Phytograph

A desktop application for measuring, comparing, and modeling plant architecture from LiDAR scans — built for plant scientists who work with point clouds, meshes, and procedural plant models.

• Import LiDAR scans

  Drag and drop .las, .laz, .xyz, .ply, or .csv point clouds into a 3D viewer that handles tens of millions of points.

• Reconstruct meshes

  Triangulate point clouds with Delaunay, Ball Pivot, or Poisson — or run multi-scan Helios triangulation for branch surfaces from terrestrial LiDAR.

• Extract skeletons

  Pull topological skeletons out of woody scans, with branch order colored by Strahler number and total length reported.

• Build QSMs

  Reconstruct dormant trees as connected cylinders with fitted radii, segment continuous shoots, and classify them by shoot rank — with woody volume, trunk diameter, and per-rank metrics.

• Generate procedural plants

  Grow Helios plant models — trees, vines, cereals, vegetables — to a target age, then morph their parameters interactively.

• Segment scans

  Classify ground, separate wood from leaf, and split a plot into individual trees — then carry the labels through the rest of the pipeline.

• Measure canopy structure

  Invert overlapping scans into a voxel grid of leaf area density (m²/m³), fit crown shapes for height and volume, and build DTM / DSM / canopy-height surfaces.

• Register and compare

  Cloud-to-cloud, mesh-to-mesh, and cloud-to-mesh ICP with RMSE, plus cloud-to-mesh distance statistics (mean / median / percentiles and coverage within 1 / 5 / 10 mm).

• Simulate a scan

  Place virtual scanners around a plant and synthesize the point cloud they would produce, with full control over beam geometry.

Start the User Guide →   Browse workflows

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Phytograph is developed at the Bailey Lab at UC Davis. Source code at github.com/PlantSimulationLab/Phytograph.