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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<title>Vessel Analyzer v2.1</title>
<style>
*{box-sizing:border-box;margin:0;padding:0}
body{font-family:'Segoe UI',Arial,sans-serif;background:#111827;color:#e5e7eb;height:100vh;overflow:hidden;display:flex;flex-direction:column}
#init-overlay{position:fixed;inset:0;background:#111827;display:flex;align-items:center;justify-content:center;z-index:100}
.init-box{text-align:center;max-width:420px;padding:40px}
.init-title{font-size:28px;color:#c084fc;margin-bottom:8px}
.init-sub{color:#6b7280;font-size:13px;margin-bottom:24px}
#init-msg{color:#9ca3af;font-size:13px;margin-bottom:16px;min-height:20px}
.pbar{background:#1f2937;border-radius:8px;height:6px;overflow:hidden}
#pfill{height:100%;background:linear-gradient(90deg,#7c3aed,#c084fc);width:0%;transition:width .4s}
.app{display:flex;flex:1;overflow:hidden}
/* sidebar */
.sidebar{width:185px;min-width:185px;background:#1f2937;border-right:1px solid #374151;display:flex;flex-direction:column;overflow:hidden}
.upload-btn{margin:10px;padding:9px;background:#7c3aed;border:none;color:#fff;border-radius:8px;cursor:pointer;font-size:13px;transition:background .15s}
.upload-btn:hover{background:#6d28d9}
#file-input{display:none}
.drop-hint{font-size:10px;color:#4b5563;text-align:center;padding:0 8px 8px;margin-top:-4px}
.img-list{flex:1;overflow-y:auto;padding:4px}
.img-item{padding:5px;border-radius:6px;cursor:pointer;margin-bottom:4px;border:2px solid transparent;transition:all .12s;position:relative}
.img-item:hover{background:#374151}
.img-item.active{border-color:#c084fc;background:#2d1b69}
.img-thumb{width:100%;height:76px;object-fit:contain;background:#111827;border-radius:4px;display:block}
.img-name{font-size:10px;color:#9ca3af;margin-top:3px;overflow:hidden;text-overflow:ellipsis;white-space:nowrap}
.img-remove{position:absolute;top:4px;right:4px;background:rgba(220,38,38,.85);color:#fff;border:none;border-radius:50%;width:18px;height:18px;font-size:11px;cursor:pointer;display:none;align-items:center;justify-content:center;z-index:5;line-height:1}
.img-item:hover .img-remove{display:flex}
.img-remove:hover{background:#dc2626}
.img-check{position:absolute;top:4px;left:4px;z-index:5;width:14px;height:14px;cursor:pointer;accent-color:#7c3aed}
/* main */
.main{flex:1;display:flex;flex-direction:column;overflow:hidden}
.controls{background:#1f2937;border-bottom:1px solid #374151;padding:8px 14px;display:flex;gap:16px;align-items:flex-end;flex-wrap:wrap}
.cgrp{display:flex;flex-direction:column;gap:4px}
.cgrp>label{font-size:10px;color:#6b7280;text-transform:uppercase;letter-spacing:.07em}
.brow{display:flex;gap:3px;flex-wrap:wrap}
.fb{padding:4px 8px;border:1.5px solid #374151;border-radius:5px;background:#111827;color:#9ca3af;cursor:pointer;font-size:11px;transition:all .12s;white-space:nowrap}
.fb:hover{border-color:#6b7280;color:#e5e7eb}
.fb.on{background:#7c3aed;border-color:#7c3aed;color:#fff;font-weight:600}
.px-wrap{display:flex;align-items:center;gap:5px}
.px-in{background:#111827;border:1.5px solid #374151;border-radius:5px;color:#e5e7eb;padding:4px 7px;font-size:12px;width:68px}
.px-in:focus{outline:none;border-color:#7c3aed}
.px-u{font-size:11px;color:#6b7280}
/* metrics */
.metrics{background:#0f172a;border-bottom:1px solid #374151;padding:6px 14px;display:flex;gap:16px;align-items:center}
.met{display:flex;flex-direction:column;align-items:center}
.met .v{font-size:17px;font-weight:700;color:#c084fc}
.met .l{font-size:10px;color:#6b7280}
.mdiv{width:1px;height:30px;background:#1f2937}
.metrics-btns{margin-left:auto;display:flex;gap:6px}
.act-btn{padding:5px 10px;border:1.5px solid #374151;border-radius:5px;background:#111827;color:#9ca3af;cursor:pointer;font-size:11px;transition:all .12s;white-space:nowrap}
.act-btn:hover{border-color:#6b7280;color:#e5e7eb}
.act-btn.green{border-color:#059669;color:#6ee7b7;background:#022c22}
.act-btn.green:hover{background:#059669;color:#fff}
.act-btn.amber{border-color:#d97706;color:#fcd34d;background:#1c1008}
.act-btn.amber:hover{background:#d97706;color:#fff}
/* results */
.results{flex:1;display:flex;gap:0;padding:10px;overflow:hidden;min-height:0}
/* remove grid-mode classes — now handled by flex-basis */
.results.mode-jenkins #frangi-panel{flex:0 0 130px;min-width:130px}
.results.mode-jenkins #jenkins-panel{flex:1;min-width:200px}
.results.mode-frangi #jenkins-panel{flex:0 0 130px;min-width:130px}
.results.mode-frangi #frangi-panel{flex:1;min-width:200px}
/* Panel drag-resizer handle */
.panel-resizer{width:8px;cursor:col-resize;flex-shrink:0;background:#1a2332;
border-left:1px solid #1f2937;border-right:1px solid #1f2937;
display:flex;align-items:center;justify-content:center;transition:background .12s;border-radius:2px}
.panel-resizer:hover{background:#374151}
.panel-resizer::after{content:'';width:2px;height:32px;background:#4b5563;border-radius:2px}
/* Menubar expandable */
.menubar{position:relative}
.menubar-handle{position:absolute;right:-4px;top:0;bottom:0;width:8px;cursor:col-resize;z-index:60}
.menubar-handle:hover::after{content:'';position:absolute;inset:0 2px;background:rgba(99,102,241,0.35);border-radius:3px}
/* Default: expanded (horizontal). Collapsed is the special class. */
.menubar.collapsed{width:38px}
.menubar.collapsed .menu-btn{writing-mode:vertical-rl;transform:rotate(180deg);padding:10px 4px;text-align:center}
.menubar.collapsed .menu-dropdown{top:0;left:100%}
/* Floating Width Log */
#wlog-float{position:fixed;bottom:0;left:50%;transform:translateX(-50%);
width:700px;max-width:95vw;background:#1f2937;
border:1px solid #374151;border-top:2px solid #38bdf8;border-radius:8px 8px 0 0;
box-shadow:0 -4px 24px rgba(0,0,0,.65);display:none;flex-direction:column;
z-index:260;overflow:hidden;min-height:90px;max-height:70vh;resize:none}
#wlog-float.open{display:flex}
#wlog-resize-bar{height:6px;cursor:ns-resize;background:#0d1117;flex-shrink:0;border-bottom:1px solid #21262d;transition:background .12s}
#wlog-resize-bar:hover{background:#21262d}
#wlog-drag-header{padding:8px 14px;display:flex;align-items:center;gap:10px;
cursor:move;user-select:none;flex-shrink:0;border-bottom:1px solid #374151;background:#111827}
/* panel tab header */
.panel-tab{display:flex;align-items:center;gap:6px;padding:5px 8px 4px;border-bottom:1px solid #374151;background:#111827;cursor:default;user-select:none;flex-shrink:0;flex-wrap:wrap}
.panel-tab-label{font-size:11px;font-weight:700;letter-spacing:.05em;text-transform:uppercase;cursor:pointer;padding:2px 6px;border-radius:4px;transition:background .12s}
.panel-tab-label:hover{background:#1f2937}
.panel-tab-label.active{color:#c084fc}
.panel-tab-expand{font-size:10px;padding:1px 6px;border:1px solid #374151;border-radius:3px;background:none;cursor:pointer;color:#6b7280;white-space:nowrap}
.panel-tab-expand:hover{border-color:#6b7280;color:#e5e7eb}
.panel-tab-expand.on{border-color:#c084fc;color:#c084fc;background:#2d1b69}
.panel{background:#1f2937;border-radius:8px;display:flex;flex-direction:column;overflow:hidden;flex:1;min-width:100px}
.ptitle{font-size:10px;color:#6b7280;padding:5px 8px;border-bottom:1px solid #374151;text-transform:uppercase;letter-spacing:.06em;flex-shrink:0;display:flex;flex-direction:column;gap:3px}
.ptitle-top{display:flex;align-items:center;gap:4px;min-height:18px}
.ptitle-btns{display:flex;gap:3px;align-items:center;flex-wrap:wrap}
.ptitle-row{display:flex;gap:3px;align-items:center;flex-wrap:wrap}
.ptitle-sep{width:1px;height:14px;background:#374151;display:inline-block;margin:0 1px;flex-shrink:0}
/* count order selector */
.order-sel{display:inline-flex;align-items:center;gap:0;background:#1c1008;border:1.5px solid #d97706;border-radius:4px;overflow:hidden;height:18px;flex-shrink:0}
.order-sel-val{font-size:11px;color:#fcd34d;font-weight:700;padding:0 5px;min-width:28px;text-align:center}
.order-sel-btn{background:none;border:none;color:#d97706;cursor:pointer;font-size:11px;padding:0 4px;line-height:1;transition:background .1s;height:100%}
.order-sel-btn:hover{background:#d97706;color:#fff}
/* zoom controls */
.zoom-ctrl{display:inline-flex;align-items:center;gap:2px;margin-left:auto;flex-shrink:0}
.zoom-btn{padding:2px 6px;border:1.5px solid #374151;border-radius:4px;background:#111827;color:#9ca3af;cursor:pointer;font-size:10px;transition:all .12s;white-space:nowrap}
.zoom-btn:hover{border-color:#6b7280;color:#e5e7eb}
.zoom-btn.active{background:#1e3a5f;border-color:#38bdf8;color:#7dd3fc}
.pb{padding:2px 7px;border:1.5px solid #374151;border-radius:4px;background:#111827;color:#9ca3af;cursor:pointer;font-size:10px;transition:all .12s;white-space:nowrap}
.pb:hover{border-color:#6b7280;color:#e5e7eb}
.pb.roi-on{background:#059669;border-color:#059669;color:#fff}
.pb.clr:hover{border-color:#dc2626;color:#fca5a5}
.pb.amber{border-color:#d97706;color:#fcd34d}
.pb.amber:hover{background:#d97706;color:#fff}
.img-wrap{flex:1;position:relative;overflow:hidden;min-height:0;background:#000}
.img-wrap img{width:100%;height:100%;object-fit:contain;display:block}
.img-wrap canvas{position:absolute;inset:0;pointer-events:none}
#paint-canvas{z-index:1}
#roi-canvas{z-index:2}
#paint-canvas.paint-active{pointer-events:all;cursor:none}
.img-wrap canvas.draw-active{pointer-events:all;cursor:crosshair}
.computing{position:absolute;inset:0;background:rgba(0,0,0,.75);display:none;align-items:center;justify-content:center;font-size:13px;color:#c084fc;z-index:10}
.empty-hint{position:absolute;inset:0;display:flex;align-items:center;justify-content:center;color:#374151;font-size:13px;pointer-events:none}
.roi-hint{position:absolute;bottom:8px;left:50%;transform:translateX(-50%);background:rgba(5,150,105,.9);color:#fff;font-size:11px;padding:4px 10px;border-radius:12px;pointer-events:none;white-space:nowrap;z-index:20}
.status{padding:5px 14px;background:#0f172a;font-size:11px;color:#4b5563;border-top:1px solid #1f2937;flex-shrink:0}
@keyframes spin{to{transform:rotate(360deg)}}
.sp{display:inline-block;width:11px;height:11px;border:2px solid #374151;border-top-color:#c084fc;border-radius:50%;animation:spin .7s linear infinite;margin-right:5px;vertical-align:middle}
/* log modal */
.log-backdrop{position:fixed;inset:0;background:rgba(0,0,0,.6);z-index:200;display:none;flex-direction:column;justify-content:flex-end}
.log-backdrop.open{display:flex}
.log-panel{background:#1f2937;border-top:2px solid #374151;max-height:55vh;display:flex;flex-direction:column}
.log-header{padding:10px 14px;display:flex;align-items:center;gap:10px;border-bottom:1px solid #374151;flex-shrink:0}
.log-header h3{font-size:13px;color:#c084fc;font-weight:600}
.log-header-btns{margin-left:auto;display:flex;gap:6px}
.log-body{overflow-y:auto;flex:1}
table{width:100%;border-collapse:collapse;font-size:11px}
thead{position:sticky;top:0;background:#111827;z-index:1}
th{padding:6px 10px;text-align:left;color:#6b7280;font-weight:600;letter-spacing:.04em;border-bottom:1px solid #374151}
td{padding:5px 10px;border-bottom:1px solid #1f2937;color:#d1d5db}
tr:hover td{background:#0f172a}
.del-btn{background:none;border:none;color:#4b5563;cursor:pointer;font-size:12px;padding:1px 4px}
.del-btn:hover{color:#f87171}
.log-empty{padding:24px;text-align:center;color:#374151;font-size:12px}
.dl-dropdown{position:absolute;top:100%;right:0;background:#1f2937;border:1px solid #374151;border-radius:6px;padding:4px;z-index:50;display:none;flex-direction:column;gap:2px;min-width:90px}
.dl-dropdown.open{display:flex}
.dl-opt{padding:5px 10px;border-radius:4px;cursor:pointer;font-size:11px;color:#d1d5db;white-space:nowrap}
.dl-opt:hover{background:#374151}
.dl-wrap{position:relative}
/* toast */
.toast{position:fixed;bottom:40px;left:50%;transform:translateX(-50%);background:#059669;color:#fff;padding:8px 18px;border-radius:20px;font-size:12px;z-index:300;opacity:0;transition:opacity .2s;pointer-events:none}
.toast.show{opacity:1}
/* Count & Width tools */
#count-canvas{z-index:4;position:absolute;top:0;left:0;width:100%;height:100%;pointer-events:none}
#width-canvas{z-index:5;position:absolute;top:0;left:0;width:100%;height:100%;pointer-events:none}
.count-badge{background:#f59e0b;color:#000;border-radius:10px;padding:1px 7px;font-size:10px;font-weight:700;margin-left:2px;vertical-align:middle;white-space:nowrap}
.width-badge{background:#38bdf8;color:#000;border-radius:10px;padding:1px 7px;font-size:10px;font-weight:700;margin-left:2px;vertical-align:middle;white-space:nowrap}
/* ── Menu bar ─────────────────────────────────────────────────────── */
.menubar{background:#0d1117;border-right:1px solid #21262d;display:flex;flex-direction:column;align-items:stretch;gap:1px;padding:6px 0;flex-shrink:0;width:108px;z-index:50;overflow:visible}
.menu-item{position:relative}
.menu-btn{background:none;border:none;color:#8b949e;font-size:12px;padding:5px 10px;cursor:pointer;border-radius:4px;transition:all .12s;white-space:nowrap;writing-mode:horizontal-tb;transform:none;width:100%;text-align:left}
.menu-btn:hover,.menu-item.open .menu-btn{background:#21262d;color:#e6edf3}
.menu-dropdown{position:absolute;top:100%;left:0;background:#161b22;border:1px solid #30363d;border-radius:6px;padding:4px;z-index:100;display:none;min-width:200px;box-shadow:0 8px 24px rgba(0,0,0,.5)}
.menu-item.open .menu-dropdown{display:block}
.menu-dd-item{padding:5px 12px;border-radius:4px;cursor:pointer;font-size:12px;color:#c9d1d9;display:flex;align-items:center;gap:8px;white-space:nowrap}
.menu-dd-item:hover{background:#21262d}
.menu-dd-item.disabled{color:#484f58;cursor:default;pointer-events:none}
.menu-sep{height:1px;background:#21262d;margin:4px 0}
.menu-dd-item kbd{margin-left:auto;font-size:10px;color:#484f58;background:#0d1117;padding:1px 5px;border-radius:3px;border:1px solid #30363d}
/* ── Modals ───────────────────────────────────────────────────────── */
.modal-backdrop{position:fixed;inset:0;background:rgba(0,0,0,.7);z-index:500;display:none;align-items:center;justify-content:center}
.modal-backdrop.open{display:flex}
.modal{background:#161b22;border:1px solid #30363d;border-radius:10px;max-width:560px;width:90%;max-height:80vh;display:flex;flex-direction:column;box-shadow:0 16px 48px rgba(0,0,0,.6)}
.modal-header{padding:14px 18px;border-bottom:1px solid #21262d;display:flex;align-items:center;justify-content:space-between;flex-shrink:0}
.modal-header h3{font-size:15px;color:#e6edf3;font-weight:600}
.modal-close{background:none;border:none;color:#8b949e;cursor:pointer;font-size:16px;padding:2px 6px;border-radius:4px}
.modal-close:hover{background:#21262d;color:#e6edf3}
.modal-body{padding:18px;overflow-y:auto;flex:1;font-size:13px;color:#8b949e;line-height:1.7}
.modal-body h4{color:#c9d1d9;font-size:13px;margin:12px 0 5px;font-weight:600}
.modal-body p{margin-bottom:8px}
.modal-body ul{padding-left:18px}
.modal-body li{margin-bottom:5px}
.modal-body code{background:#0d1117;padding:1px 5px;border-radius:3px;font-size:11px;color:#79c0ff}
.modal-footer{padding:12px 18px;border-top:1px solid #21262d;display:flex;gap:8px;justify-content:flex-end;flex-shrink:0}
.modal-btn{padding:6px 16px;border-radius:6px;border:1px solid #30363d;background:#21262d;color:#c9d1d9;cursor:pointer;font-size:12px;transition:all .12s}
.modal-btn:hover{background:#30363d}
.modal-btn.primary{background:#7c3aed;border-color:#7c3aed;color:#fff}
.modal-btn.primary:hover{background:#6d28d9}
.setting-row{display:flex;align-items:center;gap:12px;margin-bottom:10px;padding:8px;background:#0d1117;border-radius:6px}
.setting-row label{flex:1;color:#c9d1d9;font-size:12px}
.setting-row input[type=range]{width:100px;accent-color:#7c3aed}
.setting-row input[type=number]{width:70px;background:#161b22;border:1px solid #30363d;border-radius:4px;color:#e6edf3;padding:3px 7px;font-size:12px}
.setting-row select{background:#161b22;border:1px solid #30363d;border-radius:4px;color:#e6edf3;padding:3px 7px;font-size:12px;cursor:pointer}
.setting-val{min-width:36px;font-size:11px;color:#7c3aed;text-align:right}
</style>
</head>
<body>
<div id="init-overlay">
<div class="init-box">
<div class="init-title">🔬 Vessel Analyzer</div>
<div class="init-sub">Angiography segmentation · Frangi vesselness filter</div>
<div id="init-msg">Starting…</div>
<div class="pbar"><div id="pfill"></div></div>
</div>
</div>
<div class="toast" id="toast"></div>
<div class="app" id="app" style="display:none;flex-direction:column">
<div style="display:flex;flex:1;overflow:hidden">
<!-- Vertical menu bar — now a column on the far left -->
<div class="menubar" id="menubar">
<div class="menu-item" id="m-file">
<button class="menu-btn" onclick="toggleMenu('m-file')">File</button>
<div class="menu-dropdown">
<div class="menu-dd-item" onclick="document.getElementById('file-input').click();closeMenus()">📂 Open Images…</div>
<div class="menu-sep"></div>
<div class="menu-dd-item" onclick="menuSaveCurrent('vmap','png')">💾 Save Vesselness Map — PNG</div>
<div class="menu-dd-item" onclick="menuSaveCurrent('vmap','jpg')">💾 Save Vesselness Map — JPG</div>
<div class="menu-dd-item" onclick="menuSaveCurrent('overlay','png')">💾 Save Vessel Overlay — PNG</div>
<div class="menu-dd-item" onclick="menuSaveCurrent('overlay','jpg')">💾 Save Vessel Overlay — JPG</div>
<div class="menu-sep"></div>
<div class="menu-dd-item" onclick="saveAllAsZip();closeMenus()">📦 Save All Analyzed → ZIP</div>
<div class="menu-dd-item" onclick="openModal('video-modal');closeMenus()">🎬 Export Video (WebM)…</div>
<div class="menu-dd-item" onclick="exportCSV();closeMenus()">📊 Export Measurements CSV</div>
<div class="menu-dd-item" onclick="exportWidthCSV();closeMenus()">📐 Export Width Measurements CSV</div>
<div class="menu-sep"></div>
<div class="menu-dd-item" onclick="if(confirm('Start a new session? All unsaved data will be lost.'))location.reload()">🔄 New Session</div>
</div>
</div>
<div class="menu-item" id="m-edit">
<button class="menu-btn" onclick="toggleMenu('m-edit')">Edit</button>
<div class="menu-dropdown">
<div class="menu-dd-item" onclick="openModal('export-settings-modal');closeMenus()">🖼 Export Resolution…</div>
<div class="menu-dd-item" onclick="openModal('video-modal');closeMenus()">🎞 Video Settings…</div>
<div class="menu-sep"></div>
<div class="menu-dd-item" onclick="clearPaint();closeMenus()">✕ Clear Paint (current image)</div>
<div class="menu-dd-item" onclick="clearROI();closeMenus()">✕ Clear ROI (current image)</div>
<div class="menu-dd-item" onclick="resetSequence();closeMenus()">🔄 Reset Sequence Cache</div>
<div class="menu-sep"></div>
<div class="menu-dd-item" onclick="freeMemory();closeMenus()">🧹 Free Memory (clear vmap cache)</div>
</div>
</div>
<div class="menu-item" id="m-help">
<button class="menu-btn" onclick="toggleMenu('m-help')">Help</button>
<div class="menu-dropdown">
<div class="menu-dd-item" onclick="openModal('guide-modal');closeMenus()">📖 Quick Start Guide</div>
<div class="menu-dd-item" onclick="openModal('tools-modal');closeMenus()">🔧 Tool Reference</div>
<div class="menu-sep"></div>
<div class="menu-dd-item" onclick="openModal('about-modal');closeMenus()">ℹ About</div>
</div>
</div>
<div class="menubar-handle" id="menubar-handle" title="Drag to expand/collapse menu"></div>
</div>
<!-- end menubar -->
<div class="sidebar">
<button class="upload-btn" onclick="document.getElementById('file-input').click()">＋ Upload Images</button>
<input type="file" id="file-input" accept="image/*,.tif,.tiff" multiple>
<div class="drop-hint">or drag & drop anywhere</div>
<div style="display:flex;gap:4px;padding:0 8px 6px;margin-top:-2px">
<button onclick="sidebarSelAll(true)" style="flex:1;padding:3px;background:#1f2937;border:1px solid #374151;border-radius:4px;color:#9ca3af;font-size:10px;cursor:pointer" onmouseover="this.style.color='#e5e7eb'" onmouseout="this.style.color='#9ca3af'">☑ All</button>
<button onclick="sidebarSelAll(false)" style="flex:1;padding:3px;background:#1f2937;border:1px solid #374151;border-radius:4px;color:#9ca3af;font-size:10px;cursor:pointer" onmouseover="this.style.color='#e5e7eb'" onmouseout="this.style.color='#9ca3af'">☐ None</button>
</div>
<div class="img-list" id="img-list"><div style="padding:12px;font-size:11px;color:#4b5563;text-align:center">No images</div></div>
</div>
<div class="main">
<div class="controls">
<div class="cgrp">
<label>Pixel size</label>
<div class="px-wrap">
<input type="number" id="px-size" class="px-in" value="0.1" step="0.01" min="0.001">
<span class="px-u">µm/px</span>
</div>
</div>
<div class="cgrp">
<label>Vessel width — sigmas</label>
<div class="brow" id="sigma-btns"></div>
</div>
<div class="cgrp">
<label>Min segment size</label>
<div class="brow" id="minsize-btns"></div>
</div>
<div class="cgrp" style="justify-content:flex-end;flex-direction:row;gap:6px;align-self:flex-end">
<button class="act-btn amber" onclick="saveDefaults()" title="Save current settings as default for next session">⭐ Save as Default</button>
<button class="act-btn" style="border-color:#0891b2;color:#67e8f9;background:#001f2e" onclick="openSeq()">🎬 Sequence Analysis</button>
<button class="act-btn green" onclick="openLog()">📋 Measurements Log</button>
</div>
</div>
<div class="metrics">
<div class="met"><span class="v" id="m-frac">—</span><span class="l">Vessel %</span></div>
<div class="mdiv"></div>
<div class="met"><span class="v" id="m-um2">—</span><span class="l">µm²</span></div>
<div class="mdiv"></div>
<div class="met"><span class="v" id="m-mm2">—</span><span class="l">mm²</span></div>
<div class="mdiv"></div>
<div class="met"><span class="v" id="m-segs">—</span><span class="l">Segments</span></div>
<div class="metrics-btns">
<button class="act-btn" id="copy-btn" onclick="copyMetrics()">📋 Copy</button>
<button class="act-btn green" id="save-log-btn" onclick="saveToLogBtn()">＋ Save to Log</button>
<button onclick="runBtn()" id="run-btn" style="padding:6px 16px;border:2px solid #7c3aed;border-radius:6px;background:#3b0764;color:#e9d5ff;cursor:pointer;font-size:13px;font-weight:700;transition:all .15s;white-space:nowrap" onmouseover="this.style.background='#7c3aed'" onmouseout="this.style.background='#3b0764'">▶ Run</button>
</div>
</div>
<div class="results" id="results-grid">
<!-- ── Frangi Filter panel ── -->
<div class="panel" id="frangi-panel">
<div class="panel-tab">
<span class="panel-tab-label active" id="frangi-tab-label" onclick="setPanelMode('frangi')" title="Click to focus Frangi panel">🔬 Frangi Filter</span>
<span id="ptitle-vmap-name" style="color:#a78bfa;font-style:normal;font-size:9px;letter-spacing:normal;text-transform:none;font-weight:400"></span>
<button class="panel-tab-expand" id="frangi-expand-btn" onclick="setPanelMode('frangi')" title="Focus this panel">⊞</button>
</div>
<!-- Frangi tools: ROI + Paint — shown only when frangi panel is active -->
<div id="frangi-tools" style="padding:4px 6px;border-bottom:1px solid #374151;display:flex;gap:3px;align-items:center;flex-wrap:wrap;flex-shrink:0">
<button class="pb" id="roi-draw-btn" onclick="toggleDraw()">✏ ROI</button>
<button class="pb amber" id="roi-copy-btn" style="display:none" onclick="copyROI()">📋</button>
<button class="pb amber" id="roi-paste-btn" style="display:none" onclick="pasteROI()">📌</button>
<button class="pb clr" id="roi-clear-btn" style="display:none" onclick="clearROI()">✕ ROI</button>
<span class="ptitle-sep"></span>
<button class="pb" id="paint-btn" onclick="togglePaint()">🖌 Paint</button>
<button class="pb" id="erase-btn" onclick="toggleErase()" style="display:none">🧹 Erase</button>
<select id="brush-size" style="background:#111827;border:1.5px solid #374151;border-radius:4px;color:#9ca3af;font-size:10px;padding:1px 3px;cursor:pointer;display:none">
<option value="4">XS</option><option value="8">S</option><option value="14" selected>M</option>
<option value="22">L</option><option value="35">XL</option>
</select>
<button class="pb clr" id="paint-clear-btn" style="display:none" onclick="clearPaint()">✕ Paint</button>
<span class="ptitle-sep"></span>
<div class="dl-wrap">
<button class="pb" onclick="toggleDL('dl-vmap')">⬇ Save</button>
<div class="dl-dropdown" id="dl-vmap">
<div class="dl-opt" onclick="downloadImg('vmap-img','png','vesselness_map');toggleDL('dl-vmap')">PNG</div>
<div class="dl-opt" onclick="downloadImg('vmap-img','jpg','vesselness_map');toggleDL('dl-vmap')">JPG</div>
</div>
</div>
</div>
<div class="img-wrap" id="roi-wrap">
<div class="empty-hint" id="hint-vmap">Upload an image</div>
<img id="vmap-img" style="display:none">
<div class="computing" id="comp-vmap"><span class="sp"></span> Computing…</div>
</div>
</div>
<!-- ── Panel resize handle ── -->
<div class="panel-resizer" id="panel-resizer" title="Drag to resize panels"></div>
<!-- ── Jenkins panel ── -->
<div class="panel" id="jenkins-panel">
<div class="panel-tab">
<span class="panel-tab-label" id="jenkins-tab-label" onclick="setPanelMode('jenkins')" title="Click to focus Jenkins panel">📐 Pearson Method</span>
<span id="ptitle-ov-name" style="color:#a78bfa;font-style:normal;font-size:9px;letter-spacing:normal;text-transform:none;font-weight:400"></span>
<button class="panel-tab-expand" id="jenkins-expand-btn" onclick="setPanelMode('jenkins')" title="Focus this panel">⊞</button>
</div>
<!-- Jenkins tools — shown in full -->
<div id="jenkins-tools" style="flex-shrink:0">
<!-- Row 1: zoom controls -->
<div style="padding:3px 6px;border-bottom:1px solid #2a3441;display:flex;gap:3px;align-items:center;flex-wrap:wrap">
<span style="font-size:10px;color:#6b7280">Zoom:</span>
<span id="zoom-label" style="font-size:10px;color:#6b7280;margin-right:1px">100%</span>
<button class="zoom-btn" onclick="ovZoomIn()">🔍+</button>
<button class="zoom-btn" onclick="ovZoomOut()">🔍−</button>
<button class="zoom-btn" id="pan-btn" onclick="togglePan()" title="Pan mode · Alt+drag · Space+drag">🖐</button>
<button class="zoom-btn" onclick="resetOvZoom()" title="Reset zoom">⊙</button>
<span class="ptitle-sep"></span>
<div class="dl-wrap">
<button class="pb" onclick="toggleDL('dl-ov')">⬇ Save</button>
<div class="dl-dropdown" id="dl-ov">
<div class="dl-opt" onclick="downloadImg('overlay-img','png','vessel_overlay');toggleDL('dl-ov')">Clean PNG</div>
<div class="dl-opt" onclick="downloadImg('overlay-img','jpg','vessel_overlay');toggleDL('dl-ov')">Clean JPG</div>
<div style="height:1px;background:#374151;margin:3px 0"></div>
<div class="dl-opt" style="color:#f59e0b" onclick="saveAnnotatedOverlay('png');toggleDL('dl-ov')">📌 PNG + Annotations</div>
<div class="dl-opt" style="color:#f59e0b" onclick="saveAnnotatedOverlay('jpg');toggleDL('dl-ov')">📌 JPG + Annotations</div>
</div>
</div>
</div>
<!-- Row 2: Count + Width tools -->
<div style="padding:3px 6px;border-bottom:1px solid #374151;display:flex;gap:3px;align-items:center;flex-wrap:wrap">
<button class="pb" id="count-btn" onclick="toggleCount()" title="Left-click: place marker at current order · Left-click marker: cycle order · Right-click / ×: delete · ESC: stop">🔢 Count</button>
<div class="order-sel" id="order-sel-wrap" style="display:none">
<button class="order-sel-btn" onclick="changeCountOrder(-1)">‹</button>
<span class="order-sel-val" id="count-order-val">1</span>
<button class="order-sel-btn" onclick="changeCountOrder(1)">›</button>
</div>
<span id="count-badge" class="count-badge" style="display:none">0</span>
<button class="pb clr" id="count-clear-btn" style="display:none" onclick="clearCounts()">✕ Count</button>
<span class="ptitle-sep"></span>
<button class="pb" id="width-btn" onclick="toggleWidth()" title="Click: start line · Click again: measure · Right-click / ×: delete line · ESC: cancel">📏 Width</button>
<span id="width-badge" class="width-badge" style="display:none">0</span>
<button class="pb clr" id="width-clear-btn" style="display:none" onclick="clearWidths()">✕ Widths</button>
<button class="pb" id="width-log-btn" style="display:none;border-color:#38bdf8;color:#7dd3fc" onclick="openWidthLog()">📋 Width Log</button>
</div>
</div>
<div class="img-wrap" id="ov-wrap">
<div class="empty-hint" id="hint-ov">Upload an image</div>
<img id="overlay-img" style="display:none;transform-origin:50% 50%">
<canvas id="ov-canvas"></canvas>
<canvas id="paint-canvas"></canvas>
<canvas id="roi-canvas"></canvas>
<canvas id="count-canvas"></canvas>
<canvas id="width-canvas"></canvas>
<div class="computing" id="comp-ov"><span class="sp"></span> Computing…</div>
</div>
</div>
</div>
<div class="status" id="status">Upload an image to begin</div>
</div>
</div><!-- end outer flex row -->
</div>
<!-- Sequence drawer -->
<div class="log-backdrop" id="seq-backdrop" onclick="closeSeqOnBd(event)">
<div class="log-panel" id="seq-panel" onclick="event.stopPropagation()" style="max-height:70vh">
<div class="log-header">
<h3>🎬 Sequence Analysis</h3>
<div class="log-header-btns">
<button class="act-btn" style="border-color:#dc2626;color:#fca5a5;background:#1c0a0a" onclick="resetSequence()" title="Clears all projection and sequence cache — fixes display glitches">🔄 Reset Sequence</button>
<button class="act-btn" onclick="closeSeq()">✕ Close</button>
</div>
</div>
<div style="display:flex;flex:1;overflow:hidden;min-height:0">
<!-- Left: setup -->
<div style="width:280px;min-width:280px;border-right:1px solid #374151;padding:12px;overflow-y:auto;display:flex;flex-direction:column;gap:10px">
<div>
<div style="font-size:10px;color:#6b7280;text-transform:uppercase;letter-spacing:.07em;margin-bottom:6px">1 · Select frames</div>
<div style="display:flex;gap:6px;margin-bottom:6px">
<button class="act-btn" onclick="seqSelAll(true)" style="font-size:10px;padding:3px 8px">Select All</button>
<button class="act-btn" onclick="seqSelAll(false)" style="font-size:10px;padding:3px 8px">Deselect All</button>
</div>
<div id="seq-img-list" style="display:flex;flex-direction:column;gap:3px;max-height:120px;overflow-y:auto"></div>
</div>
<div>
<div style="font-size:10px;color:#6b7280;text-transform:uppercase;letter-spacing:.07em;margin-bottom:6px">2 · Projection method</div>
<div style="display:flex;gap:4px;flex-wrap:wrap">
<button class="fb" id="proj-maxv-btn" onclick="setProjMethod('max_v')" title="Best for cardiac: captures vessel at any cardiac phase">Max Vesselness ★</button>
<button class="fb" id="proj-min-btn" onclick="setProjMethod('min')" title="Min pixel = most contrast-filled frame per pixel">Min Intensity</button>
<button class="fb" id="proj-std-btn" onclick="setProjMethod('std')" title="High std = pixels that move = vessels">Std Dev</button>
<button class="fb on" id="proj-mean-btn" onclick="setProjMethod('mean')">Mean</button>
<button class="fb" id="proj-med-btn" onclick="setProjMethod('median')">Median</button>
</div>
<div id="proj-method-hint" style="font-size:10px;color:#4b5563;margin-top:4px">Mean: averages all frames (baseline)</div>
</div>
<button class="act-btn" style="border-color:#0891b2;color:#67e8f9;background:#001f2e" onclick="computeProjection()">▶ Compute Projection</button>
<div id="proj-thumb-wrap" style="display:none">
<div style="font-size:10px;color:#6b7280;margin-bottom:4px">Projection preview:</div>
<img id="proj-thumb" style="width:100%;border-radius:4px;border:1px solid #374151">
<div style="font-size:10px;color:#6ee7b7;margin-top:4px" id="proj-info"></div>
</div>
<div>
<div style="font-size:10px;color:#6b7280;text-transform:uppercase;letter-spacing:.07em;margin-bottom:6px">3 · Auto-optimize settings</div>
<div style="font-size:10px;color:#4b5563;margin-bottom:6px">Finds the min segment size where removing more stops reducing noise and starts cutting real vessels (the elbow point).</div>
<button class="act-btn amber" onclick="runAutoOptimize()">🔍 Auto-Optimize Min Size</button>
<div id="optimize-result" style="margin-top:8px;display:none">
<canvas id="elbow-chart" height="80" style="width:100%;border-radius:4px;background:#0f172a"></canvas>
<div id="optimize-msg" style="font-size:11px;color:#6ee7b7;margin-top:5px"></div>
<button class="act-btn green" style="margin-top:5px;width:100%" onclick="applyOptimized()">✓ Apply Recommended Settings</button>
</div>
</div>
<div id="guide-section" style="display:none">
<div style="font-size:10px;color:#0891b2;text-transform:uppercase;letter-spacing:.07em;margin-bottom:6px">3b · Projection-guided fill</div>
<div style="font-size:10px;color:#4b5563;margin-bottom:6px">Uses the projection as a spatial prior: where a vessel is seen in <em>any</em> frame, it relaxes the threshold for that region in each individual frame — filling gaps where a vessel is only partially visible.</div>
<div style="display:flex;align-items:center;gap:8px;margin-bottom:6px">
<label style="font-size:10px;color:#6b7280;white-space:nowrap">Guide strength</label>
<input type="range" id="guide-slider" min="0" max="100" value="40" step="5" style="flex:1;accent-color:#0891b2" oninput="document.getElementById('guide-val').textContent=this.value+'%'">
<span id="guide-val" style="font-size:11px;color:#67e8f9;min-width:32px">40%</span>
</div>
<div style="font-size:10px;color:#4b5563">0% = no guidance · 100% = max fill (may add noise)</div>
<hr style="border-color:#1f2937;margin:8px 0">
<div style="font-size:10px;color:#0891b2;font-weight:600;margin-bottom:4px">Or: hard projection template</div>
<div style="font-size:10px;color:#4b5563;margin-bottom:6px">Builds the projection vessel mask and shows it as a <span style="color:#67e8f9">cyan overlay</span> on every frame. Press ▶ Run on any frame — the template forces vessel detection wherever the projection saw them (very relaxed threshold within template region).</div>
<button class="act-btn" style="border-color:#0891b2;color:#67e8f9;background:#001f2e;width:100%" onclick="applyProjTemplate()">📐 Apply Projection Template to All Frames</button>
<button class="act-btn" id="clear-template-btn" style="display:none;border-color:#dc2626;color:#fca5a5;width:100%;margin-top:4px" onclick="clearProjTemplate()">✕ Remove Template</button>
</div>
<div>
<div style="font-size:10px;color:#6b7280;text-transform:uppercase;letter-spacing:.07em;margin-bottom:6px">4 · Apply to all frames</div>
<div style="font-size:10px;color:#4b5563;margin-bottom:6px">Uses current sigma + min size on every selected frame. First run takes ~20–40 s per frame.</div>
<button class="act-btn green" style="width:100%" onclick="applySequence()">▶▶ Analyze All Frames</button>
<div id="seq-progress" style="display:none;margin-top:8px">
<div style="font-size:10px;color:#9ca3af;margin-bottom:4px" id="seq-prog-msg">Processing…</div>
<div style="background:#1f2937;border-radius:4px;height:6px;overflow:hidden"><div id="seq-prog-fill" style="height:100%;background:linear-gradient(90deg,#0891b2,#67e8f9);width:0%;transition:width .3s"></div></div>
</div>
</div>
</div>
<!-- Right: results -->
<div style="flex:1;display:flex;flex-direction:column;overflow:hidden">
<div style="padding:8px 14px;border-bottom:1px solid #374151;display:flex;align-items:center;gap:8px">
<span style="font-size:11px;color:#6b7280" id="seq-result-info">Run analysis to see results</span>
<button class="act-btn" style="margin-left:auto" id="seq-export-btn" onclick="exportSeqCSV()" style="display:none">⬇ Export CSV</button>
</div>
<div style="flex:1;overflow-y:auto" id="seq-results-body">
<div class="log-empty">Select frames and run "Analyze All Frames"</div>
</div>
<canvas id="seq-chart" height="90" style="width:100%;background:#0f172a;flex-shrink:0;display:none"></canvas>
</div>
</div>
</div>
</div>
</div>
<!-- Floating Width Log panel (draggable + resizable) -->
<div id="wlog-float">
<div id="wlog-resize-bar" title="Drag top edge to resize"></div>
<div id="wlog-drag-header">
<span style="font-size:13px;font-weight:600;color:#38bdf8">📏 Vessel Diameter Measurements</span>
<span style="font-size:10px;color:#6b7280" id="wlog-count">0 measurements</span>
<div style="margin-left:auto;display:flex;gap:6px;align-items:center">
<span style="font-size:10px;color:#4b5563">⠿ drag to move</span>
<button class="act-btn" onclick="exportWidthCSV()">⬇ Export CSV</button>
<button class="act-btn" onclick="clearAllWidths()">🗑 Clear All</button>
<button class="act-btn" onclick="closeWidthLog()">✕</button>
</div>
</div>
<div id="wlog-body" style="overflow-y:auto;flex:1;min-height:0">
<div class="log-empty">No measurements yet.<br>Use 🔢 Count to mark vessels, then 📏 Width to measure diameters.</div>
</div>
</div>
<!-- Log modal -->
<div class="log-backdrop" id="log-backdrop" onclick="closeLogOnBd(event)">
<div class="log-panel" onclick="event.stopPropagation()">
<div class="log-header">
<h3>📋 Measurements Log</h3>
<span style="font-size:10px;color:#6b7280" id="log-count">0 entries</span>
<div class="log-header-btns">
<button class="act-btn" onclick="exportCSV()">⬇ Export CSV</button>
<button class="act-btn" onclick="clearLog()">🗑 Clear All</button>
<button class="act-btn" onclick="closeLog()">✕ Close</button>
</div>
</div>
<div class="log-body" id="log-body">
<div class="log-empty">No measurements saved yet.<br>Run an analysis and click "＋ Save to Log".</div>
</div>
</div>
</div>
<script src="https://cdn.jsdelivr.net/pyodide/v0.25.1/full/pyodide.js"></script>
<script src="https://cdnjs.cloudflare.com/ajax/libs/jszip/3.10.1/jszip.min.js"></script>
<script>
// ── Config ────────────────────────────────────────────────────────────────
const SIGMAS=[
{l:'2+', s:[2,4,6,8,10,12,14,16,18]},
{l:'4+', s:[4,6,8,10,12,14,16,18]},
{l:'6+', s:[6,8,10,12,14,16,18]},
{l:'8+', s:[8,10,12,14,16,18]},
{l:'10+',s:[10,12,14,16,18]},
{l:'12+',s:[12,14,16,18]},
{l:'14+',s:[14,16,18]},
{l:'16+',s:[16,18,20,22]},
];
const MINSIZES=[10,50,100,200,500,1000,2000,3000,5000,8000,15000,30000,60000];
// Load defaults from localStorage
let curSI=parseInt(localStorage.getItem('va_si')??'4');
let curMI=parseInt(localStorage.getItem('va_mi')??'5');
let py=null,images=[],curI=-1,busy=false;
let runSelected=new Set(); // indices selected for batch run
function toggleRunSelect(i,checked){
if(checked)runSelected.add(i);else runSelected.delete(i);
updateRunBtn();
}
function sidebarSelAll(v){
runSelected.clear();
if(v) images.forEach((_,i)=>runSelected.add(i));
renderList();updateRunBtn();
}
function updateRunBtn(){
const btn=document.getElementById('run-btn');
if(btn){
if(runSelected.size>1) btn.textContent=`▶ Run Selected (${runSelected.size})`;
else btn.textContent='▶ Run';
}
const slb=document.getElementById('save-log-btn');
if(slb){
if(runSelected.size>1) slb.textContent=`＋ Save Selected to Log (${runSelected.size})`;
else slb.textContent='＋ Save to Log';
}
}
let roi=null,drawingROI=false,hoverPt=null;
let roiClipboard=null; // copied ROI points
let logEntries=[];
let lastResult=null;
// ── Python ─────────────────────────────────────────────────────────────────
const PY=`
import numpy as np, io, base64, json
from PIL import Image, ImageDraw
from skimage.filters import frangi, threshold_otsu
from skimage.morphology import remove_small_objects, binary_closing, disk
from skimage import measure
_imgs={}; _vmaps={}
def _b64png(rgba):
buf=io.BytesIO(); Image.fromarray(rgba,'RGBA').save(buf,format='PNG')
return base64.b64encode(buf.getvalue()).decode()
def _thumb(gray,size=200):
h,w=gray.shape; s=size/max(h,w)
img=Image.fromarray(gray).resize((max(1,int(w*s)),max(1,int(h*s))),Image.LANCZOS)
buf=io.BytesIO(); img.save(buf,format='JPEG',quality=75)
return base64.b64encode(buf.getvalue()).decode()
def load_img(name,fb_js):
arr=np.array(Image.open(io.BytesIO(bytes(fb_js))).convert('L'))
_imgs[name]=arr
return json.dumps({'thumb':_thumb(arr),'w':int(arr.shape[1]),'h':int(arr.shape[0])})
def make_vmap(name,sk):
arr=_imgs[name]; inv=(255-arr.astype(np.float32))/255.0
_vmaps[(name,sk)]=frangi(inv,sigmas=json.loads(sk),black_ridges=False).astype(np.float32)
return 'ok'
def _roi_mask(h,w,roi_json):
if not roi_json: return np.ones((h,w),dtype=bool)
pts=json.loads(roi_json)
if len(pts)<3: return np.ones((h,w),dtype=bool)
mask=Image.new('L',(w,h),0)
ImageDraw.Draw(mask).polygon([(float(p['x']),float(p['y'])) for p in pts],fill=255)
return np.array(mask)>0
def run_filters_with_extras(name,sk,min_size,px_um,roi_json='',paint_json='',guide_strength=0.0):
vmap=_vmaps[(name,sk)]; orig=_imgs[name]; h,w=orig.shape
roi=_roi_mask(h,w,roi_json); nz=vmap[vmap>0]
if len(nz)<10:
empty=np.zeros((h,w,4),dtype=np.uint8)
ov=np.stack([orig,orig,orig,np.full_like(orig,255)],axis=-1)
return json.dumps({'fraction':0.0,'vessel_um2':0.0,'vessel_mm2':0.0,'n_segments':0,'vmap_b64':_b64png(empty),'overlay_b64':_b64png(ov)})
thresh=threshold_otsu(nz)
binary=binary_closing(vmap>thresh,disk(4))
binary=remove_small_objects(binary,min_size=int(min_size))
# Projection-guided fill
gs=float(guide_strength)
if gs>0:
sk_key=(name,sk); proj_key=('__proj__',sk)
if proj_key in _vmaps:
pv=_vmaps[proj_key]; pmax=pv.max()
if pmax>0:
pnorm=pv/pmax
# Where projection is confident above guide threshold, relax frame threshold
guide_thresh=thresh*(1.0-gs*0.7)
weak_binary=vmap>guide_thresh
guide_mask=(pnorm>gs*0.4)&weak_binary
guide_mask=binary_closing(guide_mask,disk(3))
guide_mask=remove_small_objects(guide_mask,min_size=max(10,int(min_size)//4))
binary=binary|guide_mask
tmask=binary_closing(orig<250,disk(10))&roi; binary=binary&tmask
# Manual paint mask (strokes applied in order; erase strokes clear)
if paint_json:
pts=json.loads(paint_json)
pmask=Image.new('L',(w,h),0)
pdraw=ImageDraw.Draw(pmask)
for p in pts:
r=int(p['r']); x=int(p['x']); y=int(p['y'])
fill=0 if p.get('erase') else 255
pdraw.ellipse([x-r,y-r,x+r,y+r],fill=fill)
binary=binary|(np.array(pmask)>0)
tpx=int(tmask.sum()); vpx=int(binary.sum())
frac=vpx/tpx*100 if tpx>0 else 0.0
n=len(measure.regionprops(measure.label(binary)))
px2=float(px_um)**2
vm=vmap.copy(); vm[~binary]=0; mx=vm.max()
vn=(vm/mx*255).astype(np.int32) if mx>0 else np.zeros((h,w),np.int32)
r=np.clip(vn*3,0,255).astype(np.uint8); g=np.clip(vn*3-255,0,255).astype(np.uint8)
b=np.clip(vn*3-510,0,255).astype(np.uint8)
vrgba=np.stack([r,g,b,np.full((h,w),255,np.uint8)],axis=-1)
ov=np.stack([orig,orig,orig,np.full_like(orig,255)],axis=-1).copy(); ov[binary]=[255,40,40,255]
return json.dumps({'fraction':round(float(frac),2),'vessel_um2':round(float(vpx*px2),1),
'vessel_mm2':round(float(vpx*px2/1e6),4),'n_segments':n,
'vmap_b64':_b64png(vrgba),'overlay_b64':_b64png(ov)})
def apply_sequence_guided(names_json,sk,min_size,px_um,roi_json='',guide_strength=0.0):
names=json.loads(names_json); results=[]
for name in names:
if name not in _imgs: continue
if (name,sk) not in _vmaps:
arr=_imgs[name]; inv=(255-arr.astype(np.float32))/255.0
_vmaps[(name,sk)]=frangi(inv,sigmas=json.loads(sk),black_ridges=False).astype(np.float32)
r=json.loads(run_filters_with_extras(name,sk,int(min_size),float(px_um),roi_json,'',float(guide_strength)))
results.append({'name':name,'fraction':r['fraction'],'vessel_um2':r['vessel_um2'],
'vessel_mm2':r['vessel_mm2'],'n_segments':r['n_segments']})
return json.dumps(results)
def build_proj_template(sk, min_size):
proj_key=('__proj__',sk)
if proj_key not in _vmaps: return json.dumps({'error':'Compute projection first'})
pv=_vmaps[proj_key]; nz=pv[pv>0]
if len(nz)<10: return json.dumps({'error':'No signal in projection'})
thresh=threshold_otsu(nz)
pb=binary_closing(pv>thresh,disk(4))
pb=remove_small_objects(pb,min_size=int(min_size))
# store for later use in guided fill
_imgs['__proj_binary__']=pb.astype(np.uint8)*255
return json.dumps({'h':int(pb.shape[0]),'w':int(pb.shape[1]),'n_px':int(pb.sum())})
def get_template_overlay(name, sk):
if '__proj_binary__' not in _imgs:
return json.dumps({'error':'Build projection template first'})
orig=_imgs[name]; h,w=orig.shape
pb_raw=_imgs['__proj_binary__']
# Resize if needed
if pb_raw.shape!=(h,w):
pb=np.array(Image.fromarray(pb_raw).resize((w,h),Image.NEAREST))>0
else:
pb=pb_raw>0
# Composite: vesselness map + cyan projection overlay
if (name,sk) in _vmaps:
vm=_vmaps[(name,sk)]; mx=vm.max()
vn=(vm/mx*255).astype(np.int32) if mx>0 else np.zeros((h,w),np.int32)
r=np.clip(vn*3,0,255).astype(np.uint8)
g=np.clip(vn*3-255,0,255).astype(np.uint8)
b=np.clip(vn*3-510,0,255).astype(np.uint8)
else:
r=g=b=np.zeros((h,w),np.uint8)
rgba=np.stack([r,g,b,np.full((h,w),255,np.uint8)],axis=-1).copy()
# Cyan overlay where projection template is active
rgba[pb,0]=np.clip(r[pb].astype(int)+0,0,255).astype(np.uint8)
rgba[pb,1]=np.clip(g[pb].astype(int)+160,0,255).astype(np.uint8)
rgba[pb,2]=np.clip(b[pb].astype(int)+220,0,255).astype(np.uint8)
return json.dumps({'b64':_b64png(rgba)})
def run_filters_template(name, sk, min_size, px_um, roi_json='', paint_json=''):
"""Like run_filters_with_extras but uses hard projection template mask."""
if '__proj_binary__' not in _imgs:
return run_filters_with_extras(name,sk,min_size,px_um,roi_json,paint_json,0.0)
vmap=_vmaps[(name,sk)]; orig=_imgs[name]; h,w=orig.shape
roi=_roi_mask(h,w,roi_json); nz=vmap[vmap>0]
if len(nz)<10:
empty=np.zeros((h,w,4),dtype=np.uint8)
ov=np.stack([orig,orig,orig,np.full_like(orig,255)],axis=-1)
return json.dumps({'fraction':0.0,'vessel_um2':0.0,'vessel_mm2':0.0,'n_segments':0,'vmap_b64':_b64png(empty),'overlay_b64':_b64png(ov)})
thresh=threshold_otsu(nz)
binary=binary_closing(vmap>thresh,disk(4))
binary=remove_small_objects(binary,min_size=int(min_size))
# Template guided: where template says vessel + frame has any signal → include
pb_raw=_imgs['__proj_binary__']
pb=np.array(Image.fromarray(pb_raw).resize((w,h),Image.NEAREST))>0 if pb_raw.shape!=(h,w) else pb_raw>0
relaxed=vmap>(thresh*0.25) # very relaxed threshold within template
guided=pb&relaxed
guided=binary_closing(guided,disk(3))
guided=remove_small_objects(guided,min_size=max(10,int(min_size)//6))
binary=binary|guided
# Paint
if paint_json:
pts=json.loads(paint_json); pmask=Image.new('L',(w,h),0); pdraw=ImageDraw.Draw(pmask)
for p in pts:
r=int(p['r']);x=int(p['x']);y=int(p['y']);fill=0 if p.get('erase') else 255
pdraw.ellipse([x-r,y-r,x+r,y+r],fill=fill)
binary=binary|(np.array(pmask)>0)
tmask=binary_closing(orig<250,disk(10))&roi; binary=binary&tmask
tpx=int(tmask.sum()); vpx=int(binary.sum())
frac=vpx/tpx*100 if tpx>0 else 0.0
n=len(measure.regionprops(measure.label(binary)))
px2=float(px_um)**2
vm=vmap.copy(); vm[~binary]=0; mx=vm.max()
vn=(vm/mx*255).astype(np.int32) if mx>0 else np.zeros((h,w),np.int32)
r=np.clip(vn*3,0,255).astype(np.uint8); g=np.clip(vn*3-255,0,255).astype(np.uint8); b=np.clip(vn*3-510,0,255).astype(np.uint8)
vrgba=np.stack([r,g,b,np.full((h,w),255,np.uint8)],axis=-1)
ov=np.stack([orig,orig,orig,np.full_like(orig,255)],axis=-1).copy(); ov[binary]=[255,40,40,255]
return json.dumps({'fraction':round(float(frac),2),'vessel_um2':round(float(vpx*px2),1),
'vessel_mm2':round(float(vpx*px2/1e6),4),'n_segments':n,'vmap_b64':_b64png(vrgba),'overlay_b64':_b64png(ov)})
def free_vmaps(names_json):
names=json.loads(names_json)
freed=0
keys=[k for k in list(_vmaps.keys()) if k[0] in names]
for k in keys:
del _vmaps[k]
freed+=1
import gc; gc.collect()
return json.dumps({'freed':freed,'remaining':len(_vmaps)})
def reset_sequence():
_imgs.pop('__proj__', None)
keys_to_del = [k for k in _vmaps if k[0] == '__proj__']
for k in keys_to_del: del _vmaps[k]
return 'ok'
def compute_projection(names_json, method, sk=''):
names=json.loads(names_json)
arrays=[_imgs[n] for n in names if n in _imgs]
if not arrays: return json.dumps({'error':'No images loaded'})
n_loaded=len(arrays)
stack=np.stack(arrays,axis=0).astype(np.float32)
if method=='median':
proj=np.median(stack,axis=0).astype(np.uint8)
elif method=='min':
proj=stack.min(axis=0).astype(np.uint8)
elif method=='std':
s=stack.std(axis=0); mx=s.max()
proj=(s/mx*255).astype(np.uint8) if mx>0 else s.astype(np.uint8)
elif method=='max_v':
# Maximum vesselness projection — uses pre-computed vmaps
if not sk: return json.dumps({'error':'Sigma key required for max vesselness'})
vmaps_list=[_vmaps[(n,sk)] for n in names if (n,sk) in _vmaps]
if not vmaps_list: return json.dumps({'error':'Compute vmaps first (run Analyze All Frames once, or switch to another method)'})
max_v=np.stack(vmaps_list,axis=0).max(axis=0)
_vmaps[('__proj__',sk)]=max_v.astype(np.float32)
mx=max_v.max()
proj=(max_v/mx*255).astype(np.uint8) if mx>0 else max_v.astype(np.uint8)
_imgs['__proj__']=proj
return json.dumps({'thumb':_thumb(proj),'w':int(proj.shape[1]),'h':int(proj.shape[0]),'n':len(vmaps_list),'vmap_ready':True})
else:
proj=stack.mean(axis=0).astype(np.uint8)
_imgs['__proj__']=proj
return json.dumps({'thumb':_thumb(proj),'w':int(proj.shape[1]),'h':int(proj.shape[0]),'n':n_loaded,'vmap_ready':False})
def auto_optimize(sk,roi_json=''):
name='__proj__'
if name not in _imgs: return json.dumps({'error':'Compute projection first'})
if (name,sk) not in _vmaps:
arr=_imgs[name]; inv=(255-arr.astype(np.float32))/255.0
_vmaps[(name,sk)]=frangi(inv,sigmas=json.loads(sk),black_ridges=False).astype(np.float32)
vmap=_vmaps[(name,sk)]; orig=_imgs[name]
roi=_roi_mask(*orig.shape,roi_json)
tmask=binary_closing(orig<250,disk(10))&roi
nz=vmap[vmap>0]
if len(nz)<10: return json.dumps({'error':'No vessel signal in projection'})
thresh=threshold_otsu(nz)
base_binary=binary_closing(vmap>thresh,disk(4))
test_sizes=[10,50,100,200,300,500,750,1000,1500,2000,3000,5000,8000,15000,30000]
areas=[]
for ms in test_sizes:
b=remove_small_objects(base_binary.copy(),min_size=ms)&tmask
areas.append(int(b.sum()))
arr_a=np.array(areas,dtype=float)
# Elbow: where relative drop first stays below 8%
elbow_idx=len(test_sizes)-1
if arr_a[0]>0:
drops=np.abs(np.diff(arr_a))/(arr_a[:-1]+1)
for i,d in enumerate(drops):
if d<0.08: elbow_idx=i+1; break
return json.dumps({'test_sizes':test_sizes,'areas':[int(a) for a in areas],
'recommended_min_size':test_sizes[elbow_idx],'elbow_idx':elbow_idx})
def apply_sequence(names_json,sk,min_size,px_um,roi_json=''):
names=json.loads(names_json); results=[]
for name in names:
if name not in _imgs: continue
if (name,sk) not in _vmaps:
arr=_imgs[name]; inv=(255-arr.astype(np.float32))/255.0
_vmaps[(name,sk)]=frangi(inv,sigmas=json.loads(sk),black_ridges=False).astype(np.float32)
r=json.loads(run_filters(name,sk,int(min_size),float(px_um),roi_json))
results.append({'name':name,'fraction':r['fraction'],'vessel_um2':r['vessel_um2'],
'vessel_mm2':r['vessel_mm2'],'n_segments':r['n_segments']})
return json.dumps(results)
def run_filters(name,sk,min_size,px_um,roi_json=''):
vmap=_vmaps[(name,sk)]; orig=_imgs[name]; h,w=orig.shape
roi=_roi_mask(h,w,roi_json); nz=vmap[vmap>0]
if len(nz)<10:
empty=np.zeros((h,w,4),dtype=np.uint8)
ov=np.stack([orig,orig,orig,np.full_like(orig,255)],axis=-1)
return json.dumps({'fraction':0.0,'vessel_um2':0.0,'vessel_mm2':0.0,'n_segments':0,'vmap_b64':_b64png(empty),'overlay_b64':_b64png(ov)})
thresh=threshold_otsu(nz); binary=vmap>thresh
binary=binary_closing(binary,disk(4))
binary=remove_small_objects(binary,min_size=int(min_size))
tmask=binary_closing(orig<250,disk(10))&roi; binary=binary&tmask
tpx=int(tmask.sum()); vpx=int(binary.sum())
frac=vpx/tpx*100 if tpx>0 else 0.0
n=len(measure.regionprops(measure.label(binary)))
px2=float(px_um)**2
vm=vmap.copy(); vm[~binary]=0; mx=vm.max()
vn=(vm/mx*255).astype(np.int32) if mx>0 else np.zeros((h,w),np.int32)
r=np.clip(vn*3,0,255).astype(np.uint8); g=np.clip(vn*3-255,0,255).astype(np.uint8); b=np.clip(vn*3-510,0,255).astype(np.uint8)
vrgba=np.stack([r,g,b,np.full((h,w),255,np.uint8)],axis=-1)
ov=np.stack([orig,orig,orig,np.full_like(orig,255)],axis=-1).copy(); ov[binary]=[255,40,40,255]
return json.dumps({'fraction':round(float(frac),2),'vessel_um2':round(float(vpx*px2),1),
'vessel_mm2':round(float(vpx*px2/1e6),4),'n_segments':n,'vmap_b64':_b64png(vrgba),'overlay_b64':_b64png(ov)})
`;
// ── Pyodide init ───────────────────────────────────────────────────────────
async function initPy(){
const msg=document.getElementById('init-msg'),fill=document.getElementById('pfill');
try{
msg.textContent='Loading Pyodide runtime…'; fill.style.width='15%';
py=await loadPyodide();
fill.style.width='40%'; msg.textContent='Loading scikit-image & Pillow…';
await py.loadPackage(['scikit-image','pillow','numpy']);
fill.style.width='85%'; msg.textContent='Initialising…';
await py.runPythonAsync(PY);
fill.style.width='100%'; msg.textContent='Ready!';
await new Promise(r=>setTimeout(r,350));
document.getElementById('init-overlay').style.display='none';
document.getElementById('app').style.display='flex';
initCanvases();
// Restore pixel size default
const px=localStorage.getItem('va_px');
if(px) document.getElementById('px-size').value=px;
}catch(e){msg.textContent='Error: '+e.message;msg.style.color='#f87171';console.error(e);}
}
// ── Save / load defaults ───────────────────────────────────────────────────
function saveDefaults(){
localStorage.setItem('va_si',curSI);
localStorage.setItem('va_mi',curMI);
localStorage.setItem('va_px',document.getElementById('px-size').value);
toast('⭐ Settings saved as default');
}
// ── Buttons ────────────────────────────────────────────────────────────────
function mkBtns(){
const sb=document.getElementById('sigma-btns');
SIGMAS.forEach(({l},i)=>{const b=document.createElement('button');b.className='fb'+(i===curSI?' on':'');b.textContent=l;b.onclick=()=>{curSI=i;upBtns();analyze();};sb.appendChild(b);});
const mb=document.getElementById('minsize-btns');
MINSIZES.forEach((sz,i)=>{const b=document.createElement('button');b.className='fb'+(i===curMI?' on':'');b.textContent=sz>=1000?(sz/1000)+'k':sz;b.onclick=()=>{curMI=i;upBtns();analyze();};mb.appendChild(b);});
}
function upBtns(){
document.querySelectorAll('#sigma-btns .fb').forEach((b,i)=>b.classList.toggle('on',i===curSI));
document.querySelectorAll('#minsize-btns .fb').forEach((b,i)=>b.classList.toggle('on',i===curMI));
}
// ── Canvases / ROI ─────────────────────────────────────────────────────────
function initCanvases(){
// ov-canvas (ROI outline mirror) resizes with ov-wrap — not used for drawing now
// roi-canvas and paint-canvas are in ov-wrap
const resize=(wrap,canvas)=>new ResizeObserver(()=>{canvas.width=wrap.offsetWidth;canvas.height=wrap.offsetHeight;drawROI(canvas,true);}).observe(wrap);
resize(document.getElementById('ov-wrap'),document.getElementById('roi-canvas'));
resize(document.getElementById('ov-wrap'),document.getElementById('ov-canvas'));
const rc=document.getElementById('roi-canvas');
rc.addEventListener('click',onROIClick);
rc.addEventListener('dblclick',onROIDblClick);
rc.addEventListener('mousemove',onROIMove);
rc.addEventListener('mouseleave',()=>{hoverPt=null;drawROI(rc,true);});
initPaintCanvas();
initCountCanvas();
}
// ── Overlay Zoom state ────────────────────────────────────────────────────
let ovZoomS=1, ovPanX=0, ovPanY=0, panActive=false, panDragging=false, panDragStart=null;
function getT(wrapId,imgId){
const wrap=document.getElementById(wrapId),img=document.getElementById(imgId);
const cw=wrap.offsetWidth,ch=wrap.offsetHeight,iw=img.naturalWidth||cw,ih=img.naturalHeight||ch;
const ia=iw/ih,ca=cw/ch;let rw,rh,ox,oy;
if(ia>ca){rw=cw;rh=cw/ia;ox=0;oy=(ch-rh)/2;}else{rh=ch;rw=ch*ia;ox=(cw-rw)/2;oy=0;}
if(wrapId==='ov-wrap'&&(ovZoomS!==1||ovPanX!==0||ovPanY!==0)){
// zoom centered on wrap center + pan offset
const zcx=cw/2+ovPanX, zcy=ch/2+ovPanY;
return{ox:zcx+(ox-cw/2)*ovZoomS, oy:zcy+(oy-ch/2)*ovZoomS,
sx:rw/iw*ovZoomS, sy:rh/ih*ovZoomS};
}
return{ox,oy,sx:rw/iw,sy:rh/ih};
}
function c2i(mx,my,t){return{x:(mx-t.ox)/t.sx,y:(my-t.oy)/t.sy};}
function i2c(ix,iy,t){return{x:t.ox+ix*t.sx,y:t.oy+iy*t.sy};}
function drawROI(canvas,withHover){
const ctx=canvas.getContext('2d');ctx.clearRect(0,0,canvas.width,canvas.height);
if(!roi||!roi.points.length)return;
const t=getT('ov-wrap','overlay-img');
const pts=roi.points.map(p=>i2c(p.x,p.y,t));
ctx.strokeStyle='#34d399';ctx.lineWidth=2;ctx.setLineDash([]);ctx.fillStyle='rgba(52,211,153,.12)';
ctx.beginPath();pts.forEach((p,i)=>i===0?ctx.moveTo(p.x,p.y):ctx.lineTo(p.x,p.y));
if(roi.closed){ctx.closePath();ctx.fill();}ctx.stroke();
if(withHover&&drawingROI&&hoverPt&&pts.length){
const last=pts[pts.length-1];
ctx.strokeStyle='rgba(52,211,153,.4)';ctx.setLineDash([5,4]);
ctx.beginPath();ctx.moveTo(last.x,last.y);ctx.lineTo(hoverPt.x,hoverPt.y);ctx.stroke();ctx.setLineDash([]);
if(pts.length>=3){const f=pts[0];if(Math.sqrt((f.x-hoverPt.x)**2+(f.y-hoverPt.y)**2)<14){ctx.strokeStyle='#34d399';ctx.lineWidth=2;ctx.beginPath();ctx.arc(f.x,f.y,8,0,Math.PI*2);ctx.stroke();}}
}
ctx.fillStyle='#34d399';pts.forEach((p,i)=>{ctx.beginPath();ctx.arc(p.x,p.y,i===0?5:3.5,0,Math.PI*2);ctx.fill();});
}
function syncOv(){/* ROI now lives on overlay panel — no sync needed */}
function onROIClick(e){
if(!drawingROI)return;
const rc=document.getElementById('roi-canvas'),rect=rc.getBoundingClientRect();
const mx=e.clientX-rect.left,my=e.clientY-rect.top;
const t=getT('ov-wrap','overlay-img'),ip=c2i(mx,my,t);
if(!roi)roi={points:[],closed:false};
if(roi.points.length>=3){const fp=i2c(roi.points[0].x,roi.points[0].y,t);if(Math.sqrt((fp.x-mx)**2+(fp.y-my)**2)<14){closeROIPoly();return;}}
roi.points.push({x:ip.x,y:ip.y});drawROI(rc,true);syncOv();
}
function onROIDblClick(e){if(!drawingROI||!roi||roi.points.length<3)return;roi.points.pop();closeROIPoly();}
function onROIMove(e){
if(!drawingROI||!roi)return;
const rc=document.getElementById('roi-canvas'),rect=rc.getBoundingClientRect();
hoverPt={x:e.clientX-rect.left,y:e.clientY-rect.top};drawROI(rc,true);
}
function closeROIPoly(){
roi.closed=true;drawingROI=false;hoverPt=null;
document.getElementById('roi-canvas').classList.remove('draw-active');
document.getElementById('roi-draw-btn').classList.remove('roi-on');
document.getElementById('roi-draw-btn').textContent='✏ Draw ROI';
document.getElementById('roi-clear-btn').style.display='';
document.getElementById('roi-copy-btn').style.display='';