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Manual Zeiss LSM 900
Saving the image
There are 2 ways of saving your image in .CZI format: uncompressed or compressed
Uncompressed:
1. Click 'File' and choose 'Save as CZI'
2. Go to the right network-folder, give your image a name and press 'Save'
Compressed:
1. Go to 'File' and choose 'Save with options'
2. Go to the right network-folder, give your image a name
3. Choose a compression method at 'Compression' and press 'Save'
Making images with old or the same settings
Open a CZI-image that was made earlier; NOT a tif or jpg image!
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Go to the left top of the screen next to 'Smart setup' and press 'Reuse'.
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Activate a track, press 'Live' and if necessary adjust 'Master Gain', 'Digital Offset' and if
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necessary 'Digital Gain' per Track. Press 'Stop' and go to the next track for adjusting.
Check on all tracks and press 'Snap'
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Making a Z-stack
1. Check in 'configuration' the 'Z-stack' on
2. Click on the 'Z-stack' bar: the settings appear
3. At 'Interval' set a value; this is the space between 2
consecutive slides. If you press 'Optimal' that value will be
taken over in 'Interval' (half of the pinhole-setting)
4. Press 'Center', the other 'Center', press "First last'
5. Activate the track with the biggest volume
6. Click 'Live'
7. Move the fine coarse adjustment knob of the microscope
forwards until there is no more signal. The figure in 'Z-
stack' shows a blue square going up towards 'L'.
8. Click 'Set last'
9. Move the fine coarse adjustment knob of the microscope
towards you until there is no more signal. The figure in 'Z-
stack' shows a blue square going down towards 'F'.
10. Click 'Set first'; the number of slices will be automatically
set
11. Move the fine coarse adjustment back to put the current level to the middle and click 'Stop'
12. Select "full Z-Stack per Track" to speed up the acquisition
13. Be sure all tracks are on, set 'Averaging' to 2 or 4 and click
'Start experiment'
14. A series of images will be taken with a distance of 'interval'
between every slice. Save the series. On the left of the image
a series of buttons appear (2d, Gallery, 3D etc.): try them out,
see what happens. Nothing can go wrong.
15. In 'Dimensions' a slider appears at 'Z-position for stepping through the series
Erasmus Optical Imaging Centre
document version #1
6
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