analySIS®

IX-
Add-In
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 Olympus IX81

Introductory comments 1

Installation 1
Olympus IX81

Software control of the IX81 4

Main tasks when working with the IX Add-In .............................4

The IX button bar .......................................................................5
User administration in the IX Add-In ..........................................6
Workflow for the first configuration ........................................... 8

Configuring the microscope 9

Entering microscope components .......................................... 10

Setting up a new key configuration .........................................16
The key configuration dialog box .............................................19
Defining frame keys and handswitch keys ..............................21
Defining Softkeys ....................................................................23
Defining observation methods .................................................25
Defining combined observation methods ................................26
Completing the key definition ..................................................27
IX81-221203En

Working with the microscope 28

Selecting combined observation methods ...............................30

The IX image information 32

The IX-UCB control box light panel 33

Saving Configuration Files 34

Index 37
 Introductory comments

Introductory comments
This documentation This documentation describes the IX software Add-In - the software control
for the motorized microscopes of the Olympus IX product line. This Add-In
is fully integrated with image-analysis software. It is assumed that the micro-
scope, including the camera, has already been assembled and that the soft-
ware has been installed on your PC.
Other documentation For detailed information on all microscope components, hints on assembly,
and technical specifications, please see the Olympus IX users’ manuals. To
familiarize yourself with the broad range of possibilities of the image analysis
software, please have a look at the "Step by Step" manual.
The explanations and examples in this documentation refer to a IX81 micro-
scope type. IX Add-In can also be used with the IX51/71 microscope. Thus,
you can control all motorized components.
With or without a PC All controllable microscope components are connected to the control box via
cable. A single serial cable connects the control box to the PC. You may also
run your microscope without the PC. In this case, the functions concerning
digital image acquisition, image processing, analysis, database archiving
and report generation will not be available. The frame keys and handswitch
keys for controlling the microscope will have the default settings.
System requirements When operating the microscope via PC, you need to have a display with a
minimum of 65536 colors (16 bits) and a minimum size of 1024x768 pixels.

Installation
The description of the installation process only refers to the IX Add-In The
general procedure is the same than with a "normal" analySIS-installation. As
a precondition, the dongle must be set on a serial port of your PC and you
must be logged in with administrator rights. For the installation of additional
software or hardware (e.g. a digital camera), please refer to the correspond-
ing manual.
For the installation of the software proceed as follows:
1) Insert the analySIS-CD into the CD-ROM drive of your PC.

1
" Normally, the Setup dialog box will open automatically. Should that
not be the case or if you have closed it, you can open it again by
clicking on the Setup.exe on the CD-ROM.
2) Select the menu entry analySIS 3.2 for the installation of the software.
3) Follow the instructions of the Setup Wizard. As refers to the IX Add-In
you must pay special interest to two settings (see below).
4) When asked for the microscope, select the Olympus manufacturer and
the option IX2 Remote and Control.
 Olympus IX81 • Installation

5) When asked for the stage, select the Olympus manufacturer and the
option IX81 Z-Stage.
2

6) Go on with the installation.

 Installation

Configuration of the input channel

For the use of the IX Add-In, some settings of the input channel have to be
adjusted. We recommend to do this directly after the installation. However,
if you forget it, you will receive a message when starting the IX Add-In.
How to... Configuration of the input channel
1) Open the dialog box Set input via the key F6 or via the menu
Image>Set Input.
" You see all existing input channels. The active input channel is
highlighted in blue.
2) Select the input channel or create a new one, which you would like to
use for the IX remote control.
3) Doubleclick on the input channel you want to use.
" The dialog box Set Input appears.
4) Select the Magnification tab.
" Select the option Olympus IX from the picklist in the Device field.

5) Click the Set COM port... button and in the Set Remote COM port dia-
log box select the port used for the RS232 serial cable that connects
your PC with the control box of the microscope.
6) In the Remote group select the On check box.
" This enables the remote control.
7) If you want to read out the magnification currently set at the micro-
scope, click the Read button.
" Once these settings are done, you can start the IX Add-In as
described on page 8.
 Olympus IX81 • Software control of the IX81

Software control of the IX81

The IX software Add-In makes operation of your microscope even easier and more efficient, and to some
extent, automated. Furthermore, the image-analysis software provides you with easy-to-use digital image
acquisition, image processing, analysis, database archiving and report generation.

Configuration via The IX software interface must be configured prior to remote operation. Con-
dialog boxes figuration is done via dialog boxes onscreen (of your PC). You will be auto-
matically prompted through the configuration process to select all the micro-
scope components and key assignments from picklists.
Control via dialog You may use dialog boxes, softkeys, frame keys and/or handswitch keys on
boxes, handswitch the microscope (all user-definable) to control the lamp voltage and all motor-
keys, frame keys and ized parts including the built-in Z-drive and filter wheels. You can also mon-
softkeys itor the status of your microscope. The integrated user-administration dialog
enables multiple users to save their configurations according to their own
particular needs and reload them as needed.
Note You may only redefine how keys are to be used if the PC is on, the software
has been started and the user is logged on.

Main tasks when working with the IX Add-In

User administration Key configuration

¾ create/delete users ¾ add or change definition of
¾ change password frame/handswitch keys
¾ change user‘s rights ¾ set up a new key configuration
¾ assign key/microscope configuration ¾ define softkeys
¾ define observation methods
4

The IX Add-In

Microscope configuration Microscope control

¾ define a new configuration ¾ control microscope from
¾ change an existing configuration computer
 The IX button bar

The IX button bar

Use the IX button bar to
access all
dialog boxes.
Use the Special > Edit But-
ton Bars... command to
show the
IX Log On/Off
button bar if it is currently
hidden. User Settings (p. 6)
Microscope Configuration (p. 10)
Depending on the user’s Key Configuration (p. 19)
rights, one or more buttons
are not available, e.g., for a Microscope Control (p. 28)
user with Standard rights, Optional button: Show/Hide SoftKeys (p. 23)
the Microscope Configura-
tion button will be disabled.

Log On This button is used to identify the current user and for password verification.
As soon as the user has logged on, the other buttons will become active.
The password for the administrator for the initial log-on is: a .
User Settings This button enables you to determine the standard microscope and key con-
figurations which the user utilizes. You can select from all existing configu-
rations. If an administrator is logged on, this dialog also contains options to
create users and assign user’s rights.
Microscope This button is used to define a hardware configuration. To do this, simply
Configuration select the existing microscope components from picklists.
Key Configuration This button is used to assign functions or observation methods of your
microscope to keys on the frame or handswitch.
Microscope Control This button is used to monitor the status of the microscope, to control the Z-
drive and motorized parts of the microscope (if present) and to select an
observation method.
Softkeys This button is only active if softkeys have been defined by the logged-in

5
user. In this case, clicking on the button will open the IX softkey button bar:
Example of a Softkey button
bar. The name of a softkey
can be freely defined.
 Olympus IX81 • User administration in the IX Add-In

User administration in the IX Add-In

The IX Add-In offers four user levels, each provided with different rights.
Thus, depending on the user’s rights, some buttons of the IX button bar will
be inactive with some users:
• Trainee:
lowest rights, can only use the microscope control, making use of the
key and/or microscope configuration assigned to him by the adminis-
trator.
• Standard:
can select a key and a microscope configuration, can create a key con-
figuration of his own.
• Advanced:
can select a key and a microscope configuration, can create a key con-
figuration and a microscope configuration of his own.
• Administrator:
has all the rights. He can create new users and assign them certain
rights. He can also change the rights of existing users. Additionally, he
can assign a default microscope and a key configuration to a user.
To do so, the User Settings dialog box has additional functions:
Appearance of the User
Settings dialog box when
logged in with administrator
rights
6

Appearance of the User

Settings dialog box when
logged in with Standard or
Advanced rights.
 User administration in the IX Add-In

Creating new users

Note Only the administrator (or a user with administrator rights) can create new
users.
1) To create a new user, click the New User.... button and enter a user
name in the New User dialog box.
" The new user is added to the list. Per default, he has Trainee rights.
" The password for the new user will initially be the same as the user
name. The user can change it afterwards (except users with the
Trainee rights). Upper and lower case are relevant when entering
the password.
2) If required, change the rights by selecting the corresponding option in
the Rights group and click Save.
3) You can assign a microscope configuration to a user. In this case, the
user will start a session with this microscope configuration. He can,
however, select another microscope configuration (if there is one) in
the User Settings dialog box.
4) Users with Trainee rights are not allowed to select a microscope con-
figuration. Therefore, the administrator must assign one to them.Other-
wise the Microscope Control button will not be available and the new
user cannot work with the software! (You can also assign a key config-
uration, but this is optional as the new user can also work with the
default key configuration.)

Changing the settings for existing users

Change password The administrator can change the password for all users. This may be useful
if a user has forgotten his password. By changing a user’s password, the
administrator is also able to deny the access to the software.
Assign a microscope The administrator can assign a microscope configuration to a user. In this
configuration case, the user will start a session with this microscope configuration. He
can, however, select another microscope configuration (if there is one) in the
User Settings dialog box.
Assign a key A new user is automatically given the Default Key configuration. This
configuration means, that no special key configuration has been defined. When clicking

7
on the key configuration button for the first time, the user has to create a new
key configuration (except users with the Trainee rights, who cannot make up
a key configuration of their own and will use either the Default key configu-
ration or one assigned to them by the administrator).
 Olympus IX81 • Workflow for the first configuration

Workflow for the first configuration

How to... Follow these steps for the first configuration of the microscope:
1) As you assemble the Olympus IX microscope, make a list of all the
components and their positions. The list should include objectives, filter
cubes, phase contrast and DIC inserts and other filters and optical ele-
ments.
2) Make sure that all cable plugs are firmly inserted into their jacks: the
connector cables between the microscope components and the control
box; the handswitch cable; the RS232 serial cable between the control
box and PC; and the power supply cables for the control box and the
PC.
3) Turn on the control box and wait until the initialization process has com-
pleted.
4) Start the image-analysis software.
5) Click the Log On button in the IX button bar.
" The Open a IX Session dialog box will be opened.
" "administrator" will appear in the User name field.
6) Enter the preliminary password (a) into the Password field.
" You will be logged in with administrator rights and therefore will be
able to create other users and assign user’s rights.
7) Confirm by clicking OK.
" The other buttons of the IX button bar will now become active.
" If the message "Cannot communicate with the microscope. The IX
remote may not be assigned to the active logical input channel."
appears, you did not configure the active logical input channel after
the installation. If you confirm the question Do you want to select/
create a logical input channel? with Yes, the IX Add-In will create a
new logical input channel and configure it for you. If you do not
want to create a new logical input channel, click No and read the
chapter "Configuration of the input channel" on page 3.
8) Leftclick once on the Acquire button and once on the Snapshot button
in the Standard button bar to ensure that the live-image display and
snapshot acquisition are functioning.
9) Click the Microscope Configuration button in the IX button bar to inform
8

the software of the exact microscope components.

" A series of dialog boxes will now guide you through the configura-
tion process. For additional explanations, see the chapter entitled
"Entering microscope components" on page 10.
10) Click the Key Configuration button to assign functions to the keys and
to define observation methods. For additional explanations, see the
chapter entitled "Setting up a new key configuration" on page 16.
 Configuring the microscope

11) Once you have completed the configuration, you may click the Micro-
scope Control button to begin using the microscope.
" For additional explanations, see the chapter entitled "Working with
the microscope" on page 28.
12) You should change your password now to make sure that data is only
accessible by you. Keep in mind that upper and lower case are relevant
when you enter your password.
13) If you want to create new users, see "Creating new users" on page 7.
Note If you have altered any component on your microscope, always remember
to change your microscope configuration or make up a new one.

Configuring the microscope

Defining the frame is part of
the configuration of the
microscope.

You can accept or alter the

proposed key configuration.

The illustration shows the

location of these keys.

9
frame keys
1-7

frame keys 8 and 9

(also on the opposite side)
 Olympus IX81 • Entering microscope components

Entering microscope components

You must first inform the software what components are attached to your microscope. Click the micro-
scope configuration button in the IX button bar. A Wizard will take you through a series of dialog boxes
in which you select the names of each component, thus ensuring that no entries are left out. This chapter
contains a number of supplementary remarks on these dialog boxes.

Warning When defining microscope components, be very careful! The entries you
make within the dialog boxes must correspond exactly to the actual micro-
scope components installed. If they do not, it could result in damage to
your device or even damage to your health (e.g., when object illumination
is too intense or unfiltered!).
Remember to redefine your configuration or to select a new configuration
if you make changes to the microscope hardware!

• Click the Microscope Configuration button.

" The first dialog box will be opened:
Components shown in blue
on the microscope diagram
are those affected by the
entries in the current dialog
box.

• Click the New... button to enter an appropriate name for the new con-
10

figuration.
" You may select whether fields are to remain empty or be filled out
with the data of the previously-active configuration in the Hardware
Configuration dialog box.
" The name of the new configuration will be added to theName-field
picklist and become available for selection.
• Select the picklist entries corresponding exactly to your microscope as-
sembly in this dialog box and all others following. Explanations to indi-
vidual options can be found on the next pages.
• Simply continue clicking on the Next button to move on to the next dia-
log box.
 Entering microscope components

Heat protection of optical Select this check box (only available for fluorescence microscopy) to close
components the shutters after 10 minutes of inactivity and, if available, to move the filter
wheel to a free position.
Motorized Prism The prism directs the light path either to the binocular or to the side port cam-
era. If your microscope has a motorized prism, you can control it via analy-
SIS. In this case, select this check box. The control panel then shows the
buttons illustrated to the left to redirect the light path (see page 30).

Shutter IX81 can control two shutters: one for reflected light and the other for trans-
mitted light. This is where you set with which shutter your microscope is
equipped. The position of the shutter (open/closed) can be controlled using
the control panel (see page 28).
Bottom Port Bottom Port Cameras are attached to the lower part of the microscope and
use the most effective light path. They do, however, require a special stage.
A motorized mirror directs the light path either to the binocular or to the cam-
era.
Select the Motorized Bottom port check box if a bottom port camera is
attached to your IX81-microscope. The buttons illustrated to the left are then
at your disposal in the control panel to redirect the light path.
Three buttons are available in the control panel, if, apart from a side port
camera, you also have attached a bottom port camera.

11

N.A. The abbreviation N.A. stands for numeric aperture. Here you can enter the
objective's numerical aperture. These fields are only for your information
and do not influence the analySIS functions.
Cap Here you can enter whether or not you use caps for your objective (i.e. sam-
ples in petri dishes). These fields are only for your information and do not
influence the analySIS functions.
Focus speed analySIS automatically enters the preset focus speed when you select an
objective. You normally do not have to change this. Should it be necessary,
however, select a new value from the picklist.
Magnification changer This is where you select the type of magnification changer you have, should
your microscope be equipped with one. The current position of the magnifi-
cation changer can be set in the control panel.(see page 30)
 Olympus IX81 • Entering microscope components

Here you can define the

parfocality
correction (see page 15).

Stage Limits Set the correct stage limits here in order to protect the samples and objec-
tives. Once these values are set, you only have to confirm them when asked
for them during other operations with the IX Add-In.
How to... Set the Stage Limits:
1) Make sure the stage is sufficiently far away from the biggest objective.
2) Switch to the highest magnification.
3) Focus the sample (at the microscope).
4) Should the Stage limits dialog box not appear, click the Limits... button
to access it.
5) Bring the sample a little closer to the objective and read out the upper
limit by clicking Read.
6) This fixes the upper stage limit for the Z-drive.
7) Now select the smallest magnification.
8) Focus the sample (at the microscope).
9) Move the sample a little bit away from the objective and read out the
lower limit by clicking Read.
10) This fixes the bottom limit for the Z-drive.
12
 Entering microscope components

In the Mirror unit type field

you can select the option
Motorized, Non motorized
and Not used.

Note:
The default value for the
optical components is Skip
position. However, one of
the positions should always
be defined as free, in order
to keep the light path free
from any optical elements.

If you forget to define one of

the positions as free, the IX
Add-In will define it for you
when you go on to the next
dialog box. Should that not
be possible, because all
positions are used, you will
get a warning message.

In the Condenser type field

you can select the option
motorized, non motorized
and not used (if the micro-
scope does not have a
condenser).

Note:
The default value for the
optical components is Skip
position. However, one of
the positions should always
be defined as free, in order
to keep the light path free
from any optical elements.

13
 Olympus IX81 • Entering microscope components

Note:
The default value for the
optical components is Skip
position. However, one of
the positions should always
be defined as free, in order
to keep the light path free
from any optical elements.

Filter wheels Each of the three possible filter wheels has its own separate dialog box.
Click the Move the Wheel button to be able to identify the active filter wheel
(simply listen for the sound of its motor).
Simply continue clicking on the Next button to move on to the next filter
wheel.
Note The filter wheels, the motorized condenser (LWUCDA), and the motorized
mirror unit (RFACA) use the same plugs located at the back of the UCB con-
trol box. Since only three plugs are available, you can only use one filter
wheel if your microscope uses a motorized condenser and motorized mirror
unit.
The plugs for the filter
wheel, condenser, and mir-
ror unit located at the back
of the UCB control box.
14

The following configurations are possible:

Illuminator Condenser available filter wheels
non-motorized/not used non-motorized/not used 3 filter wheels
motorized non-motorized/not used 2 filter wheels
non-motorized/not used motorized 2 filter wheels
motorized motorized 1 filter wheel
 Entering microscope components

• Click the Finish button in the final dialog box to conclude definition of
the microscope components.

How to... Use a parfocality correction:

1) Make sure, the stage limits are set.
2) Find a detail of the sample that is recognizable with different magnifi-
cations.
3) In the Define Microscope Configuration: Parfocality Correction dialog
box, enable the Use parfocality correction check box.
4) Select the objective with the highest magnification and focus the sam-
ple (The camera will automatically switch to live mode. So you can do
it either in the live image, by moving the slider control of the Z-axis, or
at the microscope).
5) When you are content with your results, click the <<Read Z button.
" (Alternatively, if you know the correct Z-value, enter the value in the
Value field and click the Set Z >> button.)
6) Select the objective with the second highest magnification and focus
the sample again.
7) Click the <<Read Z button again.
" The IX software will save the difference between the two Z values
(not the absolute values!). This difference will always be added or
reduced when the objectives are changed.
8) Repeat these steps with the other objectives. Take the objective with
the smallest magnification as the last one.
9) The software will save the differences between all the objectives. So,
you can directly change from the smallest objective to the biggest one,
with an automatic correction of the parfocality.
" However, when changing an objective, you will have to adjust the
exposure time manually in the camera control, as the intX function
does not work in the Microscope Configuration dialog box.

15
 Olympus IX81 • Setting up a new key configuration

Setting up a new key configuration

Every user has to define his personal key configuration for each microscope configuration he wants to
use. For example, if a user wants to use 3 microscope configurations, he will have to define 3 key con-
figurations.
However, in order to make the setting up of a key configuration easier, it is possible to select one of the
existing key configurations as a template. The key configurations can be of any other user who uses this
microscope configuration. Just select one as a template, save it under a new name and change or add it
as you like.

User Miller
uses microscope configuration
„Brightfield“ with the personal key
configuration „Brightfield-Miller“

User Smith
uses microscope configuration
„Brightfield“ with the personal key
configuration „Brightfield-Smith“
16

New User Brown

also wants to use microscope
configuration „Brightfield“.
Before, he has to set up his
personal key configuration.

As a template, he can select one

of the two existing key
configurations: „Brightfield-Miller“
or „Brightfield-Smith“.
 Setting up a new key configuration

How to... Set up a new key configuration:

1) Before clicking on the Key Configuration button, make sure that the
current microscope configuration has been selected in the User Set-
tings dialog box.
2) Click the Key Configuration button.
" A message will appear: "No key configuration is assigned to your
user settings. Please choose (or create) one with the following dia-
log."
3) After clicking on OK, the following dialog box will be opened:

" If key configurations have already been defined for other users (for
the current microscope configuration) and you wish to use one of
these as a template for your own new key configuration, then select
the one desired in the Name picklist. The entry "[Personal]" indi-
cates that the original configuration cannot be altered by you.
4) Click the New... button and enter an appropriate name into the New
Key Configuration dialog box.
" You may select whether the new configuration is to be based on the

17
default setting or, if applicable, on the most recently active existing
configuration.
" If you did not select an existing key configuration, you will be asked
if you would like to use predefined observation methods. If you click
Yes, a new dialog box opens, in which you select the observation
methods you want to use (several selections are possible):
 Olympus IX81 • Setting up a new key configuration

For transmitted light microscopy you can select 4 predefined observation

methods: BF=Bright Field, PO=Polarized Light, PH=Phase Contrast and
DIC=Differential Interference Contrast.
For fluorescence microscopy you can select 8 predefined observation meth-
ods: FL1-8.

For reflected light microscopy you can select 4 predefined observation

methods: BF=Bright Field, DF=Dark Field, PO=Polarized Light and DIC=Dif-
ferential Interference Contrast

5) After clicking on OK, the Stage Limits dialog box will be opened. You
will see the Z-values as defined during the microscope configuration.
You will only have to apply any changes here if you did not define the
Z-limits properly during microscope configuration (see "Stage Limits"
on page 12).
6) The Key Configuration dialog box will open. Here you can define your
personal key settings.
18

" From now on, this dialog box will open right away when you click
the Key Configuration button.

Deleting a key configuration:

If you want to delete a key configuration, click the Select Key Configuration
button, select the key configuration from the Name picklist and click
Delete.... Please note that you can only delete your own key configurations.
The key configurations of other users are protected, which is indicated by
the entry "[Personal]" following the name.
 The key configuration dialog box

The key configuration dialog box

Overview In the Key Configuration dialog box you can:
• look up and change the default definition of the frame keys
• look up and change the default definition of the handswitch keys
• define new softkeys (no default definition available)
• define new observation methods or change the settings of the selected
predefined observation methods
• define the settings when two observation methods are combined (only
Transmitted Light and Fluorescence)
It is advisable to assign certain basic functions to the buttons on the frame
or handswitch, e.g., active lamp ON/OFF. It is also very convenient to assign
the snapshot function to a key. This enables you to work at the microscope
and collect images without having to look at the PC monitor. As the majority
of the frame and handswitch keys are already defined with default settings,
you will probably only have to define some additional keys for your personal
settings. Please note that you can also assign macros or observation meth-
ods to a key, not only microscope functions.
Defining a key Simply select a key in the Key Configuration dialog box (it turns yellow when
selected), select the desired function or combination of functions and click
Save.

Available buttons in this dialog box:

Frame keys
Handswitch Keys
Softkeys
Observation methods

Acquire (in live mode: Snapshot

)
Reflected light Shutter Open/Close

19
Transmitted light Shutter Open/Close
Select (or create new) Key Configuration
Save
Print Key Configuration
Delete active Key definition
Help
 Olympus IX81 • The key configuration dialog box

The Delete active Key definition button deletes the setting of the selected
key. If you click this button while pressing [Shift], the settings for all the keys
of this mode will be deleted.
If you want to delete an entire key configuration, see page 18.
Clicking on the Save button will save the settings for the selected key or
observation method (shown in yellow).
The Print Key Configuration button prints the key configuration of the active
mode as a sheet for reference purposes.

An easy way to define a particular microscope observation method is by first

setting all variables on the microscope appropriately for that mode. Then, in
the software, select the desired key in the frame or handswitch dialog and
upload the status of the microscope to the computer by clicking the Get
Microscope Status button. Save this "status" by clicking the Save button.
Every time the chosen button is clicked, the microscope will be set to the
desired condition by the software.
With this button you can easily restore the default setting for a button (e.g.
in case you changed the setting of a button temporarily and now want to
restore the defaults). Just select the button, click the Get Factory Settings
button and click Save.
20
 Defining frame keys and handswitch keys

Defining frame keys and handswitch keys

Use the Key Configuration: Frame and the Key Configuration: Handswitch dialog boxes to define the
desired settings for the frame keys and for the handswitch keys.

The colors of the frame keys

indicate their status: green
signifies that the key is
defined and white that the
key is free. The currently
selected key is yellow

21
Default settings of the frame keys
(when IX-Add-In is running)
1 Toggle binocular / camera (LED Display)
2 Stage step 100.00 µm
3 Stage step -100.00 µm
4 Toggle Focus step Fine/Coarse (LED display)
5 Lamp voltage Up
6 Lamp voltage Down
7 Toggle Active Lamp On/Off
8 Stage Escape/Return
9 Snapshot
 Olympus IX81 • Defining frame keys and handswitch keys

The colors of the hand-

switch keys indicate their
status: green signifies that
the key is defined and white
that the key is free. The cur-
rently selected key is yellow

Note Please note that during key configuration, the default frame and handswitch
functions are active. Newly defined functions only become active after clos-
ing the dialog. They can first be tested, however, by positioning the cursor
on the desired button and then clicking the right mouse key.

Default setting of handswitch keys

22

A "Toggle reflected light shutter Open/Close", if microscope is equipped

with a reflected light shutter. If not, this key will be free.
B "Toggle transmitted light shutter Open/Close", if microscope is
equipped with a transmitted light shutter. If not, this key will be free.
C "Bottom port open/close", if microscope is equipped with a bottom
port camera. If not, this key will be free.
D "Filter wheel backwards", if the microscope is equipped with a filter
wheel. If not, this key will be free.
E "Filter wheel forwards", if the microscope is equipped with a filter
wheel. If not, this key will be free.
F "Contrast insert backwards", if the microscope is equipped with a mo-
torized condenser. If not, the key is either free or is being used by a
filter wheel.
G "Contrast insert forwards", if the microscope is equipped with a mo-
torized condenser. If not, the key is either free or is being used by a
filter wheel.
H "Mirror cube backwards", if the microscope is equipped with a motor-
ized mirror unit. If not, the key is either free or is being used by a filter
wheel.
 Defining Softkeys

Default setting of handswitch keys

I "Mirror cube forwards", if the microscope is equipped with a motor-
ized mirror unit. If not, the key is either free or is being used by a filter
wheel.
1 Objective 1
2 Objective 2
3 Objective 3
4 Objective 4
5 Objective 5
6 Objective 6
7 This key is always free since IX cannot be equipped with a 7th objec-
tive.

Defining Softkeys
After having assigned your most important microscope functions (or macros or observation methods) to
the buttons on the frame or on the handswitch, you have the possibility of assigning them to a softkey.
You can then utilize these via the software, instead of having to go over to the microscope.
Besides, the use of softkeys enables a change of the microscope configuration without any need to make
adjustments in dialog boxes. Just select another softkey. The image window can remain open. Only a
minimal part of the user interface is needed for the softkey command bar. You can define up to 24 soft-
keys. The procedure is exactly the same as with the definition of frame or handswitch keys.

23
 Olympus IX81 • Defining Softkeys

The defined softkeys are added to a command bar which you call up via the
IX button bar. To hide the softkey command bar, click the button again.
You can place the command bar freely within the software interface:
The IX softkey command
bar can be a separate com-
mand bar or can be docked
to the other button bars
(below).
24
 Defining observation methods

Defining observation methods

The Key Configuration: Observation methods dialog box is designed to help advanced microscope users
in placing the correct optical components in the light path, and automatically adjusting the illumination for
various types of microscopy (e.g., Fluorescence, DIC). The ability to define observation methods provides
the user with a powerful tool to switch quickly from one type of microscopy to another, with minimal
manual adjustments.

How to... Defining observation methods 25

1) Configure the microscope according to your needs.
2) Select the key you want to define.
3) Upload this setting to the IX Add-In software by clicking on the Get
Microscope Status button.
" Alternatively, you can define all the settings in the software, without
having to go over to the microscope.
4) Name the observation method accordingly, e.g., enter "GFP" for a flu-
orescence mode with a U-MWIB mirror cube. A maximum of 5 charac-
ters is possible.
" This name will be shown on the Observation tab in the IX Control
Panel.
5) Click the Save button to save the observation method.
" Every saved observation method button will turn green within the
dialog box image.
 Olympus IX81 • Defining combined observation methods

6) If you want to load the newly defined observation method, just mark the
corresponding key and press the right mouse button.
Additional Information:
ND filters Note that it is possible to set ND filters to balance brightness differences for
various fluorescence and brightfield modes.
DIC and PH Differential Interference Contrast (DIC) and Phase Contrast (PH) observa-
tion methods permit setting the contrast insert individually for each objective
on separate tabs (only for transmitted light).

Defining combined observation methods

If, for example, you are working with fluorescence microscopy and you need
a weak transmitted light in order to be able to recognize sample’s structure,
you can combine the two observation methods fluorescence and transmitted
light-brightfield.
However, in this case the lamp voltage must of course be considerably lower
than in the standard transmitted light-brightfield observation method. This is
why you have the separate keys PH+, DIC+ and BF+ for defining an obser-
vation method when it is used in combination with fluorescence microscopy.
How to... define a combined observation method
1) If necessary, go to the Key Configuration: Observation methods dialog
box.
2) Select the key for the observation method you want to be used in com-
bination with another one (either PH+, DIC+ or BF+).
" You can only combine transmitted light microscopy (only
PH=Phase Contrast, DIC=Differential Interference Contrast,
BF=Bright Field) with fluorescence microscopy.
" All the settings of the standard observation method are copied to
this key.
3) Apply the necessary changes (i.e. reduce the voltage of the lamp).
" In the text field the difference between the same observation
method when being used alone or when combined with another
observation method will be indicated:
26

Detail from the Key Configu-

ration: Observation meth-
ods dialog box.
In this example the voltage
of the lamp will be set to 3 V
when the Brightfield obser-
vation method is used in
combination with another
observation method.

4) Click Save.
 Completing the key definition

5) For loading the newly defined observation method, see page 30.

Completing the key definition

Once the definitions are done, you are ready to use the microscope through
the IX software control to full capacity.

27
 Olympus IX81 • Working with the microscope

Working with the microscope

Once the preparatory tasks like setting up a microscope and a key definition are over, the Control Panel
is the part of the IX Add-In with which you will mostly work. It permits the control of the microscope via
the PC and will save you a lot of time in going back and forth between microscope and PC.

• Click the Microscope Control button to open the IX Control Panel dialog
box:

The Control Panel offers a

continuous status overview
of the microscope. This
overview is updated several
times per second.

The current microscope

configuration and key con-
figuration are displayed at
the top of the dialog box.

The middle part of the dialog

box contains tabs to select
observation methods and to
make adjustments from
picklists or sliders.

The dialog box can be made

smaller or larger by clicking
the small arrow buttons.
28

Mouseover function The IX Control Panel dialog box is dynamically adjusted to reflect the com-
ponents and options present on your microscope. The illustration at the top
of the dialog box is a control element using a mouseover function. If you
guide the mouse over the image, you can select the motorized parts of the
microscope. The selected component turns blue.
Example How to change the position of the shutter with the mouseover function:
This example assumes that your microscope is equipped with 2 shutters.
Momentarily, the transmitted light shutter is open and the reflected light
shutter is closed. Accordingly, the position of your shutters will be displayed
as follows:
 Working with the microscope

The position of your shutter

will be displayed graphically
in the control panel.

In order to close the transmitted light shutter, move the mouse to the trans-
mitted light shutter so that it is shown in blue. Click the left mouse key to
close the shutter. The display now shows that the light path to the sample
has been interrupted.
The position of the shutter
has been altered with the
help of the mouseover func-
tion.

The same functional principle enables you to use the control panel to turn-
on or turn-off lamps, or change objectives. When turning-on or turning-off
components, it does not matter if you alter the settings by clicking with the
left or right mouse key. Please mind the following when working with com-
ponents with numerous settings: a click with the left mouse key moves the
preferences ahead by one, whereas rightclicking moves the part one step in
the reverse direction.

29
Z drive For a frame with a built-in Z drive, the values of the Z drive are displayed
together with a slider control for adjusting the Z value. By clicking on the
arrows of the slider control, you can move the stage in 1-micron increments.
By clicking the center portion of the slider between the two arrows, you can
move the stage in 10-micron increments. The relative position box allows a
basic height measurement. Simply set the value to zero by clicking Reset.
Upon moving the Z drive, the distance traveled will be indicated.
Note If the Z-slider in the dialog box has been selected (the slider is flashing in
this case), you have alternative options to change the Z-values:
• Use the wheel (on a wheel mouse) to move the Z-drive slider by turning
the wheel.
• Use the Page Up and Page Down keys on the keyboard to move the Z-
slider in steps of 10 microns.
• The up and down arrows of the keyboard represent steps of 1 micron.
Limits... The Limits... button permits the setting of stage limits. If the upper limit of the
Z-drive is set too low, the sample cannot be moved into focus. In this case,
you will have to increase the upper stage limit see page 12.
The tabs The Observation tab allows you to alternate between the defined observa-
tion methods and the objectives.
 Olympus IX81 • Selecting observation methods with the IX control panel

The General tab allows you to do the following:

• change the objective,
• enter the position of the magnification changer on the microscope,
• adapt the lamp voltage,
• change the light path (should your microscope be equipped with a
motorized prism).

Warning The magnification changer in IX81 is neither motorized nor equipped with
a sensor. analySIS therefore cannot know the position of the magnifica-
tion changer. In order to still have your images correctly calibrated, you
must inform analySIS about the current position. Do not forget to update
these settings if you change the position of the magnification changer on
the microscope!
On the Filters tab, you can select the filters to be loaded for every existing
filter wheel.
Should your microscope be equipped with a motorized condenser, you can
change the contrast inserts on the Other tab. If your microscope is equipped
with a motorized mirror unit, you can change the mirror cubes here.

Selecting observation methods with the IX control panel

30

In the Control Panel you can select the observation methods which you have
defined in the Key Configuration: Observation Methods (page 26) dialog
box. An observation method is loaded by simply clicking the corresponding
button. The button will have a depressed appearance as long as the obser-
vation method is active.

Selecting combined observation methods

If you have defined the keys for combined observation methods in the Key
Configuration: Observation methods dialog box, some keys for observation
methods will have a plus-sign after the abbreviation. You can use these
observation methods either alone or in combination with a fluorescence
observation method.
 Selecting observation methods with the IX control panel

Only the
observation
method Bright-
field Reflected is
selected.

The observation
method Brightfield
Transmitted is selec-
ted in combination
with a Fluorescence
observation method.

Note If the Observation tab is not present, no observation methods have been
defined yet. Simply return to the Key Configuration dialog box and define
observation methods there.
Termination of an observation method
You can end an active observation method by either turning it off or selecting

31
another observation method, or by selecting another mirror cube or contrast
insert.
Changing the objectives, the filters or the lamp voltage does not terminate
the observation method. However, these settings are not saved and the next
time the observation method is loaded, the original settings (i.e. those
defined in the Key Configuration dialog box) will be activated.
 Olympus IX81 • The IX image information

The IX image information

Any tif-image acquired while the IX Add-In is running contains, apart from
general information, data regarding the used microscope configuration. This
data is saved on the IX Info tab of the Image Information.

File formats The image information is only saved along with the image if you save your
image in the tif format. With other file formats, this image information will not
be available.
How to open the image information window.
32

1) Select one of the options described below:

• Click the Image Information button in the Standard button bar (the
image information window for the selected image will appear).
• Double click the image buffer with the required image.
• Click on the required image buffer with the right mouse key. In the con-
text menu select the Image Information... command.
• Mark the required image buffer and press [Alt]+[Enter].
2) Click the IX Info tab to see the information stored along with the image
concerning the
microscope configuration.
" You are shown the details of the microscope configuration which
was used during the image acquisition. This data is automatically
saved. So you do not have to enter important information concern-
ing the microscope configuration manually in the Comment field on
the General tab.
 The IX-UCB control box light panel

Apply this configura- You can even set your current microscope configuration to the configuration
tion to the microscope which was true during the image acquisition - provided that all the required
components are named identically and still available. To do so, click the but-
ton Apply this configuration to the microscope.

The IX-UCB control box light panel

The light panel on the IX-UCB control box indicates the functioning of the various components. It can pro-
vide valuable information in case of difficulties.

Green signifies OK. The

blinking of one or more
lights indicates a problem Remote
with the respective compo- Error
nent. An extinguished light
signifies the absence of the Nosepiece
component. If the red "ERR" Prism Control
(error) light is on, this indi- Mirror unit
cates that a component has Condenser turret
been incorrectly plugged in. Filter wheel
Bottom Port
Z-axis

An orange RMT light signifies control by the PC. The RMT light blinks
orange when a PC connection cannot be established.
Interruption in power to any component (e.g. removing the reflected light fil-
ter cube turret) while logged on to the software will also result in a red ERR
light.
How to... Please check the status on the light panel in case of software problems for
an appropriate diagnosis.
1) Close down the software and shut off the control box.
2) Switch on the control box ONLY.

33
3) Check the status of the light panel.
" One or more blinking lights indicate problems with the microscope
itself. Please refer to the respective Olympus manuals to trouble-
shoot such microscope problems (see manual Olympus IX-UCB).
4) If the light panel displays no errors, then start up the software.
5) Click the Log On button in the IX button bar.
6) Check the microscope configuration and compare the entries with the
components present on the microscope; adjust the configuration if nec-
essary.
7) Check the definition of the key configuration; adjust where necessary.
8) Now you may continue with your work at the microscope via software
control.
 Olympus IX81 • Saving Configuration Files

Saving Configuration Files

You can save and reload the IX Add-In configuration files. This can be of use, for example, when the com-
puter on which analySIS operates is replaced, thus requiring analySIS to be reinstalled. If you save your
configuration files onto a removable data medium before the computer is replaced, for example, you can
have quick access to your usual IX-configurations after you have reinstalled and loaded them on your
new computer.

How to... Saving Configuration Files

1) If need be, start the IX Add-In software and log in. Make sure you log
in with administrator rights.
2) Press the SHIFT key on your keyboard and keep it depressed while
clicking the User Settings button.
" The User Settings dialog box appears with the additional buttons
Import Configurations... and Export Configurations....
34

3) To save your configuration files, use the Save Configurations... button.

Your corresponding key configurations are automatically exported as
well.
Note You can only save all of the configurations on your computer; there is no
possibility to select a certain one.
4) Once you have saved your configuration files, you or another user can
reload them anytime on another computer on which IX Add-In has been
installed.
 Saving Configuration Files

How to... Import the configuration files

1) Press the SHIFT key on your keyboard and keep it depressed while
clicking the User Settings button.
" The User Settings dialog box appears, with the additional buttons
Import Configurations... and Export Configurations....
2) Click Import Configurations… in the User settings dialog box.

3) Select the location where you have saved your configuration files and
click OK. (You can only import all demo configuration files, there is no
option to select a special one.)
" Your configurations will now be imported. Open the list in the Micro-
scope configuration field to view them.
4) To load one of the configurations, select the configuration in the field
Microscope configuration. Also select the corresponding key configura-
tion in the Key configuration field.
5) Click Save and Close.

35
6) From now on, your selected configurations will be loaded when you
access the IX Control Panel. If need be, check again to see if this con-
figuration is still completely in agreement with the currently available
microscope components.
 Olympus IX81 • Saving Configuration Files
36
 Index

A E
Administrator rights 8 Error
Apply this configuration to the microscope 33 all buttons of the IX Add-In are disabled 7
Assign a microscope configuration 6 falsely calibrated images 30
Assigning a macro to a key 19, 23
Available filter wheels 14
F
First configuration of the microscope 8
B Focus speed 11
BF 18, 26 Frame
Bottom Port Camera 11 key configuration 21
Button bar IX 5 Free position 14
Button bar IX Softkey 5
Button Get Microscope Status 20
Button Set COM port... 3 G
General Tab 30
Get Factory Values 20
C Get Microscope Status button 20
Cap 11
Change password 8
Changing the microscope hardware 10 H
Changing the settings for existing users 7
Close shutter 11 Handswitch, key configuration 21, 22
Configuration files Heat protection of optical components 11
import 35
save 34
Configure input channel for IX remote control 3 I
Correctly calibrated images 30 Image calibration 30
Create new users 6 Image information 32

37
Installation 1
intX (intelligent exposure) 15
D IX button bar 5
Default password for new users 7 IX info 32
Default settings IX Softkey button bar 5
Handswitch keys 22 IX2 Remote and Control 1
Default settings frame keys 21 IX51/71 microscope 1
Default user’s right 7 IX81 Z-Stage 2
Define microscope configuration 5 IX-UCB light panel 33
Defining combined observation methods 26
Defining Softkeys 23
Delete the settings for all keys 20 K
Deleting a single key definition 20 Key Configuration
DF 18 assign 6, 7
DIC 18, 26 define 21
Dongle 1 delete 18
select 19
 Index

test 22 Read Z 15
RS232-cable 8

L
Log On 5
M Set stage limits 12
Magnification changer 11, 30
Microscope Control 5, 9
Motorized mirror 11
Motorized Prism 11
Mouseover function 28
S
Set COM port... button 3
Set remote COM Port 3
Set Z >> 15
Shutter position 11
Shutter, close automatically 11
Side Port-Camera 11
Skip position 14
Stage limits 12

N T
ND filters 26 Template for key configurations 16
New user password 7 tif-format 32
New users 6

U
O
UCB control box plugs 14
Observation method User Settings 6
combined 26 User’s rights 6
define 25, 26
end 31
predefined 17

P
38

Parfocality correction 12
Password
case-sensivity 7
for new users 7
forgotten 7
Personal entry 17, 18
PH 18, 26
Plugs 14
Plus-sign 30
PO 18
Predefined observation methods 17
Prism 11

R
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