utils/3d

3D Export & Quantification

Turn segmentations into STL and OBJ meshes, 3D renders and rotating videos, and volume measurements.

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Overview

What it does

3D Export & Quantification turns a volume and its segmentation into things that are used outside the viewer: surface meshes for visualisation and patient education, rendered images and rotating videos of the anatomy, and per-structure measurements of volume and shape.

Three tools make up the model. Mesh, the default, builds a smoothed, decimated and watertight surface for every segmented structure. Render produces maximum-intensity projections, multiplanar reformats and volume-rendered thumbnails, rotating MP4 videos and cine previews. Volume measures each structure: volume, surface area, maximal diameters, sphericity and intensity statistics.

Intended use

Visualisation, communication and measurement. Meshes support teaching and patient education, renders illustrate reports and case discussions, and volumetry supplies the numbers that many CT and MR models reuse. Thumbnails and rotating videos also serve as study previews in a viewer or a teaching library.

Who it is for

Surgeons and radiologists preparing case discussions, educators, researchers who need volumetry across cohorts, and developers who want previews and meshes from their own segmentations.

Inputs and protocol

Accepted input

Volume: a CT or MR series as DICOM or NIfTI.
Segmentation: DICOM SEG or a NIfTI label map with one label per structure, from MedRun or from any other source.
Render also accepts a volume alone, with or without masks.

Requirements

Requirement	Why
Segmentation on the same grid as the volume	Meshes and measurements are placed in patient space
Correct voxel spacing	Volumes, areas and diameters are only as good as the spacing
Labelled structures	Each mesh and measurement is named after its structure

Voxel spacing and geometry are checked with the DICOM inspection step before any value is computed. Smoothing is limited so that thin structures keep their shape in the mesh.

Optional context

The mesh format (STL, OBJ or 3MF) and the structures to include are chosen in options.

Outputs and standards

The result

Each tool returns its own result. The default run returns the meshes.

Tool	Content
Mesh (default)	Smoothed, decimated, watertight surface per structure as STL, OBJ or 3MF, optionally DICOM-encapsulated
Render	MIP, MPR and volume-rendered thumbnails, rotating MP4 videos and cine previews
Volume	Volume, surface area, maximal diameters, sphericity and intensity statistics per structure

Standards

Meshes: Encapsulated STL, OBJ and MTL Storage; Surface Segmentation Storage; plain STL, OBJ and 3MF files.
Measurements: Comprehensive 3D SR with the TID 1500 Measurement Report.
Renders: PNG and MP4, or DICOM Secondary Capture for PACS.

Related tools

utils/3d/mesh: segmentation to surface meshes; the default run.
utils/3d/render: previews, projections and rotating videos of a volume.
utils/3d/volume: per-structure volume and shape measurements.

Measurement notes

Volumes and diameters are computed from the segmentation as given, so their quality follows the quality of the masks and of the voxel spacing. Masks from MedRun models and masks drawn in other tools are measured the same way.