analySIS®

User’s Guide
3D-Processing
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 Contents

First steps in 3-D ............................................................................................................................ 2

Matrox G400 settings............................................................................................................ 2
Activating the module ........................................................................................................... 2
A simple example ................................................................................................................. 4
The 3-D window.............................................................................................................................. 8
Overview............................................................................................................................... 8
The object directory .............................................................................................................. 9
Preparing images ......................................................................................................................... 10
Arranging planes................................................................................................................. 10
Defining heigt distance ...................................................................................... 10
Tilting planes...................................................................................................... 12
Decompressing planes ...................................................................................... 12
Aligning planes .................................................................................................. 14
3-D model construction ............................................................................................................... 18
Creating polygons............................................................................................................... 18
Creating polygons sequentially.......................................................................... 18
How do I use the magic wand?.......................................................................... 23
Creating lateral surfaces..................................................................................................... 24

Which version is described by this documentation

This documentation describes the 4.15.720 version of the 3D-Processing module. This version is
included in analySIS® starting with Build 478.
You find the version number in the Add-In Manager in the Special menu. To locate your analySIS®
build number look in the About dialog box in the ? menu.
 First steps in 3-D
Matrox G400 settings
Activating the module
A simple example
This chapter is meant as an introduction
to the 3D-Processing module.
• The chapter describes the settings of
the graphic card you need and how to
activate the module.
• includes a simple example demon-
strating how you can reconstruct your
first 3-D model. This is how you be-
come familiar with what the typical 3-
D reconstruction procedure involves.
• includes definition of terms of all 3-D
objects and sub-objects that you work
with during the reconstruction.
This user’s manual offers you a quick
start in working with the 3D-Process-
ing module - to get you in a position The 3D menu’s standard position within analySIS® pro is before the C-
where you can get working on your own Module menu.
reconstructions.
Required apparatus
We recommend the following hardware
components to ensure it works quickly
enough even when a great number of
images are involved:
• 32MB VGA card
• 128MB RAM,
• Windows NT.
Original images
An image series containing section
planes of a three-dimensional sample is
required for 3-D reconstruction. You
have to save these image files in a
separate directory on the hard disk first.
The original images' properties must
include the following:
• All images require the same unit or
have to be able to be scaled in the
same unit.
• All images of a plane stack must have The 3D-Processing entry within the Add-In Manager has to be selected to
comparable length and width inas- make module commands available to you.
much that their respective dimen-
sions differ little from one another.
• If possible, images ought to be posit-
ioned parallel and one atop the other.
But they can also be displaced at
varying tilt angles with respect to one
another. The angle of the tilt may not,
however, be within the region of 90%
or 270%.
• Images should include natural or
artificial alignment criteria.

2
What are the settings required for operating the Matrox G400?
When working with the Matrox G400 VGA board, the following settings must be conducted to ensure your
work with the 3D-Processing module goes smoothly.
 Go to the Matrox homepage at www.matrox.com and load the most recent driver.
 Select the Windows command Settings, Control Panel. Click on the Matrox Image
Properties.
 Select the True Color (32-bit) entry in the Color Palette list in the Settings tab.
→ 3-D acceleration will not be in effect otherweise.
 Select the Use 3D acceleration and Use 32-bit Z-buffering check boxes in the Performance
tab.

How do I activate the 3-D Processing module?

The following series of steps is only necessary if the 3D-Processing module commands are not
available in your current analySIS® configuration.
 Open the Special menu.
 Select the Add-In Manager... command.
→ The Add-In Manager dialog box will be opened.
 Select the check box next to the 3D Processing entry in the Available add-ins list.
 Click on the Close button.
 Now, close analySIS® and re-start it.
→ It is only once you’ve closed analySIS® and re-started it that the commands of the module
will become available to you.
→ The 3D menu will now appear within the menu bar.

How do I remove the Viewport and Image Managers from view?

You do not need either the Viewport nor the Image Managers for the 3-D reconstruction most of the
time. You can remove them from view and thus enlarge the document area for the 3-D window.
 To remove the Viewport Manager from view, press the following keys: [Alt+1].
 To remove the Image Manager from view, press the following keys: [Alt+2].
→ You can use the same key combinations to have Viewport and Image Managers re-appear
once you’ve completed the 3-D reconstruction - at any time.

3
 First steps in 3-D
Matrox G400 settings
Activating the module
A simple example (1)
The simple example
involves your reconstructing a rectan-
gular cuboid and a pyramid. Use these
basic geometric shapes to create your
first 3-D model quickly. While doing so,
you’ll be going through the fundamental
sequence of steps involved, and you’ll
learn the most important 3-D commands
- starting with the definition of a work-
space, all the way to the display of the
completely-reconstructed 3-D model.
You’ll find more detailed instructions and
definitions of terms and commands on
the pages indicated.
Definitions
A Workspace is a directory on your The figure shows the 3-D window following step 7 - after you’ve added the
hard drive that you create or select in "Rectangles 1-5" images to the stack called "Stack_Rectangles" and have
the 3D-Processing module. The soft- sorted (the images).
ware saves all files of a 3-D reconstruct-
ion in the workspace selected.
A Layout contains the
information on the 3-D
objects currently loaded are how these 3-
D objects are being displayed. A work-
space can contain several layout files. This is what the image stack looks like following tilting (in step 8) and
Planes are the 2-D original ima- definition of the height distance (step 9 or 10).
ges you use to create the 3-D
model.
A Stack contains the 2-D
original images, i.e. the
planes, you reconstruct the 3-D model
with.
Polygons are the image areas
of the original images that are
assembled into a 3-D model.
A Linkage is the assembly of
the separate polygons into a
unified 3-D model having one lateral
surfac. The polygons have been linked
via triangulation.
An Element is a contain-
er. It is comprised of the
polygons and the linkages of the poly-
gons that you use to combine the Polygons - used to construct a cuboid (right) - are defined via particle
composite model. An element is the 3- detection (left) - (step 12). A 3-D model can be opened at its upper and/or
D model comprised of polygons. Each lower surface (step 14).
element refers to a stack of images
(from which the polygons originate).

4
How do I create a basic 3-D model?
Constructing a cuboid
 Save the "Rectangle1-5" and "Pyramid1-4" images from the "Demo" database to a separate
hard-disk directory. Images are appended to the "Element_Cuboid" and "Element_Pyramid"
images as documents.
 Set up a new workspace "First_Steps" and a new layout "My_example".
→ This is done using the Workspace, New... command (in the 3D menu).
→ Enter the name "My_Example" into the Layout name field.
→ The path for the workspace directory "First_Steps is defined via the Browse... button.
 Select the units for all planes of the workspace.
→ This is done using the Workspace, Select Unit... command - enter "µm".
 Create a new stack and call it "Stack_Rectangles".
→ This is done using the New Stack... command.
 Load the "Rectangle1-5" images from their directory into the stack called "Stack_Rectangles".
→ This is done using the Planes, Add... command.
→ The planes will be copied into the "Stacks" sub-directory located within the workspace.
 Select the planes to be able to execute the following steps.
→ This is done by keeping the [Shift] key depressed while you leftclick on the first and last
planes. The plane symbols will turn red.
 Sort the planes so that they are sorted in the correct order within the stack.
→ This is done using the Planes, Sort... command. Sort by counter in name, position in name
"10". "Rectangle1" should be at the bottom.
 Tilt the image stack away from you so that you can view it laterally.
→ This is done by showing the navigation wheel (3D Navigation command, Window menu) and
clicking several times on the arrow button on the navigation wheel.
 Define a height distance between the planes of 2 µm.
→ This is done using the Planes, Define Height Distance... command. Enter the number
"2" into the Distance field and confirm with OK.
 Turn ‘on’ the control lines, if they are not visible.
→ This is done by disabling the Hide Control Lines button in the 3-D button bar (along the
top of the 3-D window).
 Create a new element called "Element_Cuboid".
→ This is done using the New Element... command.
 Define polygons within the planes that outline the square of the images.
→ Select the Polygon, Create Sequentially... command to do so.
→ Click on the Particle button in the Create Polygons Sequentially dialog box.
→ Select thresholds in the Set Thresholds dialog box so that phase 1 contains the white
square of the image, but excludes the black outline.
→ Leftclick on the cross-hatched area within the square.
→ Disable the two Create series/thresholds buttons in the Create Polygons Sequentially
dialog box. Click on the Particle button. The Set Thresholds and Create Polygons
Sequentially dialog boxes will not be opened again.
→ Select (via mouse) all cross-hatched areas within the squares.
→ You’ll be asked whether you wish to create a linkage: Confirm the settings Skeleton,
Respect orientation, and Proportional progress in the Select Segmentation dialog box
with OK.
 Have a look at the cuboid from various perspectives.
→ This is done by clicking on the various buttons of the navigation wheel.
 Open up the cuboid.
→ This is done by selecting the uppermost polygon (the one called "Rectangle 5 [0]"). Click
on the Open button in the 3-D button bar (at the top of the 3-D window).
 You can delete a 3-D object at any time you like and re-start again with the appropriate step if
a step fails.

5
 First steps in 3-D
Matrox G400 settings
Activating the module
A simple example (2)
Definitionen
A segment is an area of
the lateral surface of the
3-D model that links two polygons. The
segments between two polygons
always belong to the upper polygon. This is what the image stack looks like before (left) and after (right)
alignment of the planes (step 20). The white dot within the image is your
Segments can be opened, thus permit-
ting you to view the interior of the 3-D point of orientation - a marker - it is your reference point to aid you in aligning
model from the side. the planes correctly.

A hole is a opening within a

polygon. Use holes to draw, eg,
an opening or window in the upper or
lower surface of 3-D models - thus
permitting you to view the interior of the
3-D model.
A group entry or an
entry is usually an
element, but can also be a stack or
another 3-D model.
(left): You can open the 3-D object laterally (step 23).
A group contains the
(right): You can define an hole within the upper or lower surface (step 24).
entries - these are general-
ly elements. You can combine several
single elements within one group, thus
resulting in one whole structure or
scene.
Alignment
refers to the relative alignment of the
image planes from one to another.
In order to reconstruct a realistic 3-D
model, the planes within the stack have
to be positioned such that the structures
are aligned as closely as possible in
correspondence with the actual sample.
Sample preparation may result in the
sections of the specimen being different
in size, orientated differently, position-
ally displaced or distorted. If this is the
case, you’ll need to align the planes
with one another.
One Point Alignment enables you to
correct horizontal and vertical
displacements.
You can have the individual 3-D objects assembled into a single composite
model (instruchtion "Ceating a composite model"). The figure shows cuboids
and pyramids: as they appear in their original positioning (upper); after
displacement (lower left); or after rotation (lower right) of the pyramid with
respect to the unaltered cuboid.

6
Constructing a pyramid
 Create a new stack and call it "Stack_Pyramid".
 Load the "Pyramid 1-4" images from your directory into the stack called "Stack_Pyramid".
 Select the 4 "Pyramid 1-4" planes via [Shift] key and mouse.
 Sort the planes by counter in name, position in name "8". "Pyramid1" should be at the bottom.
 Define a height distance of 10 µm.
 Align the 4 planes so that the squares are atop each other in the shape of a pyramid.
→ This is done using the Planes, One Point Alignment... command.
→ Select the marker point within each plane - this is your point of reference for aligning the
squares. Markers are respectively located in the center, below the squares.
→ You’ll be asked whether you wish to accept the alignment. Click on Yes.
 Create a new element and call it "Element_Pyramid".
 Define polygons within the planes that outline the white squares within the planes.
→ Disable the two Create series/thresholds buttons in the Create Polygons Sequentially
dialog box. Click on the Rectangle button. Position the rectangle at the upper-left corner
on the white square. Keeping the mouse button depressed, move the mouse to expand
the rectangle to fit the size of the white square precisely. Confirm the size of the rectangle
by rightclicking.
→ You’ll be asked whether you wish to create a linkage: Confirm the settings Skeleton,
Respect orientation, and Proportional progress in the Select Segmentation dialog box
with OK.
 Open the pyramid laterally.
→ This is done by doubleclicking on the "Pyramid3[0]" polygon symbol in the object directory.
Select a segment - eg, "Segment1". Click on the Open button in the 3-D button bar.
 Create a circular hole within the bottom surface of the pyramid.
→ This is done by selecting the bottom polygon (called "Pyramid1[0]"). Use the Polygon,
Create Hole... command.
→ Click on the Rectangle button in the dialog box. Draw up a rectangle within the image and
position this rectangular hole at the center of the white square.
 Tilt the pyramid and look at it from the top and from below.

Creating a composite model

 Set up a new group and call it "Group_Model".
→ This is done using the New Group... command.
 Insert the following two elements - "Element_Cuboid" and "Element_Pyramid" - into the
"Group_Model".
→ This is done by activating the "Group_Model" symbol and using the Create Group Entry...
command. Select the "Element_Cuboid" command in the 3D-Object list in the dialog box.
Confirm with OK.
→ Create the "Element_Pyramid" group entry in the same way.
 Cuboid and pyramid can be positionally displaced with respect to one another as you like.
→ To do so, select the "Element_Pyramid" group-entry symbol within the object directory.
The lateral surface of the pyramid remains filled. The cuboid is visible by its outlines only.
→ Disable the Lock button in the 3D button bar.
→ What happens now is that the buttons of the navigation wheel affect the pyramid only. This
allows you to, eg, displace, tilt or rotate the pyramid with respect to the cuboid.
→ Push the Lock button again inwards.
 Activate the group. All 3-D models will be displayed filled.

7
 Button bars
The 3-D window Frequently-used commands are linked to buttons. These buttons are
Overview organized into topically-related button bars. The standard position for the 3-
The object directory D and 3D Position button bars is along the upper border of the 3-D window.
All other button bars are context sensitive. One of these is usually shown
along the lower border of the 3-D window.
The Status bar
The 3-D window is a separate is where analySIS® shows you the result of the most recent 3-D object
window within analySIS®. The 3-D transformation - eg, "Tilt X". Moreover, you can have displayed here the
window, the navigation window, the 3D position of an arbitrary point on the surface of the 3-D object. This is done
menü and the analySIS® status bar by leftclicking on the point desired.
form the whole Graphical User Interface
for 3-D processing.
Opening the 3-D window
The 3-D window is opened when you
define a new workspace and a new
layout, or simply open a layout
(Workspace, New... or Open... in the
3-D menu). Only one 3-D window (ie,
layout) can be open at one time.
3-D window arrangement
The 3-D window acts like any other
analySIS® window: you can arrange the
3-D window within the Graphical User
Interface using the Window-menu
commands, maximize, or minimize it.
The 3-D window will appear in the list of
currently-opened documents at the
bottom of the Window menu. Click on
the entry here to have the 3-D window
appear as the foremost document.
• eine weitere kontext-sensitive
Symbolleiste (unten),
• das Navigationsrad,
• kontext-sensitive Menüs.
3-D-window structure
The 3-D window includes
• the object directory (to the left),
• the view area (to the right),
• (default setting) both the 3-D and 3D
Position button bars (along the top),
• one additional context-sensitive
button bar (along the bottom),
• the navigation wheel dialog box,
• context-sensitive menus.
View area
The 3-D view area is the large, colored
region taking up the right side of the 3-D
window. It is for constructing, displaying
and animating 3-D models.

8
The Object directory
takes up the left side of the 3-D window. All objects and sub-objects of the
Das 3-D window
layout are listed in a tree control. The object directory is NO directory on the Overview
hard drive. (The directory on the hard drive containing the files of the The object directory
reconstruction is denoted workspace.) To enlarge the object
directory, position the mouse
cursor right on the borderline
between the directory and the
3-D view area. The mouse cursor will
change shape. Keeping the left mouse
button depressed, move the mouse to
move the borderline in the direction
desired.
3-D objects of a 3-D reconstruction are
stacks, elements and groups.
Sub-objects:
• of a stack are: planes
• of an element are: polygons,
linkages, segments, holes
• of a group are: group entries, sub
groups
Select planes
To select planes or polygons,
you’ll need to make a ‘red selection’.
This simply refers to the fact that
symbols of planes or polygons that
have been selected turn red in color. In
contrast, the symbol of the active plane
remains yellow - and is highlighted in
blue.
• To make a single ‘red selection’ - ie,
to select one plane, keep the [Ctrl]
key depressed while you leftclick on
the plane desired.
• To select several planes, keep the
[Shift] key depressed while
leftclicking on the first and last of a
series of consecutive planes.
• The same keys are used to switch the
object directory entries back to yellow.
A number of commands - eg, alignment
commands - are only available when
several planes have been selected.

The symbols next to the various 3-D objects listed indicate what they are.
The current 3-D object is generally highlighted in blue or gray (Windows
default setting). Symbols of 3-D objects that have been selected are red.

9
 Preparing images The Navigation wheel
Arranging planes
Defining height distance
Tilting planes
Decompressing planes
Aligning planes
Scaling planes
Planes must be correctly scaled on both
x- and y-axes to ensure you obtain a 3-D
model that is true to scale, allowing you
to measure distance, surface and
volume in three-dimensional space. If
this is not the case, you should scale all
the planes of a stack uniformly. To do so
you have to select all the planes.
Scaling planes separately
A plane’s scaling is linked to that plane
and saved along with it. As needed,
you can scale separate planes indi-
vidually. This is done by selecting that/
those plane(s) involved.
Transferring calibration The navigation wheel is for rotating, displacing and zooming the image stack
If planes have not been correctly cali- within the view area. The navigation wheel can be turned ‘on’ or ‘off’ via the
brated, or have not been calibrated, you 3D Navigation command, Window menu.
can load a single planes into an The image stack can also be moved using the keyboard.
analySIS® image buffer, and calibrate it
using the Calibrate Image... command, Using the keyboard transformation (resulting motion)
Image menu. You can then have this [Shift] + [→] rightward motion
image’s calibration transferred to all
[Shift] + [←] leftward motion
planes selected of the stack.
[Shift] + [↑] upward motion
View scaling
[Shift] + [↓] downward motion
You can also use the Scale Planes...
command to view the current scaling of [Shift] + [PgUp] zoom out, ie, move further away
the plane selected. You do this by [Shift] + [PgDn] zoom in, ie, move closer
simply selecting the current plane. If [Shift] + [Home] reset to original setting
several planes have been selected, the [Ctrl] + [→] rotate rightward round the z axis
dialog box will show the scaling of the
[Ctrl] + [←] rotate leftward round the z axis
plane you selected last.
[Ctrl] + [↑] horizontal backward tilt
Unit selection
[Ctrl] + [↓] horizontal forward tilt
The unit selected applies to the entire
layout. This is done by using the Work-
space, Select Unit... command. The Warning A transformation may move a 3-D object outside of the
unit selected will appear in the Scale view area. In this case, you doubleclick on the hub of
Planes dialog box. The unit selected the navigation wheel or press [Shift] + [Home] to reset
cannot be altered in this dialog box. the 3-D object to its original position.

10
How do I define height distance between planes?
A MUST!
You have sorted the planes into the right order within the stack. A constant height distance is to be as-
signed to the images (ie, the planes).
 Select all planes (ie, ‘red-select’ them).
→ This is done by keeping the [Shift] key depressed while selecting (via leftclick) the first and
last planes. The plane icons will turn red.
→ Only planes that have been selected will be assigned a new height.
Available This command is only available if plane(s) have been selected.

 Turn ‘on’ the bottom grid and control lines (Hide Bottom Grid and Hide Control Lines
buttons, 3-D button bar).
‡ You have less than 16 planes: in this case you can have all planes of the stack displayed
continuously, so you can see which planes’ respective height distances change. This is done
by clicking on the Display Texture button while pressing [Shift].
 Select the Planes, Define Height distance... command (3D menu).
→ The dialog box of the same name will be opened. It indicates the unit of the layout.
 Tilt the image stack so you can view the planes from the side.
→ One way to tilt the image stack is via the tilt buttons on the navigation wheel.
 Enter the distance between planes into the Distance field.
→ If all the planes of a stack have been selected, the Base height field will only be relevant for
measurement purposes.
 Click on the Execute button.
→ You can see how the height of the planes is changed within the 3-D view area. The dialog
box will remain open, allowing you to continue entering other values and to then see how
different distances appear in comparison to the x/y width.
 Click OK to confirm the height distance and you’ll exit the dialog box.
→ The stack’s position will be reset in the 3-D view area.
 Disable the planes ([Shift] + Deselect command, Stack context menu).
‡ You wish to have a look at a plane’s height: select this plane ([Ctrl] + leftclick) and you can look
up its base height in the Define Height Distance dialog box.
‡ You wish to alter the height of a single plane, leaving the other planes untouched: just select
this one plane. Enter the desired base height into the Define Height Distance dialog box.
→ You can see how the plane is displaced relative to the bottom grid in the 3-D view area.
The heights of all other planes in the stack remain the same.
‡ You wish to alter the distance of two planes, leaving the other planes untouched: just select
the two planes you’re interested in. The dialog box will show the distance last entered, not the
current actual distance. Enter a new distance.
→ You can see how the upper plane is displaced relative to the lower plane in the 3-D view
area. The heights of all other planes in the stack remain the same.
‡ You wish to alter the distance of two planes. All other planes’ distances are to remain the same
- ie, all planes that are above the two planes have to be displaced. Just select the uppermost
plane (of the two planes you’re interested in) along with all other planes above those two
planes. Enter a new base height into the Define Height Distance dialog box so that the
distance of the upper to the lower plane is altered as desired.
→ You can see how all the upper planes are displaced relative to the lower plane in the 3-D view
area. The heights of all the planes that are below the selected planes remain the same.
‡ You have had the planes displayed continuously: have the texture of all the planes removed.
(Select all the planes, click on the Display Texture button while pressing [Shift].)

11
 Preparing images
Arranging planes
Defining height distance
Tilting planes
Decompressing planes
Aligning planes
Tilting planes
The ideal position for planes is parallel
and above the base area. Depending
on the technique you use for preparing
your sample or the image-acquisition
method of sample sections, planes may
be tilted relative to the base area (and (left): You first set the directional angle of the tilt axis along the z axis, and
possibly relative to each other as well). then you set the tilt angle of the planes along the tilt axis.
In this case, you have to correctly orient (right): In most cases, the intersecting planes are positioned parallel and
the planes spatially to be able to obtain above the x-y plane.
a realistic 3-D model of the sample.
Correcting image distortion(s)
When preparing your sample sections,
the sample material may be stretched
or compressed. The sample material
may be compressed, eg, while being
cut. These kinds of distortions alter the
actual structures and will be visible in
the 3-D model. Using the Decompress
Planes command, you can compen-
sate for homogeneous distortion. You
do this by using a reference image
whose actual structures - if possible -
are well known to you. Correct the (left): The planes are tilted at the same orientation relative to the x-y plane:
distortions of all planes selected using directional angle = 90°, tilt angle = 30°.
the reference image to compare with. (right): The planes are also tilted relative to each other: directional angle 90°,
Distortions of individual planes can also tilt angle from bottom to top: 350°, 355°, 0°, 355° and 350°.
be corrected using the Align manually
command.

(left): You first set the directional angle of the decompression line and then
set the decompression factor.
(right): Planes are stretched at a factor of 2 along the decompression line:
directional angle 60°, decompression factor 2.

12
How do I tilt planes?
You’ll only need to tilt planes relative to the base surface, and possibly relative to one another, if they are
oriented differently than the base surface.
 Select all the planes you wish to tilt relative to the base surface.
Available This command is only available if plane(s) have been selected.

 Turn ‘on’ the bottom grid and the control lines (3-D button bar).
 Tilt the stack to be able to view the planes from the side.
 Select the Planes, Tilt... command (3D menu).
 Enter the directional angle into the Direction field of the Tilt Planes dialog box.
→ The directional angle is the angle that the tilt axis is rotated within the x/y plane along the
z axis. This angle is determined beginning at the x axis, going clockwise: 0-360°. Planes
are tilted along the x axis at 0°; along the y axis at 90°.
 Enter the tilt angle into the Tilt field (0-360°).
→ The tilt angle is the angle at which the planes are rotated around the tilt axis. The tilt axis is
located within the x/y plane and runs through the origin. Planes are within the x/y plane at 0°
and are positioned perpendicular to the x/y plane at 90°. The planes selected are tilted simul-
taneously relative to the bottom grid within the 3-D view area when you alter the tilt angle.
 Clicking OK confirms the planes’ position and you exit the dialog box.
 Disable the planes ([Shift] + Deselect command, Stack context menu).
‡ You wish to align individual planes, changing their orientation: select the respective plane
desired only. And then define the directional and tilt angles desired.
‡ You wish to have a look at the orientation of a single plane: select the plane desired only. The
Tilt Planes dialog box will contain the angle of the plane selected.
How do I correct image distortion?
You only have to decompress if sample sections have been somehow compressed or stretched.
 Select all the planes that have the same compression problem (‘red-select’).
Available This command is only available if plane(s) have been selected.

 Activate one of the planes selected for use as a reference plane.

→ This reference image ought to include image structures whose shape is known, thus
enabling you to use this image to help you get the images into their actual shape.
 Turn ‘on’ the bottom grid and control lines (3-D button bar).
 Doubleclick on the hub of the navigation wheel so you get a bird’s-eye view of the planes. Adjust
the zoom for the stack until the reference plane fills out the space within the view area optimally.
 Select the Planes, Decompress... command.
→ The dialog box of the same name will be opened. A red line will appear within the reference
plane. The line indicates the direction in which the plane selected will be distorted.
 Enter the directional angle of the decompression (0-360°) into the Direction field.
→ The decompression line will be rotated within the plane of the reference image by the amount
of the decompression angle. The angle is determined beginning from the y axis, going
clockwise. Planes will be decompressed along the y axis at 0°, and along the x axis at 90°.
 You determine to what extent planes are to be decompressed in the Factor field.
→ Planes are compressed toward the decompression line when the value is less than 1, and
stretched when greater than 1). Continue to adjust the factor until image structures reassume
their original shape.
‡ You wish to correct distortion within individual planes: Select a reference plane and the plane
you wish to correct. Use the Align Manually... command to compare the image structures of
both planes directly and correct the plane desired.

13
 Preparing images
Arranging planes
Defining height distance
Tilting planes
Decompressing planes
Aligning planes
Defining Alignment
Alignment refers to the actual
‘lining up’ of image planes
relative to one another.
In order to be able to reconstruct a 3-D single-point alignment (left): using the respective 1st point, you can correct
model that looks realistic, the planes of a horizontal and vertical plane displacement: planes are displaced so that the
stack have to be arranged in such a way respective 1st points coincide positionally.
that the structures of the sample are dual-point alignment (right): using the 2nd point(s) you can also correct
positioned accurately in relation to one rotationally: planes are rotated such that (imagined) connecting lines
another - ie, as much like the sample as between the respective 1st points and 2nd points coincide positionally.
possible. Sample sections may, how-
ever, have been shifted positionally relat-
ive to one another, rotated , or have in
some way been distorted. Therefore,
you have to align the planes involved.
analySIS® provides semi-automatic
single-point alignment (One Point
Alignment) and dual-point alignment
(Two Point Alignment), as well as
manual alignment. In addition, you can
use stack animation to supervise and
adjust alignment.
Semi-automatic alignments
Use One Point Alignment for correcting stack: before (left), and after (right) single-point alignment - planes have
horizontal and vertical displacement. Use been horizontally and vertically displaced relative to one another during the
Two Point Alignment for correcting x/y course of the alignment until the contours of the head are correlated
displacement and plane rotation as well. correctly.
This is where you define separate points
for plane alignment.
Fixed points
are used as aids for correct plane align-
ment. You can use, e.g., object struc-
tures whose position(s) are known to
you for reference purposes. The ideal
aids are markers that have been inser-
ted into/onto the object before the
object has been cut or before anything
has been removed. Depending on the
kind of sample material you’re working
with, that could be, eg, holes that are
burned through the object using lasers
(along the z axis); or grooves that are
cut mechanically into the sides of the
sample block, or, fibers that are insert-
ed into the resin before it hardens.

14
How can I correct displacements and rotations semi-automatically?
You only have to align planes if the planes are horizontally or vertically displaced or rotated relative to each
other.
 Select all the planes (‘red-select’).
Available The One Point and Two Point Alignment commands are only available if two
or more planes have been selected.

→ The context-sensitive 3D-Stack button bar will appear.

 Select the Planes, One Point Alignment command (3D menu) to have only horizontal and
vertical displacements corrected, and Two Point Alignment to have rotations corrected as
well.
→ All planes will disappear from view. Only the bottommost image (of the planes selected)
will be displayed in the view area such that you’ve got a bird’s-eye view of the whole image.
→ The mouse cursor will appear within the view area and change shape, now looking like
crosshairs with a "1" attached to it.
 Define the 1st point to be used for positioning the planes atop one another.
→ A red circle will appear, indicating the position of this point.
→ Two Point Alignment: The mouse-cursor crosshairs shape will have a "2" attached to it.
 Two Point Alignment: Define the 2nd point you wish to orient the planes with.
→ A red circle will appear, indicating the position of this point.
→ The 1st red circle will be changed to a red point; the 2nd red circle into a green point.
→ The image next-up in height will be shown.
 Define the next point, or, define the next two points, as the case may be.
→ After defining the 1st point, the 2nd image will be displaced such that the point is located
above the 1st point of the 1st image.
→ After defining the 2nd point, the 2nd image will be rotated such that (imagined) connecting
lines between the 1st and 2nd points would be directly atop one another.
 Define the point, or two points for all images of the stack.
→ After you’re done with the last and topmost image you’ll receive the following message:
"Would you like to accept the modified alignment?".
 Confirm this alignment by clicking Yes if you’ve set the points correctly.
 Disable the planes ([Shift] + Deselect command, Stack context menu).
‡ You wish to reverse the alignment of individual planes: activate the plane desired. Select the
Planes, Remove alignment command.
→ You’ll receive a message: "Do you really want to remove the alignment of plane <name of
plane>?". Confirm by clicking Yes.
‡ You wish to reverse the alignment of several, or all planes: select the planes desired. Select
the Planes, Remove alignment command while pressing [Shift]. Confirm the message by
clicking Yes.

15
 Preparing images
Arranging planes
Defining height distance
Tilting planes
Decompressing planes
Aligning planes
Aligning selected planes
It may be a good idea, to select and
align planes separately: eg,
• if you wish to realign particular
planes, or
• if you wish to use not the previous,
rather a further-down plane as an
alignment aid.
You do this by selecting the plane(s)
you wish to align, along with the
reference plane(s).
Having the 3-D model shown
Sometimes you don’t notice that your
alignment is inadequate until after
you’ve created polygons and created
the 3-D model from these polygons.
Relevant criteria are, eg, if the lateral
surface of the 3-D model is the wrong
shape or isn’t smooth enough. To
improve an existing alignment, you can
have the 3-D model shown (for You can have the 3-D model displayed along with its corresponding stack.
reference purposes) while you realign.
Stack and Element display
If you’re not satisfied with the appear-
ance of a 3-D model because of plane
alignment problems, have the stack
along with one or more corresponding
elements displayed. Using the polygon
lines of the 3-D model within the image,
you’ll be able to position the planes as
best as is possible.
To have the 3-D model and the stack
displayed at the same time, drag the
element icon along with the 3-D model
(via drag&drop) onto the icon of the
relevant stack. The respective outlines
The respective outline of the lateral surface of the 3-D model will be drawn
of the 3-D model will now appear within
within the current plane (left) in the color of the current 3-D object (Scene
the corresponding planes, as you align
tab, Rendering Settings... command). The (differently-colored) outline of
manually.
the reference plane will also be shown in the transparency (right).

16
How do I realign planes separately?
This is only necessary if you’ve already created a 3-D model and wish to correct the alignment.
The planes had been aligned semi-automatically. You had created an element and polygons to construct
a 3-D model. The lateral surface of the 3-D model however, still has depressions, grooves, protrusions
and bulges which are not visible within the separate planes; ie, some planes remain incorrectly positioned
and thus have to be realigned.
 Select all the planes (‘red-select’).
 Disable the Hide Control Lines button (3-D button bar) to have the outlines of all planes
selected shown.
 Drag the element icon along with the 3-D model onto the icon of the relevant stack (via
drag&drop).
→ The 3-D model and the stack will be shown within the view area together.
→ The Disconnect Object button (in the 3D-Stack button bar) will be pushed in.
 The plane(s) selected at a height where the lateral surface of the 3-D model is faulty are to
remain selected. The plane(s) located directly below - the correctly-aligned one(s) - should
remain selected as well. You disable all other planes.
 Select the Planes, Align manually command (3D menu).
→ Everything will disappear from view, except that the bottommost image of the planes selected
will be shown in the parallel perspective such that you’ve got a bird’s eye view of the whole
image. The respective outline of the lateral surface of the 3-D model will appear on this plane.
→ The Align manually dialog box will be opened. The navigation-wheel buttons’ functions will
change and some of their symbols will change as well. You have now entered the alignment
mode.
 Reduce/zoom, or displace the plane if the plane is not fully visible within the view area
(Position Scene button).
 Decompress the planes if necessary (using navigation-wheel buttons).
 Set fixed points at significant image structurres (Fix-Points button).
 Click on the Next Plane button in the Align manually dialog box to have the next-higher plane
shown of those selected.
→ You’ll receive a message asking you whether you wish to align the other next-higher
planes of the stack along with the currently-active plane. Confirm by clicking Yes to have
all displacements and rotations (not decompressions, however) transferred to all the next-
higher planes as well.
→ The respective outline of the lateral surface of the 3-D model will appear on this plane.
 Position this plane. Decompress it if necessary.
→ This is done using the corresponding buttons of the navigation wheel. The current plane will
appear transparent so you can see the (selected) plane below it. The colored outline (of the
lateral surface of the 3-D model) on the (selected) plane below will appear through the current
plane. Use the two outlines as well as the fixed points for reference purposes. Any
displacement, rotation or decompression you carry out, is shown in the status bar.
 Click on the Next Plane button in the Align manually dialog box to have the next-higher plane
shown (of those selected).
→ You’ll receive a message asking you whether you wish to align the other next-higher
planes of the stack along with the currently-active plane. Confirm by clicking Yes. Semi-
automatic alignment remains valid.
 Align these and the next-higher planes (of those selected).
 After finishing with the last plane, confirm the alignment by clicking OK; and for the message
on Yes.
→ The lateral surface of the 3-D model will be recalculated and displayed.
 Disable the planes ([Shift] + Deselect command, Stack context menu).
 Correct the alignments for the entire lateral surface of the 3-D model.
 Disable the Disconnect Object button in the 3D-Stack button bar.

17
 3-D model construction
Creating polygons
Creating lateral surfaces
The following commands are to:
• Create Polygons
Sequentially, to define
respective polygons on all
planes selected of the associated
stack. This is how you extract an
image structure from/onto each
plane. If necessary, you can directly
redefine faulty polygons. After you’ve
defined polygons, you can combine
them to form a linkage. Polygons are
thus given a lateral surface within
three-dimensional space and thus
become a 3-D model.
• Create Polygons from
Plane, to define one or more
polygons on a plane. This is
how you can quickly create multiple
polygons per plane within one
element.
• Modify Object (Polygon context
menu), to redefine an existing
polygon. This is how you replace a
faulty polygon with a new polygon.

The image structure is displayed small-sized onscreen.

(left): large distance between points (40), detail lost in 3-D model.
(right): little distance between points (5), the polygon is quite round and one
only notices any squareness when one looks at it more closely.

The image structure is displayed large-sized onscreen.

(left): large distance between points (40), the polygon is quite round.
(right): little distance between points (5), the polygon is round. The 3-D
model includes much detail from the separate planes.

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How do I semi-automatically create polygons using multiple planes?
A MUST!
The quickest and easiest way to create polygons is by setting thresholds and using particle detection. To
be able to do this, you have to distinguish between the relevant image structures and the neighboring im-
age areas - using their gray-/color-value phases as distinguishing criteria.
 Select all planes (from which you wish to extract polygons) of the associated stack of the
element.
 Leftclick on the icon of the element intended to become the 3-D model.
→ The 3D-Element context-sensitive button bar will appear.
Warning The Create Polygons Sequentially... command is only available if two or more
planes have been selected.
 Select the Polygons, Create Sequentially... (3D menu).
→ The Create Polygons Sequentially dialog box will be opened.
→ The size of the 3D window will be maximized.
→ The bottommost of the planes selected will be shown in the view area giving you a bird’s
eye view of the image. The plane icon will be highlighted in gray within the object area.
→ The name of the bottommost plane selected will be suggested in the Name field. Use this
name.
Setting point distance and initiating polygon definition
 Enlarge the plane using the zoom buttons on the navigation wheel so the visibility of the image
structure you wish to define as a polygon is optimal.

 Enter a value of 5 pixels into the Point distance field of the Create Polygons Sequentially
dialog box.
→ A point distance of 5 pixels means that, onscreen, every fifth point of the outline of the area
detected is considered a node of the polygon: ie, you use point distance and display size
of the relevant image structure onscreen to determine how precisely a polygon is drawn.
→ If the image structure is clearly visible onscreen a point distance of 5 pixels will result in a
polygon that is sufficiently detailed and without any unrealistically sharp corners. You
won’t require a point distance that is lower than 5 unless the image structure in question is
very craggy and extremely jagged. The lower the point distance, the more memory
required for the polygon and all subsequent transformations take longer.
Warning The distance between nodes depends on the relative size of the image structure
onscreen and on point distance - NOT on the absolute size (of the image struc-
ture).

19
  Leave both the Stop Automatic Progress/Verify Particle Thresholds buttons pushed
inward.
→ Then you can have the polygon defined redrawn immediately if necessary, and set new
respective thresholds.
 Initiate definition of the polygon by clicking on the Particle button.
→ The dialog box will disappear
from view and the Set
Thresholds dialog box
containing the Manual tab will be
opened. This dialog box will
suggest the settings from your
most recent threshold setting.
The standard setting is one
phase.
→ When working with RGB true-
color images, an intensity extract
of the color image is generated.
The intensity image is an 8-bit
gray-value image. The Set
Thresholds dialog box is also
opened in this case.
→ A scale bar will be drawn (using the unit of the workspace).
Setting thresholds and image structure selection
 Define one or more phases depending on your needs. The phase(s) must frame the image
structure in its entirety, but need not necessarily fill it out. Check the thresholds on the plane.
 Click OK to confirm your phases and to exit the dialog box.
→ analySIS® will conduct a particle detection. The particles found will appear on the plane in
gray-blue cross-hatching.
→ Particle detection makes use of settings in the Define Detection dialog box (Analysis menu):
Particle filter: Minimum: 0 pixels; Fill holes selected; Use ranges not selected; Connectivity:
include diagonals (8); Border particles: Truncate; Search area: Frame.
→ The mouse cursor will appear within the view area.

 Leftclick the particle desired.

→ The cross-hatching will disappear from view. A colored outline will be drawn around the
edges of the particles. This is what the new polygon consists of.
→ The Create Polygons Sequentially dialog box will reappear.

20
Correcting parameters
‡ Now check and make sure that the polygon represents the image structure with sufficient
precision. Structures that have a width of one monitor pixel will be, due to the point distance
of 5 pixels, be dilated by about 1, 2, or 3 pixels: needle-like and beam-like shapes which are
displayed small-sized onscreen, will become somewhat wider and rounded. The polygon
should, however, include any larger protrusions and pointy aspects of the image structure
(with respect to onscreen display). Moreover, the polygon should not have unrealistically-
sharp corners. If you are having problems (as described above), then do the following:
→ Solution: Lessen the point distance and/or enlarge the view showing the plane. Then re-
conduct detection of the polygon.
‡ You’ve received an error message that the polygon overlaps itself and thus cannot be drawn.
The reason being that the particle may only be one monitor pixel wide at some spots, meaning
that the resulting polygon will certainly not be a "simple" one.
→ Solution: Lessen the point distance and/or enlarge the view showing the plane. Then re-
conduct detection of the polygon. If necessary, you can also adjust thresholds as well. This
makes narrow beam-like and bridge-like shapes of the particle somewhat wider.
‡ The image structure desired has to exactly comprise a single unified particle: the image
structure may not be comprised of more than one particle, nor may the particle be joined to
any neighboring image regions. If you are having problems (as described above), then do the
following:
→ Solution: Detect the polygon once again. Define new thresholds.
→ If this doesn’t help: use the magic wand to define the polygon.
→ If this doesn’t help: use the interpolating polygon.
Creating polygons on subsequent planes
 Click on the Stop Automatic Progress button to disable it in the Create Polygons
Sequentially dialog box.
‡ The planes of the stack have similar gray-/color-value distributions meaning you can detect the
image structure desired using the thresholds set the first time, for detection on the subsequent
planes: in this case, click on the Verify Particle Thresholds button to disable it.
 To continue defining the polygon, click on the Particle button.
→ The next-higher plane (of those selected) will be shown in the view area.
‡ The Verify Particle Thresholds button is pushed in: in this case, the Set Thresholds
dialog box will be opened. (Re-)set or use the thresholds shown and confirm via OK.
→ The particle detection will be conducted. Moreover, the polygon of the plane below will
appear in magenta. Leftclick the particle on the image structure.
 The next-higher plane (of those selected) will automatically be loaded respectively after you’ve
selected the particle on the image structure of a plane. The Create Polygons Sequentially
dialog box will not be opened. The Set Thresholds dialog box will appear for each respective
plane if you haven’t disabled the Verify Particle Thresholds button. In this case, you set
thresholds for each respective plane separately. Leftclick the respective particle on the image
structure until a polygon has been defined on all the planes selected.
Deleting and redrawing polygons
‡ You have defined a polygon incorrectly and wish to redraw it: to interrupt polygon definition,
simply middleclick (middle mouse button) or press [Esc]. Alternatively, you can click on the
Cancel button in the Set Thresholds dialog box (if it’s been opened).
→ The Create Polygons Sequentially dialog box will be opened. The last plane will be
shown.
‡ You wish to redefine the polygon on the next plane: push the Verify Particle Thresholds button
inwards. Detect the polygon using the Particle button once more, or use another means of
creating a polygon if necessary.

21
 ‡ You wish to delete the polygon on the current plane and then redefine it: push the Stop
Automatic Progress button inwards. Push the Verify Particle Thresholds button inwards.
Detect the polygon using the Particle button once more, or use another means of creating a
polygon if necessary.
→ After you’ve defined the polygon correctly, disable the Automatic Progress button once
again, and continue with the subsequent planes.
‡ You wish to delete polygons that are on planes located further down in the stack, to then
redraw them: use the Back to last polygon button to flip back through the planes. This
involves you first deleting the polygon on the respectively-current plane. Return to the plane
where you wish to redraw the polygon. Push the Automatic Progress button inwards.
Redraw the polygon. Disable the button once again and redefine the polygons on the
subsequent planes as well.
Creating linkages
 After you’ve defined the polygon on the uppermost (selected) plane the Create Polygons
Sequentially dialog box will appear. Confirm the polygons defined via OK.
→ You’ll receive a message inquiring whether or not you’d like to create a linkage using the
polygons defined. Confirm via Yes to create a 3-D model using the polygons.
→ The Select Segmentation dialog box will be opened.
 Enter the following settings for your first model into the Select Segmentation dialog box:
Segmentation: Skeleton, Respect orientation and Triangulation: Proportional progress.
Confirm via OK.
→ A linkage will be created using the polygons defined:
the polygons will be linked with one another in three-
dimensional space via a lateral surface, resulting in a
3-D model. The 3-D model will be shown in the view
area.
→ Double-decker polygon icons will appear within the
object directory. The number of the linkage will
appear in square brackets following the name of the
polygon. The first linkage of an element is numbered
"[0]".
→ Segments are saved in the element file. You can
have the segment icons shown in the object directory
simply by doubleclicking on the icon of a polygon.
Deleting individual polygons later on and redrawing them
‡ You notice that certain polygons do not adequately represent the image structure: in this case,
you can redefine the polygons one at the time.
→ Activate the corresponding polygon. To be able to locate the faulty polygon, have the
control lines appear. Keeping the [Ctrl] key depressed, leftclick on the polygon right in the
view area. The polygon icon within the object directory will turn red. Click on the polygon
icon. Then rightclick.
‡ Using the Show Plane command of the Polygon context menu, you can have the plane shown
that the (faulty) polygon is located on. This is how you can have a look at the shape of the
extracted image structure.
→ Select the Modify Object... command in the Polygon context menu and redefine the
polygon. Set, eg, different thresholds, or redraw the polygon freehand. The previous
polygon will be deleted. The new polygon will be automatically integrated into the linkage
and the lateral surface will be recalculated.

22
How do I use the magic wand?
You’ve tried to define a polygon via particle detection and were not able to detect the image structure de-
sired. You’ve interrupted definition of the polygon, set the plane in question, and turned off the automatic
progress option.
 Set the following options for the magic wand in the
Create Polygons Sequentially dialog box:
→ Tolerance: 50
→ Outlines
‡ when working with 24-bit color-value images: Color
space: Intensity
 Click on the Magic wand action button.
→ The mouse cursor will immediately appear within the image. Leftclick on a typical gray- or
color value on the image structure to be used as the point of origin.
→ The point of origin will be blue.
→ All pixels within the region of the point of origin, whose pixel values are within the tolerance of
the point of origin’s pixel value, are considered part of the particle. The outline of the particle
is red.
 Raise or lower the tolerance so that the particle fits the image structure.
→ To raise tolerance, keep the left mouse button depressed while moving the mouse
rightwards; to lower tolerance, the mouse is moved leftwards. The further you move the
mouse, the greater the change to tolerance.
→ The new outline will be shown right within the image.
‡ You’re not able to frame the image structure in its entirety: in this case, select another point of
origin with a different pixel value.
→ It’s a good idea to try out various points of origin: try out points that have lighter as well as
darker pixel values. Then try to adjust tolerance to correspond to the image structure.
‡ for color images: you’re still not able to frame the image structure in its entirety: in this case,
interrupt polygon creation by middleclicking or by pressing [Esc].
→ Select the next color space; eg, Hue. Now try again to define the polygon using the magic
wand. Try out points of origin with various color values.
‡ If you’re still having trouble, try the other two color spaces (HSI and RGB).
 If the outline frames the image structure correctly, confirm the polygon by rightclicking.

23
 3-D model construction How do I create a linkage?
Creating polygons There are various ways of creating a linkage:
Creating lateral surfaces  Create Polygons Sequentially: you create 2 or more
polygons using the Polygons, Create Sequentially...
Defining a linkage
command. After you’ve defined a polygon on the last of the
A linkage involves assembling
planes, you’ll receive a message asking you whether you would like
the separate polygons to form
to create a linkage using the polygons you’ve just defined. Respond
one single, unified 3-D model
in the affirmative by clicking Yes and confirm the settings in the
using a lateral surface. The polygons
Select Segmentation dialog box by clicking OK.
are linked via triangulation. Because
the polygons do not touch, nor  Create Linkage: select the polygons you wish to have linked
intersect, a 3-D model results - which and select the Linkage, Create command (3D menu).
has a continuous lateral surface and  Connecting linkage sets: you can join multiple linkage sets
defined interior and exterior surfaces. to form a linkage. This is necessary, eg, if you hadn’t created
An element may include one or more all the polygons successively, or you’ve linked some of the
linkage sets (you distinguish between polygons manually. Select a polygon from each linkage and, while
them by the number of the linkages). keeping [Shift] depressed, select the Linkage, Create command (3D
A double-decker polygon menu).
icon is to be found next to all
component polygons of a linkage within
the object directory. Moreover, the
number of the linkage appears next to
the polygon icon in square brackets.
Segmentation/Triangulation
2 polygons, one atop the other, may be
linked at respectively different points.
The lateral surfaces involved may be
very different, depending on which
points you have linked. You determine
these points via the segmentation
process and the triangulation method.

The illustrations show a reconstrution of the brain: before (left), and after
(right) you had assembled the polygons to form a linkage.

24
 What properties does a linkage have?
How many A linkage is similar to a thread or piece of string that traces an image structure
polygons per through all the planes - and - assembles the polygons, ie, the outlines of the image
plane? structure, to form a linkage. A linkage requires at least 2 polygons. However, each
plane can only supply a maximum of one polygon for any given linkage. If you have
several polygons from one plane in one element, you can only link these with other
polygons that are from respectively-different linkage sets. Ramifications are, eg, not
allowed for linkages.
Which polygons The lateral surfaces link the polygons, starting with the polygon at the top (uppermost
are linked? z position) on through to the lowest polygon (lowest z position). The z position of a
polygon is the z position of its plane within the associated stack.
Note The z position of the polygons and the corresponding planes do not necessarily
have to correspond to the order of the planes in the stack (as shown in the object
directory). Z position and order may differ, eg, if you have re-sorted the planes
after having defined the height distance (eg, in the By name mode). To sort the
stack according to z values, you have to sort the stack using the Planes, Sort...
command (3D menu) in the By Z-Value mode.
Where is lateral- Each polygon contains all the following information: on the lateral surface which is
surface between it (the polygon) and the next-lower polygon; on the segmentation points; and
information on the triangulation mode of the lateral surface. The last polygon at the bottom of the
stored? thread does not have any of its own lateral surfaces (it may, however, be filled in).
How are the You determine how polygons are linked via the segmentation process and via the tri-
polygons linked? angulation method. The Skeleton segmentation process and the Minimum Dis-
tance triangulation method are the presets. Leftclick on the element icon within the
object directory and select the Segmentation, Select... command (3D menu) to set
other modes. You can have the lateral surface of a linkage recalculated using these
new settings.
Which polygons The bottommost and uppermost polygons within a linkage are the ones that are
are shown filled shown filled in. The two exterior polygons receive an orientation involving their being
in? filled in with the same color as the lateral surfaces (standard setting: red exterior,
green interior). This means, that when you create a linkage, the resulting 3-D model
- no matter where you view it from - from above, below, or from any side - is an en-
closed model. Any and all polygons in between are not filled in because they are nor-
mally hidden behind the lateral surfaces.
Note The colors of the exterior and interior surfaces can be changed using the Select
Colors..., Element context menu.
You can, eg, use the Open command (Polygon context menu) to open up or
close a polygon.

25