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Measurement tables and units

For graph construction and export, follow the object-measurement tutorial. Use this reference to check identities, units, and unavailable measurements.

Table identity

Measurement nodes produce tables, not images. Each table carries ordered columns, a table kind, row/column counts, a source name where available, and per-column units where the calculation defines them.

Keep the keys that distinguish observations:

  • leading-axis indices, such as t_index, c_index, and z_index;
  • object/graph IDs, such as label_id, mesh_id, component_id, branch_id, node_id, and edge_id;
  • experimental fields added with Add Metadata Columns, such as treatment, replicate, and batch.

Equal row counts are not proof that two tables describe the same observations.

Units through table composition

Node Unit handling
Merge Tables Preserves units; duplicate names and their units receive matching suffixes.
Select Table Columns Preserves the selected columns' units.
Add Metadata Columns Keeps existing units; new metadata columns are unitless.
Summarize Measurements Propagates numeric units except for count statistics.

Object morphology

Measure Objects returns one row per label object. Basic fields include ID, pixel/voxel area or volume, centroid, bounding box, equivalent diameter, extent, and Euler number. Optional groups add shape, axis/inertia, derived ratios, 2D boundary descriptors, and 2D moments.

With calibration, supported physical columns include:

  • area/volume, centroid, and bounding-box coordinates;
  • equivalent diameter, bounding/fill size, and maximum Feret diameter;
  • major/minor axis lengths, bounding-box side lengths, and inertia eigenvalues.

Physical perimeter, Crofton perimeter, and perimeter-to-area ratio are available for isotropic 2D pixels. For anisotropic 2D pixels these physical perimeter columns remain NaN; VIPP does not apply a misleading single scale factor.

Measure Objects + Intensity takes matching Labels and Intensity image inputs and adds per-object mean, minimum, maximum, sum, and standard deviation.

3D mesh morphology

With true 3D labels and correct Z/Y/X spacing, Measure 3D Mesh Morphology extracts a marching-cubes surface for each object.

Field group Outputs
Size voxel_count, voxel_volume_physical, mesh_volume_physical, mesh_surface_area_physical
Shape surface_area_to_volume, equivalent-sphere radius/diameter, sphericity, physical extents and extent ratios
Optional convex hull Hull volume/area, solidity_3d, surface_area_to_convex_hull_area
Diagnostics mesh_status, mesh_error

Tiny or invalid objects remain as rows with NaN mesh metrics and an explanatory status. Check those fields before summarizing results.

Segmentation, voxel spacing, and surface approximation all affect these measurements. Very small or flat objects may not support stable mesh or hull metrics. Mesh viewing/export belongs to the separate 3D Meshes nodes; specialist repair is not supplied.

Existing mesh objects

The mesh input measures current geometry directly, with one row per explicit object. It never remeshes, rejoins disconnected shells, or infers voxel counts.

Field Meaning
mesh_id Stable mesh object identity, not a row number. Label extraction retains source label IDs.
vertex_count, triangle_count Counts in that mesh object.
watertight Edge/orientation checks passed; not a general self-intersection or print-validity certificate.
mesh_status, mesh_error Explain empty or invalid geometry and unavailable metrics.

Physical metrics use compatible units converted to the mesh X-axis unit; uncalibrated data remains in voxel-coordinate units. Open, degenerate, non-manifold or inconsistently wound surfaces keep area/extents where defined, but volume-derived fields are NaN. Smoothing and simplification can change measurements, even when the object ID stays the same.

Filtering retains IDs; combining remaps collisions, and splitting assigns IDs to additional parts. Keep source/parent IDs from mesh metadata when tracing those changes. Do not join pre- and post-operation tables by row position.

Skeleton and association tables

Expensive measurement nodes are manual/cached by default. Recalculate stale results before export; changing table sorting does not recalculate the data.