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.
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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
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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.
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(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.
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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)
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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.
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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
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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
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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.
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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
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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
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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
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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.
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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
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