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1The Stage Manager

Stage management using the Stage Manager

Th e S t a g e M a n a g e r What is the Stage Manager for? ....................................2


Stage Manager and Automater ......................................2
Preconditions for using the Stage Manager ...................2
STAGE MANAGER... ................................................................3
The Overview Image ............................................................5
The Stage Manager Dialog Box ...........................................6
Defining Stage Paths .........................................................14
Defining Rectangular Stage Paths ...............................14
Defining Circular Stage Paths ......................................15
Defining Grid Stage Paths ...........................................16
Defining Arbitrary Stage Paths .....................................17
ACQUIRE OVERVIEW IMAGE... ............................................19
PREFERENCES... ..................................................................21
EStage0402
Stage management using the Stage Manager

Stage management using the Stage Manager


What is the Stage Manager for?
Using the Stage Manager you can ...
1) acquire overview images of the specimen. On these overview
images you can define a set of stage positions which can be moved to
for later analysis. For the actual image acquisition you can later use a
higher microscope magnification than the one used for the overview
image acquisition.
2) create an overview image by combining single images with high
resolution. The resolution of the overview image can be adjusted. In
this way larger objects, too, may be represented in an image in higher
resolution.
3) define individual stage positions for the acquisition of a series of
images.

Stage Manager and Automater


A process automater is integrated into analySIS. The core of the automater
is the Define Processing dialog box, in which you define the whole
automatic process. You open this dialog box with the Stage > Define
Processing... command. With the automater you move to previously defined
and saved stage positions one by one, acquire an image at each position
and carry out previously defined processing steps.

Preconditions for using the Stage Manager


Warning So that your microscope stage can be correctly controlled by the image
analysis software, please follow the instructions in this chapter carefully.

Sequence when To avoid errors, please use the following sequence when switching on the
switching on equipment:
equipment 1) Firstly, switch on the computer.

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2) The stage controller must be switched on before the software is
started. Otherwise the stage driver must be reloaded in Special >
Preferences > Stage .
3) Start your image analysis software last.
? Remember that the stage must be reinitialised following each start.
Calibrated input The input channel must be correctly calibrated. If the input channel is not
channel correctly calibrated, the wrong positions will be moved to.
Arrangement of The camera must be positioned parallel to the stage movement direction.
camera and stage Otherwise the individual images of the overview image will be turned against
each other. Small rotation angles of less than 3° can be compensated by the
software. To do so, use the Stage > Preferences... command.
Stage Manager...

How to... adjust the camera parallel to the stage movement direction.
If you are using a digital camera with the GrabBit, you can use the live
overlay to adjust the camera and the stage:
1) Mount the camera onto the microscope as parallel as possible to the
stage movement direction.
2) Switch on the live overlay for the active input channel: to do so, mark
the Image > Configure Input... > Display > Live overlay check box.
3) Position a specimen which shows vertical and horizontal lines or
structures under the microscope. The edges of the microscope slide
glass serve this purpose.
4) Switch into live image.
5) Paste a rectangle into the image. To do so, click on the Overlay Button
Bar button in the standard button bar and subsequently on the
Rectangle button.
6) Move the object along the horizontal object line, using the joystick. The
object must move exactly parallel to the displayed frame.
7) Correct the camera position by loosening the camera screws and
turning the camera slightly.
8) Repeat the last two steps until the camera and the stage are correctly
adjusted.

Stage Manager...
Use the Stage Manager...command to define and save a stage path for the object.

Stage Manager and The Stage Manager is a non-modal dialog box, i.e., you can leave the dialog
other functions box open and still have access to a range of important analySIS functions.
Thus you can, for example, change the magnification using the Image > Set
Magnification... command, without having to close the Stage Manager.
However, you should not carry out any image processing operations when
the Stage Manager is open, since the live mode has to be closed to do this
and the allocation of the image buffer to both viewports will generally be
altered. Thus you lose, amongst other things, the possibility of navigating on

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the overview image. The system expects the live image in the upper
viewport and the overview image in the lower viewport following Stage
Manager access.
The Special > Preferences... command cannot be accessed when the Stage
Manager is opened either.
Before you use this Use the Image > Set Magnification...command to provide the system with
command the current microscope magnification. This magnification will be adopted by
the Stage Manager.
What will happen... 1) when the live mode is activated
when the command is activated, the system switches into live mode
automatically.
2) when the viewport sequence is changed
The viewport sequence is automatically changed so that you can see
the live image and the current overview image simultaneously. After
the Stage Manager is closed the original viewport sequence is
restored.
The image buffer used for the live image is always the first image
buffer. Remember that the image which is located in this buffer will
Stage Manager...

NOT be overwritten, even if the definition of the stage paths is covered


by the live image.
Single screen system If you are working with a single screen system, the image document is
split: in the upper viewport you see the live image, while the current
overview image is displayed in the lower viewport.
Note It is recommended that the size of the image document be adjusted
before the Stage Manager is activated: the image document should
allow space for the Stage Manager dialog box and be large enough to
display two overlaid images optimally. The following figure shows an
example for a suitable user interface.
If you often work with the Stage Manager, it is worth saving a user
interface as a working area for working with the stage. To do so, use
the File > Workspace > Save As...command.
Dual screen system If you are working with a dual screen system, you have the possibility
of using the dual monitor for the live image and thus to display both the
overview image and the live image in an optimum size: to do so, select
the Stage > Preferences... command. Select the Dual option in the
Stage Preferences dialog box . If you now activate the Stage Manager,
the system switches the viewports on both screens to single image
display. The live image is displayed on the dual monitor, the overview
image is displayed on the windows monitor.

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The Overview Image

Following activation of the


Stage Manager the system
switches into live mode. The
current overview image is
displayed together with the
live image.

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The Overview Image
Following activation of the Stage Manager the system shows the last
acquired overview image of the object. Remember that in the overview
image only the object areas which have already been scanned can be
displayed. All object areas which have not yet been scanned are displayed
in black.
Number of possible The overview image shows you automatically the number of image
acquisitions acquisitions which are required to cover the defined area. The system uses
the magnification shown in the Stage Manager dialog box and the current
calibration data to calculate the number of images required. If the area
covered is altered, the number of positions will be adjusted automatically in
the overview image.
The Stage Manager Dialog Box

Distance between single The system positions the single images either edge to edge. You define the
images distance between images in the Stage Preferences dialog box in the Default
frame distance group.
A change in the distance will not automatically be taken into account. To do
this, click on the Adjust Frame Distance button.
Text in overview image The following additional information is displayed in the overview image:
Current stage The red X cross marks the current stage position.
position The system makes a standard update of the stage position every second.
You can also change this updating interval. To do so, use the Stage
Preferences... command and enter the required time in the Update rate of
stage position field.
The stage position can naturally only then be displayed when it is within the
object area which is covered by the current overview image. If the stage
position is outside the overview image, use one of the buttons in the Move
stage group to move the stage back to the covered area.
Image frames All individual images which belong to the current stage path are represented
by frames. You can also make the frames of the individual images
disappear: unmark the Show frames check box in the Stage Preferences
dialog box. You can also change the color of the frames in the Stage
Preferences dialog box.

Current stage path Small +-crosses mark the image center points of all individual images which
belong to the current stage path. You can change the color of the crosses in
the Stage Preferences dialog box.
Current stage You can move to the individual stage positions of the stage path using the
position on stage Stage Manager. To do so, click on one of the buttons of the Move stage
path group. The position moved to in this way is marked with a filled red square
in the overview image.

The Stage Manager Dialog Box


With the exception of the Define shape group, all tabs in the Stage Manager
have the same structure. All elements which you will find on all four tabs are
described below.

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The individual dialog box
tabs differ only through the
Define shape group. The
functions of this group are
described separately for
each tab.

Move stage Use the Move stage group buttons to move to individual positions of the
current stage path. You can also enter the number of the required position
directly or select on the overview image. The position moved to is displayed
in the overview image by means of a filled red square. The group is only
The Stage Manager Dialog Box

available when a stage position has been defined.


The numbering of the stage position depends on the acquisition procedure.
Click on the Details>>button to select the required acquisition procedure
from the Position route list..

First Position
Previous Position
Next Positon
Last Position
Select Position

Select Position Click on the Select Position button to move directly to any required position
of the current stage path. After you click on the button, the mouse pointer
jumps to the overview image. Click on the required position on the overview
image. You can move to several positions in series. Click the right hand
mouse button to return to the Stage Manager dialog box.
Scan Use the Scan group to acquire a new overview image. The overview image
contains the current stage path.
Scan Positions Click on the Scan Positions button to move to all the positions of the
previously defined stage path in series. The sequence depends on the
acquisition procedure which is selected. The acquired images are displayed
in the lower viewport in their position in the overview image. To save working
storage space, analySIS reduces the resolution of the overview image
automatically. The image size of the overview image is set at 1000x1000
pixels.
Scan Area Click on the Scan Area button to scan the whole object area which is
covered by the current overview image. The overview image can be far
larger than the object area which is covered by the current stage path.
The area is always moved across vertically, meandering, independent of
which acquisition path has been currently selected.

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The Scan Positions and Area buttons for example always supply differing
results if the images are not acquired edge to edge.
In cases of higher
magnification the individual
images of the stage path
move apart. Left: overview
image after clicking on the
Scan Positions button
Right: overview image after
clicking on the Scan Area
button.

Adjust Frame Distance Click on the Adjust Frame Distance button when you have changed the
magnification or the distance between the individual images. The overview
image will then be adjusted to the changed settings.
The Stage Manager Dialog Box

Changing the distances If you have changed the distances between the individual images in the
between the individual Stage Preferences dialog box, click on the Adjust Frame Distance button to
images adopt the settings for the current stage path.
Changing magnification 1) Use the Stage > Stage Manager... command and define a stage path:
Select for example the Grid tab. Click on the Set Center button and
enter a 2 into the Rows and Column fields.
2) Change the magnification on the microscope.
3) Use the Image > Set Magnification... command to give the system the
current magnification.
? The system shows the new magnification in Stage Manager.
? If you close Stage Manager again and then restart it, the images will
be smaller (the enlargement has been increased) or larger (the
enlargement has been decreased) in the overview image.
? The position of the individual images remains unchanged, i.e., in
case of a higher magnification the images are further apart. In case
of reduced magnification the individual images will overlap.
4) Click on the Adjust Frame Distance button to adjust the image positions
to the changed magnification.
? Grid layout: the number of individual images remains unchanged
and the distances are adjusted to the magnification. In case of a
higher magnification, a smaller object area will be covered by the
stage path. In case of lower magnification, a larger area will be
covered.
? Rectangular and circular layout: The object area covered by the
stage path remains the same and the number of individual images
is adjusted to the changed magnification. For a higher
magnification, more images will be required in order to screen the
same area.
? Any layout: The Adjust Frame Distance button is not available.

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The Stage Manager Dialog Box

For a magnification of 6.3 a


stage path with 20 images is
defined. There is no
distance between the
images of the stage path.

Magnification change
After changing the
magnification to 16x an
individual image acquisition
shows a smaller area with
higher resolution. The
individual images in the
overview image are
accordingly smaller.

Adjust Frame Distance


Grid stage path
After clicking on the Adjust
Frame Distance button:
The stage path images are
put together edge to edge.
In the case of a grid stage
path a smaller object area
with the 20 images will be

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screened.

Adjust Frame Distance


Rectangular stage path
After clicking on the Adjust
Frame Distance button:
The stage path images are
once again placed edge to
edge. In the case of a
rectangular stage path the
same object area is
represented as for a x6.3
magnification. The number
of images increases from 20
to 130.
The Stage Manager Dialog Box

Number of positions The Number of positions field shows how many stage positions belong to
the current stage path.
If you, for example for the ’Grid’ stage path, change the matrix from 2x2 to
4x4, the number of positions changes from 4 to 16.
Magnification The Magnification field shows the magnification which you have set using
the Image > Set Magnification... command. Check whether this
magnification matches the current microscope magnification. You can also
set the magnification without having to close the dialog box.
OK Click on the OK button to close the dialog box.
If the image buffers 1 and 2 did not contain any images before the command
was used, the last live image will be written into image buffer 1 and the
overview image into image buffer 2.
If image buffers 1 and 2 contained images before the command was used,
the original images are reloaded into the image buffer.
The live mode is ended and the original viewport layout reinstated.
File... Click on the File...button to save the settings in the Stage Manager dialog
box in a file. Please note that the settings for all tabs are saved and not only
those of the active tab. You save four individual stage paths in one file.
Which parameters are The overview image, the acquisition path and the number and position of the
saved? individual images are saved with each parameter file. The positions are
absolute stage positions.
Write the required name for the stage path in the File input field and click on
the Save button.
To load parameters, select the appropriate name from the list field and click
on the Load button.
To delete single stage paths, select the file name and click on the Delete
button.
Stage paths in an To use a stage path within an automatic process, you have to previously
automatic process save it in a file. All saved files are offered as possible stage paths for the
Stage source of images in the Define Processing dialog box.
Details Click on Details >> button to extend the dialog box. You can now set a
different acquisition path and different image distances for the stage path.
Click on the Details << button to close the general settings. Use this option

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especially when you are not working with a dual screen, so that the dialog
box is covered as little as possible by the user interface.
The Stage Manager Dialog Box

All settings that you


generally only define once
for a stage path can be
closed. To do so, click on
the <<Details button . Use
this option if you are
working with one screen
only so that the dialog box
takes as little space as
possible away from the user
interface.

Position distance You change the distance between individual stage path images in the
Position distance group. The default value is the one that you previously
defined using the Stage > Preferences... command in the Default frame
distance group. Here the distances are entered absolutely, as opposed to
the input in the stage settings.
Horizontal In the Horizontal or Vertical field the absolute distance between two
Vertical neighboring images is entered for the current stage path. The distances
represent the distance from image center point to image center point. You
can change the distances so as to move the images closer together. The
images may also overlap. Enlarge the distances to move the images further
apart. If the image distances are changed the image frames are
automatically updated in the overview image.
Position route Select the order in which the individual stage positions are to be moved to
from the Position route list. Four different acquisition procedures are

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available: vertical meander, horizontal meander, horizontal comb and
vertical comb. If you are working with autofocus, you should select a
meander route order, so that the autofocus produces better working results
at the end of the lines.
Remember that the selected acquisition path can only be taken into account
if you click on the Scan Positions button. Clicking on the Scan Area button
means that the Vert. meander acquisition path is always used.
The illustration shows the
different options for sorting
the images within a stage
path.
The Stage Manager Dialog Box

Fit overview area Mark the Fit overview area check box to recalculate the size of the overview
image for the current magnification and the set stage path.
When must the overview • Change of magnification:
image be adjusted? If by selecting a different magnification you change the object area
covered by the stage path, the size of the overview image will be
recalculated. The new overview is exactly as big as required by the
number of images and the position distances which have been set.
In the case of a magnification reduction, the object area covered by the
overview image is enlarged, with a higher magnification it is reduced.
• You move the second reference point and thus change the rectangular
stage area. If you adjust the overview, all the areas in the overview
image which are not covered by the current stage area are cut off.
• You reduce the distances between the individual image positions. Thus
all images are pushed together. If you adjust the overview, the
unnecessary edges will be cut off.
"Fit overview area " The adjustment of the overview image only takes effect in the case of a
means cutting off edges reduction of the area covered by the stage path. In this case, the edges
which are not covered by the current object area are cut off.
If you enlarge the area covered by the current stage path, for example by
increasing the number of stage positions, the overview image is also
adjusted even if the check box is not marked.

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The Stage Manager Dialog Box

The illustration shows the


effect of the status of the Fit
overview area check box on
the overview image:
· The stage is at position 1.
· Clicking on the Scan
Area button delivers an
overview image to position
1.
· The stage is moved to
position 2.
· Clicking on the Set
Center button moves the
grid to position 2.

The Fit overview area check


box is unmarked:
The overview image is
extended by the area which
is covered by the current
stage path.

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The Fit overview area check
box is marked:
The overview image now
only shows the area which is
covered by the current stage
path.
Defining Stage Paths

Defining Stage Paths


The object area which is to be scanned by the stage path can be defined in
four different ways. For each of these methods the Stage Manager dialog
box provides a separate tab:
• You can define a rectangular or circular image area,
• For a grid you define the number of images which are to be positioned
horizontally or vertically next to each other. The object area thus
covered is naturally also rectangular.
• You can also compose a stage path using any single positions
required.

Defining Rectangular Stage Paths


On the Rectangle tab you define a rectangular area on the object. The area
is clearly defined through two positions which lie diagonally to each other:
for example through its upper left and lower right corner.
Move stage Following the area definition you can move the stage to any position
required within this rectangle. To do so, use the buttons in the Move stage
group.
Difference to Grid The area covered by the rectangle stage path remains the same when the
stage path magnification is changed. In case of a change in the magnification the
system automatically increases or decreases the number of stage positions.
In the case of the grid stage path, the number of stage positions and their
positions in relation to each other remain constant when the microscope
magnification changes.
You can define a
rectangular image area by
using diagonally opposing
positions .

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Set Reference Click on one of the Set Reference Point buttons to define the current stage
Point position as a reference point of a rectangular object area. Before doing so,
move the required position into the center of the image using the joystick.
The image area now shown is definitely contained in the stage area. Use the
live image shown for orientation purposes.
Defining Circular Stage Paths

A reference point exists A previously-defined reference point will be over written. If no reference
already point was defined, the color of the check lamp changes from red to green
Overview image The size of the overview image is automatically adjusted to the new stage
area. The system calculates automatically the number of images which are
required to scan the necessary area. The image distance previously defined
in the stage settings are taken into account in the process.
Possible error messages If one or more part images are outside the current maximum stage area, you
will receive an error message. If you scan the stage area regardless, the
positions which cannot be covered remain black.
Clear Click on the Clear Reference Points button to delete a previously defined
Reference stage path. The check lamp next to the Set Reference Point buttons are now
Points red. The Move stage group is no longer available because no stage path is
defined. In the Scan group only the Scan Area button is available.
How to.... define a rectangular area on the specimen:
1) Click on the Clear Reference Points button to remove all existing
reference points.
? The digital check lamps in the Define shape group will now show
red.
2) Using the joystick move the stage to a corner of the object area which
you want to cover. The live image is shown in the upper viewport for
orientation purposes.
3) Click on the Set Reference Point 1 button to define a reference image
for the rectangular area.
? The upper check lamp will now show green.
4) Using the joystick move the stage to the second corner of the specimen
area which you want to cover.
5) Click on the Set Reference Point 2 button to define the rectangular
area. The lower check lamp is now also showing green.
? The system now automatically sets as many images to the
previously defined image area as required to form a rectangle, with
both reference points inside the rectangle.
6) The image positions in the overview image are adjusted accordingly.
? You can now move to the individual stage positions. To do so, use

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the buttons in the Move stage group.

Defining Circular Stage Paths


Define a circular area on the object on the Circle tab. The area is clearly
defined by three points on the circumference.
Move stage Following the area definition you can move the stage to any position within
the circle: to do so, use the buttons in the Move stage group.
Defining Grid Stage Paths

You can define a circular


image area using three
positions on the
circumference.

Set Reference Click on one of the Set Reference Point buttons to set the current stage
Point position as the reference point. Before you do so, move the required
position into the center of the image using the joystick. Use the displayed
live image for orientation.
A reference point already A previously-defined reference point will be overwritten in this process. If no
exists reference point was defined, the color of the check lamp changes from red
to green.
Overview image The size of the overview image will be automatically adjusted to the new
stage area. The system automatically calculates the number of images
necessary to screen the defined area. The image distances previously
defined in the stage settings will be taken into account in the process.
Clear Click on the Clear Reference Points button to delete a previously-defined
Reference stage path. The check lamps next to the Set Reference Point buttons now
Points show red. The Move stage group is no longer available since no stage path
is defined. In the Scan group only the Scan Area button is available.

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Defining Grid Stage Paths
Define a rectangular area on the object on the Grid tab. The area is defined
through the number of images which are to be positioned horizontally and
vertically next to each other.
Move stage Following the definition of the area, you can move the stage to any required
position within the rectangle. To do so, use the buttons in the Move stage
group.
Difference to rectangle In the case of the rectangle stage path, the number of stage positions and
stage path their position to each other remains constant when the microscope
magnification is changed. Thus the area covered by the stage path depends
on the microscope magnification.
An area covered by the rectangle stage path remains constant when the
magnification changes.
Defining Arbitrary Stage Paths

You define a rectangular


image area around a central
point.

Set Center Click on the Set Center button to set the current stage position as the center
of the grid. The grid will be arranged around the center.
Use this button to move a grid stage path to another object position with one
mouse click.
Rows Enter the number of stage positions which you later want to move to in series
Column in horizontal or vertical direction into the Rows and Column fields.

Defining Arbitrary Stage Paths

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You compose a stage path using individual positions on the Arbitrary tab.
You can also use this option to manually edit stage paths which you have
defined on other tabs. You can delete single positions from a previously-
defined stage path or add individual positions.
Move stage Following the definition of the area, you can move the stage to any required
position within the rectangle. To do so, use the buttons in the Move stage
group.
Defining Arbitrary Stage Paths

You can compose a stage


path using any individual
positions. Use this stage
path if you particularly want
to move to single interesting
areas within an overview
image.

Add Current Click on the Add Current Position button to add the current stage position to
Position the current stage path. Before you do so, move to the required position using
the joystick and use the displayed live image for orientation purposes.
Add Positions Click on the Add Positions by Polygons button to define an arbitrary image
by Polygons area. The system then automatically sets as many image positions in the
area as are required to screen the arbitrary object area using the defined
image distances.
Remember: when you add single positions as a polygon, you define a new
stage path. All existing positions will be deleted in the process.
Definition of the polygons You define the polygon directly in the overview image: after clicking on the
Add Positions by Polygons button the mouse pointer jumps to the overview
image. Click on the left hand mouse button once to define single fulcrums
for the polygon. Close the polygon by clicking with the right hand mouse
button.
You can also define the polygon in freehand mode: to do so, hold the left
hand button down and move around the area of interest with the mouse.

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Close the polygon by clicking with the right hand mouse button.
Delete Click on the Delete Positions button to delete positions from an existing
Positions stage path or positions imported from another tab:
As soon as you have clicked on the button, the mouse pointer jumps to the
overview image. Using the left hand mouse button, click on all the image
frames that you want to delete from the stage path. The selected positions
are marked by a red point in the overview image. Confirm this selection
using the right hand mouse button.
Delete all Click on the Delete all Positions button to delete all previously-defined stage
Positions areas. The Move stage group is no longer available since no stage path is
defined. In the Scan group only the Scan Area button is available. Click on
this button to adopt the current live image as the overview image.
Rectangle You can also edit stage paths on this tab which you have defined on the
Circle other tabs. Select from the list one of the three tabs Rectangle, Circle or
Grid Grid, to import the current stage path from the selected tab. You can now
delete single positions from the stage path or add new individual positions.
Remember that the selected stage path will only be imported if you click on
the Apply button.
Acquire Overview Image...

Apply Click on the Apply button to adopt the current stage path from the selected
tab. In doing so, you define a new stage path. All previously-defined stage
positions are deleted in the process.
Adjust Frame Distance The Adjust Frame Distance button is not available for this tab.

Acquire Overview Image...


Use this command to acquire an image of a larger object area using the current Stage Manager settings.
The overview image is composed of several individual images. The resolution of the overview image can
be adjusted.

What will happen... • Following the start of image acquisition the system scans the area
which is covered by the current stage path. At overview image
acquisition the images are definitely acquired edge to edge, even when
you have defined image distances in the stage settings or the Stage
Manager.
• An image is acquired at each position. All acquired images are
composed to an image in the random access memory.
• The result image is written into the destination image buffers.
Characteristics of the • The overview image is always correctly calibrated, i.e., the pixel
overview image calibration data is adjusted to the selected image resolution.
• The name of the overview image is adopted from the current tab of the
Stage Manager: Rectangle, Circle, Grid or Arbitrary.
Preconditions for the • Stage Precision: The individual images from which the overview
acquisition of an image is composed are positioned edge to edge. Any imprecision in
overview image your stage will inevitably lead to misalignment of the individual images.
• Homogenous Illumination: if the individual images are not illuminated
homogenously, this leads to differences in intensity in the composed
image. Remember that for the human eye even small differences in the
intensity are clearly visible.
The overview image that you acquire using this command differs from the
overview image that can be acquired during the definition of the Stage
Manager.

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Overview Image Stage Manager Overview Image
Acquisition Use the Stage > Acquire Overview Click on the Scan Positions or Scan
Image... command Area button in the Stage Manager dialog
box.
Purpose The overview image is a high resolution The overview image in the Stage
image of a larger object, composed of Manager is merely an orientation aid
several individual images placed edge to acquired during the definition of a stage
edge. The positions for the acquisition of path.
the individual images are moved to
automatically by the stage.
Resolution The resolution can be freely selected. The resolution is defined by the system
and is definitely lower than the resolution
of the individual images.
Saving The image can be saved like a normal The system saves each overview image
image using any name. automatically using a standard name in
the ’Stage’ sub-directory. The overview
image is overwritten at every further
acquisition.
Acquire Overview Image...

Zoom An individual stage path can contain any number of individual images. The
overview image, which is composed of all of these individual images, can
thus be relatively large. You can limit the resolution of the overview image
to prevent it becoming too large.
Enter the required resolution into the Zoom field as a percentile value.
100% Select a zoom factor of 100% to set the individual images next to each other
in full resolution. The result image is a high resolution overview image.
Example An individual image has for example a size of 1280x1024 pixels, with a zoom
factor of 30% an overview image which is composed of 9 images has a size
of 1149x916 pixels.
Width The Width and Height fields show the pixel sizes of the result image. If you
Height change the zoom factor, the values are recalculated automatically.
Required RAM The Required RAM field shows you how much RAM the result image
requires at the selected zoom factor in MB. If you change the zoom factor,
this value will be recalculated automatically.
The RAM required is retained as preset for the next acquisition of an
overview image. The zoom factor is adjusted accordingly.
Example You are using a color camera. An individual image has a size of 1280 x 1024
pixels, for example, at a zoom factor of 100% an overview image composed
of 9 images requires 33.75 MB RAM. A zoom factor of 50% reduces the
RAM required to 8.4 MB, a quarter of the RAM.
OK With OK you confirm the settings and start the acquisition of the individual
images.

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Preferences...

Preferences...
Use this command to define general settings for the Stage Manager.

Available This command is also available when the Stage Manager is open. You can,
for example, change the distances between the individual images within a
stage path without closing the Stage Manager. You should, however,
remember that some changes in the Stage Preferences dialog box only take
effect after the Stage Manager has been closed and reopened.

Display In the Display group you can change what is displayed in the image
document after Stage Manager has been activated.
Single Select the Single option to display the live image and the overview image in
the image document on the windows screen.
The image document is divided: in the upper viewport you see the current
live image and in the lower viewport you see the current overview image.

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After closing the dialog box the original viewport layout is restored.
The image buffer used for the live image is always the first image buffer. The
image which is in this buffer will NOT be overwritten, even if it is covered
during the definition of the stage path by the live image.
Dual Select the Dual option to display the live image and the overview image in
the image document of the dual screen. The advantages of a dual screen
system are: the image can be shown larger on the dual screen than on the
windows screen and the Stage Manager dialog box does not cover any of
the image.
Show frames Mark the Show frames check box so as to show the individual images of a
stage path as frames in the overview image. In this way you can see directly
in the overview image which image areas in the individual images are shown
or check whether the overlap areas or image distances are properly defined.
Unmark the Show frames check box so as to show only the center points of
the images in the overview image. In this way, if you are scanning a large
object area with very many individual images, the display in the overview
image remains clear.
Preferences...

Color Select one of 16 colors from the Color palette for the representation of the
image frames and the image center point.
Update rate of stage Enter the time interval into the Update rate of stage position field following
position which the system checks the stage position. With a time interval of 50ms the
system checks the stage position every 50ms and subsequently updates the
stage position in the overview image of the Stage Manager.
The default value is 1 s. Remember that your computer may work slower if
you reduce the value.
Default frame distance In the Default frame distance group you set the horizontal and vertical
distance of the individual images within a stage path. These settings are
taken into account when you define the next stage path. To adopt a change
in the settings for the current path, click on the Adjust Frame Distance button
in the Stage Manager dialog box.
Horizontal The image distance is entered relative to the image size as a percentile
Vertical value. To acquire the images edge to edge, enter 100% into each of the
Horizontal and Vertical fields. A value of 90% leads to overlapping of the
individual part images by 10% of the image size. A value of 200% increases
the distance between the individual part images by exactly one image size.
You can set the distances in the X and Y direction separately.
Alignment The camera is generally not positioned parallel to the stage movement
direction. As a result, the X and Y direction of the microscope stage do not
concur with the image edges of an acquired image. An image acquired at
the X position X1, and a second image which is acquired following a
movement of the table at position X2, do not therefore lie horizontally next
to each other, but are shifted opposite against each other. For the
acquisition of an image series which is to be automatically composed to a
complete image, the stage must move in directions X and Y so as to order
the images horizontally next to each other or vertically under each other in
an image matrix.
Adjust Click on the Adjust button to have the angle of rotation set automatically.
Preconditions for a • If the system is to be able to calculate a correct angle of rotation, the
successful adjustment input channel used must be correctly calibrated.
• The stage must be correctly configured and initialized.
• Before you click on the button, move the stage to a specimen section

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with a lot of sharp image structures, so that the system recognises the
structures again and the positions are correctly assigned.
• Camera and stage movement direction should always be adjusted as
parallel as possible.
What does ’adjust’ After you click on the Adjust button the system acquires an image at the
mean? current stage position X0, then moves the stage in direction X by a short
distance to position X1 and acquires an image here, too. The images at
positions X1 and X0 are compared and the movement of the images
towards each other determined. The same measurement is subsequently
carried out for the movement of the stage in direction Y. The result of the
adjustment is an angle of rotation which is displayed in the Rotation field. For
a later horizontal stage movement with the Stage Manager the actual stage
movement is calculated on the basis of the calibration data.
Result of the adjustment Following the adjustment, the angle of rotation between camera and stage
movement direction is shown in the Rotation field.
If the stage alignment could not be measured, you receive an error
message. In this case, try to undertake a new adjustment at another object
position with a greater image contrast.
Preferences...

When should adjustment A new adjustment is necessary when the camera position has been
take place? changed.
Remember that the system only saves one valid angle of rotation. With
some electron microscopes the image rotates with a change of the
magnification. In this case, a new adjustment is required following each
change of the magnification.
Fine adjust Mark the Fine adjust check box to enlarge the movement path for the
acquisition of both images which are used for the calculation of the angle of
rotation. In this way a much smaller image area is searched for the same
image structure.
Unmark the Fine adjust check box to use a larger image area for the sample
recognition. The coarse adjustment can lead to better results for greater
angles of rotation.
Rotation The Rotation field contains the angle of rotation which the system takes into
account for each stage movement path. After clicking on the Adjust button
the field shows the result of the adjustment. You can reset the angle of
rotation to 0° manually if you have aligned the camera exactly parallel to the
stage movement direction.
Horizontal scale Following adjustment, the Horizontal scale und Vertical scale values show
Vertical scale pixel calibration data. The system calculates these values from the stage
movement path and the number of pixels between two identical image
points. This naturally assumes that the pitch and the resolution of the stage
are correct.
If the adjustment was successful, the calculated calibration data concurs
with the image calibration data. Remember that the calibration data of the
input channel only then tallies with the image calibration data if no binning
has been set for the current input. (Image > Configure Input > Format >
Binning > Horizontal/Vertical =1).

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