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chore: fix precommit
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1 change: 1 addition & 0 deletions docs/index.md
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Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
Expand Down
16 changes: 16 additions & 0 deletions docs/interoperability.md
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@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.
4 changes: 2 additions & 2 deletions src/spatialdata/_io/io_zarr.py
View file
Open in desktop
Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
reader_format = get_raster_format_for_read(elem_group, sdata_version)
element = read_func(
elem_group_path,
cast(Literal["image", "labels"], element_type),
element_type,
reader_format,
)
elif element_type in ["shapes", "points", "tables"]:
Expand Down
, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
 blocks
(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;
codeBlock.parentElement.setAttribute('data-copy-added', 'true');
var btn = document.createElement('button');
btn.textContent = 'Copy';
btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';
btn.onmouseover = function() { this.style.opacity = '1'; };
btn.onmouseout = function() { this.style.opacity = '0.7'; };
btn.onclick = function() {
navigator.clipboard.writeText(codeBlock.textContent).then(function() {
btn.textContent = 'Copied!';
setTimeout(function() { btn.textContent = 'Copy'; }, 1500);
});
};
codeBlock.parentElement.style.position = 'relative';
codeBlock.parentElement.appendChild(btn);
});
}
addCopyButtons();
// Re-run on dynamic content
var observer = new MutationObserver(addCopyButtons);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '
docs: add interoperability page by jan-glx · Pull Request #1180 · scverse/spatialdata · GitHub
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docs: add interoperability page#1180

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LucaMarconato
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chore: fix precommit


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Original file line numberDiff line numberDiff line change
Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
Expand Down

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docs/interoperability.md

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
 reader_format = get_raster_format_for_read(elem_group, sdata_version)
 element = read_func(
 elem_group_path,
cast(Literal["image", "labels"], element_type),
 element_type,
 reader_format,
 )
 elif element_type in ["shapes", "points", "tables"]:
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Force GitHub README to respect dark mode
(function() {
var style = document.createElement('style');
style.textContent = '
.markdown-body {
color-scheme: dark light;
}
.markdown-body pre { background: #161b22 !important; }
.markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }
.markdown-body table th, .markdown-body table td { border-color: #30363d !important; }
.markdown-body img { background: #0d1117; }
.markdown-body blockquote { border-left-color: #8b949e; }
.markdown-body hr { border-color: #30363d; }
';
document.head.appendChild(style);
})();
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
docs: add interoperability page by jan-glx · Pull Request #1180 · scverse/spatialdata · GitHub
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docs: add interoperability page#1180

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LucaMarconato
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chore: fix precommit


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Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
Expand Down

16 changes: 16 additions & 0 deletions
docs/interoperability.md

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Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
 reader_format = get_raster_format_for_read(elem_group, sdata_version)
 element = read_func(
 elem_group_path,
cast(Literal["image", "labels"], element_type),
 element_type,
 reader_format,
 )
 elif element_type in ["shapes", "points", "tables"]:
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
(function() {
var ref = document.referrer;
var terms = [];
if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {
var url = new URL(ref);
var q = url.searchParams.get('q') || url.searchParams.get('p');
if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
}
}
if (terms.length === 0) return;
var style = document.createElement('style');
style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';
document.head.appendChild(style);
function highlight(node) {
if (node.nodeType === 3) { // text node
var text = node.textContent;
var found = false;
terms.forEach(function(term) {
var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\]\\]/g, '\\') + ')', 'gi');
if (regex.test(text)) {
found = true;
var frag = document.createDocumentFragment();
var parts = text.split(regex);
parts.forEach(function(part, i) {
if (i % 2 === 0) {
frag.appendChild(document.createTextNode(part));
} else {
var span = document.createElement('span');
span.className = 'userscript-highlight';
span.textContent = part;
frag.appendChild(span);
}
});
node.parentNode.replaceChild(frag, node);
}
});
} else if (node.nodeType === 1 && node.childNodes) { // element
var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];
if (!skipTags.includes(node.tagName)) {
Array.from(node.childNodes).forEach(highlight);
}
}
}
highlight(document.body);
// Re-highlight on dynamic content
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1 || node.nodeType === 3) highlight(node);
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
docs: add interoperability page by jan-glx · Pull Request #1180 · scverse/spatialdata · GitHub
Skip to content
docs: add interoperability page#1180

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chore: fix precommit


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Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
Expand Down

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docs/interoperability.md

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
 reader_format = get_raster_format_for_read(elem_group, sdata_version)
 element = read_func(
 elem_group_path,
cast(Literal["image", "labels"], element_type),
 element_type,
 reader_format,
 )
 elif element_type in ["shapes", "points", "tables"]:
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Strip utm_, fbclid, gclid, etc. from all links on page
(function() {
var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',
'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',
'ref', 'ref_src', 'source', 'medium', 'campaign'];
function cleanUrl(url) {
try {
var u = new URL(url, window.location.origin);
var changed = false;
trackingParams.forEach(function(p) {
if (u.searchParams.has(p)) {
u.searchParams.delete(p);
changed = true;
}
});
return changed ? u.toString() : url;
} catch (e) {
return url;
}
}
function cleanLinks() {
document.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
m.addedNodes.forEach(function(node) {
if (node.nodeType === 1) {
if (node.tagName === 'A') cleanLinks();
node.querySelectorAll('a[href]').forEach(function(a) {
var clean = cleanUrl(a.href);
if (clean !== a.href) a.href = clean;
});
}
});
});
});
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '
docs: add interoperability page by jan-glx · Pull Request #1180 · scverse/spatialdata · GitHub
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docs: add interoperability page#1180

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Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
Expand Down

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docs/interoperability.md

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
 reader_format = get_raster_format_for_read(elem_group, sdata_version)
 element = read_func(
 elem_group_path,
cast(Literal["image", "labels"], element_type),
 element_type,
 reader_format,
 )
 elif element_type in ["shapes", "points", "tables"]:
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Auto-enable theater mode on YouTube
(function() {
function tryTheater() {
var btn = document.querySelector('button[aria-label="Theater mode"], ytd-player #player button[title="Theater mode"]');
if (btn && !btn.classList.contains('activated')) {
btn.click();
}
}
// Try immediately
tryTheater();
// Try after navigation (SPA)
var lastUrl = location.href;
setInterval(function() {
if (location.href !== lastUrl) {
lastUrl = location.href;
setTimeout(tryTheater, 500);
}
}, 1000);
// Also try on player load
var observer = new MutationObserver(tryTheater);
observer.observe(document.body, { childList: true, subtree: true });
})();
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
docs: add interoperability page by jan-glx · Pull Request #1180 · scverse/spatialdata · GitHub
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docs: add interoperability page#1180

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Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
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docs/interoperability.md

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@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
 reader_format = get_raster_format_for_read(elem_group, sdata_version)
 element = read_func(
 elem_group_path,
cast(Literal["image", "labels"], element_type),
 element_type,
 reader_format,
 )
 elif element_type in ["shapes", "points", "tables"]:
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Remove or un-stick sticky/fixed headers that block content
(function() {
function unstick() {
document.querySelectorAll('header, nav, [role="banner"], .header, .navbar, .sticky, .fixed-top, [style*="position: fixed"], [style*="position:sticky"]').forEach(function(el) {
if (el.style.position === 'fixed' || el.style.position === 'sticky' || getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {
el.style.position = 'static';
el.style.top = 'auto';
el.style.zIndex = 'auto';
}
});
}
unstick();
var observer = new MutationObserver(unstick);
observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });
})();
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '
docs: add interoperability page by jan-glx · Pull Request #1180 · scverse/spatialdata · GitHub
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docs: add interoperability page#1180

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docs: add interoperability page


jan-glx Aug 18, 2026
8b9ba34

chore: fix precommit


LucaMarconato Aug 19, 2026

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docs/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
Expand Down

16 changes: 16 additions & 0 deletions
docs/interoperability.md

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
 reader_format = get_raster_format_for_read(elem_group, sdata_version)
 element = read_func(
 elem_group_path,
cast(Literal["image", "labels"], element_type),
 element_type,
 reader_format,
 )
 elif element_type in ["shapes", "points", "tables"]:
Expand Down

, 'i');
if (__m === '*' || __re.test(location.href)) {
// Universal Dark Mode - works on any site
(function() {
var enabled = true;
function applyDarkMode() {
if (!enabled) return;
// Create style element if it doesn't exist
var style = document.getElementById('universal-dark-mode-style');
if (!style) {
style = document.createElement('style');
style.id = 'universal-dark-mode-style';
document.head.appendChild(style);
}
// Dark mode CSS - inverts colors but preserves images/video
style.textContent = '
/* Invert everything except media */
html {
filter: invert(1) hue-rotate(180deg) !important;
background: #1a1a2e !important;
}
/* Restore images, videos, iframes, canvas */
img, video, iframe, canvas, svg, picture, [style*="background-image"] {
filter: invert(1) hue-rotate(180deg) !important;
}
/* Preserve specific elements that should not be inverted */
.no-dark-mode, .no-dark-mode *,
[data-theme="light"], [data-theme="light"],
.ace_editor, .ace_editor *,
.CodeMirror, .CodeMirror *,
.monaco-editor, .monaco-editor *,
.markdown-body pre, .markdown-body pre *,
.highlight, .highlight *,
pre code, pre code * {
filter: none !important;
}
/* Fix common UI elements */
.modal, .popup, .dropdown-menu, .tooltip, .popover {
filter: invert(1) hue-rotate(180deg) !important;
background: #2d2d44 !important;
border-color: #444 !important;
}
/* Scrollbars */
::-webkit-scrollbar { background: #1a1a2e !important; }
::-webkit-scrollbar-thumb { background: #444 !important; }
::-webkit-scrollbar-thumb:hover { background: #555 !important; }
/* Selection */
::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }
';
}
function removeDarkMode() {
var style = document.getElementById('universal-dark-mode-style');
if (style) style.remove();
}
// Toggle with Alt+Shift+D
document.addEventListener('keydown', function(e) {
if (e.altKey && e.shiftKey && e.key === 'D') {
e.preventDefault();
enabled = !enabled;
if (enabled) {
applyDarkMode();
console.log('[Universal Dark Mode] Enabled');
} else {
removeDarkMode();
console.log('[Universal Dark Mode] Disabled');
}
}
});
// Apply on load
applyDarkMode();
// Re-apply on dynamic content
var observer = new MutationObserver(function(mutations) {
if (enabled && !document.getElementById('universal-dark-mode-style')) {
applyDarkMode();
}
});
observer.observe(document.head, { childList: true });
console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');
})();
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();
docs: add interoperability page by jan-glx · Pull Request #1180 · scverse/spatialdata · GitHub
Skip to content
docs: add interoperability page#1180

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 Merged

LucaMarconato
merged 2 commits into

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Aug 19, 2026

+19

−2

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docs: add interoperability page
#1180
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9c26df3

docs: add interoperability page


jan-glx Aug 18, 2026
8b9ba34

chore: fix precommit


LucaMarconato Aug 19, 2026

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docs/index.md

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Original file line numberDiff line numberDiff line change
Expand Up@@ -110,6 +110,7 @@ tutorials/notebooks/notebooks.md
tutorials/notebooks/datasets/README.md
glossary.md
design_doc.md
interoperability.md
contributing.md
changelog.md
references.md
Expand Down

16 changes: 16 additions & 0 deletions
docs/interoperability.md

View file


Open in desktop

Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
# Interoperability

The on-disk representation of SpatialData can be read from other languages. Here we list interfaces for working with SpatialData from your language of choice:

## R

- [spatialdataR](https://helenalc.github.io/spatialdataR/) provides an R implementation of the `SpatialData` object, with out-of-memory images and labels, `duckdb`-backed points and shapes, and tables represented as `SingleCellExperiment` objects.

## JavaScript and TypeScript

- [SpatialData.js](https://github.com/Taylor-CCB-Group/SpatialData.js) provides a TypeScript and JavaScript library for interfacing with SpatialData stores.
- [Vitessce](https://vitessce.io/docs/data-file-types/#spatialdatazarr) reads `spatialdata.zarr` stores directly and uses them for interactive visualization.

## File format

The SpatialData on-disk format builds on [OME-NGFF](https://ngff.openmicroscopy.org/latest/). See the [design document](design_doc.md) for details of the current on-disk layout.

4 changes: 2 additions & 2 deletions
src/spatialdata/_io/io_zarr.py

View file


Open in desktop

Original file line numberDiff line numberDiff line change
Expand Up@@ -5,7 +5,7 @@
from collections.abc import Callable
from json import JSONDecodeError
from pathlib import Path
from typing import Any, Literal, cast
from typing import Any, Literal

import zarr.storage
from anndata import AnnData
Expand DownExpand Up@@ -71,7 +71,7 @@ def _read_zarr_group_spatialdata_element(
 reader_format = get_raster_format_for_read(elem_group, sdata_version)
 element = read_func(
 elem_group_path,
cast(Literal["image", "labels"], element_type),
 element_type,
 reader_format,
 )
 elif element_type in ["shapes", "points", "tables"]:
Expand Down