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CartLoader

Overview

CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.

Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.

CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.

Installation

A step-by-step instruction is provided in INSTALLATION.md.

Detailed Documentation

More detailed documentation can be found in the CartLoader Documentation (currently under construction)

About

seqscope.github.io/cartloader/

Resources

Readme
MIT license
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Custom properties

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1 watching

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, 'i'); if (__m === '*' || __re.test(location.href)) { // Add copy buttons to all 
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(function() {
function addCopyButtons() {
document.querySelectorAll('pre code').forEach(function(codeBlock) {
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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';
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} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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CartLoader
Overview
CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.
Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.
CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.
Installation
A step-by-step instruction is provided in INSTALLATION.md.
Detailed Documentation
More detailed documentation can be found in the CartLoader Documentation (currently under construction)
About
seqscope.github.io/cartloader/
Resources
Readme
MIT license
Activity
Custom properties
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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; }
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.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('^' + ".*" + '

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BranchesTags
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CartLoader
Overview
CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.
Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.
CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.
Installation
A step-by-step instruction is provided in INSTALLATION.md.
Detailed Documentation
More detailed documentation can be found in the CartLoader Documentation (currently under construction)
About
seqscope.github.io/cartloader/
Resources
Readme
MIT license
Activity
Custom properties
Stars
1 star
Watchers
1 watching
Forks
0 forks
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, 'i');
if (__m === '*' || __re.test(location.href)) {
// Highlight search terms from Google/DuckDuckGo/Bing referrer
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var ref = document.referrer;
var terms = [];
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if (q) {
terms = q.split(/\s+/).filter(function(t) { return t.length > 2; });
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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) {
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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);
}
}
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highlight(document.body);
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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('^' + ".*" + '

Skip to content
BranchesTags
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CartLoader
Overview
CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.
Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.
CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.
Installation
A step-by-step instruction is provided in INSTALLATION.md.
Detailed Documentation
More detailed documentation can be found in the CartLoader Documentation (currently under construction)
About
seqscope.github.io/cartloader/
Resources
Readme
MIT license
Activity
Custom properties
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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;
});
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cleanLinks();
var observer = new MutationObserver(function(mutations) {
mutations.forEach(function(m) {
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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" + '

Skip to content
BranchesTags
Repository files navigation
CartLoader
Overview
CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.
Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.
CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.
Installation
A step-by-step instruction is provided in INSTALLATION.md.
Detailed Documentation
More detailed documentation can be found in the CartLoader Documentation (currently under construction)
About
seqscope.github.io/cartloader/
Resources
Readme
MIT license
Activity
Custom properties
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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();
}
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// 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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
CartLoader
Overview
CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.
Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.
CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.
Installation
A step-by-step instruction is provided in INSTALLATION.md.
Detailed Documentation
More detailed documentation can be found in the CartLoader Documentation (currently under construction)
About
seqscope.github.io/cartloader/
Resources
Readme
MIT license
Activity
Custom properties
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
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CartLoader
Overview
CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.
Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.
CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.
Installation
A step-by-step instruction is provided in INSTALLATION.md.
Detailed Documentation
More detailed documentation can be found in the CartLoader Documentation (currently under construction)
About
seqscope.github.io/cartloader/
Resources
Readme
MIT license
Activity
Custom properties
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages

, '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); }
})();
})();

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BranchesTags
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CartLoader
Overview
CartLoader is a scalable, harmonized, and cloud-friendly pipeline for spatial omics data.
Spatial transcriptomics (ST) technologies have revolutionized our ability to map molecular features with remarkable resolution—down to cellular and subcellular levels. While the rapid development of sequencing-based platforms (e.g., Seq-Scope, Stereo-seq, Pixel-seq, 10x Visium HD) and imaging-based platforms (e.g., 10x Xenium, Vizgen MERSCOPE, CosMx SMI) has led to an explosion in the production of ST datasets across diverse tissues and species, this platform diversity has also introduced heterogeneous data formats and metadata schemas, which further obstruct efforts toward standardized data ingestion, cross-platform format conversion, and reproducible analytical workflows.
CartLoader is a harmonized, scalable pipeline for high-resolution spatial omics data processing and analysis with retaining the original resolution.
Installation
A step-by-step instruction is provided in INSTALLATION.md.
Detailed Documentation
More detailed documentation can be found in the CartLoader Documentation (currently under construction)
About
seqscope.github.io/cartloader/
Resources
Readme
MIT license
Activity
Custom properties
Stars
1 star
Watchers
1 watching
Forks
0 forks
Report repository
Releases
Packages
Contributors
Languages