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Linajea

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Linajea

This is the main software repository for the linajea cell tracking project. It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.

Installation

git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning

The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main. The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility. A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.

Use

Have a look at the jupyter notebook examples or look at the run scripts directly.

Contributing

If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge. Help is always appreciated!

Other

If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!

About

No description, website, or topics provided.

Resources

Readme
MIT license
Activity
Custom properties

Stars

19 stars

Watchers

5 watching

Forks

6 forks
Report repository

Releases

Packages

Used by

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n 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;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
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Linajea
Publications
Linajea
This is the main software repository for the linajea cell tracking project.
It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.
Installation
git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning
The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main.
The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility.
A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.
Use
Have a look at the jupyter notebook examples or look at the run scripts directly.
Contributing
If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge.
Help is always appreciated!
Other
If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!
About
No description, website, or topics provided.
Resources
Readme
MIT license
Activity
Custom properties
Stars
19 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
Linajea
Publications
Linajea
This is the main software repository for the linajea cell tracking project.
It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.
Installation
git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning
The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main.
The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility.
A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.
Use
Have a look at the jupyter notebook examples or look at the run scripts directly.
Contributing
If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge.
Help is always appreciated!
Other
If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!
About
No description, website, or topics provided.
Resources
Readme
MIT license
Activity
Custom properties
Stars
19 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
Linajea
Publications
Linajea
This is the main software repository for the linajea cell tracking project.
It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.
Installation
git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning
The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main.
The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility.
A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.
Use
Have a look at the jupyter notebook examples or look at the run scripts directly.
Contributing
If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge.
Help is always appreciated!
Other
If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!
About
No description, website, or topics provided.
Resources
Readme
MIT license
Activity
Custom properties
Stars
19 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} 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
Linajea
Publications
Linajea
This is the main software repository for the linajea cell tracking project.
It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.
Installation
git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning
The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main.
The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility.
A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.
Use
Have a look at the jupyter notebook examples or look at the run scripts directly.
Contributing
If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge.
Help is always appreciated!
Other
If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!
About
No description, website, or topics provided.
Resources
Readme
MIT license
Activity
Custom properties
Stars
19 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} 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
Linajea
Publications
Linajea
This is the main software repository for the linajea cell tracking project.
It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.
Installation
git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning
The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main.
The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility.
A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.
Use
Have a look at the jupyter notebook examples or look at the run scripts directly.
Contributing
If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge.
Help is always appreciated!
Other
If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!
About
No description, website, or topics provided.
Resources
Readme
MIT license
Activity
Custom properties
Stars
19 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
Linajea
Publications
Linajea
This is the main software repository for the linajea cell tracking project.
It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.
Installation
git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning
The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main.
The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility.
A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.
Use
Have a look at the jupyter notebook examples or look at the run scripts directly.
Contributing
If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge.
Help is always appreciated!
Other
If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!
About
No description, website, or topics provided.
Resources
Readme
MIT license
Activity
Custom properties
Stars
19 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages

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

Skip to content
BranchesTags
Repository files navigation
Linajea
Publications
Linajea
This is the main software repository for the linajea cell tracking project.
It includes tools and infrastructure for running a pipeline that starts from 3d+time light sheet data and ends in extracted cell lineage tracks.
Installation
git clone https://github.com/funkelab/linajea.git
cd linajea
conda create --name linajea python pytorch pylp -c pytorch -c funkey
conda activate linajea
pip install numpy cython jupyter
pip install -r requirements.txt
pip install -e .

Versioning
The main branch contains the current version of the code. New features and bugfixes will be developed in separate branches before being merged into main.
The experiments in the Nature Biotechnology paper have been conducted with v1.3, the experiments in the MICCAI paper with v1.4 (see tags). For the public release we refactored major parts of the code, breaking backwards compatibility.
A separate repository (https://github.com/linajea/linajea_experiments) contains all the scripts necessary to replicate the paper results, using the appropriate release.
Use
Have a look at the jupyter notebook examples or look at the run scripts directly.
Contributing
If you make any improvements to the software, please fork, create a new branch named descriptively for the feature you are upgrading or bug you are fixing, commit your changes to that branch, and create a pull request asking for permission to merge.
Help is always appreciated!
Other
If you have any questions and can't find the answers you need in the examples or in the code documentation, feel free to contact us!
About
No description, website, or topics provided.
Resources
Readme
MIT license
Activity
Custom properties
Stars
19 stars
Watchers
5 watching
Forks
6 forks
Report repository
Releases
Packages
Used by
Contributors
Languages