3d image processing

Simpleware ScanIP

3D Image Segmentation and Processing Software

ScanIP provides a software environment for comprehensively processing 3D image data (MRI, CT, micro-CT, FIB-SEM…). The software offers powerful image visualisation, analysis, segmentation, and quantification tools.

ScanIP is easy-to-learn and use, and includes video recording features and options to export surface models/meshes from segmented data for CAD and 3D printing. Additional modules are available for exporting CAE meshes, integrating image data and CAD, exporting NURBS and calculating effective material properties from scans.

segmentation software

New in Version M-2017.06

Read the ►Release Blog and sign up for the ►Release Webinar

New Segmentation and Processing Capabilities
  • Reduce segmentation time with smooth interpolation tool
  • Use mask ungroup tool to automate difficult segmentation tasks
  • Achieve better segmentation with complex image data using 3D wrap tools
  • Save significant time and effort with one-click fill gaps tool
  • See a major speed increase with 3D editing enhancements
Enhanced Visualisation and Inspection
  • Faster visualisation capabilities include a ~10x increase in average dataset sizes, as well as 10% reductions in preview rendering time and 50% drops in animation preview rendering time
  • Work with large datasets with no noticeable performance decrease up to 55M triangles
  • Speed up inspection workflows by displaying multiple measurements simultaneously in 2D and 3D
  • Use probe centreline measurements to allow cross-section measurements to be obtained interactively


  • Intuitive user interface
    Easy-to-learn and easy-to-use
  • Generate high quality, multi-part STL and surface models
    No need for manual fixing or remeshing
  • Scripting
    Automate repeatable tasks and operations
  • Direct image to surface conversion for surface export and visualisation
    Accurate, high quality representations of your data

Key features

  • Import a wide range of file formats
  • Customisable workspace with multiple 2D/3D viewing modes
  • Volume rendering of background images and masks
  • Record animations and export video files for presentations
  • Comprehensive measurements and statistics tools
  • Powerful, semi-automated segmentation tools
  • Volume and topology preserving smoothing
  • Robust multi-part surface mesh/STL generation


ScanIP Technical Data

ScanIP offers an intuitive and interactive environment to assist the user in segmenting 3D data into masks, ready for surface and/or volume meshing.

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Import Formats

  • DICOM (version 3.0 and 2D stacks)
  • ACR-NEMA (versions 1 and 2)
  • Interfile
  • Analyze
  • Meta-image
  • Raw image data
  • 2D image stacks:
    • BMP
    • GIF
    • JPEG
    • PCX
    • PNG
    • TIFF
    • XPM
  • Natively supported pixel types:
    • 8-bit Unsigned Integer
    • 16-bit Unsigned Integer
    • 16-bit Signed Integer
    • 32-bit Floating Point

Export Formats

  • Background image:
    • RAW image
    • MetaImage
    • Stack of images (BMP, JPG, PNG, TIF)
  • Segmented image:
    • RAW image
    • MetaImage
  • Surface model:
    • STL
    • IGES
    • ACIS (SAT)
    • ANSYS surface
    • ABAQUS surface
    • MATLAB file surface
  • Animations:
    • AVI
    • Ogg Theora
    • H.264/MPEG-4 AVC
    • Windows Media Video (WMV)
    • PNG sequence
  • 2D and 3D screenshot:
    • JPEG
    • PNG
    • VRML
    • Postscript (*.eps)
    • BMP
    • PNM
    • PDF

General User Interface

  • Modern ribbon interface
  • User defined interface: dockable tool boxes, range of 2D/3D view options
  • Undo/redo operation support
  • Independent part visibility control in 2D and 3D
  • Ability to import multiple image sets into the workspace to aid segmentation
  • Histogram and profile line utilities assist in finding optimal threshold values
  • Automatic logging and timestamp of filters and tools applied since the creation of a project
  • Workspace tabs: toggle between the active document, mask statistics, model statistics, centreline statistics, the document log and the scripting interface
  • Preferences: a number of different options available for default settings:
    • General: number of undos to save, default startup layout, max permissible CPUs for parallelized operations
    • Slice views: display orientation labels, choose whether to use a dark background, specify model contour and mask voxel outline colours
    • 3D view: save last camera position before exiting the document, stereo rendering settings, options to further divide higher order mesh elements (for FE meshes and NURBS patches)
    • Volume rendering: GPU rendering supported, Background volume rendering visibility on startup
    • Folders: options to change locations of temporary files
    • Statistics: default template for Mask, Model and Centreline statistics
    • Scripting: enable/disable supported scripting languages

2D User Interface

  • 3x 2D views
  • Orientation labels
  • Ability to work on single slice, selection of slices or whole volume
  • Slice cursors to identify the position of 2D slices
  • Mask visualisation options: solid, translucent, voxel outline
  • View 3D model contours on 2D slices

3D User Interface

  • Background volume rendering: using standard presets or greyscale mapping
  • Single mask volume rendering
  • Interactive cropping using 3D view
  • Clipping box: unconstrained, interactive sectioning of 3D rendering
  • Fast 3D preview mode for rapid visualisation of segmentation: ability to change preview quality to speed up rendering and reduce memory consumption
  • Mask transparency
  • 3D stereoscopic visualisation with selected hardware modes available:
    • Crystal eyes
    • Red/blue
    • Interlaced
    • Left
    • Right
    • Dresden
    • Anaglyph
    • Checkerboard
  • Wireframe mode
  • Vertex lines superimposed over surfaces mode
  • Lighting and 3D rendering adjustments
  • Background gradient adjustments
  • View surface entities: CFD boundary conditions, node sets, contacts, shells
  • View contours of greyscale based material properties
  • Model shading options: None, flat, Gouraud, hardware shader
  • Full screen mode
  • Load and save 3D view camera positions
  • View slice planes
  • Show image dimensions on scale axes

Statistical Analysis

  • Quick statistics: quickly compute commonly required quantities (volume, surface area, average greyscale, etc.)
  • Mask statistics (based on voxel information):
    • Built-in templates: general statistics, contact statistics, material statistics, orientation, pore sizes, surface statistics
    • Ability to generate user defined templates
    • Variety of statistical information pertaining to:
      • Voxels: count, volume, surface area, etc.
      • Greyscales: mean, standard deviation, minimum, maximum, etc.
      • Surface estimation: area, area fraction, volume, volume fraction, etc.
      • Material properties: mass, mass density, Young’s modulus, Poission’s ratio, moment of inertia, etc.
      • Axis aligned bounding boxes
      • Axis aligned bounding ellipsoids
      • Object oriented bounding boxes
      • Object oriented bounding ellipsoids
      • Create a user defined statistic
  • Model statistics (based on polygon information):
    • Ability to generate user defined templates
    • Built-in templates: general statistics (perimeters, surfaces, volumes and NURBS surfaces), mesh quality (CFD, FE-linear elements and FE-quadratic elements), orientation (perimeters, surfaces, volumes), pore sizes, surface quality (linear, quadratic)
    • Variety of statistical information pertaining to:
      • Surface parameters: element count, node count, edge count, etc.
      • Perimeters: length, mean edge length, mean dihedral angle, etc.
      • Surface triangle and quadrilateral primitives: edge-length, in-out ratio, distortion, etc.
      • Tetrahedral, hexahedral, pyramid and prismatic volume element primitives: angular skew, volume skew, shape factor, Jacobian, etc.
      • Axis aligned bounding boxes
      • Axis aligned bounding ellipsoids
      • Object oriented bounding boxes
      • Object oriented bounding ellipsoids
      • Create a user defined statistic
  • Centreline statistics:
    • Built-in templates: line orientation, lines by network, lines by node, constriction, shape, twist, nodes by network
    • Ability to generate user defined templates
    • Variety of statistical information pertaining to:
      • Lines: count, network, length, Euclidean length, curvature, torsion, closed, looped, positions, orientation, connection count, cross-sectional area and perimeter, incircle radius, twist, control points, object-oriented bounding boxes, mean orientation vector, best fit circle, inscribed radius, circumscribed radius, bounding ellipse radius
      • Nodes: name, mask, network, position, line count, connection count
      • Create a user defined statistic
  • Probe centrelines to get measurements at specific locations
  • Save and import user-defined templates and statistics
  • Compute statistics within user-defined regions of interest (ROIs)

Measurement tools

  • Create and save points, distances and angles in 2D/3D
  • Visualisation options to display all at once or selected
  • Snap to 3D surface option
  • Profile line
  • Histogram
  • Export as comma separated values

Image Processing Tools

  • Data processing:
    • Crop
    • Pad
    • Rescale
    • Shrink wrap
    • Resampling using various interpolation techniques: nearest neighbour, linear, majority wins and partial volume effects
    • Flip
    • Shear
    • Align
  • Basic Filters (most commonly used):
    • Smoothing: Recursive Gaussian
    • Noise filtering: mean filter, median filter
    • Cavity fill
    • Island removal filter
  • Advanced Filters (more specialist applications):
    • Histograms slice equalisation
    • CT image stabiliser
    • Binarisation filter
    • Gradient magnitude filter
    • Gradient anisotropic diffusion
    • Curvature anisotropic diffusion
    • Curvature flow
    • Discrete Gaussian filter
    • Min/max curvature flow
    • Skeletonisation
    • Metal artefact reduction
    • Fill gaps tool (using largest contact surface or mask priority)
  • Level set methods: allow segmentation based on implicit surfaces. Contour specific features can therefore be controlled during the region growing/surface adjusting process
  • Morphological filters:
    • Erode
    • Dilate
    • Open
    • Close
    • 3D Wrap
  • Lattice factory: allows masks to be filled with a user defined internal structure
  • Segmentation tools:
    • Paint/unpaint
    • Paint with threshold
    • Interpolate between slices (smooth or linear)
    • Propagate to next slice(s) – adapts to image or uses direct copy
    • Confidence connect region growing
    • Floodfill
    • Thresholding
    • 3D editing tools for application of filters to local regions
    • Automated generation of masks for pre-segmented images
    • Magnetic lasso
    • Multilevel Otsu segmentation
    • Split regions tool
    • Merge regions tool
    • Watershed segmentation tool
  • Particle segmentation tools:
    • Automated watershed segmentation
    • Split/merge segmentation
    • Particle size analysis and visualisation
  • Boolean operations: applied to/between masks. General and Venn diagram UI options
    • Union
    • Intersect
    • Subtract
    • Invert
  • Multi-label tools: use mask labels to label different regions within a mask. Use for statistics and visualisation
    • Label disconnected regions
    • Split mask into pores
    • Combine masks to multi-label mask
    • Mask label editor
    • Reports: automatically generate pre-formatted reports of common metrics using a multi-label mask or full model's mesh
      • Particles report
      • Pores and throats report
  • Window/level tool
  • Overlap Check: display/generate mask to check overlap volume in active masks

Surface Mesh Generation

  • Topology and volume preserving smoothing
  • Triangle smoothing
  • Decimation
  • Multipart surface creation
  • Surface element quality control (for volume meshing in third party software)
  • So-called ‘sub-pixel accuracy’ through the use of partial volume effects data

Surface Mesh Quality Inspection Tool

  • Inspect surface triangles or clusters of triangles
  • Option to show mesh errors (for e.g. surface holes, surface intersections) and warnings
  • Show distorted elements above a user-defined threshold
  • Zoom into the pathological element to inspect it more closely


  • Create and export animations in the 3D view
  • Built in-quick animations: Rotations, slice reveals and volume rendering
  • User defined animations cues:
    • Background colours
    • Camera (orbits, follow path and key frame based)
    • Clipping
    • Opacity
    • 2D slice planes
    • Volume rendering
  • Variety of export formats:
    • AVI
    • Ogg Theora
    • H.264/MPEG-4 AVC
    • Windows Media Video (WMV)
    • PNG sequence
  • Variety of export sizes: from 480p to 2160p (4K)


  • ScanIP API: ScanIP Application Programming Interface (API) is an object-oriented programming library that allows access to most of the features of ScanIP
  • Support for a variety of scripting languages:
    • Python
    • Iron python
    • C#
    • Visual basic
    • Boo
    • Java
  • Macro recording: record, save and play macros
  • Convert log entry to script


  • Seamless integration with Simpleware's +CAD module for interactive CAD/STL object integration and positioning
  • Seamless integreation with Simpleware's +FE module for direct volume element generation suitable for FE and CFD simulations
  • Seamless integreation with Simpleware's +NURBS module for robust NURBS patch generation
  • Seamless integration with Simpleware’s +SOLID, +FLOW and +LAPLACE modules for numerical homogenisation of materials

Download Technical Datasheet