Zeiss ConfoCor 3, Quick Manual

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Page 3: ...es 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...

Page 4: ...or 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...

Page 5: ...tes 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 ac...

Page 6: ...4 04 2009 Fig 4 ZEN Main Application Window after Startup with empty image container Fig 5 ZEN Main Application Window after Startup with several images loaded...

Page 7: ...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 a...

Page 8: ...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...

Page 9: ...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...

Page 10: ...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...

Page 11: ...the lasers are turned on automatically The Laser Life Extender function of the software shuts all lasers off if ZEN is not used for more than 15 minutes To manually switch lasers on or off Click the...

Page 12: ...press the Online button for your actions to take effect immediately Then open the Ocular tool to configure the components of your microscope like filters shutters or objectives Fig 11 Selecting an obj...

Page 13: ...icroscope settings Microscope settings can be stored as configurations Fig 13 by typing a config name in the pull down selector and pressing the save button Fast restoration of a saved config is achie...

Page 14: ...rrow in the dye list and simply choose the dye s you want to use in your experiment from the list dialogue In this dialogue the dyes can be also searched by typing the name in the search field Fig 14...

Page 15: ...n If the option Linear Unmixing is selected the system is set in the lambda mode automatically Pressing the Auto Exposure button will then optimize the settings of the Gain Master and offset for the g...

Page 16: ...uble and triple labeling line by line or frame by frame Advantage Only one detector and one laser are switched on at any one time This reduces cross talk Disadvantage slower image acquisition Open the...

Page 17: ...box of the selected channel Ch 1 4 monitor diode ChM QUASAR detectors ChS1 8 transmission ChD for the scanning procedure and assigning a color to the channel Select the appropriate filters and activat...

Page 18: ...and channels Frame Tracks are switched during scanning frame by frame The following settings can be changed between tracks Laser line and intensity all filters and beam splitters the channels incl se...

Page 19: ...the Acquisition Mode tool Fig 20 to adjust the scan speed A higher speed with averaging results in the best signal to noise ratio Scan speed 8 usually produces good results Use speed 6 or 7 for superi...

Page 20: ...mode in the Acquisition Mode tool Select the number of lines or frames to average Adjusting pinhole size Select the Channels tool in the Left Tool Area Set the Pinhole size to 1 AU Airy unit for best...

Page 21: ...pre adjustment of detector gain and offset Select Live for continuous fast scanning useful for finding and changing the focus Select Continuous for continuous scanning with the selected scan speed Se...

Page 22: ...1 Airy Unit Fig 25 Set the Gain Master high When the image is saturated reduce AOTF transmission in the Laser control section of the Channels Tool Fig 25 using the slider to reduce the intensity of th...

Page 23: ...Stack Then focus on the lower specimen area where the recording of the Z Stack is to end Click on the Set Last button to set this lower position Click on the button to set number of slices to match th...

Page 24: ...r experiment Click on the Save button If you close an image which has not been saved a pop up window will ask you if you want to save it Choosing yes will lead you to the WINDOWS Save As window To exp...

Page 25: ...itch off the Ar ML laser with first the idle run switch Fig 2 3 and second the key switch Fig 2 1 then wait until the fan of the Argon laser has switched off Don t switch off the main power yet On the...