Tour of the interface¶
This page is a reference map of the Viewer — what each region is and what lives there. Skim it once to know where things are; you don't need to memorize anything.
Top bar¶
| Region | What's there |
|---|---|
| Top-left | Phytograph logo and the current scene summary ("N Clouds, M Meshes…") |
| Top-center | The active mode label |
| Top-right | Report a Bug and Request a Feature buttons (see Reporting bugs & requesting features) |
Import is via drag-and-drop onto the window or the File → Import
menu — choose Auto-detect, or an explicit Point Cloud, Mesh,
or Skeleton when auto-detection picks the wrong type for an ambiguous
format like .ply. To remove scans, select them in the Scans panel
and delete.
File → New (⌘/Ctrl+N) clears everything — all point clouds, meshes, skeletons, plant models, scans, and analysis results — and resets the app to a fresh start, the same as relaunching it. It asks for confirmation first because it can’t be undone.
Left tool column¶
A vertical column down the left side. At the top are the view controls (command-palette search, Set Scene Origin — the rotation pivot — and Pick Point, which labels individual points with their coordinates and attributes) and the snap-view gizmo. Below those are two always-visible blocks — Create and Tools:
| Block | Buttons |
|---|---|
| Create (build the scene) | Generate Plant, Import Model, Create Voxel Grid, Create Plane, Add Scan |
| Tools › Pre-processing | Transform, Crop, Erase, Filter, Resample, Move to Origin, Backfill Misses, Align (ICP), Stitch |
| Tools › Segmentation | Segment Ground, Segment Wood / Leaf, Segment Trees |
| Tools › Reconstruction | Triangulate, Generate DEM, Extract Skeleton, Build QSM, Leaf Area Density, Fit Crown & Metrics |
Create is kept separate from Tools on purpose: Create builds a scene (generating geometry, placing scanners), whereas Tools operate on data you already have. The Tools block holds only the three analysis stages of a typical pipeline. Synthetic scanning (Simulate) has no left-column block of its own — run it from the Simulate menu (Run Synthetic Scan) or the Run Synthetic LiDAR Scan button at the top of the Scans panel once a scanner is placed.
Hover any button to see its name. Buttons no longer appear and disappear with your selection — they're always shown so you can see what's available.
- Single-input tools (Filter, Segment Ground, Triangulate, …) act on the selected cloud. They're greyed out until you select one; the tooltip tells you what to pick.
- Multi-input tools (Align, Stitch, Leaf Area Density) stay enabled and open a dialog where you pick their inputs explicitly — for example, Leaf Area Density lets you choose the scans and the voxel grid. If a needed input doesn't exist yet, the dialog tells you.
Everything in these blocks is also in the menu bar — under the Tools, Create, and Simulate menus, grouped the same way — and in the command palette.
The same operation can often be reached from a tool's results, too — running a Helios triangulation, for instance, defines the voxel grid that the Leaf Area Density dialog then reuses automatically.
Bottom-left view gizmo¶
A small XYZ orientation gizmo and a row of view-snapping buttons: Left, Right, Front, Back, Top, Bottom, plus Isometric. Click any button to rotate the camera to that view — it only reorients (Z stays up), keeping your current target and zoom rather than reframing. The gizmo tracks the current orientation; clicking one of its axis heads does the same thing. After snapping you can still orbit freely. To reframe, use Reset View (fit all) or Zoom to Selection.
3D canvas¶
The main interactive area. Camera controls:
| Action | Mouse | Trackpad |
|---|---|---|
| Orbit | Left-click drag | One-finger drag |
| Pan | Right-click drag, or ⌘/Ctrl + left-click drag | Two-finger drag |
| Zoom | Scroll wheel | Pinch |
| Zoom to selection | F (or the Zoom to Selection toolbar button) | Same |
Orbiting turns the view about the scene origin (the red-and-white ring marker, which starts laterally centered on your loaded content at ground level, and can be dragged elsewhere) — panning does not move that pivot. Zooming is independent of the origin: the scroll wheel flies the camera toward whatever is under your mouse cursor, so anything you can see, you can zoom to. See Viewer navigation.
A reference grid on the world XY plane gives you a sense of scale. It adapts as you zoom: the cell size steps through round values (…10 cm, 20 cm, 50 cm, 1 m, 2 m, 5 m…) so cells stay legible instead of packing together, with a heavier line every fifth cell.
Labels dropped by the Pick Point tool also live here: each one is a small bubble tethered by a dashed leader line to the point it describes, and it stays pinned to that point as you orbit. See Inspect a point.
Right-side scene panel¶
Three stacked lists — Scans, Meshes, Skeletons. Each scan entry shows:
- a color dot (also acts as a selection indicator); click it to pick a custom per-scan color, which drives the Per-scan color mode
- the scan label and a subtitle (point count, scanner origin, or both)
- visibility, duplicate, and remove controls
- a paperclip to attach point data (if the scan only has parameters)
- a radio icon to add scan parameters (if the scan only has data)
- an expand chevron that reveals the full parameter readout
The duplicate button (a copy icon) makes an independent copy of the
scan — its point data and any scan-parameter metadata — named
… (copy) (then … (copy 2), and so on). The copy is fully separate:
editing, cropping, or deleting one never affects the other. It's handy
for branching experiments — run two different crops or segmentations off
the same import, or place a second scanner with the same sweep settings.
(For a one-off non-destructive crop you don't need to duplicate first —
tick Keep original cloud in the crop panel instead.)
A scan can hold point data, scan parameters (origin, sweep, return mode), or both — see Scans for details.
Multi-select with Shift+click (range) or ⌘/Ctrl+click (toggle). Single-input tools (Filter, Segment, …) act on the current selection, so being deliberate about what's selected matters; multi-input tools (Stitch, Align, Leaf Area Density) seed their dialog from the selection but let you change it there.
Selecting meshes in the viewport¶
Meshes are also selectable directly in the 3D view. Click a mesh to select it; ⌘/Ctrl+click adds or removes meshes from a multi-selection. Selecting a mesh — whether in the viewport or in the Meshes panel — draws a bright highlight outline around it in the 3D view and highlights its row in the panel, so the two stay in sync. Click an empty area to clear the selection. (Viewport mesh selection pauses while an edit tool such as Crop, Erase, or Transform is active, since those clicks belong to the tool.)
Bulk show/hide and delete¶
Each list's header has an eye and a trash button that act on multiple entries at once:
- With one or more rows selected, they apply to just the selection — "hide the 3 selected scans", "delete the 2 selected meshes".
- With nothing selected, they apply to the whole list — hide or show every entry, or clear the list.
The eye button toggles to a single uniform state: if any target is visible it hides them all; press again to show them all. A bulk delete asks for confirmation once for the whole batch, rather than once per entry. The same multi-select + header buttons work for Meshes, Skeletons, and QSM results.
The colormap legend in the bottom-right shows the current scalar-to-color mapping (e.g., height in meters → viridis). Different color modes change the legend.
Bottom status bar¶
Cursor world coordinates ("X, Y, Z"), the active modifier-state indicators (Left/Right/Scroll meanings depending on tool), and the last operation's status message (e.g., "Loaded 84,795 points from scan.xyz").
Opening the documentation¶
Open Help → Phytograph Documentation to open this documentation site in your web browser.
About / version info¶
Open Phytograph → About Phytograph (macOS) or Help → About Phytograph (Windows/Linux) to see the versions Phytograph is running: the Application and Backend versions, plus the PyHelios and Helios (C++) engine versions. These are handy to quote when reporting a bug — the same numbers are auto-attached to the bug/feature reports you send from within the app.
Checking for updates¶
Open Phytograph → Check for Updates… (macOS) or Help → Check for Updates… (Windows/Linux) to see whether a newer release is available. If you're already on the latest version, it tells you so.
Phytograph also checks automatically once each time it starts. Either way, it always asks before downloading — the installer is several hundred megabytes, so it never starts a large download on its own.
While the download runs, a progress pill appears at the top of the viewer, the same indicator used for other long-running operations. The download continues in the background; you can keep working.
Once it finishes, Phytograph asks whether to restart. Choosing Restart now closes the app, installs the update, and reopens it — the window disappears for up to a minute while that happens, which is normal. Choosing Later keeps the downloaded update and installs it the next time you quit.
Command palette¶
Press ⌘+K (macOS) or Ctrl+K (Windows) anywhere in the Viewer to open a searchable list of commands.
The palette is the fastest way to find a feature when you don't remember which button hides it. Start typing to filter; press Enter to run the highlighted command, Esc to close.
Undo / redo¶
⌘/Ctrl+Z undoes the last edit; ⌘/Ctrl+Y or ⌘/Ctrl+Shift+Z redoes it. Undo covers the whole scene: adding objects (import, triangulate, generate plant, extract skeleton, build QSM, compute LAD), deleting them, transforms (move/rotate/scale), pre-bake erase/crop edits, stitching, and renaming/recoloring. Deleting several selected objects undoes in a single step. View settings (visibility, color mode, point size, camera) are not undoable. A few destructive operations that rewrite point data or recreate a backend session — baking edits, segmentation, ICP registration, and plant morph/age changes — are one-way: instead of being reversible they clear the undo history for the affected object.
What's next¶
Pick a workflow that matches what you want to do: