Label points by hand¶

The automatic classifiers — ground, leaf/wood, individual trees — get most of a cloud right, but not all of it. Label Points lets you assign classes by hand: to correct what a classifier got wrong, or to build ground truth for checking how well it did.

Classes are yours to define. Phytograph ships four starting sets, but you can label anything you like.

Label¶

Select the point cloud (or clouds) you want to label.
Click Label Points (the brush icon in the Tools › Segmentation group), or open the command palette and choose Label Points. Under Clouds, the panel lists every point cloud in the scene with the ones you had selected checked; check or uncheck them there (see Label several clouds at once).
Pick the class you want to paint by clicking it in the class list. The number keys 1–9 and 0 pick the first ten classes, in the order the panel numbers them.
Choose how you want to select points — Lasso or Brush (see Lasso, rectangle or brush? below).
Paint. With the lasso, click to place each corner of an outline, then press Enter (or double-click) to close it. With the brush, just drag. Points selected take the active class and recolor straight away.
Repeat with different classes as needed. Undo (or Cmd+Z) removes the last stroke, and Shift+Cmd+Z puts it back.
Close the panel when you are done.

The labels are on the point cloud from the moment you paint them: export and every other tool read them straight away. What catches up in the background is the cloud's display index, which is rebuilt when you close the panel, and also after two minutes without a stroke. There is nothing to press and nothing to wait for; the labels stay on screen throughout.

Undo in the panel is the app's own Undo, so the two always agree. It is available when the most recent edit is a stroke on the column in front of you; if you cropped or moved something since, Cmd+Z undoes that first. Undo stops where the display was last rebuilt: it steps back through the strokes painted since, but not into the ones before it.

Each class row shows how many points currently carry it, so you can see the counts move as you work.

Press L to look around

While the lasso is armed every viewport click places a corner, so you can't orbit. Press L — or click Drawing — view frozen — to disarm it, move the camera freely, then press L again to carry on. The panel stays open and your class selection is kept.

The brush leaves orbiting alone — only dragging paints. Because the wheel sizes the brush while it is active, zoom moves to Alt+scroll.

The panel states what the next stroke will do in words, e.g. "Painting Leaf over any visible class". Read that line if a stroke does not do what you expect.

Export to keep your labels

Phytograph has no project file: labels live on the point cloud while the app is open, and are lost when it closes unless you export the cloud. Until you do, the panel says Labels changed since this cloud was last exported, and closing the app or File › New names how many clouds have labels that would be lost. An export clears it for the label columns it wrote.

Label several clouds at once¶

The Clouds list at the top of the panel decides what a stroke paints. It starts with the clouds selected in the Scans pane checked — with nothing selected, nothing is checked and the panel asks you to check one. Once the panel is open, clicking in the Scans pane no longer changes what you are labeling; only the checkboxes do.

With more than one cloud checked:

Every stroke labels all of them. A lasso, rectangle or brush stroke paints the points it covers in each checked cloud, in the same column and with the same class, and Undo takes the whole stroke back from all of them in one step. This is the way to label overlapping scans of the same plants without repeating every stroke per scan.
The counts are totals. Each class row shows how many points carry it across the checked clouds.
They share one column and one class list: the ones shown in the panel. The column list offers every column any checked cloud carries; a cloud that does not have the chosen column yet gets it on the first stroke.
Pick labels the piece under the click in each checked cloud that has points there. The Line tool paints only the checked clouds that the cross-section cuts.
Save strokes… and Load strokes… are for one cloud at a time, and are disabled until only one is checked.

Unchecking a cloud takes it out of the next stroke; the labels it already has stay on it. Checking a hidden cloud shows it for as long as it stays checked. A cloud with no editable session is listed but cannot be checked.

Lasso, rectangle or brush?¶

All three are always available (G, R and B switch between them); they answer different questions.

	Lasso	Rectangle	Brush
How you paint	Click each corner, `Enter` to close	Drag a box	Drag
Best for	A precise outline around an irregular region	Sweeping a block quickly	Fast touch-up and correction
Depth	Selects at every depth inside the outline	Every depth, like the lasso	Stops at the surface you are pointing at

X swaps the paint class with the class it paints over (when exactly one over dot is set): after painting Wood over Leaf, one key sets up painting Leaf over Wood. Keyboard shortcuts, at the bottom of the panel, lists them all.

The brush is a sphere that sits on the geometry under your cursor, so it does not paint the trunk behind the leaf you aimed at. Set its size with the scroll wheel or the [ and ] keys; the panel shows the current size in pixels. The size is in screen pixels, so the circle stays the same on screen as you zoom, and the sphere it corresponds to grows or shrinks in the cloud to match.

If the cursor is not over any geometry the brush shows nothing and paints nothing, rather than guessing a depth and labeling points you cannot see.

Pick a whole piece with one click¶

The Pick tool (K) labels a whole piece of the cloud per click — a leaf, a stretch of branch, or a whole plant — instead of tracing it:

Pieces cuts the cloud into compact pieces about Size across. A piece never jumps a gap, so a leaf stays separate from the leaf behind it.
Connected takes everything joined up, bridging gaps up to Gap: a plant standing apart from its neighbors, or a fruit hanging clear.

Leave the size at 0 and the first click chooses one from the point spacing and fills it in; change it to pick smaller or larger pieces. Shift+click also takes the neighboring pieces facing the same way — a flat leaf blade, or the ground around a stem — and stops at a fold. A drag still turns the view, so you can look around between clicks.

The first click on a cloud takes a moment while it is cut into pieces; later clicks at the same size are immediate. Each click is one stroke, undone and redone like any other.

How deep a stroke reaches¶

The panel's Depth row decides how far behind the outline a stroke paints:

Through (the default) — the lasso and rectangle select every point inside the outline at every depth, as if the outline were pushed through the cloud.
Front — the lasso and rectangle select only the surface you can see inside the outline, so outlining a leaf no longer paints the branch behind it. The surface is taken from the points drawn on screen when you close the outline. Also keep adds a little depth behind that surface, in cloud units, for a surface that is rough or thick; 0 allows only for the surface's own slope.
Box — every stroke, including the brush and the line, selects only inside a limiting box. Click Draw box, then click two opposite corners in the view; the box spans the cloud's full height, and the Z fields trim it. Until a box is drawn, strokes are refused rather than painting everywhere.

The lasso remains the better tool for covering a large region in one go — and, paired with a cross-section, for classifying a cloud systematically. Inside a section there is a fourth tool, the line (P).

Choose what you are labeling¶

The Column dropdown at the top of the panel picks which classification your strokes write to. Every classification the cloud carries is listed, so a classification that came out wrong can be fixed by hand rather than only recomputed.

Labeling — the hand-labeling column, where your own classes live. It is offered even on a cloud that has none yet; it is created the first time you paint.
Classifications — the class columns the cloud already has: a tree_instance from Separate trees, a ground_class from Segment ground points, a classification byte carried in from a LAS file, or any column you marked Label in the import wizard.
Other columns — continuous measurements. These are offered because Phytograph cannot always tell a class column from a measurement, but painting one replaces the measured values, so the panel warns before you do.
+ New classification… — start your own column; see Create a new classification.

When you open the tool on a cloud that carries exactly one classification, it opens on that column with its real classes and counts already listed. With several clouds checked, the first one in the list decides which column the tool opens on.

Fixing a tree segmentation by hand

Separate trees sometimes merges two trees into one, or splits one across two ids. Select the cloud, open Label Points, and it opens on Tree instance showing the trees the segmentation actually found. Pick the tree you want a region to belong to, lasso the points that were assigned wrongly, and close the panel. To split a merged tree, use Edit → Add class first: on a classification the cloud already carries, a new class continues that column's own numbering (Tree 3 after Tree 2) rather than starting a separate custom range.

Re-running a tool replaces its column

Running a segmentation again (or recomputing a scalar field) rewrites its whole column, so your hand corrections on it are replaced by the new result, and Undo can no longer step back into them. Export first if you want to keep the corrected version.

Class 0 is always available

Every column offers Unclassified (class 0), even when the data has no zeros in it — a tree segmentation numbers its trees from 1. It is how you take a classification away from points that should not have had one, and it reads 0 points until you use it.

Strokes stay with their column and cloud

Strokes belong to the column and the cloud you painted them on. Switching column, or checking a different cloud in the panel, starts that one clean; switching back finds your strokes still pending, and Undo only ever undoes strokes on the column and cloud in front of you.

Class sets¶

A class set is a vocabulary for the column you are painting. Preset in the panel switches between the built-in sets that describe that column — it never moves you to a different one. A column with no built-in vocabulary (a tree segmentation's instance ids, or a classification of your own) has no presets, and the button is grayed out; its classes come from the data itself.

The built-in sets are:

Wood / leaf (the default) — matches what Separate leaf and wood writes, so you can correct its output in the same vocabulary.
Plant organs — leaf, petiole, shoot, peduncle, fruit, petiolule. These are the same organ codes a simulated scan carries, so hand-labeled and simulated data can be compared directly.
Ground / non-ground — matches Segment ground points.
ASPRS standard — the LAS classification codes (Ground, Low/Medium/High Vegetation, Building, Water…), for data that has to line up with other LiDAR software.

Every set includes Unclassified (class 0), which is what points start as.

Each set belongs to a column: ground / non-ground describes what the ground-segmentation tool writes, ASPRS describes an imported LAS classification byte, and wood/leaf and organs describe the hand-labeling column. Pick the column first, in the Column dropdown, and the presets that apply to it follow.

Define your own classes¶

The presets are starting points, not the vocabulary. Edit in the panel opens the class editor, where you can add classes, rename and recolor them, and save the result as a palette of your own.

Add class appends a new class in the 64–255 band, which LAS reserves for user-defined codes — so your classes never collide with the ASPRS standard ones, and they fit the LAS classification byte they are exported into. On a classification the cloud already carries, a new class instead continues that column's numbering — Tree 3 after Tree 2 — because those ids are data the segmentation wrote, not a vocabulary you chose. Each new class starts with a color that is distinct from every class already in the palette (never Unclassified's gray); click its swatch to change it.
Class values run from 0 to 255, the range of the LAS classification byte. Instance columns, which number objects rather than classes (a tree_instance from Separate trees, or any column whose name ends in _instance), take ids up to 16,777,216, so a plot with hundreds of trees can still be split and renumbered by hand.
Save palette applies it, binds it to the cloud (so it is still there when you reopen the tool), and adds it to your saved palettes. Saving an edited built-in set, or a column's own classes, stores a copy of your own, so it never replaces a palette you saved for another project. A copy of a column's classes is named after its cloud and column.
Export / Import move palettes between projects or collaborators as a JSON file, so a labeling scheme agreed once can be reused by everyone.

Two rules the editor enforces, both to protect points you have already painted:

Unclassified (class 0) cannot be removed or renumbered. Points from an unlabeled or merged cloud arrive as 0, so 0 has to mean "unclassified" everywhere. You can rename it — a tree segmentation's class 0 reads "Unassigned" — because only the number is the contract.
A class that already has points keeps its value. The class number is what gets stored in the file, so repointing a class that is in use would leave those points holding a number the palette no longer describes. Renaming and recoloring stay available — only the number is fixed.

Create a new classification¶

+ New classification… in the Column dropdown makes a column of your own, alongside the ones the cloud already has, rather than mixing your classes into the hand-labeling column. Give it a name — "Row QC" — and the editor shows the name it will carry in the data (row_qc) beneath it.

A name is refused if it collides with a standard LAS dimension name or with a column this cloud already has; Create classification stays disabled until it is usable, so a name that could not be written is caught before you paint rather than after.

Once you paint it, it is a real column like any other: it appears in Color by, in the scalar filter, in split-by-class, and in an export.

Only repaint certain classes¶

The class list has two distinct controls, and it is worth being clear about which is which:

Clicking the row picks the class a stroke paints (the highlighted row).
The dot in the over column picks which classes a stroke is allowed to paint over.

Switch the dot on for one or more classes and a stroke only affects points already in those classes — everything else inside the lasso is left alone. This is what makes fast, rough lassos safe: to reclassify some leaf points as wood, select Wood as the paint class, set the over dot on Leaf, and paint freely. The ground and trunk points your lasso also covers are untouched.

With no dot set, a stroke repaints any visible class.

Painting a class over itself does nothing

Selecting Wood and setting the over dot on Wood means "paint wood only where it is already wood" — a no-op. The panel warns you when the two line up like this.

Show, hide and lock classes¶

The eye icon on each row hides that class's points from the viewer. Hidden classes are also never repainted: a stroke skips them whatever the over column says, so hiding a class you have finished with protects it while you work on the rest, and "any visible class" means exactly that.

Alt-click a class row to show only that class, which is the quickest way to check what a class really contains. Alt-click the same row again to show every class.

The padlock on each row locks a class: no stroke changes its points, and unlike hiding it stays on screen. Protect labeled points, under the class list, locks every class except Unclassified, so strokes only ever label points that have no label yet, which makes it safe to sweep a big lasso over a half-finished cloud. Click it again to unlock everything.

Find what is still unlabeled¶

Find unlabeled points (or N) shows only the Unclassified points and moves the camera to where most of them are. Press N again for the next such area, largest first, and Shift+N to go back; the panel says which area you are on and how many unlabeled points are left. Each step re-reads the cloud, so areas you label drop out as you go, and when nothing is left the panel says so. Alt-click a class row to see the labeled points again.

Instances: this tree, that leaf¶

A column whose name ends in _instance (tree_instance from a tree segmentation, or one you create such as leaf_instance) numbers objects rather than naming classes. Its class list is the list of instances, with their point counts, and show, hide, isolate and lock work as for any class. An Instances box in the panel adds what numbering objects needs, acting on the instance selected in the list:

New instance adds the next free id after the highest in use, named like its siblings (Tree 18 after Tree 17), and makes it the paint class. Paint with it to split a wrongly merged instance — with the old instance as the only over class, so nothing else is touched.
Frame moves the view to the instance.
Merge into… gives every point of this instance another instance's id.
Delete returns every point of this instance to Unassigned.
Also set paints a class in another column with every stroke — say Hand labels: Wood while you paint Tree 3 — so an instance and what it is are labeled together. Both columns change in one step, and one undo takes both back.

Merge and delete are strokes like any other: undo reverses them, and the id stays in the list (with no points) so an undo has somewhere to put them back.

Pre-label from another column¶

Rather than start a column from nothing, seed it from a result another tool already wrote — ground segmentation's ground_class, wood/leaf segmentation's wood_class, a tree segmentation's tree_instance, or any other class column on the cloud. Choose it under Pre-label from another column…, check how its classes map onto yours (classes with the same name are matched for you; the rest you pick, or leave as they are), and click Pre-label. Only points still Unclassified keeps what you have already painted. Instance ids copied into another instance column are kept as they are.

It is one stroke: the result shows at once, undo takes it back, and you then correct it by hand like any painting.

Save and load strokes¶

Save strokes… writes every stroke the column has had since the cloud was loaded to a small .json file. Load strokes… replays such a file onto the column being edited, as one undoable step. The strokes are stored in the cloud's own coordinates, so they land in the same place on a re-import of the same scan — to carry work across a re-import, or to share it with a colleague who has the same file. Classes are stored by number: load onto a column whose class set uses the same numbers, and the panel says if the file uses classes the set does not have.

What happens to the labels¶

Labels are stored in whichever column you picked: the hand-labeling column (manual_class) by default, the cloud's own classification when you chose one, or a column you created. Either way they behave like any other scalar:

color the cloud by them (they appear in the color-by list with your class names and colors),
filter to particular classes,
split the cloud into one cloud per class,
export them to LAS/LAZ, where they are written both as their own named column and into the standard LAS classification byte (classes 0–255), so other LiDAR software sees them too. The file also carries the class names and colors: other programs read the names of the classification byte's classes, and a re-import into Phytograph brings back every labeled column's class set.

LAS flags¶

LAS files mark points withheld, synthetic or as key-points with flags in each point rather than with classes. The column list offers one column for each (LAS flag: Withheld, and so on): paint Withheld onto the points to flag, exactly as you would a class, and the LAS export sets the flag. Re-importing the file brings the flag back as the same column.

Work in a cross-section¶

A lasso is drawn on screen, so on its own it selects every point inside it at every depth — including the far side of the canopy you cannot see. A cross-section is the fix, and it is how professional LiDAR classification is normally done.

Open Tools › Pre-processing › Cross-section. Under Clouds, check the clouds the section should cut — the ones selected in the Scans pane start checked — then click Draw section.
Click two points in the view to set the line the section runs along. As you move toward the second point, the slab you are about to create is drawn so you can see the volume before committing to it.
Set Thickness thin enough that nothing hides behind anything.
Open Label Points — the section stays active, and the panel says so. Paint normally; strokes only affect points inside the section.
Step through the cloud with ◀ ▶, or from the keyboard with , / ← (back) and . / → (forward) — the keys work with the Label panel open, so you can page and paint without reaching for the section panel. They step by the panel's Step size. The default half-thickness step makes consecutive sections overlap, so no point is skipped, and the "Section 7 of 42" readout tells you when you have covered everything.

The section is drawn as a thin, vertical-walled box: bounded by your two clicks along the line, half the thickness either side of it, and spanning the full height of the cloud.

One section can cut several clouds at once: every cloud checked in the panel is clipped to the same slab, and the slab is sized to all of them together. A cloud you leave unchecked is drawn whole. You can check or uncheck clouds after the section is drawn, and the set is kept while the section exists, even with the panel closed. Checking a hidden cloud shows it until you uncheck it or the section ends. Label Points has its own Clouds list: a stroke is bounded by the section on every cloud checked in both panels, and paints a cloud checked only for labeling at every depth.

A small map in the lower-left corner of the viewport shows the cloud from above with the section as a blue band, so you can tell where you are while every face-on slice looks alike. The band moves as you step.

Paint above or below a line¶

With a section drawn, the Label panel's Line tool (P) cuts the section in one stroke — a stem from its crown, or a trunk from the ground. Click along the section to draw a line through the points, then Enter or double-click to finish. Every point in the section on the chosen side is painted:

Above or Below the line. Set Within ± to paint only a band that close to the line — the 20 cm of ground under a profile, say. 0 means the whole side.
Near — within ± of the line on either side. Left at 0, the band is the section's own thickness.

Past either end the line keeps the height of its last point, so a line that stops short of the section's edge still covers it. The line is drawn in the section, so it needs a view facing the section; a view looking along the section cannot place it. Like every stroke drawn in a section, it paints nothing outside the slab.

Getting back to the whole cloud¶

The section is a view, not a mode: it stays in effect while you use other tools, and both panels are visible at once. That also means closing the panel does not remove it — otherwise opening the Label tool, which shares the same panel slot, would silently switch off the section you set up to paint inside.

While a section is active a small indicator sits at the top of the viewport with two ways out, so you never have to remember which tool put it there:

Show full cloud — stop clipping temporarily. The section keeps its colors and every point outside it is drawn gray, so you see the whole cloud and still see where the section sits. Its thickness and its place in the traverse are all kept, so you can look around and drop straight back into it.
Clear — remove the section and return to a normal view.

Both are also in the Cross-section panel, and the Label panel's "Strokes are limited to the cross-section" notice carries its own Clear. Redraw section shows the whole cloud while you pick the new line, so you are never aiming at points the old section is hiding.

Without a section, a lasso still cuts through

If no section is active, switch to the Brush, which is depth-limited and needs no section. Otherwise orbit to an angle where the points you want are not in front of anything else, or hide the classes you have already finished.