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Shift + click
Set a filament vertex
Shift + click plane & drag Draw a filament
Ctrl + click plane
Change the plane orientation (from XY to YZ to XZ)
Mouse wheel
Change the filament diameter (to visualize change to Style Cone - Tab Settings)
PageUp
Increase the filament diameter (to visualize change to Style Cone - Tab Settings)
PageDown
Decrease the filament diameter (to visualize change to Style Cone - Tab Settings)
Num plus
Increase the extended section (of the drawing plane)
Num minus
Decrease the extended section (of the drawing plane)
X
Set the plane orientation to YZ
Y
Set the plane orientation to XZ
Z
Set the plane orientation to XY
See also:
Addendum - Mouse
&
Keyboard
Mac
13.6
Frame
The Frame serves to outline the object in the viewing area. In the Surpass Tree check the check-box Frame
to display the frame in the viewing area. Un-check the box to make the frame invisible.
How
to
Add
a
new
Frame?
Select menu Surpass - Frame.
The Surpass Tree list is automatically updated and in the Frame - Properties the Settings parameter are
displayed.
13.6.1
Tab Settings
Highlight Frame in the Surpass Tree and click on the tab Settings. The Frame Settings display in the
properties area.
Box
and
Time
Settings
Box
Check the parameter to display a box around the Frame.
Line Width
Adjust the box line width with the respective slider.
Shading
Check this parameter to display a shading. Use the slider to adjust the shade contrast.
Shadow
The entire Surpass scene can produce shadows on the three planes of the Frame object. Check this box to
display the shadows. Use the Shading slider (see above) to adjust the contrast. The rendering is done in
real-time, and it requires a good performance of the graphics board (depending on the complexity of the
scene).
Time Colorbar
Only available if you work with a time data set. Check this box and the Time Colorbar displays in the upper
left corner of the viewing area.
Grid
and
Tickmarks
Settings
Grid
Check the box Grid to display a grid. The grid serves as a scale bar in 3D perspective views. Use the slider
to adjust the grid width.
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Imaris Reference Manual
Tickmarks
Check the box Tickmarks to display tickmarks on the edges of the frame.
Fix to Data Set
Check Fix to Data Set to fix the x-, y-, and z-axes to the same side when navigating the object.
Spacing
Specify the grid and tickmark spacing.
Labels
Settings
Axis Labels
Check the box Axis Labels to display the x, y, and z axes to clearly show the orientation of the object. If this
box is checked the parameter Label Color and Label Font is available (see below).
Label Color
Only available if the parameter Axis Labels (see above) is checked. Click on the icon to open the Color Editor
window to change the color of the label on the coordinate axes.
Label Font
Only available if the parameter Axis Labels (see above) is checked. Click on the icon to open the Font Editor
window to change the font to label the coordinate axes.
13.6.2
Tab Color
To change the color use the color wheel or type in the color combination.
13.7
Group
Groups are folders in the Surpass Tree that contain other Surpass objects. They are visible in the objects
area and allow you to create a treelike hierarchy of Surpass objects. When the first Surpass object is
created, it is automatically placed in a Group called Surpass Scene. Additional Groups can be created in
order to sort objects of the scene.
How
to
Add
a
new
Group?
Select menu Surpass - Group.
The Surpass Tree list is automatically updated and in the Group - Properties the Settings parameter are
displayed.
How
to
Add
Items
in
a
new
Group?
Click on an Item in the Surpass Tree list and drag it onto the Group object. Once released, the Item is
added to the Group.
Like all other objects, Groups have a visibility check-box. This box affects the visibility of all objects in the
Group.
See also:
Surpass View - Overview - Surpass
Tree
Surpass View - Overview - Scene
File
Concept
13.7.1
Tab Settings
Number of Objects
Displays the number of objects in the Group.
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Button
Show All
If you click this button the check-box(es) of the Item(s) in the Group are checked.
Button
Hide All
If you click this button the check-box(es) of the Item(s) in the Group are un-checked.
13.7.2
Tab Color
The color change applies to all Items in the Group.
13.7.3
Tab Sort
The tab Sort is available when a Group contains at least one Surpass Tree Item.
Highlight the Group and select the tab Sort. Adjust the parameters to sort the objects within the Group by
statistical values.
Sort
Objects
by
(Various sorting criteria)
Select the desired sorting criteria.
Ascending
In the Surpass Tree the objects are arranged in ascending order.
Show All
In the Surpass Tree the objects are checked and displayed in the viewing area.
Button
Select Hidden
All objects in the Surpass Tree that are un-checked (hidden) are highlighted at once. Use this function to
move the objects in a different group or delete them at once.
Show
Objects
between
two
Values
Enable
Check this box to enable the function and enter the two values.
Histogram
The numerical range of the statistics value (e.g. Track length), and the number of objects (e.g. Tracks)
depending on the statistics value is displayed. By clicking into the histogram you move the colored line and a
reduced/enlarged set of objects is visualized. The visualized objects are checked in the Surpass Tree.
13.8
Light Source
A Light Source serves to illuminate objects in the viewing area.
How
to
Add
a
new
Light
Source?
Select menu Surpass - Light Source.
The Surpass Tree list is automatically updated and in the Light Source - Properties the Settings parameter
are displayed. Multiple light sources can be added in the Surpass Tree.
Move
Light
Source
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Imaris Reference Manual
To move the Light Source in the viewing area, choose the pointer mode Select and drag the cone or line.
Light
Intensity
Click on the cylinder above the cone and move it closer or further away from the object to change the light
intensity.
See also:
Surpass View - Overview - Surpass
Tree
Surpass View - Overview - Camera Toolbar - Pointer
(Mode Select)
13.8.1
Tab Settings
Fix to Data Set
Check the box to fix the x-, y-, and z-axes to the same side when navigating the object. When the box is
un-checked, the light source is fixed to a particular position in space and remains in place when the object
moves or rotates.
13.8.2
Tab Color
To change the color of the light source use the color wheel or type in the color combination.
13.8.3
Mouse & Keyboard PC
Light
Source
Mouse
&
Keyboard
Functions
Left-click cone (or line) & drag
Change direction
Left-click cylinder & drag
Change intensity
See also:
Addendum - Mouse
&
Keyboard
PC
13.8.4
Mouse & Keyboard Mac
Light
Source
Mouse
&
Keyboard
Functions
Click cone (or line) & drag
Change direction
Click cylinder & drag
Change intensity
See also:
Addendum - Mouse
&
Keyboard
Mac
13.9
Measurement Point
How
to
Add
a
new
Measurement
Point?
Select menu Surpass - Measurement Point.
The Surpass Tree list is automatically updated and in the Measurement Point - Properties the Edit
parameters are displayed.
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© Bitplane 2008
13.9.1
Tab Settings
Point
Shape
Tetrahedron
Cube
Sphere
Here you can choose from three different shapes for the Measurement Points (tetrahedron, cube, or sphere).
Filled
Check the box and the point shape is solid.
Point
Diameter
Here you can define the Measurement Point diameter.
Point
Labels
Name
Check the check-box to display the name of a Measurement Point in the viewing area.
Intensity
Check the check-box to display the intensity of a Measurement Point in the viewing area. The intensity of the
channel is displayed in brackets.
Line
Mode
Pairs (AB, CD, ...)
Any two consecutive points are connected by a line.
Polygon (ABCD ...)
All points in the Group are connected consecutively (P1-P2-P3-P4, etc.).
Line
Width
Here you define the line width.
Line
Labels
Distance
The measured distance between two points is displayed next to the line connecting the two Measurement
Points. Check the check-box to display the distances in the viewing area.
Velocity
Only accessible if you have a time data set. Check the box to display the speediness between two
Measurement Points.
Tip:
If
you
do
not
have
the
module
ImarisTrack
you
can
easily
use
the
velocity
function
to
track
single
objects
over
several
time
points
and
measure
the
velocity.
Button
Color
Button
Font
Label Color and Font
To change the color or font of the label (display of the line length) click on the respective icon.
Tip:
You
can
find
the
parameters
to
change
the
color
of
the
Measurement
Points
and
connecting
lines
on
the
tab
Colors.
Visible for all Time Points
Only accessible if you have a time data set. Check the box to display the inserted Measurement Points, lines,
and annotations at all time points.
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Imaris Reference Manual
See also:
Surpass View - Measurement Point - Tab
Color
13.9.2
Tab Edit
Autodepth
Position
In the mouse pointer mode Select:
Shift-click with the left mouse button to add a new point. Left-click to select an existing point. Shift-
left-click to reposition a selected point.
Intersect
with
The first two parameters are relevant if you want to insert Measurement Points in a volume rendered data
set. For the rest the last parameter is crucial.
first visible Channel
In the Display Adjustments you decide, whether a channel is visible or not in the viewing area. Select this
parameter and only the first visible channel is relevant for the placement of the Measurement Points.
all visible Channels
In the Display Adjustments you decide, whether a channel is visible or not in the viewing area. Select this
parameter and all visible channels are relevant for the placement of the Measurement Points.
solid Objects
Check this box and the Measurement Points are placed on the surface of an object. Un-check the box and
you can also place Measurement Points in an object.
Button
Delete All Points
Click on this button to delete all Measurement Points. Alternatively click on the Delete-key on the keyboard.
Selected
Point
Click to select an existing point. If no point is selected the following parameters are grayed. Re-click on a
selected point to un-select the point.
Button
Delete
Click on this button to delete the selected Measurement Point.
Name
Text field to edit the Measurement Point name.
Position
X
Y
Z
T
Data field of the x-, y-, z- and t-coordinates.
See also:
Menu Edit - Show
Display
Adjustment
Surpass View - Overview - Camera
Toolbar
(Pointer Select)
13.9.3
Tab Intensity
Imaris reads out the intensity profile of each voxel against the distance. Here you select the channels that
should be displayed in the histogram and you choose the desired connecting lines between the Measurement
Points.
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© Bitplane 2008
Histogram
The histogram displays the intensity profile along the lines. The labeled lines represent the Measurement
Points. The x-axis represents the length of the profile. On the left hand side of the histogram you find the
display of the channel(s) intensity range. The channel selection is located below the histogram. Here you can
switch channels in the intensity profile on or off. Below the channel selection you find the profile selection. In
the drop-down list select the desired line and the histogram updates accordingly.
Button
Snapshot
Click on this button to do a Snapshot of the histogram. The window Save Snapshot as... opens.
See also:
Menu File - Save as... Snapshot
13.9.4
Tab Statistics
Measurement Point statistics are automatically computed. For the statistical variable values please refer to
the chapter Menu Edit - Preferences... - Statistics - Measurement
Points
.
Tab
Overall
Display of the general statistical values.
Tab
Detailed
Drop Down List
Select in the drop down list the statistical variable.
List
Display of the corresponding detailed statistical variable values. The order is: Value, Unit and ID.
Interactive two-way Selection
Select in 3D to get the corresponding row in the statistics table highlighted.
Select in the table to get the corresponding object in the 3D view highlighted.
Buttons Overview
PC:
Mac:
Select Spot
Left-click
Click
Select multiple Spots
Ctrl + left-click
Command + click
Tab
Selection
Display of the selected statistical values.
Buttons
at
the
bottom
of
the
Statistics
tab
Button
Settings - Configure List of visible statistics values.
Click on the button
Settings
and you switch to the window Preferences - Statistics - Measurement Points
.
Button
Search
- Search by object ID.
Type in the object ID in the data field. Click on the button Search.
Highlight the object in viewing area
Highlight the object on the tab Detailed
Display of the values on the tab Selection
Button
Measurement
Points
- Duplicate Selection to new Measurement Points.
Click on this button and all selected objects are copied to a new group. The new group displays in the
Surpass Tree.
Documents you may be interested
Documents you may be interested
