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Segment individual trees

Separate a point cloud containing many trees into individual trees, giving every point a per-tree instance ID. Phytograph uses TreeIso — a classical cut-pursuit graph method that runs on the CPU (no GPU required).

When to use this

  • Your scan covers a forest plot, orchard row, or any scene with more than one tree, and you want to isolate each tree.
  • You need per-tree point sets for downstream analysis (height, crown, skeleton) or to export each tree separately.

Before you start

TreeIso isolates above-ground tree structure, so deal with the ground first with Segment ground points. You have two options:

  • Remove the ground points, or
  • Label them (run ground segmentation and keep the labelled cloud without deleting the ground). When the cloud carries a ground_class label, Segment Trees automatically excludes the ground points — TreeIso only sees the plant points, and the ground keeps tree ID 0 ("Unassigned").

If ground appears to still be present and unlabelled when you run the tool, Phytograph warns you (but still runs).

Steps

  1. Import your scan (see Import & export) and, if needed, run Segment ground points — either keep the non-ground cloud or keep the labelled cloud (the ground is excluded automatically).
  2. Select the cloud in the scan list.
  3. Open the Segment Trees tool from the toolbar (the trees/forest icon in the Tools › Segmentation group) or the command palette (Cmd/Ctrl-K → "Segment Trees").
  4. Adjust parameters if needed. The size-dependent settings (the internal decimation and the max-gap below) are seeded from the cloud's extent each time the panel opens — fine for a close-range scan, coarser for a field- or airborne-scale tile — so a large-area scan is handled as efficiently as a close-range one instead of stalling:
    • 3D reg. strength (λ₁) — regularization for the initial 3D segmentation. Default 1.0.
    • 2D reg. strength (λ₂) — regularization for the intermediate 2D grouping; the most influential knob. Default 15.
    • Max intra-tree gap (m) — the largest gap (from occlusion) still treated as belonging to one tree. Default 2.0 (seeded larger for very large tiles). Lower it when trees stand close together so neighbours aren't merged.
    • Split into one cloud per tree — when checked, also adds a separate cloud for each tree to the scan list.
  5. Click Segment Trees. While it runs, the button shows a spinner and a Cancel button appears beside it — click Cancel to stop a long or stuck run immediately (the computation is killed and the cloud is left unchanged).

Results

The cloud is recoloured by the tree_instance attribute: each tree gets a distinct colour. Points TreeIso could not assign keep ID 0 ("Unassigned", shown grey). (No legend is shown for tree instances — with one entry per tree it would fill the viewport and the IDs are arbitrary anyway.) If you enabled Split, one new cloud per tree (… (tree N)) is added to the list.

The split runs after the recoloured cloud appears, and each per-tree cloud gets its own display octree — on a large plot with many trees that takes a while. A Building n of N clouds… status pill at the top of the viewer tracks the progress; the per-tree clouds all appear in the scan list when it finishes. Cancelling from the pill leaves the recoloured parent cloud in place and adds no per-tree clouds.

Seeding trunks (optional)

For tricky scenes you can guide the result by marking trunks yourself:

  1. In the panel, turn on Seed trunks.
  2. Left-click each trunk in the viewer — a numbered marker drops at that spot. Right-click removes the last seed; Clear seeds removes all. (The camera is locked while seeding; turn the mode off to orbit.)
  3. Click Segment Trees. Each seed yields exactly one tree, and ambiguous segments are assigned to their nearest seed.

Refining the result

Once a cloud is segmented (flat clouds), a Refine section appears:

  • Merge — combine two tree IDs into one (e.g. when one tree was split in two): enter the two IDs and click Merge.
  • Split — separate a tree that actually contains two by spatial gaps: enter the tree ID and click Split; disconnected blobs become new trees.

Tips

  • Results are best on ground-removed, reasonably dense clouds.
  • If neighbouring trees merge into one, lower Max intra-tree gap or add trunk seeds.
  • If one tree is split into several, raise 2D reg. strength or Merge the pieces afterward.
  • Segmentation runs in the background, so the rest of the app stays responsive while it works. Use the panel's Cancel button to stop a run — closing the panel does not cancel it.

See also