Zeiss LSM 5 MP User manual

LSM 5 MP, LSM 510 and
LSM 510 META
Laser Scanning Microscopes
LSM Software ZEN 2007
August 2007
Quick Guide
Microscopy from Carl Zeiss
We make it visible.

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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............................................................................................................... 15
Storing and exporting image data ..................................................................................... 20
Switching off the system..................................................................................................... 21
Introduction
This LSM 510 / LSM 510 META / LSM 510 NLO Quick Guide describes the basic operation of the
LSM 510 / LSM 510 META / LSM 510 NLO Laser Scanning microscope with the ZEN 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, Axioskop 2 FS MOT). 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 510 / LSM 510 META / LSM 510 NLO 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
" When set to ON the REMOTE CONTROL switch
labeled System/PC provides power to the
computer. This allows use of the computer and
ZEN software offline (Fig. 1).
" 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 Enterprise UV-Ar Laser
" If the UV laser is required, switch it on via the
toggle switch (Fig. 2/1) on the power supply.
! It will be ready for operation after a few
seconds.
Fig. 1 REMOTE CONTROL switch
Fig. 2 Power supply of UV-Ar laser

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Starting the ZEN software
" Double click the ZEN icon on the WINDOWS desktop to start the Carl Zeiss LSM
software.
The ZEN Main Application Window and the LSM 510 Startup window appear on the
screen (Fig. 3)
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.
Fig. 3 ZEN Main Application Window at Startup (a) and the LSM 510 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
ZEN - Efficient Navigation - is the new software for the LSM 5 Family 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 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 image acquisition, image processing and
system maintenance, easily accessible via 3 Main Tabs (
Fig. 5/1). All functions needed to control the
microscope and to acquire images are bundled in 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 Blocks 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 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:
Fig. 6 Basic and Pro Mode

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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).
More features of ZEN 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 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 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 "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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Advanced data browsing is available through the File Browser (Ctrl-F or from the File Menu). The File
Browser can be used like the WINDOWS program file browser. Images can be opened by a 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

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Turning on the lasers
" Open the Laser Tool in the left tool area (always the first in the list) and activate the lasers you need
for your experiment (Fig. 10). Remember, the argon multi-line laser has to first be put to standby for a
5 minute warm-up before it changes to on.
" Zeiss recommends operating the Argon multi-line Laser at a tube current of about 6 A (#50 %
output). This is the best compromise between laser stability/power and laser life-time. (tube-current
control can be found in Pro Mode).
$
Fig. 10 Laser Control tool (in Pro Mode)