Clean a point cloud¶

Raw LiDAR data almost never lands ready for analysis. This workflow covers the five operations you'll reach for most often: transform, crop, erase, filter, and resample. Apply them in roughly that order.

Transform (translate and rotate)¶

Use Transform (in the tool column, or right-click the cloud → Transform) to move and rotate a cloud in world space — most often to bring it to the origin, level a tilted scan, or line it up with another cloud before registration.

Opening the tool shows a Transform panel with Position and Rotation (°) sections, plus translation arrows and rotation rings at the cloud. Set the change any of these ways — all update the viewport live so you can see the result before committing:

Type exact X / Y / Z values (metres for position, degrees for rotation) in the panel.
Drag the gizmo's arrows to translate along an axis, or its colored rings to rotate about an axis.
Use the Blender-style shortcut for translation: press T, optionally lock an axis with X / Y / Z, type a distance, then click (or Enter) to set it. See Keyboard shortcuts.

Rotation turns the cloud about the scene origin (see below). There is always one: until you place it yourself it sits at the center of the loaded scene, marked in the viewport by a red-and-white ring. Move it first when you need to pivot around a specific point — for a single cloud, Center on selection puts it on the cloud's own center, which spins the cloud in place.

Nothing is applied until you decide:

OK applies the transform (see the note below) and closes the panel.
Cancel discards it — the cloud snaps back to where it started.
Reset Position / Reset Rotation zero the pending values without closing, so you can start over.
Closing with the ✕ while you have unsaved changes asks whether to Apply or Discard first.

While the panel is open the other tools are locked, so you always finish (or cancel) a change before doing anything else — a half-entered transform can never leak into a later step.

OK bakes the transform into the geometry

Clicking OK writes the translation and rotation into the cloud's actual point coordinates rather than keeping a display-only offset. This is what guarantees that every later tool — triangulation, leaf area density, skeletons, QSM, export — operates on the cloud where and how you placed it.

Two consequences worth knowing:

Everything tied to the scan's world position moves and rotates with it: the recorded scanner origin (and, for a moving-platform scan, the whole trajectory and its per-pose orientation), the sky/miss points, per-pulse beam origins, and the miss overlay. So a transformed scan stays internally consistent — the scanner still sits in the right place relative to its points, which is what LAD and triangulation depend on.
Like applying a crop or a filter, an applied transform is a permanent edit to the working copy — it is not on the undo stack. Your source file on disk is never modified.

The toolbar also has a one-click Move to Origin that centers the cloud's bounding box at (0, 0, 0) without rotating it.

Setting the scene origin¶

Set Scene Origin (the crosshair button in the top View Controls box, next to the command-search icon / Tools → Pre-processing → Set Scene Origin) moves the pivot point, like CloudCompare's. It's a scene control rather than an analysis tool, so it sits with the view controls. The origin is the rotation center for both the Transform tool and the camera: a left-drag in the viewport turns the whole view about it, so panning no longer changes what you rotate around. Zoom is not tied to it — the scroll wheel flies toward whatever is under your cursor — so the origin only decides what you circle. Moving the origin does not move the camera: the view stays exactly where it is, it just pivots somewhere else. Use Zoom to origin in the panel if you do want the camera to go there.

With no placement of your own, the origin sits laterally at the center of the loaded scene but vertically at its base — on the ground rather than halfway up — which is usually the point you want to circle.

That ground level is measured robustly, so a handful of erroneous returns below the terrain (multipath, birds, scanner artefacts) will not drag it down: it ignores the lowest 0.5% of points rather than taking the single lowest one. The ground grid uses the same estimate.

A red-and-white ring marker (a 3D cursor) shows the origin in the scene, at a constant size no matter how far you zoom. Click the ring to select it: an X/Y/Z arrow gizmo appears, and dragging an arrow slides the origin along that axis. Click anywhere else in the viewport (or press Esc) to put the gizmo away. (Opening the panel arms Pick in viewport, which takes over viewport clicks — click that button once to turn it off if you want to grab the marker instead.) The marker only appears once something is loaded, so it never sits on top of the empty-viewport import prompt.

In the Scene Origin panel you can:

Pick in viewport — click-to-place. This is already armed when the panel opens, so you can just click a point straight away; it snaps to the cloud surface where you click, or drops onto the ground plane if you click past the cloud. (The view does not move when you pick.) Placing a point disarms it, and the button toggles it off and on again by hand.
Type exact X / Y / Z world coordinates.
Center on selection — snap the origin to the middle of the selected cloud(s).
Show origin marker — uncheck to hide the marker (and its gizmo). The pivot itself is unchanged; it just stops drawing over your scene.
Reset to scene center — drop your placement and return the origin to its default: laterally the middle of the loaded scene, vertically its base.

The origin returns to that default when you start a new scene (File → New).

Crop¶

Use Crop (scissors icon) to keep only points inside (or outside) a region. Three shapes are supported — a 3D Box, a screen-space Rect(angle), and a freeform Polygon lasso — and the same region applies to every scan you have selected.

Click Crop. A green box appears around the union of the selected scans' bounding boxes.
In the panel choose Box, Rect, or Polygon at the top, then a Mode below it: Keep Inside (default), Keep Outside, or Segment. The first two discard the points you don't keep; Segment keeps both halves as separate clouds (see below).
Shape the region (see below).
Click Apply at the bottom of the panel. A Cropping… indicator appears while the crop is processed, and the removed points stay hidden the whole time (in Segment mode nothing is hidden, since both halves are kept). Click the × in the panel header to dismiss without applying.

When more than one scan is selected, the panel shows "Applies to N scans" and each scan gets its own cropped result — identities are preserved.

Preview detail while cropping

For large (LOD-streamed) scans, the live crop preview renders at reduced point density so it stays responsive while you position the box — you may see the displayed density change as you move or zoom. This affects only the preview; Apply re-crops the scan at full resolution.

Box mode¶

Two ways to shape the box:

Type dimensions / center in the panel for an exact axis-aligned box.
Click "Draw box in viewport" then click two opposite corners on the ground plane. After the first click a marker shows where it landed and a live preview box follows the cursor until you click the second corner. The box's Z extent auto-spans the data; refine with the dimension / center fields afterwards. Esc cancels.

Box mode is axis-aligned and easiest from a roughly top-down view. To crop from an angled view, use Rect instead.

Cropping out the ground

For TLS scans of a single plant, raise the box's lower Z bound to the level of the lowest branch (adjust the Z center / dimension fields). With Keep Inside selected, this removes the ground in one step — much faster than filtering by height.

Rect mode¶

Rect mode is a screen-space rectangle — the quick, any-view counterpart to Box. Unlike the world-space box, it works from any camera angle.

Pick Rect in the panel; the view switches to a straight-on (orthographic) projection and the camera locks so the rectangle stays anchored to the view.
Click-drag in the viewport from one corner to the opposite corner. A dashed preview rectangle follows the cursor; release to commit it.
Click Apply in the panel, or use Redraw rectangle to start over. Esc cancels.

Like the polygon, the rectangle lives in screen space, so the in/out test uses the camera as it was when you released the drag — orbiting afterwards doesn't change the result. Because the draw is orthographic, the selection extrudes straight into the scene: the cropped region is a true rectangular slab from any viewing angle, not a perspective wedge. So you can, for example, orbit to a side view, drag a rectangle around the part of a plant you want, and get a clean axis-true cut.

Polygon mode¶

Polygon mode is a screen-space lasso — useful when the region you want isn't a tidy box.

Pick Polygon in the panel; the camera locks so the lasso stays anchored to the view.
Click in the viewport to add vertices. Right-click or Backspace removes the last vertex.
Press Enter to close the polygon. A filled preview shows what will be kept (green) or removed (red).
Click Apply in the panel, or use Redraw polygon to start over.

Because the polygon lives in screen space, the in/out test uses the camera as it was when you closed the polygon — orbiting afterwards is fine and doesn't change the result.

Segment mode (keep both halves)¶

Keep Inside and Keep Outside discard the points you don't keep. Segment instead splits each selected scan in two: the original scan keeps the in-region points (the same set Keep Inside would keep), and a new "… (segment)" cloud is added to the scene holding the cropped-out points. No points are lost. It works with all three shapes — Box, Rect, and Polygon.

The new cloud inherits the colour of the scan it came from, so the two halves read as one family in the scan list — tell them apart by the "… (segment)" name. Recolour or rename it from the scan list like any other scan. It's handy for separating a plant from its ground, or splitting one scan into named regions without re-importing.

The whole cloud stays visible in Segment mode

Keep Inside and Keep Outside hide the points they are about to discard, so the preview shows you what will survive. Segment discards nothing — both halves become clouds — so it leaves the entire cloud on screen and draws only the region outline to show where the split will fall. Switching between the modes turns that culling on and off.

Keep original cloud¶

By default a crop replaces the scan: the points outside the kept set are discarded, and because the cropped points become the new ground truth the apply also clears that scan's undo history — ⌘/Ctrl+Z will not bring them back.

Tick Keep original cloud to crop non-destructively. The source scan stays in the scene untouched (just hidden, so the viewport looks the same as a normal crop) and the kept points are added as a new "… (cropped)" cloud, which inherits the source scan's colour. Click the eye icon next to the original to show it again.

Because nothing is destroyed, a retained crop is undoable — one ⌘/Ctrl+Z removes the new cloud and leaves the original exactly as it was. The new cloud also inherits the scanner origin, so origin-dependent analyses (Backfill Misses, Helios triangulation, Leaf Area Density) still work on it.

The option is unavailable in Segment mode, which already keeps every point across its two output clouds.

Which to use

Use Keep original cloud when you're isolating a region for analysis and may want to go back to the full scan — cropping one tree out of a plot, say. Use a plain crop when you're cleaning a scan down to what you actually want to keep and the discarded points are just noise.

How edits are applied (the in-memory model)

When you import a point cloud, Phytograph reads the file once and holds the points in memory as the working copy — the source of truth for every edit. Crop, erase, filter, and segment all operate on that in-memory copy; the file is never re-read. Crops and filters rebuild the displayed octree from the in-memory points (a brief step on large scans), while erase deletes are applied as an instant visibility mask. Either way nothing touches the original file on disk — your edits live in the session until you Export.

Export edited clouds you want to keep

Because edits live in the session and never touch the source file, an edited cloud cannot be rebuilt from that file. Phytograph caches the displayed octree on disk, but that cache can be cleared (by the OS, by an app update, or when the backend restarts). If it goes missing for a cloud you have edited, Phytograph tells you the cloud is unavailable rather than silently rebuilding it from the original file — which would restore points you deleted and undo transforms you applied. Export any edited cloud you need to keep.

Erase¶

Use Erase Brush (eraser icon) for irregular regions a box can't capture — stray points, noise behind the plant, isolated outliers.

The brush is a square stamp that cuts straight through the cloud along your view direction — like the rectangle/polygon crop, but a pre-shaped square you paint freely. It shows a live preview of what it removes; nothing is deleted until you apply.

Click Erase Brush to open the tool. The panel opens but the view stays interactive — orbit/pan/zoom to frame the angle you want to erase from.
Click Start Erasing in the panel (or press E) to turn erase mode on. This freezes the viewport so every stamp shares the same view, and a square brush follows your cursor (orange → red).
Click on the cloud to stamp a square, or click-drag to paint a strip of squares. The points behind each square disappear in the live preview — and because the square extrudes through the whole cloud, it removes points at every depth behind it, not just the near surface.
Press E (or the button) again to turn erase mode off without closing the tool — the view unfreezes so you can reorient, then turn erase back on and keep stamping. Painted strokes are kept across toggles.
Click Apply Erase to delete the painted points, or Clear Strokes to discard the preview. The point count drops immediately — the erase is applied as an instant visibility mask, with no waiting.

Adjust brush size (in screen pixels) with the slider; because the brush is screen-space, its size stays constant on screen regardless of the cloud's distance.

Erase composes: each apply removes the painted union from the current point set, so you can apply, reorient, and stamp again to clear points hidden behind a surface. Because deletes are masked (not yet written to a new octree), they're cheap and reversible:

Undo last deletion restores the most recent erase.
Permanently apply deletions bakes the survivors into a fresh octree — the one slower step, and the point at which the deletions become permanent (no longer undoable). You only need this before exporting, or to free the deleted points' memory; until then the masked result is already what every other operation (triangulate, skeleton, segment, export) sees.

How erase works

Erase is instant because it sets a per-point visibility mask on the in-memory cloud rather than rebuilding anything — the deleted points vanish on the GPU the moment you apply. While erase mode is on, the view is projected orthographically (as the Rect crop does) so the square extrudes as a straight prism and the cleared region matches the brush outline exactly rather than flaring into a perspective trapezoid. Since the test is in screen space the stamp is depth-independent: it removes every point behind the square, not just the near surface — reorient and paint again to clear points it was shielding. Permanently apply deletions is what actually rebuilds the octree from the survivors.

Filter¶

Use Filter Points (filter icon) to keep only points whose values fall within a range — useful when the file carries intensity, classification, or custom scalars. This works for large, octree-backed clouds too: their imported scalar attributes (the same ones offered in the Color by picker) appear in the filter field list alongside X, Y, and Z.

To set a filter:

Pick a field from the dropdown (X, Y, Z, intensity, or any scalar).
Set the criterion:
- Continuous fields (intensity, height, deviation, …) show min and max inputs — points in the inclusive range are "in range". The range takes effect immediately.
- Class fields — ground_class (from Segment ground) and tree_instance (from Segment trees) — are categorical, so instead of a range you get a checkbox per class (Ground, Non-ground, or Tree 1…N). Tick the classes to keep; use All / None to toggle the whole set. This is the natural way to isolate, say, just the non-ground points after a ground classification.
Repeat for other fields to stack filters — they compose with AND, so only points passing every active filter are "in range".

Then choose how to commit (there is no separate Apply step):

Filter (remove points) — deletes the out-of-range points, keeping only the in-range ones.
Segment (split into two clouds) — keeps the in-range points on the original cloud and adds the out-of-range points as a second cloud (<name> (filtered out)). Nothing is discarded; the two clouds together equal the original. Handy for separating, say, a canopy from the rest by height without losing the rest.

Use ⌘/Ctrl+Z to undo. If a filter excludes every point, you're offered the chance to delete the cloud instead.

Small vs large clouds

Small (in-memory) clouds preview the filter live in the viewport as you edit the range. Large, octree-backed clouds have no live preview — committing applies the filter to the in-memory points and rebuilds the displayed octree from the survivors (the file is not re-read), so the change appears once that brief step finishes. A second filter composes on the first result, never re-admitting points an earlier filter removed.

Resample¶

Use Resample Point Cloud (scatter icon) when a cloud is too large to work with interactively or when you want a uniformly sparser version for export.

Click Resample Point Cloud.
Type a Keep fraction between 0.001 and 1.0 (it's a number field, not a slider).
Quick presets: 100%, 50%, 25%, 10%, 5%, 1%.
Click Preview to see the resampled cloud. The preview isn't live — changing the fraction clears it, so press Refresh Preview to update. Cancel Preview discards it.
Click Permanently Resample Point Cloud to commit.

Both buttons are disabled at a fraction of 1.0, since keeping everything is a no-op.

Resampling is uniform-random, not voxel-based. For voxel downsampling, export to .ply and use a tool like CloudCompare.

A typical cleaning order¶

Transform — translate and rotate the cloud level and centered.
Crop — remove the ground and far-field noise with a single box.
Filter — drop low-intensity returns if intensity is reliable.
Erase — clean up stragglers a box couldn't reach.
Resample — only if needed for performance.

Save (Export → .ply) at each milestone if you want backup checkpoints.