Zeiss LSM 700 User manual

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Microscopy from Carl Zeiss

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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............................................................................... 13
Scanning an image............................................................................................................... 19
Storing and exporting image data ..................................................................................... 24
Switching off the system..................................................................................................... 25
Introduction
This LSM 700 Quick Guide describes the basic operation of the LSM 700 Laser Scanning Microscope with
the ZEN 2012 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).
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 700 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 700 system
xTurn on the LSM 700 system via the switch-
operated multipoint connectors (power strips 1
and 2) on the system. This switches on all
system components except attached scanning
stages, the microscope and its illumination
(HBO 100, XBO 75 or HXP 120).
xIf using the Axio Observer microscope stand,
push the power button at the left hand side
first to switch on the microscope.
xTurn the key switch (Fig. 1/1) of the electronics
and laser module to the right to start the laser.
The yellow LED in return turns on. If this is not
the case, check the power switch (Fig. 2/2) on
the back of the laser module.
xOn the back of the system there is a plastic
screw (Fig. 2/1). This is a laser interlock which
can be used for coupling the laser module e.g.
to doors. If this screw is unscrewed the lasers
will not turn on!
Switching on the HXP 120 or the HBO 100
or the XBO 75 lamps
xSwitch on the main switch of the HXP 120 /
HBO 100 / XBO 75 lamps for reflected light
illumination via the power supply as described
in the respective operating manual.
Switching on the scanning stage
xIf attached, switch on the scanning stage via the
controller.
Fig. 1 Electronics and laser module
Fig. 2 Electronics and laser module

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Starting the ZEN software
xDouble click the ZEN 2012 icon on the WINDOWS desktop to start the Carl Zeiss LSM
software.
The ZEN Main Application window and the LSM 700 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 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 700 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 2012 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 Locate 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 2012 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 2012 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 2012 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 2012 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
Set Exposure button. For an empty image document press the New button.
The new document is immediately presented in the Images andDocuments panel of the Right Tool
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 in case 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
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