Zeiss LSM 710 User manual

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04/2009 1
Contents
Page
Contents ................................................................................................................................. 1
Introduction............................................................................................................................ 1
Starting the System ............................................................................................................... 2
Introduction to ZEN – Efficient Navigation .......................................................................... 5
Setting up the microscope................................................................................................... 10
Configuring the beam path and lasers ............................................................................... 12
Scanning an image............................................................................................................... 17
Storing and exporting image data ..................................................................................... 22
Using the ConfoCor 3 module............................................................................................. 23
Switching off the system..................................................................................................... 29
Introduction
This LSM 710 / LSM 710 NLO and ConfoCor 3 Quick Guide describes the basic operation of the
LSM 710 / LSM 710 NLO and ConfoCor 3 Laser Scanning microscopes with the ZEN 2009 software.
The purpose of this document is to guide the user to get started with the system as quick as possible in
order to obtain some first images from his samples.
This Quick Guide does NOT replace the detailed information available in the full user manual or in the
manual of the respective microscopes (Axio Imager, Axio Observer, Axio Examiner).
Also, this Quick Guide is written for a user who is familiar with the basics of Laser Scanning Microscopy.
For your safety!
Observe the following instructions:
The LSM 710 / LSM 710 NLO and ConfoCor 3 Laser Scanning Microscope, including
its original accessories and compatible accessories from other manufacturers, may
only be used for the purposes and microscopy techniques described in this manual
(intended use).
In the Operating Manual, read the chapter Safety Instructions carefully before
starting operation.
Follow the safety instructions described in the operating manual of the microscope
and X-Cite 120 lamp / HBO 100 mercury lamp.

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Starting the System
Switching on the LSM system
!Switch on the main switch (Fig. 1/1) and the
safety lock (Fig. 1/2).
!When set to ON the power remote switch
labeled System/PC provides power to the
computer. This allows use of the computer and
ZEN software offline
!To completely switch on the system, now press
the Components switch to ON. This starts the
other components and the complete system is
ready to be initialized by the ZEN software.
Switching on the X-Cite 120 or the HBO
100 mercury lamp
!Switch on the main switch of the X-Cite 120 /
HBO 100 lamp for reflected light illumination
via the power supply as described in the
respective operating manual.
Switching on the Ar-ML Laser
!If the Ar-ML laser is required, switch it on via
the toggle switch (Fig. 2/2) on the power supply
and turn the key (Fig. 2/1).
The laser is automatically kept in standby mode
for 5 minutes to warm up.
!Set the idle-run-switch (Fig. 2/3) to run. It takes
about 50s until the laser has reached the set
output power (green LED) provided the warm
up time of 5 minutes is already completed.
!Adjust the required power level with the control
knob (Fig. 2/4) (default position should be
11 o’clock).
Fig. 1 Power remote switch
0
Laser - Fertigung GmbH
laser
run
Fig. 2 Power supply of Ar-ML laser
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Starting the ZEN software
!Double click the ZEN 2009 icon on the WINDOWS desktop to start the Carl Zeiss LSM
software.
The ZEN Main Application window and the LSM 710 Startup window appear on the
screen (Fig. 3)
In the small startup window, choose either to start the system (Start System hardware for acquiring new
images) or in Image Processing mode to edit already existing images. Toggle the little
symbol to
view the Boot Status display and get the additional Offline / Demo button option:
Choosing Start System initializes the whole microscope system and activates the entire software
package for new image acquisition and analysis.
The Image Processing mode ignores all hardware and activates only data handling and image
processing functionality for already acquired images.
The Offline / Demo mode reads the current hardware database but does not activate the system
hardware for use. Instead, it simulates the system hardware for training purposes.
Upon clicking the Start System button, the Image Processing button changes to a Cancel
button. Click Cancel to interrupt/stop the Startup of the system.
After Startup, the ZEN Main Application Window (Fig. 4 and Fig. 5) opens. To benefit from all of ZEN's
features, run the window in its full screen mode.
Fig. 3 ZEN Main Application window at Startup (a) and the LSM 710 Startup window (b
and c)

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Fig. 4 ZEN Main Application Window after Startup with empty image container
Fig. 5 ZEN Main Application Window after Startup with several images loaded

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Introduction to ZEN – Efficient Navigation
The ZEN 2009 interface is clearly structured and follows the typical workflow of the experiments
performed with confocal microscopy systems:
On the Left Tool Area (Fig. 4/D) the user finds the tools for sample observation, image acquisition,
image processing and system maintenance, easily accessible via four Main Tabs (Fig. 5/1). All functions
needed to control the microscope can be found on the Ocular Tab, to acquire images use the
Acquisition Tools (Fig. 5/3and 4). Arranged from top to bottom they follow the logic of the
experimental workflow. The area for viewing and interacting with images is centered in the middle of the
Main Application Window: the Center Screen Area. Each displayed image can be displayed and/or
analyzed with many view options available through view tabs which can be found on the left side of the
image. According to the chosen view tab, the required view controls appear in View Control Tabs below
each image. File management and data handling tools are found in the Right Tool Area (see Fig. 4 and
Fig. 5).
Color and brightness of the interface have been carefully adjusted to the typical light conditions of the
imaging laboratory, guaranteeing optimal display contrast and minimal stray light for high-sensitivity
detection experiments. The ZEN software is optimized for a 30" TFT monitor but can also be used with
dual-20" TFT setups.
A focus in the development of ZEN 2009 was to fulfill the needs of both basic users and microscopy
specialists. Both types of users will appreciate the set of intuitive tools designed to make the use of a
confocal microscope from Carl Zeiss easy and fast:
The Show all concept ensures that tool panels are never more complex than needed. With Show all de-
activated, the most commonly used tools are displayed. For each tool, the user can activate Show all
mode to display and use additional functionality (Fig. 6).
Fig. 6 Show all mode

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More features of ZEN 2009 include:
The user can add more columns for tools to the Left Tool Area or detach individual tools to
position them anywhere on the monitor. To add a column, drag a tool group by the title bar (e.g.,
Online Acquisition) to the right and a new tool column automatically opens. Alternatively use the
context menu "move toolgroup to next column". To detach a tool, click on the little icon on the
very right end of the blue tool header bar (Fig. 7).
Another unique feature in Imaging Software is the scalable ZEN interface. This Workspace Zoom
allows adjustment of the ZEN 2009 window size and fonts to the situational needs or your
personal preferences (Fig. 7).
Setting up conventional confocal software for a specific experiment can take a long time and is
often tedious to repeat. With ZEN these adjustments have to be done only once – and may be
restored with just two clicks of the mouse. For each type of experiment one can now set-up and
save the suitable Workspace Layout. These configurations can also be shared between users.
For most controls, buttons and sliders, a tool tip is available. When the mouse pointer is kept over
the button, a small pop-up window will display which function is covered by this tool/button.
These are just some of the most important features of the ZEN interface. For a more detailed description
of the functionality for the ZEN 2009 software, please refer to the User Manual that is provided with
your system.
Fig. 7 ZEN Window Layout configuration

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Setting up a new image document and saving your data
To create a new image document in an empty image container, click the Snap or the
Auto Exposure button. For an empty image document press the New button.
The new document is immediately presented in the Open Images Area. Remember, an unsaved 2D
image in the active image tab will be over-written by a new scan. Multi-dimensional scans or saved
images will never be over-written and a new scan will then automatically create a new image document.
Acquired data is not automatically saved to disc. Make sure you save your data appropriately and back it
up regularly. The ZEN software will ask you if you want to save your unsaved images when you try to
close the application with unsaved images still open.
There is no image database any more like in the earlier Zeiss LSM software versions.
Fig. 8 New image document in the Open Images Areas

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Advanced data browsing is available through the ZEN File Browser (Ctrl + F or from the File Menu).
The ZEN File Browser can be used like the WINDOWS program file browser. Images can be opened by
double-click and image acquisition parameters are displayed with the thumbnails (Fig. 9). For more
information on data browsing please refer to the detailed operating manual.
Fig. 9 File Browser