Manual
labSens
IMAGING SOFTWARE
Any copyrights relating to this manual shall belong to Olympus Soft Imaging
Solutions GmbH.
We at Olympus Soft Imaging Solutions GmbH have tried to make the information
contained in this manual as accurate and reliable as possible. Nevertheless,
Olympus Soft Imaging Solutions GmbH disclaims any warranty of any kind,
whether expressed or implied, as to any matter whatsoever relating to this
manual, including without limitation the merchantability or fitness for any
particular purpose. Olympus Soft Imaging Solutions GmbH will from time to time
revise the software described in this manual and reserves the right
to make such changes without obligation to notify the purchaser. In no event
shall Olympus Soft Imaging Solutions GmbH be liable for any indirect, special,
incidental, or consequential damages arising out of
purchase or use of this manual or the information contained herein.
No part of this document may be reproduced or transmitted in any form or by any
means, electronic or mechanical for any purpose, without the prior written
permission of Olympus Soft Imaging Solutions GmbH.
© Olympus Soft Imaging Solutions GmbH
All rights reserved
Printed in Germany
Version 510_UMA_labSens_Fraser_EN_00_19.11.2010
Olympus Soft Imaging Solutions GmbH, Johann-Krane-Weg 39, D-48149 Münster,
Tel. (+49)251/79800-0, Fax: (+49)251/79800-6060
Contents
1. Before you start............................................................................................. 4
1.1.About this manual .......................................................................................................... .....4
1.2.What is labSens?................................................................................................................4
2. Working with labSens................................................................................... 5
2.1.User interface......................................................................................................................5
2.2.Layout..................................................................................................................................6
2.3.Document group..................................................................................................................8
2.4.Tool Windows......................................................................................................................9
2.5.Working with documents...................................................................................................10
3. Configuring the system.............................................................................. 12
3.1.Overview - System Configuration .....................................................................................12
3.2.Device Settings - Nosepiece.............................................................................................13
3.3.Setting up a new database................................................................................................14
4. Tool window - labSens................................................................................ 17
4.1.Starting and ending cases.................................................................................................19
4.2.Acquiring images...............................................................................................................20
4.3.Annotating and measuring images ...................................................................................21
5. Acquiring specific images.......................................................................... 28
5.1.Acquiring a single image...................................................................................................28
5.2.Acquiring a Z-stack ...........................................................................................................29
5.3.Creating stitched images...................................................................................................32
1. Before you start
1.1. About this manual
The documentation for your software consists of two parts: the online help and
this manual.
Where do you find
which information?
Writing convention
used in the
documentation
1.2. What is labSens?
Main features of
your software
Additional
functionality
labSens
tool window
In the manual, you will find both an introduction to the product and an explanation
of the user interface. By using the extensive step-by-step instructions you can
quickly learn the most important procedures for using this software.
In the online help, you will find detailed help for your software.
In this documentation, the term "your software" will be used for labSens.
labSens is a software used for microscopy in laboratory environments and in a
pathological routine environment. It supports various kinds of hardware such as
digital cameras and motorized microscopes and stages.
The main functions of labSens ensure quick and handy workflows for the
following tasks:
Controlling digital cameras
Acquiring images
Annotating images
Measuring images
There are additional software solutions available for labSens offering enhanced
functionality.
NetCam
NetCam enables the user to transmit/stream a live image via a web
server to browser based clients.
Patho
The Patho solution extends the workflow and enables the case wizard.
This package contains a dedicated database system. The Patho solution
guides the users through image acquisition and allows them to sav e all
acquired images by case and slide in dedicated folders in the database.
The labSens tool window guides users during image acquisition and helps to
store all acquired images by case and slide.
Before you start
00018
20001
4
2. Working with labSens
2.1. User interface
The graphical user interface determines your software's appearanc e. It specifies
which menus there are, how the individual functions can be called up, how and
where data, e.g. images, is displayed, and much more. Here, the basic elements
of the user interface are described.
Appearance of the user interface
Working with labSens
(1) Menu bar
(2) Document
group
(3) Toolbars
(4) Tool windows
The illustration shows the schematic user interface with its basic elements.
You can call up many commands by using the corresponding menu. Your
software's menu bar can be configured to suit your requirements. Use the Tools
> Customization > Start Customize Mode... command to add menus, modify, or
delete them.
Further information is available in the online help.
The document group contains all loaded images.
When you start your software, the document group is empty. While you use your
software, it gets filled - e.g., when you load or acquire images, or perform various
image processing operations to change the source image and create a new one.
Commands you use frequently are linked to a button providing you with quick
and easy access to these functions. Please note that there are many functions
which are only accessible via a toolbar, e.g., the drawing functions required for
annotating an image. Use the Tools > Customization > Start Customize Mode...
command to modify a toolbar's appearance to suit your requirements.
Tool windows combine functions into groups. These may be very different
functions. For example, in the Properties tool window you will find all the
information available on the active document.
In contrast to dialog boxes, tool windows remain visible on the user interface as
long as they are switched on. That gives you access to the settings in the tool
windows at any time.
5
(5) Status bar
2.2. Layout
Working with labSens
The status bar shows a lot of information, e.g., a brief description of each
function. Simply move the mouse pointer over the command or button for this
information.
Further information is available in the online help.
00108
Overview - Layouts
To switch backwards and forwards between different layouts, click the name of
the layout you want in the menu bar, or use the View > Layout command.
Please note: There is usually only one layout available in your software version.
A description of this layout can be found in the online help. If only one layout is
available, the name of the layout is not displayed in the menu bar.
If you received the "Patho" solution with your software, the following layouts are
available:
Acquire images ("Acquisition" layout)
Manage records and measurements ("Review" layout)
00013
What is a layout?
The user interface is configurable, so that you can easily adapt it to meet the
requirements of individual users or tasks. You can choose a so-called "layout"
that is suitable for the task on hand. A "layout" is an arrangement of the control
elements on your monitor that is optimal for the task at hand. In any layout, only
the software functions that are important in respect to this layout will be available.
Please note: There is usually only one layout available in your software version.
6
Working with labSens
Which elements of the user interface belong to the layout?
The illustration shows you the elements of the user interface that belong to the
layout.
(1) Toolbars
(2) Tool windows
(3) Status bar
Activating a layout
Please note: There is usually only one layout available in your software version.
For this reason, you can't activate any other layouts and no other layouts are
displayed in your menu bar.
There are several ways in which you can activate a layout.
1. Use the View > Layout command to open a menu containing all of the
available layouts. Select the layout you want from this menu.
2. You will find a tab for each layout at the top right corner of the user
interface. Click the name of the desired layout (1).
3. For each layout, you will find the Layout (2) button next to the tabs
located to the right side of the menu bar. Click this button to open a
menu with all of the available layouts. Select the layout you want from
this menu.
Editing layouts
You can
have the user interface's individual elements shown or hidden.
You have not only the possibilities of hiding or showing the user interface's
elements and changing their size and position. As well as that, you can also
change existing toolbars, or even set up your own. These changes will not be
saved in the layout, but instead, in the configuration. They will remain available to
you, even when you return the layout to its standard form.
change a layout at any time. Use the commands in the View menu to
7
Saving and resetting layouts
Changes made in layouts will be automatically saved. Use the View > Layout >
Reset Current Layout command to reset the layouts to their default configuration.
2.3. Document group
The document group contains all loaded documents.
Appearance of the
user interface
Working with labSens
00014
Button with a hand
On the left, the illustration shows a schematic representation of a user interface.
On the right, the document group is shown enlarged.
(1) Document group in the user interface
You will find the document group in the middle of the user interface. In it you will
find all of the document
and the images resulting from, e.g., any image processing function, will be
displayed there.
(2) Document bar in the document group
The do
For every loaded document, an individual field will be set up in the document
group. Click the name of a document in the document bar to have this document
displayed in the document group. The name of the active document will be
shown in color. Each type of document is identified by its own icon.
(3) Buttons in the document bar
At the top right of the document bar you
Click the button with a hand on it to extract the document group from the user
interface. In this way you will create a document window that you can freely
position or change in size.
If you would like to merge two document groups, click the button with the hand in
one of the two document groups. While pressing the left mouse button, drag the
document group with all the files loaded in it, onto an existing one.
cument bar is the document group's header.
s that have been loaded or acquired. Also the live-image
will see several buttons.
8
You can only position document groups as you wish when you are in expert
mode. In standard mode the button with the hand is not available.
Arrow button
Button with a cross
The arrow buttons located at the top right of the document group are, to begin
with, inactive when you start your software. The arrow buttons will only become
active when you have loaded so many documents that all of their names can no
longer be displayed in the document group. Then you can click one of the two
arrows to make the fields with the document names scroll to the left or the right.
That will enable you to see the documents that were previously not shown.
Click the button with a cross to close the active document. If it has not yet been
saved, the Unsaved Documents dialog box will open. You can then decide
whether or not you still need the data.
(4) Navigation bar in the image window
Some image
this navigation bar, e.g., to specify how a Z-stack is to be displayed on your
monitor, or to change this.
2.4. Tool Windows
Tool windows combine functions into groups. These may be very different
functions. For example, in the Properties tool window you will find all the
information available on the active document.
Working with labSens
s have their own navigation bar directly in the image window. Use
00139
Docked tool
windows
Freely positioned
tool windows
Position of the tool windows
The user inte
windows can be docked, freely positioned, or integrated in document groups.
Tool windows can be docked to the left or right of the document window, or
below it. To save space, several tool windows may lie on top of each other. They
are then arranged as tabs. In this case, activate the required tool window by
clicking the title of the corresponding tab below the window.
You can only position tool windows as you wish when you are in expert mode.
You can set a tool window to float at any time. The tool window then behaves
exactly the way a dialog box does. To release a tool window from its docked
position, click on its header with your left mouse button. Then while pressing the
left mouse button, drag the tool window to wherever you want it.
Buttons in the header
In the heade
Hide and Close.
rface is to a large degree configurable. For this reason, tool
r of every tool window, you will find the three buttons Help, Auto
9
Click the Help button to open the online help for the tool window.
Click the Auto Hide button to minimize the tool window.
Click the Close button to hide the tool window. You can make it reappear at any
time, by using the View > Tool Windows command.
Context menu of the header
To open a
can contain the Auto Hide and Transparency commands. Which commands will
be shown, depends on the tool window.
Additionally, the context menu contains a list of all of the tool windows that are
available. Every tool window is identified by its own icon. The icons of the
currently displayed tool windows will appear clicked. You can recognize this
status by the icon's background color.
Use this list to make tool windows appear.
context menu, rightclick a tool window's header. The context menu
2.5. Working with documents
You can choose from a number of possibilities when you want to open, save, or
close documents.
Please note: Your software version supports only documents belonging to the
document type "Image". Thus, the term "Documents" means "Images" in this
manual.
Saving documents
Autosave and
close
You can recognize documents that have not been saved by the star icon after the
document's name.
There are a number of ways to save documents.
1. Save your documents in a database. That enables you to store all
manner of data that belongs together in one location. Search and filter
functions make it quick and easy to locate saved documents. Detailed
information on inserting documents into a database can be found in the
online help.
A database is only available if you have the "Patho" solution for your
software.
2. To save a single document, activate the document in the document
group and use the File > Save As... command.
3. Use the Gallery tool window.
Select the desired document and use the Save command in the context
menu. For the selection of documents, the standard MS-Windows
conventions for multiple selection are valid.
1. If you have purchased the "Patho" solution with your software, you have
a database available to you.
In the labSens tool window, the workflow is then organized as a series of
cases for you to work on. First, click the Start Case button and perform
all of the image acquisitions, annotations and measurements necessary
for this case. The images are automatically saved in the database.
Working with labSens
00037
10
Closing documents
Opening
documents
Working with labSens
2. When you exit the software, all of the data that has not yet been saved
will be listed in the Unsaved Documents dialog box. This gives you the
chance to decide which documents you still want to save.
3. With some acquisition processes, the acquired images will be
automatically saved after the acquisition has finished. You will find an
overview of the acquisition processes that are supported in the online
help.
4. You can also configure your software in such a way that all images are
saved automatically after image acquisition. To do so, use the
Acquisition Settings > Saving dialog box.
There are a number of ways to close documents.
1. To close a single document, activate the document in the document
group and use the File > Close command. Alternatively, you can click the
button with the cross
. You will find this button on the top right in the
document group.
2. Use the Gallery tool window.
Select the desired document and use the Close command in the context
menu. For the selection of documents, the standard MS-Windows
conventions for multiple selection are valid.
There are a number of ways to open or load documents.
1. Use the File > Open... command.
2. Use the File Explorer tool window.
3. Drag the document you want directly out of the MS-Windows Explorer,
onto your software's document group.
4. To load documents out of a database into the document group, use the
Load Documents command.
00143
11
3. Configuring the system
3.1. Overview - System Configuration
Configuring the system
Why do you have
to configure the
system?
When do you have
to configure the
system?
After successfully installing your software you will need to first configure your
image analysis system, then calibrate it. Only when you have done this will you
have made the preparations that are necessary to ensure that you will be able to
acquire high quality images that are correctly calibrated. When you work with a
motorized microscope, you will also need to configure the existing hardware, to
enable the program to control the motorized parts of your microsco pe.
You will only need to completely configure and calibrate your system anew when
you install and start the software on your PC for the first time. When you later
change the way your microscope is equipped, you will only need to change the
configuration of certain hardware components, and possibly also recalibrate
them.
Process flow of the configuration
To set up your software, the following st
Selecting the camera and the microscope
Specifying which hardware is available
Configuring the interfaces
Configuring the specified hardware
eps will be necessary:
Calibrating the system
All these commands are only available to you when you start the software as
Administrator or Power User. Further information on user rights is available in the
online help.
Selecting the camera and the microscope
The first time
quick configuration with some default settings will be made. In this step you need
only to specify the camera and microscope types in the Quick Device Setup
dialog box. The microscope will be configured with a selection of typical
hardware components. Further information is available in the online help.
Specifying which hardware is available
Your software has to kno
equipped with. Only these hardware components can be configured and
you start your software after the installation has been made, a
w which hardware components your microscope is
12
Quick Device
Setup
Quick Device
Setup
Configuring the system
subsequently controlled by the software. In the Acquire > Devices > Device List
dialog box, you select the hardware components that are available on your
microscope.
If you use a preset configuration in the Quick Device Setup dialog box, check in
this step whether the preset hardware components really comply with your
system.
Configuring the interfaces
Use the Interf
or other motorized components, and the PC on which your software runs.
If you use a preset configuration in the Quick Device Setup dialog box, you can
skip this step.
Configuring the specified hardware
Usually vario
stage, will belong to your system. Use the Acquire > Devices > Device S e ttings...
dialog box to configure the connected devices so that they can be correctly
actuated by your software.
Calibrating the system
n all of the hardware components have been registered with your software
Whe
and configured, the functionality of the system is already ensured. However, it's
only really easy to work with the system and to acquire top quality images, when
you have calibrated your software. The detailed information that helps you to
make optimal acquisitions will then be available.
Your software offers a wizard that will help you while you go through the
individual calibration processes. Use the Acquire > Calibrations... command to
start the software wizard.
aces dialog box to configure the interface between your microscope
us different devices, such as a camera, a microscope and/or a
00159
3.2. Device Settings - Nosepiece
Why must the
nosepiece be
configured?
Documentation of
the microscope
settings during
image acquisition
Your software has to know with which objectives your microscope is equipped,
and at which position in the nosepiece each one is fitted. Only then will the
buttons on the Microscope Control toolbar be correctly defined. Then you will find
that every objective has its own button on the toolbar.
Before you make an image acquisition, click the button with the objective in use,
otherwise the image you acquire will not be correctly calibrated. Only on correctly
calibrated images will the scale bar show the correct scale. Also for making
measurements, correctly calibrated images are an essential prerequisite.
When you exchange or add objectives, you must register the new objectives and
their position in the objective revolver with the system.
All of the information in this dialog box will be automatically adopted in the
Properties tool window during the acquisition. You will find this information in the
Microscope group. This information is saved with the image if you save it in the
TIF or VSI image file format. It will be displayed again when the image is loaded.
13
Configuring the objective nosepiece
1. Use the Acquire > Devices > Device Settings... command.
2. Select the Lightpath entry in the Sort by list.
3. In the tree structure, select the General > Manual Nosepiece entry (if you
have a manual microscope), resp. General > Nosepiece <Name of the
nosepiece> (if you have a motorized microscope).
On the right hand side of the dialog box, the current configuration of
the nosepiece will be displayed. When you configure the software for
the first time, the fields for the details referring to your objectives will
be empty.
4. Enter all of the objectives that are curre ntly fitted to your no sepiece.
5. Close the Device Settings dialog box with OK or continue with the
configuration of further hardware components.
Every objective you have selected will then be offered on the
Microscope Control toolbar and in the labSens tool window.
3.3. Setting up a new database
If you have purchased the "Patho" solution with your software, you have a
database available to you. In the labSens tool window, the workflow is then
organized as a series of cases for you to work on. First, click the Start Case
button and perform all of the image acquisitions, annotations and measurements
necessary for this case. The images are automatically saved in the database.
Only the database administrator can set up a database.
Use the database template that is provided to set up a new database. Only then
can you use the labSens tool window to create new cases in a database.
1. Select the Database > New... command.
The New Database dialog box will open. This dialog box works in a
similar manner to a wizard. It guides you step-by-step through the
setting up of a database.
Step 1: Selecting a
database server
2. Specify in the Database Server field on which database server the
database is to be set up. If you have already set up a database on this
server from your PC, you will find the required server in the picklist.
Alternatively, click the button [ … ] with the three points. The Select
Servers dialog box will open. Here, select the server from the
Available database servers list, then click the Add >> button. Click
the OK button to close the dialog box and return to the New
Database dialog box.
The database file is located on the database server. The documents
e.g., the images, can also be located on another PC, or even on
several different PCs. You will find more information on document
storage in a database in the online help.
3. In the User Authentication group, you select the way you (and all future
users) are to log on to this database.
Configuring the system
2288
14
Step 2: Entering
the name of the
database, and
specifying the
storage location for
documents
Step 3: Selecting a
database template
Configuring the system
Select Single Sign On entry. With Windows Authentication, the data with
which the user logs on to MS-Windows will also be used for logging on to
the database.
You can also select the SQL Authentication entry.
With SQL Authentication the log-on data that has been defined for
Microsoft SQL Server will be used. Every user of your database must
know the log-on data (supplied by the database administrator) and
has to enter them in the User Name and Password fields to be able
to open the database.
The first step in setting up a database has now been completed.
4. Click the Next > button.
5. Enter the name of the database in the Database Name field. The name
must not be longer than 20 characters and must not contain any spaces
or special characters. Under this name you'll find the database in the
Open Database dialog box later on.
6. If the new database is to become your standard database, select the Use
as standard database check box. This option makes sense when you
mostly work with the same database.
Later on, you can use the Tools > Options > Database > Standard
database command to specify that the standard database will be
automatically opened whenever you start your software.
7. Enter the directory in which the documents are to be stored. To do so,
click the button [ … ] with the three points located next to the Document
Storage Path field, then browse to the directory you want to use.
Note: When several people are to work with the database, select a
directory which is also available to other users of this database.
If you're the only user of the database, you can also choose a local
directory on your own PC.
Note: To have your database with all of its documents regularly saved,
make sure that both the database server, and the PC on which the
documents are stored are incorporated in an automatic data back-up
process (e.g., every night).
8. When you work with several databases, enter a descriptive text for the
new database in the Database Description field. This text will later be
displayed in the Open Database dialog box (when you use the Use
database connection file connection mode).
9. Click the Next > button.
10. In the Template File Path field, choose a database template. A database
template has the file extension DBE.
A database template already contains a defined database structure.
Your software will have been supplied with a database template.
During the software installation, the template is installed in the
following directory:
..\Documents and Settings\All Users\Application Data\Olympus\OSIS
\ <Name of the software>\Database\DBE
15
Step 4: Checking
the options for the
new database
Configuring the system
11. Click the Next > button.
The wizard's next dialog box shows you all of the options that you
have set up for the new database.
12. Check the options for the new database.
Should you want to correct an option, click the underlined term. For
example, click the term "Database Name", if you want to change the
name you've entered.
Should you want to change an option, your software will jump back
to the New Database wizard's corresponding dialog box.
13. Click the Finish button to have the database set up.
The Logging tool window will automatically appear. In it you can
follow the setting up of the new database.
When a database is set up, a database connection file (DBC file) will
be automatically created too. The database connection file makes it
possible for you to quickly log on to this database in the future. You
will find the DBC file in the following directory:
..\Documents and Settings\All Users\Application Data\Olympus\OSIS
\ <Name of the software>
The database will be set up and opened. You can see the database
in the Database tool window.
00337
16
4. Tool window - labSens
Use the labSens tool window as an easy-to-use graphical user interface. All of
the commands that you use on a regular basis are available in this tool window
and are displayed as large buttons.
If the labSens tool window is hidden, use the View > Tool Windows > Record
Details > labSens command to make it appear.
What can you use
the tool window
for?
Buttons colored
gray in the tool
window
Use the labSens tool window to acquire, annotate, and measure images. If you
have purchased the "Patho" solution with your software, you have a database
available to you. The workflow is then organized as a series of cases for you to
work on. First, click the Start Case button and perform all of the image
acquisitions, annotations and measurements necessary for this case. The
images are automatically saved in the database. A case folder is created in the
database for every case that you work on. Every case folder contains a subfolder
for each microscope slide that you’ve examined.
Please note: If you haven't purchased the "Patho" solution with your software,
you won't have a database and the case processing feature available to you. In
this case, use the File > Save and File > Save As... commands to save the
images on your hard disk.
In the labSens tool window, buttons are only active if their function is relevant to
the current step. Inactive buttons appear in gray. In this way, you'll be guided
through the case step by step after clicking the Start Case button.
Tool window - labSens
17
Structure of the
tool window
Tool window - labSens
(1) Starting and ending cases
(2) Acquiring images
(3) Annotating and measuring images
18
4.1. Starting and ending cases
Please note: The buttons relevant to cases are only available if you have
purchased the "Patho" solution with your software.
Click this button to start working on a new case. At the beginning of a case, this
button is the only active one.
1. Click the Start Case button.
The database opens if it is still closed.
2. In the Insert Case Folder dialog box, enter the barcode of the new case.
You can also enter an accession number and a patient ID here.
3. Click the Insert button in this dialog box.
4. In the Insert Slide Folder dialog box, enter the bar code of the
microscope slide that you want to acquire an image of.
You can also enter more information on the microscope slide here.
5. Click the Insert button in this dialog box.
A new record of the "Case Folder" type is automatically created in
the database, as well as a child record of the "Slide Folder" type for
the first microscope slide.
6. Acquire all of the necessary images of the microscope slide and use the
annotation and measurement functions if required.
Tool window - labSens
Start Case
Finishing the slide
analysis
Add Slide
Click this button if you want to acquire images of another microscope slide.
1. Click the Add Slide button.
You will then be asked whether all of the currently open images
should be saved in the slide folder of the current microscope slide.
2. In the Insert Case Folder dialog box, enter the barcode of the new case.
3. Click the Insert button in this dialog box.
In the database, a new slide folder is automatically created for the
new microscope slide. This slide folder is a child record of the current
case folder.
Only use the Add Slide button if you have finished acquiring, annotating and
measuring all necessary images from the current microscope slide. All acquire d
images of the current microscope slide are opened in the document group and
are displayed in the Gallery tool window as thumbnails. No other images will be
open if you haven't manually loaded further images into the document group
while using the labSens tool window.
You will be asked whether you want to save all images displayed in the gallery to
the current slide folder. It usually makes sense to click Yes. The images will then
19
Refusing some
images of a slide
Finishing the slide
analysis
Tool window - labSens
be saved in this slide folder. Afterwards, the images are automatically closed,
i.e., they are no longer shown in the document group or in the Gallery dialog box.
If you click No, the images aren't saved in the slide folder and remain open.
You can manually close an opened image, such as an unsuccessful image
acquisition any time you want. To do this, select the image in the Gallery dialog
box and press the [Del] key on your keyboard.
End Case
Click this button to finish working on the current case.
Only use the End Case button if you have finished acquiring, annotating and
measuring all necessary images from the current microscope slid e. Please note
the explanations from the Add Slide button.
Cancel
Click this button to cancel working on a case.
4.2. Acquiring images
Camera
Switch On Live display
Click this button to start or stop live mode. The live-image is displayed in the
document group.
Acquire a Snapshot
Click this button to stop live mode and acquire an image. The acquired image is
displayed in the document group.
Start Auto Focus
Click this button so that the software will switch to the live mode and verify the
focus of various Z-positions. The stage then returns to the Z-position with the
best focus in order to acquire the sharpest possible image.
20
Tool window - labSens
Magnification
Click one of the objective buttons to select the corresponding magnification. The
active button will then indicate the magnification you've selected. The active
button can be identified by its orange color and a check-mark.
Switch on / off NetCam
Click this button to turn the NetCam function on or off. The button will appear
clicked when NetCam is active. You can recognize this by its orange color. Users
can now make a connection between their own PCs and the NetCam server and
receive the images you have loaded. The NetCam function is only available if
you have purchased the "NetCam" solution with your software. Further
information on the NetCam function is available in the online help.
This button isn't relevant to your software version.
4.3. Annotating and measuring images
All image objects, text objects, and measurement objects you insert in the image
are written as vector graphics to a specific vector plane. Further information is
available in the online help.
General
Select a drawing or measurement object
Click this button to select an object in the image.
1. Click the Select a drawing or measurement object button.
2. Move the mouse pointer onto the image object.
The mouse pointer will then have the shape of a four-pronged
arrowhead.
3. Click on the image object to edit it.
If you want to change the position of the image object, be sure that
the mouse pointer is shaped like a four-pronged arrowhead.
If you want to change the size of the image object, move your mouse
pointer over the handles of the image object until the mouse pointer
21
Tool window - labSens
takes the shape of a small square. The small arrows next to the
square indicate that you can move the handle. This is how you
change the size of the image object.
If you want to change the properties of the image object, doubleclick
on the image object. The Drawing Object Properties dialog box
opens. Here you can change the color, for example.
Delete selected drawing or measurement
Click this button to delete the selected object from the image.
Show or hide drawings and measurements
Click this button to display or hide the drawn objects.
Drawings
Draw a free hand polygon
Click this button to draw an image object in the shape you need.
1. Click the Draw a free hand polygon button.
The software switches to drawing mode. You can see that the
software is in drawing mode by the handles.
2. Press and hold the mouse button and draw the image object.
You can still change an image object's position and shape later.
3. If you're satisfied with the position and shape of the image object, click
the Select a drawing or measurement object button.
Your software then switches off drawing mode.
Draw an arrow
Click this button to draw an arrow.
1. Click the Draw an arrow button.
The software switches to drawing mode. You can see that the
software is in drawing mode by the handles.
2. Click on the image to set the start point of the arrow.
3. Press and hold the mouse button and set the arrow.
The start point and end point are both indicated by a handle.
You can still change the arrow's length and position later.
22
Adding a text field
Changing the
width and height of
a text object at any
time
Changing the
position of a text
object at any time
Editing text in a
text object at any
time
Tool window - labSens
4. If you're satisfied with the arrow, click the Select a drawing or
measurement object button.
Your software then switches off drawing mode.
Add a text field
Click this button to add a text object to the image. Use this option to add text
directly to an interesting part of the image.
1. Click the Add a text field button.
The mouse pointer has the shape of a small cross.
2. Press and hold the mouse button and set a new text object.
Alternatively, you can doubleclick on the image: By doing so, a text
object with the default width and height is added to the image.
The software switches to text-entry mode. You can see that the
software is in text-entry mode by the blinking cursor in the text object
and dark background.
3. Enter the new text into the text object.
4. When you finish entering the text, click outside of the text object.
Your software then switches off the text-entry mode.
You can still add text objects to other parts of the image once you've
clicked the Add a text field button.
You can still change the width, height, position or text of a text object later.
1. Click the Add a text field button, and then click on the text object.
The text object is surrounded by eight handles.
2. Move the individual handles.
By doing so, you can change the width and height of the text object.
3. If you're satisfied with width and height of the text object, click in the
image outside of the text object.
Your software then switches off the text-entry mode.
1. Click the Add a text field button, and then click on the text object.
The mouse pointer will then have the shape of a four-pronged
arrowhead.
The text object is surrounded by eight handles.
2. Press and hold the mouse button, and drag the entire text object.
3. Click outside of the text object.
1. Click the Add a text field button, and then doubleclick on the text object.
The software switches to text-entry mode. You can see that the
software is in text-entry mode by the blinking cursor in the text object
and dark background.
23
Editing an image
object
Tool window - labSens
2. Edit the text.
3. When you finish editing the text, click outside of the text object.
Measurements
You can find
This tool window is at the same time the measurement display and contains all of
the values that have been measured on the active image.
Click this button to measure the area of a two-dimensional image object.
1. Click the Measure a free hand polygon button.
2. Move the mouse pointer onto a point on the object border. Click on it with
3. Move the mouse pointer onto the next point on the object border. To set
4. Set additional handles along the perimeter of the object.
5. Rightclick to finish the measurement.
You can still change the drawn image object image object later.
1. Move the mouse pointer onto the image object.
2. Move the handle to a different position.
3. Repeat the last step for any other handles that need to be moved.
4. If you're satisfied with the shape of the image object, click the Select a
more measurement functions in the Measurements tool window.
Measure a free hand polygon
The software switches to measurement mode.
The mouse pointer turns into a small cross.
the left mouse button.
The first handle, a small square, is then set.
The mouse pointer has the shape of a small square. The small
arrows next to the square indicate that you can set the next handles.
the handle, click with the left mouse button.
The area is displayed next to the drawn image object.
In the Measurement tool window, the object's perimeter is listed in
addition to the area.
As soon as you move the mouse pointer over a handle, the mouse
pointer changes from a small cross into a small square. The small
arrows next to the square indicate that you can move the handle.
By doing so, you can change the shape and area of the image object.
drawing or measurement object button.
Your software then switches off the measurement mode.
24
Tool window - labSens
Measure a length
Click this button to measure the length of a line in an image.
1. Click the Measure a length button.
The software switches to measurement mode.
The mouse pointer turns into a small cross.
2. Position the mouse pointer over the start point of the line you want to
measure. Click on it with the left mouse button.
The first handle, a small square, is then set.
The mouse pointer has the shape of a small square. The small
arrows next to the square indicate that you can set the second
handle.
3. Position the mouse pointer onto the end point of the line to be measured.
To set the handle, click with the left mouse button.
The length is displayed next to the drawn line.
Editing a line
You can still change the drawn line later.
1. Move the mouse pointer onto the image object.
As soon as you move the mouse pointer over one of the two
handles, the mouse pointer changes from a small cross into a small
square. The small arrows next to the square indicate that you can
move the handle.
2. Move the handle to a different position.
By doing so, you can change the position and length of the image object.
3. Repeat the last step for the second handle if necessary.
4. If you're satisfied with the position and length of the line, click the Select
a drawing or measurement object button.
Your software then switches off the measurement mode.
Options
Set the line color
Click this button to change the color of the selected image objects and
measurement objects. The button is also available if no object is selected. In this
case, you select the color of the next object that you want to draw. The current
color will always be displayed in the lower part of the button.
1. If the Select a drawing or measurement object button has not been
clicked: Click the Select a drawing or measurement object button.
2. Select the objects in the image whose color you want to change.
To do so, move the mouse pointer onto the objects. Once the mouse
25
Tool window - labSens
pointer has the shape of a four-pronged arrowhead, you can select the
object by clicking on it.
You can see that the object is selected by the handles around it.
It is also possible to select several objects. The standard MSWindows conventions are valid for the Multiple Selection.
If you don't select any objects, the color change will only affect the
next objects that you draw.
3. Click the Set the line color button.
A menu opens.
4. Select the color you want from this menu.
The selected objects adopt the selected color.
If you draw a new object, it will have the same color.
There are other software functions available offering additional settings for the
color of measurement objects. Further information is available in the online help.
Set the line width
Click this button to change the line width of the selected image objects. The
button is also available if no object is selected. In this case, you select the line
width of the next object that you want to draw.
1. If the Select a drawing or measurement object button has not been
clicked: Click the Select a drawing or measurement object button.
2. Select the objects in the image whose line width you want to change.
To do so, move the mouse pointer onto the objects. Once the mouse
pointer has the shape of a four-pronged arrowhead, you can select the
object by clicking on it.
3. Click the Set the line width button.
4. Select the line width you want.
The selected objects adopt the selected line width.
Set the font size
Click this button to change the font size of the selected text objects. The button is
also available if no text object is selected. In this case, you select the font size of
the next text object that you want to add to the image.
1. If the Select a drawing or measurement object button has not been
clicked: Click the Select a drawing or measurement object button.
2. Select the text objects in the image whose font size you want to change.
To do so, move the mouse pointer onto the text objects. Once the mouse
pointer has the shape of a four-pronged arrowhead, you can select the
text object by clicking on it.
3. Click the Set the font size button.
26
Tool window - labSens
4. Select the font size you want.
The text in the selected text objects adopts the selected font size.
Set the text color
Click this button to change the font color of the selected text objects. The button
is also available if no text object is selected. In this case, you select the font color
of the next text object that you want to add to the image.
1. If the Select a drawing or measurement object button has not been
clicked: Click the Select a drawing or measurement object button.
2. Select the text objects in the image whose font color you want to change.
To do so, move the mouse pointer onto the text objects. Once the mouse
pointer has the shape of a four-pronged arrowhead, you can select the
text object by clicking on it.
3. Click the Set the text color button.
4. Select the font color you want.
The text in the selected text objects adopts the selected font color.
10162
27
5. Acquiring specific images
In addition to the acquisition functions in the labSens tool window, you can use
your software to make snapshots at your microscope and save the images as a
file.
Furthermore, you can acquire images of specific types: Z-stacks and stitched
images.
What is a Z-stack?
You can combine a series of separate images into one image file. A Z-stack
contains frames acquired at different focus positions. You need a Z-stack, for
example, to calculate an EFI image (Extended Focus Image) with the Process >
Enhancement > EFI Processing... command.
A standard image is two dimensional. The position of every pixel will be
determined by its X and Y-values. With a Z-stack, the focus position resp. the
height of the sample, is an additional item of information for every pixel.
What is a stitched
image?
Use the Process > Multiple Image Alignment… menu command to have several
separate images combined, as with a puzzle, into a stitched image. (MIA stands
for Multiple Image Alignment.) The stitched image will display a large sample
segment in a higher X/Y-resolution than would be possible with a simple
snapshot.
Acquiring specific images
The illustration shows left, four individual images. On the right you see the
stitched image made up from the four images.
5.1. Acquiring a single image
You can use your software to acquire high resolution images in a very short
period of time. For your first acquisition you should carry out these instructions
step for step. Then, when you later make other acquisitions, you will notice that
for similar types of sample many of the settings you made for the first acquisition
can be adopted without change.
20002
28
Selecting the
objective
Switching on the
live-image
Setting the image
quality
Acquiring and
saving an image
Acquiring specific images
1. In the labSens tool window, click the button with the objective that you
use for the image acquisition.
2. In the labSens tool window, click the Live
3. Go to the required part of the sample in the live-image.
4. To set the image quality, activate the Camera Control tool window.
You can find a complete description of the Camera Control tool
window in the online help.
5. Bring the sample into focus. The Focus Indicator toolbar is there for you
to use when you are focusing on your sample.
6. Check the color reproduction. If necessary, carry out a white balance.
7. Check the exposure time. You can either use the automatic exposure
time function, or enter the exposure time manually.
8. Select the resolution you want.
9. Return to the labSens tool window.
10. In the labSens tool window, click the Snapshot
The image you have acquired will be shown in the document group.
11. Use the File > Save As... command to save the image. Use the
recommended TIF file format.
button.
button.
00048
5.2. Acquiring a Z-stack
With the Z-Stack acquisition process, you acquire a series of frames one after
the other, a Z-stack.
Acquiring a Z-stack
The acquisition process is only available when your microscope stage is
equipped with a motorized Z-drive.
Example: You want to acquire a Z-stack. The sample is approximately 50 µm
thick. The Z-distance between two frames is to be 2 µm.
1. Switch to the "Acquisition" layout. To do this, use, e.g., the View > Layout
> Acquisition command.
Selecting the
objective
Setting the image
quality
2. On the Microscope Control toolbar, click the button with the objective that
you want to use for the image acquisition.
3. Switch to the live mode, and select the optimal settings for your
acquisition, in the Camera Control tool window. Pay special attention to
setting the correct exposure time. This exposure time will be used for all
of the frames in the Z-stack.
29
Selecting the
acquisition process
Acquiring specific images
4. Search out the required position in the sample.
5. Activate the Process Manager tool window.
6. Select the Automatic Processes option.
Selecting the
acquisition
parameters
Acquiring the
image
7. Click the Z-Stack
The button will appear clicked. You can recognize this status by the
button's colored background.
The [ Z ] group will be automatically displayed in the tool window.
9. Select the Range entry in the Define list.
10. Enter the Z-range you want, in the Range field. In this example, enter a
little more than the sample's thickness (= 50 µm), e.g., the value 60.
11. In the Step Size field, enter the required Z-distance, e.g., the value 2, for
a Z-distance of 2 µm.
In the Z-Slices field you will then be shown how many frames are to
be acquired. In this example 31 frames will be acquired.
12. Find the segment of the sample that interests you and focus on it. To do
this, use the arrow buttons in the [ Z ] group. The buttons with a double
arrow move the stage in larger steps.
13. Click the Start
Your software now moves the Z-drive of the microscope stage to the
start position. The starting positions lies half of the Z-range deeper
than the stage's current Z-position.
The acquisition of the Z-stack will begin as soon as the starting
position has been reached. The microscope stage moves upwards
step by step and acquires an image at each new Z-position.
button.
button.
The Start Process button changes into the Pause
on this button will interrupt the acquisition process.
The Stop
stop the acquisition process. The Z-stack as acquired up till then, will
be preserved.
The acquisition has been completed when you can once more see
the Start
progress bar has been faded out.
You can see the acquired Z-stack in the image window. Use the
navigation bar located in the image window to view the Z-stack.
Further information on the navigation bar is available in the online
help.
The Z-stack that has been acquired will be automatically saved. You
can set the storage directory in the Acquisition Settings > Saving >
Process Manager dialog box. The preset file format is VSI.
button will become active. A click on this button will
button in the Process Manager tool window, and the
button. A click
30
Setting the EFI
parameters
Preparing for the
acquisition of a
Z-stack
Acquiring specific images
Tip: When other programs are running in the background on your PC, for
instance a virus scanning program, it can interfere with the performance when a
Z-stack is being acquired.
Acquiring an EFI image
Example: You have a thick section in the transmitted light mode, or a sample with
a three dimensional surface in the reflected light mode, e.g., with holes, grooves,
bumps peaks or slanting planes. In the image it's only possible to bring one focus
plane, resp. only part of the surface, sharply into focus, higher-lying or deeperlying areas are outside the depth of focus range. Acquire a Z-stack through the
complete thickness resp. height, of the sample, and have the EFI image
calculated for you.
1. Activate the Process Manager tool window.
2. To open the Acquisition Settings dialog box, click the Acquisition Settings
button in the tool window's toolbar.
3. Select the Acquisition > Automatic EFI entry in the tree view.
4. In the Algorithm list, select the Transmitted light (exp) entry, if you're
working in the transmitted light mode, and the Reflected light entry if
you're working in the reflected light mode.
5. Select the Automatic frame shift check box when you're working with a
stereo microscope and acquiring the sample at a viewing angle.
Otherwise, clear this check box.
6. Close the Acquisition Settings dialog box with OK.
1. Carry out all the microscope settings.
2. In the Microscope Control toolbar, click the button corresponding to the
objective you've set.
3. Activate the Camera Control tool window.
4. Switch to the live mode.
5. Optimize the exposure time. The exposure time will be kept constant
during the acquisition of the Z-stack.
Setting the Z-stack
parameters
6. Click the Autofocus
toolbar to focus.
1. Activate the Process Manager tool window.
2. Select the Z-Stack
3. Select the Top & Bottom entry in the Define list.
4. Use the arrow buttons in the [ Z ] group to move your stage to the Zposition at which the lowest-lying position on the sample is sharply
focused.
The arrow buttons move the stage by steps of 2 µm resp. of 20 µm.
The stage's current position will be shown to you in the Pos. field.
button in the Camera Control tool window's
acquisition process.
31
Acquiring specific images
5. Click the top Set button to define the starting position for the Z-stack
acquisition.
The current Z-position will be adopted in the Start field.
6. Use the arrow buttons in the [ Z ] group to move your stage to the Zposition at which the highest-lying position on the sample is sharply
focused.
7. Click the bottom Set button to define the position at which the Z-stack
acquisition is to end.
The current Z-position will be adopted in the Start field.
8. In the Step Size field, enter the distance between two frames in the Z-
stack. This Z-distance should be small enough to ensure that no
positions on the sample between two images remain blurred. The higher
your objective's Numerical Aperture is, the smaller the Z-spacing should
be.
9. Use the [Enterl] key to confirm the Z-distance that you've set.
The number of images in the stack will be automatically calculated
on the basis of the Start and End values, and the Z-distance.
10. Select the Extended Focal Imaging check box.
11. Finish the live mode.
12. Click the Start
The acquisition of the Z-stack will start immediately.
The acquisition will begin. After the acquisition has been completed
the EFI image will be shown in the document group. This image was
calculated from the variously focused separate images.
5.3. Creating stitched images
Without or with a
motorized
XY-microscope
stage
Acquiring a
stitched image
without a
motorized
XY-stage
(Manual MIA)
Please note: The following step-by-step-instructions describe how to acq uire a
stitched image using the Manual MIA acquisition process without a motorized
XY-microscope stage. However, you can also use the Manual MIA acquisition
process if your microscope is equipped with a motorized XY-stage. To do so,
select the Use motorized xy stage if available check box. You'll find this check
box in the Acquisition Settings > Acquisition > Manual MIA dialog box. To open
this dialog box, click, e.g., the Acquisition Settings
Manager tool window's toolbar. In this case, you won't need to move the stage
manually.
Example: You want to acquire an image of a large sample area. Use the Manual
MIA acquisition process, to acquire several individual images of adjoining
positions on the sample, and to have them combined into a stitched image.
button.
00367
button in the Process
32
Prerequisite
Selecting the
objective
Setting the image
quality
Selecting the
acquisition process
Acquiring specific images
The camera is aligned parallel to the XY-stage. The angle between camera and
stage should be smaller than 1°.
1. Switch to the "Acquisition" layout. To do this, use, e.g., the View > Layout
> Acquisition command.
2. In the labSens tool window, click the button with the objective that you
want to use for the acquisition of the stitched image.
3. Switch to the live mode, and select the optimal settings for your
acquisition in the Camera Control tool window. Pay special attention to
setting the correct exposure time. This exposure time will be used for all
of the stitched image's individual images.
4. Find the position on the sample at which you want to start acquiring the
stitched image.
5. Finish the live mode.
6. Activate the Process Manager tool window. To do this, use, e.g., the
View > Tool Windows > Process Manager command.
7. Select the Manual Processes option.
Selecting the
acquisition
parameters
Acquiring a
stitched image
8. Click the Manual MIA
The button will appear clicked. You can recognize this status by the
button's colored background.
The Manual MIA group will be automatically displayed in the tool
window.
9. Make quite certain that the Auto Align button appears clicked. It should
then look like this:
Then your software will search for the same image structures in
neighboring individual images. The stitched image will be put
together in such a way that image areas that are the same will be
superimposed.
A tip if your system is equipped with a motorized XY-stage: Some
motorized microscope stages work so precisely that you can
dispense with an overlapping of the individual images. If you want to
acquire the individual images edge to edge, release the Auto align
button. The individual images will now be set next to one another just
as they were acquired.
10. Click the Start
Your software switches into the live mode.
11. Bring the sample into focus.
12. Click on one of the arrow buttons to set the side of the current image at
which the next image is to be arranged. For example, click this button
button.
button.
.
if the next image is to be laid to the right of the current image.
Your system now acquires an image at the current position on the
sample. In the image window, you now see on the left (1) the
33
Acquiring specific images
acquired image, and on the right (2) the live-image.
Since you haven't moved the sample, the live-image still shows the
current sample position which means that you now see the current
image twice.
The two images overlap. Since the live-image is shown transparent,
you see both images in the overlap area simultaneously.
13. Make a note of a significant structure on the live-image's right border.
You will find the same sample structure in the overlap area. On the
illustration, a significant structure has been indicated by a circle.
14. Now, move the stage very slowly to make the structure on the live-image
move to the left. Keep moving the stage until the image structures in the
overlap area lie as exactly over each other as possible. The image
structures need not lie precisely over each other, since your software will
match the individual images with each other.
In the overlap area (3), the same image segments are shown now.
This enables your software to seamlessly combine the two images.
You can reverse the direction in which your stage moves, in the
Device Settings > Stage dialog box. Depending on how you can best
orient yourself, the live-image will then move to the left or to the right,
when you move your stage to the right.
15. Check whether both images have been correctly combined. Otherwise
you can undo the last step by using the Undo last frame
can then move the stage again, and match the structures better.
During the acquisition, you can change the current stitched image's
zoom factor, e.g., to see certain parts in the overlap area better. You
will find an overview on the possibilities of changing an image's
zoom factor in the online help.
16. Define your way through the sample, with the arrow buttons, and follow
that with the stage.
button. You
34
Acquiring specific images
In this manner, you can display a sample in any form you like in the
stitched image. The illustration shows a stitched image that is made up
of 9 individual images, and the stage path.
Properties of the
stitched image
17. Click the Stop
button when you want to end the acquisition of the
stitched image.
You see the completed stitched image (4) in the image window.
Since the individual images can lie a little askew of each other, the
stitched image isn't as a rule, rectangular, but contains empty areas
on its borders (5). These areas will, as a rule, be cut off in the
stitched image.
The stitched image will, by default, be automatically saved. The
storage directory is shown in the Acquisition Settings > Saving >
Process Manager dialog box. The preset file format is VSI.
By default, in the overlap area, the intensity values of two adjoining
individual images will be matched with each other to make the
image's overall impression homogeneous.
Stitched images are calibrated. This means that you can measure
distances and objects on a stitched image.
00383
35
Loading...