MitoSim · interactive (local server)

The slicing axis, in your hands

Real chromatid geometry from the simulator (dog karyotype). Pick a phase, drag the 3D panel to orbit the camera, and use the sliders to change tilt, slab offset/thickness, and focus. The bottom-right panel calls this Flask server's /api/render endpoint, which runs the actual render_patch() optics pipeline (Beer-Lambert + defocus PSF + HE colour) for the exact current parameters, at 2.5× the M4 demo's native resolution (0.1 μm/px, 320×320).

3D scene

Drag to orbit the camera. This doesn't change the section — only how you're looking at it.

Slicing controls

Tilt

Tilt direction

Slab offset (s)

Slab thickness (t)

Focus (relative to s)

Sharpness

0 = physically-derived (matches the M4 demo exactly, and looks soft — a lone chromatid is 1-2px at this NA/resolution). Higher trades that accuracy for a legible image; it only affects the exact (server) panel.

Section preview instant, approximate

Depth-based softening stands in for defocus here — not Beer-Lambert + PSF.

Section preview exact, server-rendered

waiting for first render…

What "tilt direction" means: tilt alone (0° = spindle along the section normal, 90° = 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.