Carl Zeiss LSM 710, LSM 710 NLO, ConfoCor 3 User Manual

Microscopy from Carl Zeiss

We make it visible.

Quick Guide

LSM 710 / LSM 710 NLO
and ConfoCor 3

Laser Scanning Microscopes

LSM Software ZEN 2008

August 2008

Contents

Page

Contents ................................................................................................................................. 1

Introduction............................................................................................................................ 2

Starting the System ............................................................................................................... 3

Introduction to ZEN – Efficient Navigation .......................................................................... 6

Setting up the microscope................................................................................................... 11

Configuring the beam path and lasers............................................................................... 13

Scanning an image............................................................................................................... 16

Storing and exporting image data ..................................................................................... 21

Using the ConfoCor 3 module............................................................................................. 22

Switching off the system..................................................................................................... 29

05/2008 1

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 2008 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.

2 05/2008

Starting the System

Switching on the LSM system

• Switch on the main switch (Fig. 1/1) and the

safety lock (

• 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.

Fig. 1/2).

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, turn the key

Fig. 2/1) and switch it on via the toggle switch

(

Fig. 2/2) on the power supply.

(

• After about 10 min. switch from standby to run

by the switch (

• Adjust the required power level with the control

knob (

Fig. 2/4) (default position should be 11

O’clock).

Fig. 2/3).

Fig. 1 Power remote switch

0

laser
run

Laser - Fe

rtigung GmbH

Fig. 2 Power supply of Ar-ML laser

05/2008 3

Starting the ZEN software

• Double click the ZEN 2008 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)

Fig. 3 ZEN Main Application window at Startup (a) and the LSM 710 Startup window (b and c)

In the small startup window, choose either to start the system online ("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.

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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

05/2008 5

Introduction to ZEN – Efficient Navigation

ZEN - Efficient Navigation - is the new software for the LSM Systems from Carl Zeiss. With the launch

of this software in 2007 Carl Zeiss sets new standards in application-friendly software for Laser Scanning
Microscopy.

The ZEN 2008 Interface is clearly structured and follows the typical workflow of the experiments
performed with confocal microscopy systems:

On the Left Tool Area (
system maintenance, easily accessible via 3 Main Tabs (
microscope and to acquire images are bundled in the Acquisition Tools (
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 Blocks below each image. File management and data handling tools
are found in the Right Tool Area (see

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.

Fig. 4/D) the user finds the tools for image acquisition, image processing and

Fig. 5/1). All functions needed to control the

Fig. 5/3 and 4). Arranged from

Fig. 4 and Fig. 5).

Fig. 6 Basic and Pro Mode

A focus in the development of ZEN 2008 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:

6 05/2008

The Pro-Basic concept ensures that tool panels are never more complex than needed. In Basic Mode,
the most commonly used tools are displayed. For each tool, the user can activate Pro Mode to display
and use additional functionality (

Fig. 6).

Fig. 7 ZEN Window Layout configuration

More features of ZEN 2008 include:

• The user can add more columns 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. 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 2008 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 2008 software, please refer to the User Manual that is provided with
your system.

05/2008 7

Setting up a new image document and saving your data

To create a new image document in an empty image container, click the "Single" or the "Start"

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.

Alternatively you can create a new empty image document with the "New"

button in the Action

Button area or the "New" function in the File Menu.

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.

Note: There is no "image database" any more like in the earlier Zeiss LSM software versions.

Fig. 8 New image document in the Open Images Ares

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