

	### Links and embed (tested 2026-10-24)

	```text
	Every line, scan and CT pyramid as one JSON: https://huggingface.co/spaces/SharpMeow/umbilici/resolve/main/data/lines.json
	Open a scan in a given mode and height: https://sharpmeow-umbilici.static.hf.space/?mode=scan&scan=PHerc0191&z=10400
	Page source and build scripts: https://huggingface.co/spaces/SharpMeow/umbilici/tree/main
	```