interactive_demo.html

<title>MitoSim — interactive slicing-axis explorer</title>
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<div class="page">
  <p class="kicker">MitoSim &middot; interactive</p>
  <h1>The slicing axis, in your hands</h1>
  <p class="dek">Real chromatid geometry from the simulator (dog karyotype), not an illustration. Pick a phase,
    then drag the left panel to orbit the camera, and use the sliders to change the spindle's tilt relative to
    the section, the slab's offset and thickness, and the focal plane. The right panel is what a section through
    that exact configuration would show.</p>

  <div class="phase-row" id="phaseRow"></div>

  <div class="layout">
    <div class="panel">
      <h2>3D scene</h2>
      <div class="canvas-wrap"><canvas id="scene3d" width="640" height="640"></canvas></div>
      <p class="hint">Drag to orbit the camera. This doesn't change the section — only how you're looking at it.</p>
    </div>

    <div class="panel controls-panel">
      <h2>Slicing controls</h2>
      <div class="row">
        <label><b>Tilt</b><span class="val" id="vTilt"></span></label>
        <input type="range" id="tilt" min="0" max="90" step="1" value="0">
      </div>
      <div class="row">
        <label><b>Tilt direction</b><span class="val" id="vAzimuth"></span></label>
        <input type="range" id="azimuth" min="0" max="360" step="1" value="0">
      </div>
      <div class="row">
        <label><b>Slab offset (s)</b><span class="val" id="vOffset"></span></label>
        <input type="range" id="offset" min="-10" max="10" step="0.1" value="0">
      </div>
      <div class="row">
        <label><b>Slab thickness (t)</b><span class="val" id="vThickness"></span></label>
        <input type="range" id="thickness" min="0.3" max="8" step="0.1" value="3">
      </div>
      <div class="row">
        <label><b>Focus (relative to s)</b><span class="val" id="vFocus"></span></label>
        <input type="range" id="focus" min="-4" max="4" step="0.1" value="0">
      </div>
      <div class="btn-row">
        <button class="btn" id="btnRandomTilt">Random tilt</button>
        <button class="btn" id="btnReset">Reset</button>
      </div>
      <div class="readout" id="readout"></div>
    </div>

    <div class="panel">
      <h2>Resulting section (approximate)</h2>
      <div class="canvas-wrap"><canvas id="scene2d" width="440" height="440"></canvas></div>
      <p class="hint">A simplified stand-in for the real optical model: depth-based softening approximates
        defocus here, it isn't Beer-Lambert + PSF. The M4 demo has the physically-modelled version.</p>
    </div>
  </div>

  <p class="callout"><b>What "tilt direction" means:</b> tilt alone (0&deg; = spindle along the section normal,
    90&deg; = spindle lying flat in the section plane) doesn't fully describe an orientation — direction matters
    too, the same way two ladders leaning at the same angle can fall toward different walls. Sweep tilt direction
    at a fixed tilt and watch the cell rotate around the slab rather than through it.</p>
</div>

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<script>
(function () {
  const DATA = JSON.parse(document.getElementById('data-json').textContent);
  const PHASES = ["prophase", "prometaphase", "metaphase", "anaphase", "telophase"];
  const CHROM_COLORS = ["#3f7cac","#c9622d","#4f9d5b","#a34f8c","#c2a83e","#5b6bbf","#b4483f","#3f9e94",
                        "#8a5fb0","#c77b3d","#4f8f6d","#b0507a","#6f8c3f","#9a5a3f","#4a6ea8","#c2954a"];

  let state = {
    phase: "metaphase",
    tilt: 0, azimuth: 0, offset: 0, thickness: 3.0, focus: 0.0,
    viewAzimuth: -0.55, viewElevation: 0.35,
  };

  // ---- linear algebra ----
  function normalize(v) { const n = Math.hypot(v[0], v[1], v[2]) || 1; return [v[0]/n, v[1]/n, v[2]/n]; }
  function cross(a, b) { return [a[1]*b[2]-a[2]*b[1], a[2]*b[0]-a[0]*b[2], a[0]*b[1]-a[1]*b[0]]; }
  function dot(a, b) { return a[0]*b[0] + a[1]*b[1] + a[2]*b[2]; }
  function sub(a, b) { return [a[0]-b[0], a[1]-b[1], a[2]-b[2]]; }

  function rotationAboutAxis(axis, angle) {
    const [x, y, z] = normalize(axis);
    const c = Math.cos(angle), s = Math.sin(angle), C = 1 - c;
    return [
      [x*x*C+c,   x*y*C-z*s, x*z*C+y*s],
      [y*x*C+z*s, y*y*C+c,   y*z*C-x*s],
      [z*x*C-y*s, z*y*C+x*s, z*z*C+c],
    ];
  }
  function matVec(m, v) {
    return [
      m[0][0]*v[0]+m[0][1]*v[1]+m[0][2]*v[2],
      m[1][0]*v[0]+m[1][1]*v[1]+m[1][2]*v[2],
      m[2][0]*v[0]+m[2][1]*v[1]+m[2][2]*v[2],
    ];
  }

  function cameraBasis(azimRad, elevRad) {
    const forward = normalize([
      Math.cos(elevRad) * Math.cos(azimRad),
      Math.cos(elevRad) * Math.sin(azimRad),
      Math.sin(elevRad),
    ]);
    const worldUp = [0, 0, 1];
    let right = cross(forward, worldUp);
    if (Math.hypot(...right) < 1e-6) right = [1, 0, 0];
    right = normalize(right);
    const up = normalize(cross(right, forward));
    return { right, up, forward };
  }

  // ---- membrane wireframe (unit sphere, scaled per-phase at draw time) ----
  const MEMBRANE_LINES = (() => {
    const lines = [];
    const nSeg = 28;
    for (let lat = 1; lat < 8; lat++) {
      const phi = Math.PI * lat / 8;
      const pts = [];
      for (let i = 0; i <= nSeg; i++) {
        const th = 2 * Math.PI * i / nSeg;
        pts.push([Math.sin(phi)*Math.cos(th), Math.sin(phi)*Math.sin(th), Math.cos(phi)]);
      }
      lines.push(pts);
    }
    for (let lon = 0; lon < 12; lon++) {
      const th = 2 * Math.PI * lon / 12;
      const pts = [];
      for (let i = 0; i <= nSeg; i++) {
        const phi = Math.PI * i / nSeg;
        pts.push([Math.sin(phi)*Math.cos(th), Math.sin(phi)*Math.sin(th), Math.cos(phi)]);
      }
      lines.push(pts);
    }
    return lines;
  })();

  // Returns a pole *index*, computed from the untransformed (canonical)
  // geometry -- which pole a chromatid is attached to doesn't depend on
  // the cell's current tilt, so this stays rotation-invariant. Callers
  // must look the index up in the *rotated* pole positions when drawing,
  // or poles/fibres will silently stay fixed while everything else tilts.
  function poleIndexForChromatid(c, poles) {
    if (poles.length === 2) return c.s === 0 ? 1 : 0;
    let best = 0, bestD = Infinity;
    for (let i = 0; i < poles.length; i++) {
      const d = Math.hypot(...sub(poles[i], c.cen));
      if (d < bestD) { bestD = d; best = i; }
    }
    return best;
  }

  // ============================== 3D PANEL ==============================
  const canvas3d = document.getElementById('scene3d');
  const ctx3d = canvas3d.getContext('2d');

  function project(p, basis, scale, cx, cy) {
    const sx = cx + dot(p, basis.right) * scale;
    const sy = cy - dot(p, basis.up) * scale;
    const depth = dot(p, basis.forward);
    return [sx, sy, depth];
  }

  function draw3d() {
    const W = canvas3d.width, H = canvas3d.height;
    ctx3d.clearRect(0, 0, W, H);
    ctx3d.fillStyle = getComputedStyle(document.documentElement).getPropertyValue('--plate') || '#fdfcf9';
    ctx3d.fillRect(0, 0, W, H);

    const d = DATA[state.phase];
    const R = 0.85 * Math.min(W, H) / 2 / (d.cell_radius * 1.25);
    const cx = W / 2, cy = H / 2;
    const basis = cameraBasis(state.viewAzimuth, state.viewElevation);
    const tiltAxis = [Math.cos(state.azimuth * Math.PI/180), Math.sin(state.azimuth * Math.PI/180), 0];
    const Rphys = rotationAboutAxis(tiltAxis, state.tilt * Math.PI / 180);

    const zLo = state.offset - state.thickness/2, zHi = state.offset + state.thickness/2;
    // Poles are part of the same rigid spindle apparatus as the
    // chromatids -- they must tilt with Rphys too, or they (and every
    // fibre drawn to them) stay pinned in place while the cell rotates
    // around them, which reads as "nothing is actually moving".
    const polesW = d.poles.map(p => matVec(Rphys, p));

    // membrane
    ctx3d.strokeStyle = 'rgba(120,110,90,0.28)';
    ctx3d.lineWidth = 1;
    for (const line of MEMBRANE_LINES) {
      ctx3d.beginPath();
      line.forEach((p, i) => {
        const wp = [p[0]*d.cell_radius, p[1]*d.cell_radius, p[2]*d.cell_radius];
        const [sx, sy] = project(wp, basis, R, cx, cy);
        if (i === 0) ctx3d.moveTo(sx, sy); else ctx3d.lineTo(sx, sy);
      });
      ctx3d.stroke();
    }

    // slab planes (fixed in world frame, not rotated by Rphys)
    const ext = d.cell_radius * 1.15;
    ctx3d.fillStyle = 'rgba(199,154,46,0.13)';
    ctx3d.strokeStyle = 'rgba(199,154,46,0.75)';
    ctx3d.lineWidth = 1.2;
    for (const zc of [zLo, zHi]) {
      const corners = [[-ext,-ext,zc],[ext,-ext,zc],[ext,ext,zc],[-ext,ext,zc]];
      const proj = corners.map(p => project(p, basis, R, cx, cy));
      ctx3d.beginPath();
      proj.forEach((p, i) => { if (i===0) ctx3d.moveTo(p[0],p[1]); else ctx3d.lineTo(p[0],p[1]); });
      ctx3d.closePath();
      ctx3d.fill();
      ctx3d.stroke();
    }

    // chromatid fibres (faint, drawn under chromatids)
    if (d.poles.length) {
      ctx3d.strokeStyle = 'rgba(138,31,61,0.18)';
      ctx3d.lineWidth = 0.6;
      for (const c of d.chromatids) {
        const cenW = matVec(Rphys, c.cen);
        const pole = polesW[poleIndexForChromatid(c, d.poles)];
        const [x1,y1] = project(cenW, basis, R, cx, cy);
        const [x2,y2] = project(pole, basis, R, cx, cy);
        ctx3d.beginPath(); ctx3d.moveTo(x1,y1); ctx3d.lineTo(x2,y2); ctx3d.stroke();
      }
    }

    // chromatids: transform, depth-sort, draw faded full path then bright in-slab runs
    const drawables = [];
    for (const c of d.chromatids) {
      const wpts = c.pts.map(p => matVec(Rphys, p));
      const proj = wpts.map(p => project(p, basis, R, cx, cy));
      const avgDepth = proj.reduce((a,p) => a+p[2], 0) / proj.length;
      const color = CHROM_COLORS[c.id % CHROM_COLORS.length];
      const lw = (c.rad.reduce((a,b)=>a+b,0)/c.rad.length) * R * 0.9;
      drawables.push({ proj, wpts, color, lw, depth: avgDepth, cenW: matVec(Rphys, c.cen) });
    }
    drawables.sort((a,b) => a.depth - b.depth);

    for (const item of drawables) {
      ctx3d.strokeStyle = item.color + '2e';
      ctx3d.lineWidth = Math.max(item.lw, 1);
      ctx3d.lineCap = 'round';
      ctx3d.beginPath();
      item.proj.forEach((p,i) => { if (i===0) ctx3d.moveTo(p[0],p[1]); else ctx3d.lineTo(p[0],p[1]); });
      ctx3d.stroke();

      // in-slab sub-runs at full opacity
      ctx3d.strokeStyle = item.color;
      ctx3d.lineWidth = Math.max(item.lw * 1.1, 1.2);
      let run = [];
      for (let i = 0; i < item.wpts.length; i++) {
        const z = item.wpts[i][2];
        const inSlab = z >= zLo && z <= zHi;
        if (inSlab) run.push(item.proj[i]);
        if ((!inSlab || i === item.wpts.length-1) && run.length > 1) {
          ctx3d.beginPath();
          run.forEach((p,k) => { if (k===0) ctx3d.moveTo(p[0],p[1]); else ctx3d.lineTo(p[0],p[1]); });
          ctx3d.stroke();
          run = [];
        } else if (!inSlab) { run = []; }
      }
    }

    // centromeres
    ctx3d.fillStyle = '#241f3d';
    for (const item of drawables) {
      const [sx, sy] = project(item.cenW, basis, R, cx, cy);
      ctx3d.beginPath(); ctx3d.arc(sx, sy, 1.6, 0, 2*Math.PI); ctx3d.fill();
    }

    // poles
    if (d.poles.length) {
      ctx3d.strokeStyle = 'rgba(138,31,61,0.6)';
      ctx3d.lineWidth = 1.2;
      ctx3d.setLineDash([4,4]);
      ctx3d.beginPath();
      polesW.forEach((p,i) => { const [x,y]=project(p,basis,R,cx,cy); if(i===0) ctx3d.moveTo(x,y); else ctx3d.lineTo(x,y); });
      ctx3d.stroke();
      ctx3d.setLineDash([]);
      ctx3d.fillStyle = '#8a1f3d';
      for (const p of polesW) {
        const [x,y] = project(p, basis, R, cx, cy);
        ctx3d.save(); ctx3d.translate(x,y); ctx3d.rotate(Math.PI/4);
        ctx3d.fillRect(-4,-4,8,8); ctx3d.restore();
      }
    }
  }

  // ============================== 2D PANEL ==============================
  const canvas2d = document.getElementById('scene2d');
  const ctx2d = canvas2d.getContext('2d');

  // fixed decorative background nuclei (purely cosmetic, precomputed once)
  const BG_NUCLEI = Array.from({length: 10}, (_, i) => {
    const rnd = (seed) => { const x = Math.sin(seed*999)*10000; return x - Math.floor(x); };
    return { x: rnd(i*3+1)*2-1, y: rnd(i*3+2)*2-1, r: 0.06 + rnd(i*3+3)*0.05 };
  });

  function draw2d() {
    const W = canvas2d.width, H = canvas2d.height;
    ctx2d.clearRect(0, 0, W, H);
    ctx2d.fillStyle = '#f7f4ee';
    ctx2d.fillRect(0, 0, W, H);

    const d = DATA[state.phase];
    const fov = d.cell_radius * 1.5; // half-width of the field of view, microns
    const scale = (Math.min(W,H) / 2) / fov;
    const cx = W/2, cy = H/2;
    const zLo = state.offset - state.thickness/2, zHi = state.offset + state.thickness/2;
    const focalZ = state.offset + state.focus;
    const dof = 0.9;

    // decorative background nuclei
    ctx2d.fillStyle = 'rgba(150,130,150,0.35)';
    for (const n of BG_NUCLEI) {
      ctx2d.beginPath();
      ctx2d.arc(cx + n.x*fov*scale, cy + n.y*fov*scale, n.r*fov*scale, 0, 2*Math.PI);
      ctx2d.fill();
    }

    // cytoplasm footprint -- exact sphere/slab intersection formula from M1
    const r = d.cell_radius;
    const lo = Math.max(-r, zLo), hi = Math.min(r, zHi);
    if (hi > lo) {
      const z0 = Math.min(Math.max(0, lo), hi);
      const cytoR = Math.sqrt(Math.max(r*r - z0*z0, 0));
      const grad = ctx2d.createRadialGradient(cx, cy, 0, cx, cy, cytoR*scale);
      grad.addColorStop(0, 'rgba(210,120,145,0.55)');
      grad.addColorStop(1, 'rgba(210,120,145,0.38)');
      ctx2d.fillStyle = grad;
      ctx2d.beginPath();
      ctx2d.arc(cx, cy, cytoR*scale, 0, 2*Math.PI);
      ctx2d.fill();
    }

    const tiltAxis = [Math.cos(state.azimuth * Math.PI/180), Math.sin(state.azimuth * Math.PI/180), 0];
    const Rphys = rotationAboutAxis(tiltAxis, state.tilt * Math.PI / 180);

    for (const c of d.chromatids) {
      const rad = c.rad.reduce((a,b)=>a+b,0)/c.rad.length;
      for (let i = 0; i < c.pts.length; i++) {
        const wp = matVec(Rphys, c.pts[i]);
        if (wp[2] < zLo || wp[2] > zHi) continue;
        const defocus = Math.sqrt(1 + Math.pow((wp[2]-focalZ)/dof, 2));
        const alpha = Math.max(0.12, 1 / defocus);
        const px = cx + wp[0]*scale, py = cy - wp[1]*scale;
        const pr = Math.max(rad*scale*defocus*0.8, 1.2);
        ctx2d.fillStyle = `rgba(58,47,102,${alpha.toFixed(3)})`;
        ctx2d.beginPath();
        ctx2d.arc(px, py, pr, 0, 2*Math.PI);
        ctx2d.fill();
      }
    }
  }

  // ============================== wiring ==============================
  function redraw() { draw3d(); draw2d(); updateReadout(); }

  function updateReadout() {
    document.getElementById('vTilt').textContent = state.tilt.toFixed(0) + '°';
    document.getElementById('vAzimuth').textContent = state.azimuth.toFixed(0) + '°';
    document.getElementById('vOffset').textContent = state.offset.toFixed(1) + ' µm';
    document.getElementById('vThickness').textContent = state.thickness.toFixed(1) + ' µm';
    document.getElementById('vFocus').textContent = (state.focus>=0?'+':'') + state.focus.toFixed(1) + ' µm';
    const d = DATA[state.phase];
    document.getElementById('readout').innerHTML =
      `<b>phase</b> ${state.phase}<br>` +
      `<b>chromatids</b> ${d.chromatids.length}<br>` +
      `<b>poles</b> ${d.poles.length}<br>` +
      `<b>cell radius</b> ${d.cell_radius.toFixed(1)} µm<br>` +
      `<b>slab z</b> [${(state.offset-state.thickness/2).toFixed(1)}, ${(state.offset+state.thickness/2).toFixed(1)}] µm`;
  }

  const phaseRow = document.getElementById('phaseRow');
  PHASES.forEach(p => {
    const btn = document.createElement('button');
    btn.className = 'phase-btn' + (p === state.phase ? ' active' : '');
    btn.textContent = p;
    btn.dataset.phase = p;
    btn.addEventListener('click', () => {
      state.phase = p;
      document.querySelectorAll('.phase-btn').forEach(b => b.classList.toggle('active', b.dataset.phase === p));
      redraw();
    });
    phaseRow.appendChild(btn);
  });

  function bindSlider(id, key, parse) {
    const el = document.getElementById(id);
    el.addEventListener('input', () => { state[key] = parse(el.value); redraw(); });
  }
  bindSlider('tilt', 'tilt', parseFloat);
  bindSlider('azimuth', 'azimuth', parseFloat);
  bindSlider('offset', 'offset', parseFloat);
  bindSlider('thickness', 'thickness', parseFloat);
  bindSlider('focus', 'focus', parseFloat);

  document.getElementById('btnRandomTilt').addEventListener('click', () => {
    // matches the real sampling convention: sin(tilt) uniform on [0,1]
    const tiltRad = Math.asin(Math.random());
    state.tilt = tiltRad * 180 / Math.PI;
    state.azimuth = Math.random() * 360;
    document.getElementById('tilt').value = state.tilt;
    document.getElementById('azimuth').value = state.azimuth;
    redraw();
  });
  document.getElementById('btnReset').addEventListener('click', () => {
    state.tilt = 0; state.azimuth = 0; state.offset = 0; state.thickness = 3.0; state.focus = 0.0;
    document.getElementById('tilt').value = 0;
    document.getElementById('azimuth').value = 0;
    document.getElementById('offset').value = 0;
    document.getElementById('thickness').value = 3.0;
    document.getElementById('focus').value = 0.0;
    redraw();
  });

  // orbit drag on the 3D canvas
  let dragging = false, lastX = 0, lastY = 0;
  function pointerDown(x, y) { dragging = true; lastX = x; lastY = y; }
  function pointerMove(x, y) {
    if (!dragging) return;
    state.viewAzimuth += (x - lastX) * 0.008;
    state.viewElevation = Math.max(-1.45, Math.min(1.45, state.viewElevation - (y - lastY) * 0.008));
    lastX = x; lastY = y;
    draw3d();
  }
  function pointerUp() { dragging = false; }
  canvas3d.addEventListener('mousedown', e => pointerDown(e.clientX, e.clientY));
  window.addEventListener('mousemove', e => pointerMove(e.clientX, e.clientY));
  window.addEventListener('mouseup', pointerUp);
  canvas3d.addEventListener('touchstart', e => { const t=e.touches[0]; pointerDown(t.clientX, t.clientY); }, {passive:true});
  canvas3d.addEventListener('touchmove', e => { const t=e.touches[0]; pointerMove(t.clientX, t.clientY); }, {passive:true});
  canvas3d.addEventListener('touchend', pointerUp);

  redraw();
})();
</script>