1.

Introduction to Mimics

Materialise Mimics is an image processing software for 3D design and modeling, developed
by Materialise a Belgian company specialized in additive manufacturing software and technology
for medical, dental and additive manufacturing industries. Materialise Mimics is used to create 3D
surface models from stacks of 2D image data. These 3D models can then be used for a variety of
engineering applications. Mimics uses 2D cross-sectional medical images such as from computed
tomography (CT) and magnetic resonance imaging (MRI) to construct 3D models, which can then
be directly linked to rapid prototyping, CAD, surgical simulation and advanced engineering
analysis.

Mimics is an acronym for Materialise Interactive Medical Image Control System.

Materialise is an international company, best known for its activities in the field of rapid, industrial,
and medical prototyping. Started in 1990 as a spin off corporation from the University of Leuven
in Belgium, it began as a rapid prototyping service bureau. Since then, Materialise has grown into
the world’s largest rapid prototype producer. The company also enjoys a worldwide reputation as
provider of innovative software solutions. As such, Materialise has acquired the position of market
leader for 3D printing and digital CAD software in addition to being a major player in medical and
dental image processing and surgery simulation.

For the medical and rapid prototyping industries, Materialise offers an array of software solutions;
Mimics is the medical image-based processing tool for creating 3D models and linking the models
to rapid prototyping (RP), computer aided engineering (CAE), computer aided design (CAD), and
surgery planning. SurgiCase CMF is Materialise’s CT based craniomaxillofacial surgical planning
software. It allows users to import patient data, create 3D models, plan out the surgery, and rapid
prototype surgical guides that can be used during the operation to match the surgical plan. SimPlant
is Materialise’s dental implant planning software. Similar to SurgiCase, it allows users to plan
dental implant surgeries and prepare surgical guides for the operating room. All medical software
packages developed by Materialise are FDA approved. Magics RP is considered a powerful
preprocessor for additive fabrication. It prepares 3D object (STL) files for additive fabrication as
well as performs easy mesh and geometry manipulation. 3-matic is Materialise’s forward
engineering software that allows advanced manipulation and design on an STL file. It allows a
user to perform ‘digital’ CAD operations (i.e. typical CAD operations on a STL file instead of the
traditional CAD files), and fix and remesh for CAE. Materialise ensures that all software packages
are ISO-9001 certified and that there is a seamless link between all packages.

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1.1 Mimics History:
After the start of the company Materialise in 1990 as a rapid prototyping company, it didn’t take
long for the company to see the analogy between RP and CT (or MRI) images; in RP, a 3D model
is built slice per slice, whereas a CT scanner does the reverse, it breaks down a 3D model (the
human body) into a stack of image slices. In 1992 Materialise wrote software that linked the image
information to RP models. The software allowed extracting 3D information from an image stack
and building a 3D model from it, using RP technology. Materialise’s Interactive Medical Image
Control System (MIMICS) was born.

1.2 Mimics System Requirements:

 Minimum System Requirements:
Software Hardware
Windows® 7 sp1 - 64 bit (or higher) Intel® core™ 2 duo / AMD Athlon™ X2
AM2 or equivalent
Internet explorer® 10 4 GB Ram
Pdf viewer DirectX® 11.0 compliant graphics card with 1
GB Ram
.Net framework 4.5.2 (or higher) 5 GB free hard disk space
Resolution of 1280x1024

 Recommended System Requirements:

Software Hardware
Windows® 7 sp1 - 64 bit (or higher) Third generation Intel® Core™ i5/i7 or
equivalent
Internet explorer® 10 16 GB Ram
Pdf viewer DirectX® 11.0 compliant AMD
Radeon/NVIDIA® GeForce® card with 2 GB
Ram
.Net framework 4.5.2 (or higher) 20 GB free hard disk space
Resolution of 1680x1050 or higher

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1.3 Basic Functionality of Mimics:
Mimics displays the image data in several ways, each providing unique information. Mimics
divides the screen into three or four views: the original axial view of the image, and resliced data
making up the coronal and sagittal views and 3D view (Figure 1.1). Several visualization functions
are included such as contrast enhancement, panning, zooming and rotating of calculated 3D
images. Color scales are used to enhance small differences in the soft tissue or the bone. The
alignment or scout image can be displayed. The original data can be resliced online or a resliced
project can be exported. Online reslicing allows the display of cross-sectional and parallel images
that are orthogonal and along a user-drawn curve in the axial view. The export resliced project tool
offers an interface that allows the export of resliced Mimics projects along a user-drawn line. This
line can be drawn in any view and in any direction.
Mimics enables different types of measurement to be performed. Point-to-point measurements are
possible on both the 2D slices and the 3D reconstructions. A profile line displays an intensity
profile of the grey values along a user-defined line. Accurate measurements are possible on the
basis of the grey values using three methods: the threshold method, the four-point method and the
four-interval method. These methods are ideal for technical CT users. Density measurements can
be performed in ellipses or rectangles: area, mean, grey value and standard deviation are displayed.

Figure: 1.1 Overview of Mimics layout.

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Segmentation masks are used to highlight regions of interest. Mimics enables you to define and
process images with several different segmentation masks. To create and modify these masks,
the following functions are used:

 Thresholding is the first action performed to create a segmentation mask. You can select a
region of interest by defining a range of grey values. The boundaries of that range are the
lower and upper threshold value. All pixels with a grey value in that range will be
highlighted in a mask.
 Region growing will eliminate noise and separate structures that are not connected.
 Editing (draw, erase, local threshold): manual editing functions make it possible to draw,
erase or restore parts of images with a local threshold value. Editing is typically used for
eliminating artifacts and separating structures.
 Dynamic region growing segments an object on the basis of the connectivity of grey values
in a certain grey value range. It allows for easy segmentation of tendons and nerves in CT
images, as well as providing an overall useful tool for working with MRI images.
 Morphology operations act on the ‘form’ of a segmentation mask. All these functions
remove or add pixels from the source mask and copy the results to a target mask. This tool
is extremely effective when working with MRI images.

Figure: 1.2 Examples of 3D objects in Mimics.

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  Boolean operations enable different combinations of two segmentation masks (subtraction,
union and intersection) to be made. These operations are very useful for reducing the work
needed to separate joints.
 Cavity fill fills the internal gaps of a selected mask and copies the result to a new mask.
The filling process can be applied in 2D.
 Cavity fill from polylines creates a segmentation mask, starting from a polyline set. This
tool is very useful for filling internal cavities in preparation of files for FEA.

After isolation of the region of interest, a 3D can be calculated. Therefore, parameters for
resolution and filtering can be set. Information about height, width, volume, surface, etc., is
available for every 3D model. Mimics can display the 3D model in any of the windows with
visualization functions that include real-time rotation, pan, zoom and transparency. The ability to
apply advanced rendering with OpenGL hardware acceleration offers high-quality rendering
including Gouraud shading for optimal display of the 3D objects (Figure 1.2).

1.4 Modules in Mimics:

Mimics consists of different modules. Figure 1.3 shows the links between the main program and
its modules. The different modules link Mimics to various application fields: rapid prototyping
(RP), finite element analysis (FEA) and computer-aided design (CAD).

1.4.1 Import Module:

Mimics imports 2D stacked uncompressed images such as CT, MRI or microscopy data in a wide
variety of formats, as well as offering a user-defined import tool. The import software provides
direct access to images written on proprietary optical disks and tapes, converts them into the
Materialise image format and preserves all necessary information for further processing.

A stack of images can be loaded into the software, Mimics, and this usually consists of images in
the XY plane (axial images). Mimics then calculates and creates images in the XZ (coronal) and
YZ (sagittal) direction. This enables a more comprehensive 3D feel of the 2D data.

The key to converting anatomical data from images to 3D models is a process called segmentation.
During segmentation the user indicates the structure(s) of interest in the sliced image data. This
information is then used to recreate a 3D model from the segmented structures. To describe the
outer surface of the 3D model, Mimics uses the STL format, which is the common file format in
RP. The STL format allows describing the most complex geometries accurately. This is necessary,
since anatomical data is in general very intricate. Accurate segmentation is important in order to
extract meaningful information from images.

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 CT/MRI
scanner

Import

Mimics

Simulation
surgical procedure
simulation

RP Slice STL+ MedCAD

Model and support Model generation via Interface to CAD
generation via sliced triangulated files
files

FEA
Interface to FEA
and CFD

Rapid FE Analysis CAD

Prototyping

Figure: 1.3 Modular structure of Mimics: links to different applications.

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Segmentation: The medical images coming from CT or MRI scanners consist of grayscale
information. Mimics allows the user to create models based on the grayvalues (Hounsfield units
in CT images) within these images. A grayvalue is a number associated with an image pixel
defining the shade (white, gray, or black) of the pixel. There is a direct association between
material density of the scanned object and the grayvalue assigned to each pixel in the image data.
Because of this, Mimics has the flexibility to create models from any geometry distinguishable
within the scanned data. By grouping together similar grayvalues, the image data can be
segmented, and models created. This type of segmentation is called thresholding and yields
accurate models.

Many of the segmentation tools in Mimics are common in image processing and can be applied in
any of the views (XY, XZ or YZ), but Mimics also has a unique 3D editing tool; an initial
segmentation can be optimized in a 3D preview (Figure 1). This makes editing very easy, since it
allows true editing in 3D, which is easier to comprehend than 2D editing.

Figure: 1.4 Editing a Mimics model in 3D to capture only the femoral head.

Using the segmentation and known information on the pixel size and the distance between the
image slices, Mimics can calculate a 3D model (Figure 1.4). The accuracy in a Mimics model
matches the accuracy of an object captured within the scan.

A wizard helps to guide you through the import process. It allows for the merging of multiple
image sequences into one project, to convert different image sets at once or to select specific
images prior to creating the project.

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1.4.2 RP Slice Module:

The RP slice module interfaces from Mimics to any kind of rapid prototyping system via sliced
formats and performs support generation. The 3D object created within Mimics is an STL file.
STL is the common language for rapid prototyping machines and 3D printers and it can describe
very complex geometries (like medical geometries). The 3D object can be directly exported to
rapid prototyping in either STL or Sliced file format; in the latter it also allows support generation.
Or it can be imported into Materialise’s Magics program for support generation or for build
optimization. Figure 1.5 shows how models exported from Mimics were prepared in Magics to
generate supports and duplicate the object to print multiple models at once.

Figure: 1.5 Mimics models printed on a RP machine with support generation.

Rapid prototypes from Mimics have many applications in the medical field. Considering the fact
that the human brain is optimized to work with something tangible, holding a physical model is
always easier to understand than a 3D model on a computer screen, no matter how good 3D
graphics are. Since the models accurately match patient data, the models are helpful in
communication and surgery preparation for clinical work. Medical rapid prototypes are highly
utilized by medical device design manufactures and engineers. The RP models allow engineers to
test form, fit, function, and validation of designs on actual patient data prior to testing them on
actual patients. Rapid prototyping also allows users to test and validate designs with physical
models.

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1.4.3 STL+ Module:

The Mimics STL+ module interfaces from Mimics to any kind of rapid prototyping (RP) system
via triangulated files. These files are created with a bilinear and interplane interpolation algorithm
to enhance the resolution of the RP model.

An STL file is a triangulated surface mesh file. The file contains the three nodes of each triangle
and defines the normal direction of the triangle. This file format is ideal for anatomical geometry
because of its simple file structure and flexibility to match any contour desired. It is not controlled
by parametric constraints such as true CAD files and IGES files. Below is an example of the
triangulation of an STL file. The available export formats are ASCII STL, binary STL, DXF,
VRML 2.0 and point cloud.

Figure: 1.6 Triangulation of STL file.

Several calculation parameters can be specified. STL+ makes it possible to reduce the number of
triangles of the exported files, to interpolate the images and to smoothing the 3D files.

There are two methods available for reducing the number of triangles: matrix reduction and
triangle reduction. Matrix reduction allows the grouping of voxels to calculate the triangles.
Triangle reduction makes it possible to reduce the number of triangles in the mesh. This makes it
easier to manipulate the file.

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There are also two methods available for interpolating the images and generating the 3D mesh:
grey value interpolation and contour interpolation. Contour interpolation is a 2D interpolation in
the plane of the images that is smoothly expanded in the third dimension. Grey value
interpolation is a real 3D interpolation. A smoothing algorithm can be applied to make rough
surfaces smoother.

1.4.4 Med CAD Module:

The Med CAD module provides a direct interface to CAD systems via surfaces, curves and objects
exported as IGES files.

Based on the segmentation mask, Med CAD automatically generates the contours (polylines) of
the mask. These polylines are used to fit b-spline curves, b-spline surfaces and objects (circle,
sphere, cylinder, plane, etc.). The objects can also be created interactively. All these entities can
be exported as IGES files and are directly usable for the design of custom-made prostheses in any
CAD system.

To verify the CAD implant design, Mimics imports the design as an STL file. Med CAD enables
the user to visualize and manipulate the implants within the medical images in 2D cross-sections
as well as in 3D.

1.4.5 FEA Module:

The Mimics FEA module makes it possible to link from scanned images to finite element analysis
and computational fluid dynamics by exporting the files in the appropriate file format. 3D objects
can be calculated on the basis of the scanned images and these surfaces meshes can be prepared
for finite element analysis purposes. The remesher in the FEA module ensures that the most
optimal input for that FEA package is eventually obtained. Materials can be assigned to volumetric
meshes, based on the Hounsfield units in the scanned images.

The Mimics remesher significantly improves the quality and speed of FE analyses on STL models.
It allows the easy transformation of irregularly shaped triangles into more or less equilateral
triangles and increases the reliability and accuracy of FEA results on STL models. Most FE
packages do not allow the manipulation or optimization of the mesh generated when a part is
imported. This might reduce the accuracy of the results. With the remesher it is possible to optimize
the file and deliver good meshes that will run in the FEA software (Figures 1.7 and 1.8).

After loading a volume mesh, the FEA calculates an appropriate Hounsfield value for each element
of the mesh on the basis of the scanned images. Several Hounsfield unit ranges, each representing
a material, can then be specified. A density, an elastic modulus and a Poisson’s ratio can also be
assigned for those materials. The volumetric mesh with the assigned materials can then be exported
to a Patran neutral, Ansys or Abaqus file (Figures 1.9 and 1.10).
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Figure: 1.7 3D view of the vessel before Figure: 1.8 3D view of the vessel after
Remeshing. Remeshing.

Figure: 1.9 Material distribution representation. Figure: 1.10 Material distribution histogram.

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Remeshing: Mimics has been designed to remesh 3D objects (STL files) from their original RP-
ready format to a CAE-ready format. To optimize the mesh and create equilateral triangles, Mimics
will analyze the shape quality of each triangle. After the quality of each triangle within a mesh is
understood, Mimics can automatically perform the remeshing processes described in the above
section. This will quickly prepare anatomical models for CAE analyses. For highly sensitive
analyses and for more user control and definition, Mimics has the option to perform manual
remeshing. This allows a user to manually edit triangles and control the triangle reduction and size.

The remeshing process in Mimics also allows one to analyze an anatomical assembly. Researchers
and engineers alike will use Mimics to prepare a study of multiple anatomical models interacting
together or anatomical data interacting with manufactured device designs. While running a finite
element analysis of an assembly it is important for two mating surfaces to have node-to-node
matching. Mimics will create this node-to-node matching from two separate STL files as shown
in figures 1.11 and 1.12.

Figure: 1.11 Original mesh of two surfaces Figure: 1.12 Two parts, with optimized
without node-to-node matching. Mesh and node-to node matching.

Volume Mesh: STL is a surface representation. To do an analysis, a complete volume description

is needed. Generating a volume mesh from an optimized surface mesh is straightforward. From a
triangle surface mesh, a tetrahedral volume mesh can be generated. A tetrahedral and hexahedral
mesh can be created within Mimics or within a 3rd party volume mesh generation package. This
volume mesh generation flexibility allows a user to determine what parameters and settings are
most important depending on application and preference.

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1.4.6 Simulation Module:

The Mimics simulation module is an open platform for surgical simulations that makes it possible
to perform a detailed analysis of data using the anthropomorphic analysis templates, plan
osteotomies and distraction surgeries, or simulate and explain a surgical procedure for implant
design.

To perform an anthropomorphic analysis – standard template or user defined – indicate the

appropriate points (landmarks). Planes and measurements are automatically created once the
points they depend upon are created. New landmarks can be created, copied, edited or deleted.
Each landmark can have some default properties that can be set when creating the landmark or by
editing an existing landmark. Both distances and angles can be measured. For distance, either the
distance between two points or the distance between a point and a plane can be measured. As for
an angle, this can be measured using three points or using two lines.

The Mimics simulation module offers a powerful 3D package for all kinds of surgery simulation
application. Various tools and STL operations for simulating osteotomy and distraction surgeries
are available: cut and split operations, merging of objects, mirroring of parts, distractor placement
and repositioning of objects with or without a distractor. The following examples demonstrate the
use of the simulation module.

A user can then begin to analyze the placement of the imported implant/device. This helps both
engineers designing the implant and surgeons placing the implant understand a design’s fit and
function as in figure 1.13.

Figure: 1.13 Surgical simulation of the placement of a femoral implant.

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1.5 Applications:

Mimics is a powerful image processing tool and links to many applications. Its user base consists
mostly of engineers, but also clinicians. There is a discrepancy in the demands of both engineers
and clinicians for a software like Mimics. Engineers want a powerful open toolbox, whereas
clinicians want it to be easy to use and fast. To accommodate the wishes of both, Mimics is
equipped with a very user friendly graphical user interface (GUI) as well as powerful tools to
analyze intricate data. Therefore, Mimics is an easy to use, powerful toolbox for both engineers
and clinicians.

Materialise Mimics is a platform to bridge stacked image data to a variety of different medical
engineering applications:

 3D measurements and analyses.

 Computer Aided Design.
 Computational Fluid Dynamics.
 Customized implant design.
 Finite Element Analysis.
 Rapid Prototyping.
 Surgical simulation.

The major industries that use Mimics are:

 Cardiovascular
 Craniomaxillofacial
 Orthopedic
 Pulmonology

Other industries Mimics is also used in include tissue engineering, anthropology,

technical/industrial design, and pulmonary study. Because Mimics is used in multiple markets, it
is important for the software to have features that fit each market. Therefore, Mimics has a modular
structure and users can tune the software to their needs by extending the basic package with
additional modules.

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