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36 followers · 23 following

    Achievements

    Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor

    Achievements

    Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor

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    heylf/README.md

    Hi! I am Florian - Nice to meet you 👋

    💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.

    🔥 Key Projects

    Tools

    • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
    • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
    • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.

    Workflows

    Other Projects that I am supporting

    • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
    • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
    • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
    • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.

    📭 How to reach me:

    Pinned Loading

    1. spatialaxespatialaxePublic

      Forked from nf-core/spatialaxe

      A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

      Python

    2. spoQCspoQCPublic

      A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

      Python 10

    3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic

      Python 41 6

    4. task_spatial_segmentationtask_spatial_segmentationPublic

      Forked from openproblems-bio/task_spatial_segmentation

      Shell

    5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic

      Tool Shed repositories maintained by the Intergalactic Utilities Commission

      HTML 201 524

    , '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" + '

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    36
followers
 · 23
following

      Achievements
      Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
      Achievements
      Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
      
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      heylf/README.md
      Hi! I am Florian - Nice to meet you 👋
      💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.
      🔥 Key Projects
      Tools
      • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
      • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
      • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.
      Workflows
      Other Projects that I am supporting
      • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
      • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
      • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
      • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
      📭 How to reach me:
      
Pinned
Loading
      1. spatialaxespatialaxePublic
        
Forked from nf-core/spatialaxe
        
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

        Python
      2. spoQCspoQCPublic
        
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

        Python
10

      3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic
        Python
41

6

      4. task_spatial_segmentationtask_spatial_segmentationPublic
        
Forked from openproblems-bio/task_spatial_segmentation
        Shell
      5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic
        
Tool Shed repositories maintained by the Intergalactic Utilities Commission

        HTML
201

524

      
, '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
      View heylf's full-sized avatar
      36
followers
 · 23
following

        Achievements
        Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
        Achievements
        Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
        
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        heylf/README.md
        Hi! I am Florian - Nice to meet you 👋
        💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.
        🔥 Key Projects
        Tools
        • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
        • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
        • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.
        Workflows
        Other Projects that I am supporting
        • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
        • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
        • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
        • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
        📭 How to reach me:
        
Pinned
Loading
        1. spatialaxespatialaxePublic
          
Forked from nf-core/spatialaxe
          
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

          Python
        2. spoQCspoQCPublic
          
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

          Python
10

        3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic
          Python
41

6

        4. task_spatial_segmentationtask_spatial_segmentationPublic
          
Forked from openproblems-bio/task_spatial_segmentation
          Shell
        5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic
          
Tool Shed repositories maintained by the Intergalactic Utilities Commission

          HTML
201

524

        
, '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
        View heylf's full-sized avatar
        36
followers
 · 23
following

          Achievements
          Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
          Achievements
          Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
          
Block or report heylf

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          heylf/README.md
          Hi! I am Florian - Nice to meet you 👋
          💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.
          🔥 Key Projects
          Tools
          • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
          • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
          • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.
          Workflows
          Other Projects that I am supporting
          • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
          • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
          • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
          • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
          📭 How to reach me:
          
Pinned
Loading
          1. spatialaxespatialaxePublic
            
Forked from nf-core/spatialaxe
            
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

            Python
          2. spoQCspoQCPublic
            
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

            Python
10

          3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic
            Python
41

6

          4. task_spatial_segmentationtask_spatial_segmentationPublic
            
Forked from openproblems-bio/task_spatial_segmentation
            Shell
          5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic
            
Tool Shed repositories maintained by the Intergalactic Utilities Commission

            HTML
201

524

          
, '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
          View heylf's full-sized avatar
          36
followers
 · 23
following

            Achievements
            Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
            Achievements
            Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
            
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            heylf/README.md
            Hi! I am Florian - Nice to meet you 👋
            💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.
            🔥 Key Projects
            Tools
            • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
            • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
            • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.
            Workflows
            Other Projects that I am supporting
            • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
            • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
            • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
            • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
            📭 How to reach me:
            
Pinned
Loading
            1. spatialaxespatialaxePublic
              
Forked from nf-core/spatialaxe
              
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

              Python
            2. spoQCspoQCPublic
              
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

              Python
10

            3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic
              Python
41

6

            4. task_spatial_segmentationtask_spatial_segmentationPublic
              
Forked from openproblems-bio/task_spatial_segmentation
              Shell
            5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic
              
Tool Shed repositories maintained by the Intergalactic Utilities Commission

              HTML
201

524

            
, '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
            View heylf's full-sized avatar
            36
followers
 · 23
following

              Achievements
              Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
              Achievements
              Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
              
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              heylf/README.md
              Hi! I am Florian - Nice to meet you 👋
              💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.
              🔥 Key Projects
              Tools
              • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
              • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
              • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.
              Workflows
              Other Projects that I am supporting
              • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
              • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
              • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
              • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
              📭 How to reach me:
              
Pinned
Loading
              1. spatialaxespatialaxePublic
                
Forked from nf-core/spatialaxe
                
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

                Python
              2. spoQCspoQCPublic
                
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

                Python
10

              3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic
                Python
41

6

              4. task_spatial_segmentationtask_spatial_segmentationPublic
                
Forked from openproblems-bio/task_spatial_segmentation
                Shell
              5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic
                
Tool Shed repositories maintained by the Intergalactic Utilities Commission

                HTML
201

524

              
, '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
              View heylf's full-sized avatar
              36
followers
 · 23
following

                Achievements
                Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
                Achievements
                Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
                
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                heylf/README.md
                Hi! I am Florian - Nice to meet you 👋
                💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.
                🔥 Key Projects
                Tools
                • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
                • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
                • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.
                Workflows
                Other Projects that I am supporting
                • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
                • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
                • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
                • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
                📭 How to reach me:
                
Pinned
Loading
                1. spatialaxespatialaxePublic
                  
Forked from nf-core/spatialaxe
                  
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

                  Python
                2. spoQCspoQCPublic
                  
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

                  Python
10

                3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic
                  Python
41

6

                4. task_spatial_segmentationtask_spatial_segmentationPublic
                  
Forked from openproblems-bio/task_spatial_segmentation
                  Shell
                5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic
                  
Tool Shed repositories maintained by the Intergalactic Utilities Commission

                  HTML
201

524

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

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                  Achievements
                  Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
                  Achievements
                  Achievement: Pull Sharkx3Achievement: StarstruckAchievement: Pair Extraordinairex2Achievement: QuickdrawAchievement: YOLOAchievement: Arctic Code Vault Contributor
                  
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                  heylf/README.md
                  Hi! I am Florian - Nice to meet you 👋
                  💻 I’m currently developing scalable workflows and tools to analyze and process spatial omics and single-cell multi-omics data.
                  🔥 Key Projects
                  Tools
                  • spoQC 🖖 : modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics.
                  • StoatyDive: A tool to evaluate and classify predicted peak profiles to assess the binding specificity of a protein to its targets.
                  • LiMetrack: Lightweight, modular biosample management platform designed to streamline centralized research data handling and sample tracking within biomedical research projects.
                  Workflows
                  Other Projects that I am supporting
                  • nf-core/variantbenchmarking 🏃 : A standardized Nextflow pipeline for benchmarking variant-calling workflows, enabling reproducible and FAIR analysis.
                  • nf-core/scrnaseq: Bioinformatics best-practice analysis pipeline for processing 10x Genomics single-cell RNA-seq data.
                  • SACCELERATOR: A flexible framework for applying spatially aware clustering methods.
                  • nf-core/mcmicro: Nextflow pipeline for processing highly-multiplexed imaging data, as produced by technologies such as Cycif, MIBI, CODEX, SeqIF among others.
                  📭 How to reach me:
                  
Pinned
Loading
                  1. spatialaxespatialaxePublic
                    
Forked from nf-core/spatialaxe
                    
A bioinformatics best-practice processing and quality control pipeline for Xenium and Artera data

                    Python
                  2. spoQCspoQCPublic
                    
A modular framework for multimodal quality control (QC) of imaging-based spatially resolved transcriptomics (SRT).

                    Python
10

                  3. SpatialHackathon/SACCELERATORSpatialHackathon/SACCELERATORPublic
                    Python
41

6

                  4. task_spatial_segmentationtask_spatial_segmentationPublic
                    
Forked from openproblems-bio/task_spatial_segmentation
                    Shell
                  5. galaxyproject/tools-iucgalaxyproject/tools-iucPublic
                    
Tool Shed repositories maintained by the Intergalactic Utilities Commission

                    HTML
201

524