3D Reconstruction: Decimate and Finalize

Decimate Surface

Decimation reduces the triangle count of the surface. A lighter mesh renders faster and is easier to handle downstream.

1. In the Geometry editing group, choose Decimate surface
2. Set the Decimation factor (0–100 %, default 50)
3. Press Apply

Topology is preserved, so holes and boundaries survive decimation. Use it when the auto-generated surface is denser than you need for visualization or simulation.

Remove Small Bits

Segmentation can leave small disconnected fragments around the main structure.

1. In the Geometry editing group, choose Remove small bits
2. Press Apply

⚠️ This keeps only the single largest connected region and discards everything else — it has no size threshold, despite the name. On a bilateral lung segmentation it would leave you with one lung. Run it per-segment, or use Select mask when you need finer control.

Select Mask

Select mask is an interactive region picker, not a target selector: hover and click disconnected regions in the 3D view to select them, then press Backspace to remove the selection. Use it when Remove small bits is too blunt — for example when you want to keep a fragment it would discard.

Store and Simulate

When the surface is clean, save the anatomy as a project — the same Store selection as project step described in the segmentation tutorial.

1. In the Store selection as project section, type a name into the New project input
2. Confirm to create the device/project from the cleaned anatomy

This makes the anatomy available to the lung analysis tools and the engineering simulation workflow.

Suggested Cleanup Order

A practical sequence for a noisy auto-generated surface:

1. Remove small bits — drop detached fragments
2. Smooth surface — reduce staircase artifacts
3. Decimate surface — lighten the mesh if it is too dense
4. Store selection as project — save the result

Troubleshooting

Surface Looks Blocky

• Run Smooth surface; increase the Taubin/Laplacian slider and press Start again
• Multiple light smoothing passes are safer than one aggressive pass

Stray Fragments Around the Organ

• Run Remove small bits to delete disconnected pieces

Mesh Is Too Heavy

• Run Decimate surface to reduce the triangle count

Best Practices

1. Clean before storing: tidy the surface with the geometry editing tools before Store selection as project
2. Smooth conservatively: raise the slider gradually and re-run rather than smoothing hard once
3. Remove fragments first: small bits can interfere with downstream analysis