Zeiss LSM 880 Operating Manual
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Zeiss LSM 880 Operating Manual

Zeiss LSM 880 Operating Manual

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ZEN 2 (black edition)
March 2015

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Summary of Contents for Zeiss LSM 880

  • Page 1 ZEN 2 (black edition) March 2015...

  • Page 2: Table Of Contents

    Carl Zeiss Introduction This Quick Guide describes the basic operation of the LSM 880, LSM 880 NLO Laser Scanning microscopes with the ZEN 2 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 their samples.

  • Page 3: Starting The System

    LSM880 ZEN Carl Zeiss   Work flow to acquire image    Starting the system, and turning on the lasers (P. 2~6)  ↓ Microscope observation via eye pieces (P. 7)  ↓ Configuring the LSM beam path for dye you use (P. 8~11)  ↓ Scanning an image (P. 12~17)  1. Starting the System   1‐1.  Starting the System 1‐1‐1. Switching on the LSM system  ① Switch on the Main Switch of the Power remote switch. ※ Check the safety lock is ON. ② Switch on the System/PC, and log on as ‘LSM user’ ※safety lock ③ Switch on the Components. Fig. 1 Power remote switch  ・ SYSTEM/PC provides power to the computer. This allows use of the computer and ZEN software offline ・ COMPONENTS starts the other components and the complete system is ready to be initialized by the ZEN software. 1‐1‐2. Switching on the mercury lamp (X‐Cite 120 or HBO 100)  ・ 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.
  • Page 4 1-2. Starting ZEN software Double click the ZEN icon on the desktop to start the Carl Zeiss LSM software. The ZEN Main Application window and the Startup window appear on the screen. Choose Start system to start the system hardware for acquiring new images.
  • Page 5 LSM880 ZEN Carl Zeiss 《 Introduction to ZEN – Zeiss Efficient Navigation 》 ZEN 2 interface is clearly structured and follows the typical workflow of the experiments performed with confocal microscopy systems: Left Tool Area（Fig.3-①,②,③） The user finds the tools for sample observation, image acquisition, FCS, image processing and system maintenance, easily accessible via four Main Tabs.
  • Page 6 LSM880 ZEN Carl Zeiss Show all 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.5 Show all More features of ZEN 2 include: −...

  • Page 7: Turning On The Lasers

    LSM880 ZEN Carl Zeiss 2. Turning on the lasers ZEN 2 operates all lasers automatically. Whenever they are used (manually or by loading configuration), the lasers are turned on automatically. To manually switch lasers on or off: Check the Show all tools tick box and open the Laser tool. All available lasers can be operated within this tool (Fig.

  • Page 8: Setting Up The Microscope

    LSM880 ZEN Carl Zeiss 3. Setting up the microscope Changing between direct observation and laser scanning mode The Locate and Acquisition buttons switch between the use of the microscope and the LSM: Click on the Locate tab for the direct observation mode. In this mode, lasers are blocked.

  • Page 9: Configuring The Beam Path And Lasers

    LSM880 ZEN Carl Zeiss 4. Configuring the beam path and lasers Click on the Acquisition button to change to the LSM mode. There are 3 ways to configure the beam path and lasers. We highly recommend to use ‘4-1. Experiment Manager’ especially for users who are not familiar with LSM.

  • Page 10: Smart Setup

    LSM880 ZEN Carl Zeiss 4-2. Smart Setup ① Click on the Smart Setup button to open the smart setup window. ② Click on the arrow in Configure your experiment. ③ Choose the dye(s) you use from the list dialogue. In Fig.
  • Page 11 LSM880 ZEN Carl Zeiss 4-3. Setting up a configuration manually ① Activate ‘Show all tools’. Fig.14 Show all tools ② Open the Imaging Setup tool to set-up the beam path. This tool displays the selected track configuration. ③ Users can change the settings of this panel using the following function elements.
  • Page 12 LSM880 ZEN Carl Zeiss 《 Methods for multi-color imaging: Simultaneous and Sequential 》 Simultaneous and sequential acquisition are the methods of choice for multi-fluorescence imaging. Both methods have merits and demerits, and the user can select one of the methods according to the purpose of the experiment.

  • Page 13: Scanning An Image

    LSM880 ZEN Carl Zeiss 5. Scanning an image Workflow to acquire images Adjusting pinhole size ↓ Auto Exposure ↓ Live scan Adjusting Brightness/Contrast ↓ Setting the parameters ↓ Snap Adjusting pinhole size ① Select the Channels tool in the Left Tool Area. The Channels tool provides the control of the parameters for the individual detection channels.
  • Page 14 LSM880 ZEN Carl Zeiss Image acquisition – Auto Exposure ③ Click Set Exposure button, and ZEN optimizes the settings of the Gain (Master) and offset for the given laser power and pinhole size. Users can easily optimize the image further by using this recommended parameters.

  • Page 15: Split View

    LSM880 ZEN Carl Zeiss Split View displays individual channels of a multi-channel image as well as the superimposed image. ※ The Dimensions View shows the Merged tick box to activate / deactivate the display of the channel overlay. Fig.19 Split View Adjust Brightness and Contrast ⑤...

  • Page 16: Image Optimization

    LSM880 ZEN Carl Zeiss Image Optimization Activating Range Indicator In the View – Dimensions View Option Control Block, activate Range Indicator tick box (Fig. 21). Fig.21 Dimensions Control window The scanned image appears in a false-color presentation If the image is too bright, saturated pixels are indicated as red color.

  • Page 17: Setting The Parameters For Scanning

    LSM880 ZEN Carl Zeiss Setting the parameters for scanning ⑦ Select the Acquisition Mode tool from the Left Tool Area. Fig.23 Acquisition Mode tool Frame Size Select the Frame Size as predefined number of pixels or enter any values (default is 512 x 512) in the Acquisition Mode tool.
  • Page 18 LSM880 ZEN Carl Zeiss Averaging Averaging improves the signal-to-noise ratio of images. Averaging scans can be carried out line-by-line or frame-by-frame; frame averaging helps to reduce photo-bleaching, but does not give quite as smooth as line averaging does. For averaging, select the number of lines or frames to average from the pull down menu.

  • Page 19: Storing And Exporting Image Data

    Merit) ・It stores an image together with the acquisition parameters. ・ Reloading configuration from the stored image data is available. De-merit) ・ Other software cannot load CZI images . ※ You can download the free software ‘ZEN Light Edition’ from Carl Zeiss website. (Windows OS only) http://www.microimaging.zeiss.co.jp/ 2) Save as multipurpose format (Export), like TIF, JPEG…etc.

  • Page 20: Save Image

    Fig.28 Save as window ③ Enter the file name and choose the appropriate image format. Note: the CZI and LSM format (.czi, .lsm, respectively) are the native Carl Zeiss LSM image data format and contains all available extra information and hardware settings of your experiment.
  • Page 21 LSM880 ZEN Carl Zeiss 2) Export of Images as general formats ① Select the image to be exported, and c hoose File - Export from the menu. ② Select the file format, and the data type which the image is to be exported under Data.

  • Page 22: Open Images

    LSM880 ZEN Carl Zeiss 6-2. Open images To open images, select the file from File menu – Open or New File Browser. ZEN File Browser ① Advanced data browsing is available through the New File Browser (Ctrl + F or from the File Menu).

  • Page 23: Z Stack

    LSM880 ZEN Carl Zeiss 7. Z stack (3D imaging) The Z-Stack function permits scanning a series of XY-images in different focus positions resulting in a Z-Stack, thus producing 3 dimensional data from your specimen. Scanning a Z stack ① Select Z-Stack in the main tools area.
  • Page 24 LSM880 ZEN Carl Zeiss ④ Click on the Optimal button to set number of slices to match the optimal Z- interval for the given stack size, objective lens, and the pinhole diameter. Fig.35 Optimal button ⑤ Click on the Start Experiment button to start the recording of the Z-Stack.

  • Page 25: View Tabs

    LSM880 ZEN Carl Zeiss 8. View Tabs The View tabs make all viewing options and image analysis functions directly available from the main view. Switching from one View tab to another changes the view type only for the currently activated image, keeping the image in the foreground.

  • Page 26: Histogram View

    LSM880 ZEN Carl Zeiss 8-4. Ortho View (for Z-stack) ・ displays a Z-Stack of images in an orthogonal view ・ Users can measure distances in three dimensions Fig.40 Ortho View 8-5. Cut View (for Z-stack) ・ displays a user defined section plane (= cut plane) of a Z- Stack.

  • Page 27: Co-Localization View

    LSM880 ZEN Carl Zeiss 8-8. Co-localization View ・ permits interactive analysis of two channels of an image by computing a scatter diagram (co-localization). ・ Quantitative Colocalization Parameters are shown in the Data Fig.44 Colocalization View Table. ※ Tables can be saved by right-mouse clicking on the table display! 8-9.

  • Page 28: View Option Control Tab

    LSM880 ZEN Carl Zeiss 9. View Option Control tab (View Controller) These tabs allow individual activation / deactivation of the available View Option control blocks by clicking on the tabs. (The View tab Specific control tabs are marked with a blue triangle on their upper right corner.) ※...
  • Page 29 LSM880 ZEN Carl Zeiss 9-4. Graphics ・ add a scale bar to the image, as well as text annotations, ・ use a set of interactive measurement functions for length, angle, area and size, ① ② ③ ④ ⑤ Fig.50 Graphics tab ①...
  • Page 30 LSM880 ZEN Carl Zeiss 9-5. Series This panel allows to set the axis for rotating the 3D reconstructed images. ① Select 3D View ② Select the render mode, and set the position of the image (zoom, angle) in the Image Display window Fig.

  • Page 31: Operation Of Microscope

    LSM880 ZEN Carl Zeiss 10. Operation of Light Microscope (Axio Observer. Z1) In this system, not only laser scanning microscopy, but also bright field, differential interference contrast, phase contrast and wide field fluorescent microscopy are available, depending on the system specification (e.g., objectives, filters, the type of the condenser).
  • Page 32 LSM880 ZEN Carl Zeiss TFT display touchscreen on the Axio Observer.Z1 On the motorized Axio Observer, the user can operate and configure the microscope and utilize optional functions using the TFT display. The TFT display is designed as a touch-sensitive screen.

  • Page 33: Switching Off The System

    LSM880 ZEN Carl Zeiss Controls and functional elements for Axio Observer.Z1 - 32 -...

  • Page 34: Bright Field Observation

    LSM880 ZEN Carl Zeiss Acquiring transmitted-light images For overlaying fluorescence and transmitted-light images, click on the T-PMT button in the Imaging Setup tool. All transmitted light applications like - Phase contrast - Differential interference contrast (DIC) - Polarization contrast (Pol)
  • Page 35 LSM880 ZEN Carl Zeiss 10-2. Differential interference contrast (DIC) for transmitted light ① Move the polarizer on the transmitted light illuminator carrier into position, and load the analyzer in the reflector turret to position from ZEN or TFT touchscreen. Polarizer ②...

  • Page 36: Phase Contrast

    LSM880 ZEN Carl Zeiss 10-3. Phase contrast Turn the condenser turret adjustment ring to move the condenser turret to the Ph 1 ~ 3 position for bright field according to the lens to be used. Condenser turret 10-4. Epifluorescence contrast ①...

  • Page 37: Switching Off The System

    11-4. Click on the File - Exit button to leave the ZEN software. 11-5. Shut down the computer. 11-6. Turn off the Power remote switch. ① Turn off the Components switch and the System/PC switch. ② Turn off the Main Switch. March 2015 Carl Zeiss Microscopy Co., Ltd. - 36 -...

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Lsm 880 nlo

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