3D Reconstruction

3D Reconstruction

Generating a 3D object

From the Object list, select one or more objects and choose 3D ▸ Add to scene from the context menu (or Shift+double-click an object). The first time, this opens the 3D scene window; if a scene is already open, the objects are added to it. Meshes are built on a background thread (you'll see a "Generating 3D…" progress indicator). Z-traces can also be added to the scene (as tubes) from the z-trace list.

📸 Screenshot: the 3D scene window with a few reconstructed objects and the scale cube.

3D model types

Each object has a 3D type (set in Edit 3D settings… from the object list):

• Surface (default) — a smoothed surface reconstructed from the object's traces (negative traces are subtracted, e.g. to hollow out a structure).
• Spheres — one sphere per trace, sized to the trace's radius (good for point-like or stamped objects).
• Contours — each trace rendered as a thin slab, showing the raw cross-sections.

Z-traces render as tubes. Edit 3D settings… also sets per-object opacity.

Series-wide 3D quality is controlled in Series ▸ Options (the 3D section): an XY Resolution slider (less detail/faster ↔ more detail/slower), the 3D smoothing method (Humphrey — recommended — Mutable Diffusion Laplacian, Taubin, or None), the smoothing iterations, and the screenshot resolution (dpi).

Navigating the 3D scene

• Left-drag — rotate; middle-drag — pan; right-drag — zoom. (Ctrl-drag also rotates.)
• Double-click an object — jump the 2D field to that point on the corresponding section.
• Click meshes to select them. With objects selected: arrow keys translate in X/Y, Ctrl+Up/Down translates in Z, Shift+arrows and Ctrl+Shift+Up/Down rotate. Delete/Backspace removes selected objects from the scene; [ / ] step their opacity.
• Set the camera along an axis with X / Y / Z, fit everything with Home ("Focus on all"), and center on the selection with F.
• Press ? in the scene for its full shortcut list.

The 3D window has its own menu bar:

• Scale cube — toggle a reference cube with the C key (or Scale Cube ▸ Display in scene). To move it, select it (left-click) and use the arrow keys (X/Y) and Ctrl+Up/Down (Z). Edit its edge length (µm), color, opacity, and outline width via Edit ▸ Edit attributes… (Ctrl+E) — it's a physical measuring reference.
• Scene ▸ Change background — set the background color.
• Scene ▸ Organize scene… (Ctrl+Shift+H) — line objects up side by side, by host group or individually.
• Scene ▸ Set translate/rotate step… — the movement increments (default 0.1 µm and 10°).
• File ▸ Save scene… / Load scene… — save the scene (objects, colors, camera) to a JSON file and reload it later (also Series ▸ 3D ▸ Load 3D scene… from the main window). Add to scene can also pull objects from another series.

Saving images and exporting meshes

• Scene ▸ Save scene screenshot… — save a rendered image (PNG, JPG, TIF, or BMP) at the configured DPI.
• Scene ▸ Export scene… — export the whole scene as a single Wavefront .obj (with a .mtl material file).
• From the Object list ▸ 3D ▸ Export meshes — export individual objects as Wavefront (.obj), OFF (.off), Stanford PLY (.ply), STL (.stl), or Collada (.dae). (Surface and Spheres objects export; contour and tube types do not.)
• Object list ▸ 3D ▸ Export quantitative data — write per-object surface area and volume to CSV. (Note these depend on the meshing settings; verify mesh quality before relying on the numbers.)

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