Zeiss LSM 710 User manual

ZEISS LSM 710 CONFOCAL MICROSCOPE
USER MANUAL
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START THE SYSTEM...............................................................................................2
START ZEN SOFTWARE ..........................................................................................3
SET THE TEMPERATURE AND THE CO2CONTROLLERS ..............................................4
OBSERVATION AT OCULARS ..................................................................................5
STATIF PRESENTATION..........................................................................................6
ACQUIRE ONE OR SEVERAL STAININGS ..................................................................7
SAMPLING (IMAGE RESOLUTION) ........................................................................13
ACQUIRE A Z STACK ............................................................................................14
ACQUIRE A TIME SERIES......................................................................................16
ACQUIRE A MOSAIC IMAGE.................................................................................17
ACQUIRE MULTIPLE STAGE POSITIONS.................................................................19
VISUALIZATION OF YOUR ACQUIRED IMAGES.......................................................20
SIGNAL QUANTIFICATION ...................................................................................21
SAVE YOUR IMAGES ...........................................................................................22
SWITCH OFF THE SYSTEM....................................................................................23

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START THE SYSTEM
1. Switch on « MAIN SWITCH » button.
2. Switch on « SYSTEM PC » button.
3. Switch on the PC and log in « USER » session.
4. Once Windows session starts, switch on « COMPONENT » button.
5. Light on the fluorescent lamp.
On the power supply box of Argon laser:
6. Check if the button is at the « ON » position.
7. Turn the Power key on « I ».
On the small laser box:
8. Push the button up, on « LASER RUN » position.
9. When the LED is green (5 minutes after step 7) turn the knob around 9 o'clock, avoiding the red LED
lights on.
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START ZEN SOFTWARE
1. Start the software by clicking on ZEN 2011 icon on the desktop.
2. Choose START SYSTEM to access to the acquisition menu.
3. Zen software is divided in 3 parts: the left side is dedicated to acquisition parameters, central part is for
displaying images and toolbar and the right side list acquired images.

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SET THE TEMPERATURE AND THE CO2CONTROLLERS
1. Open the INCUBATOR window.
2. Enter the temperature value that you need and tick the box.
3. Open the CO2 bottle.
4. Enter the percentage of CO2 and tick the box.
Warning !!!
At the end of your session, please untick all boxes and close the CO2 bottle.
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OPEN
CLOSE
WARNING!
Don't close the air bottle!

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OBSERVATION AT OCULARS
1. Choose the 1er tab : LOCATE.
2. Choose the adapted configuration for
fluorescence or transmission.
According to the type of illumination that you
use, you can :
3. Light on/light off/choose the intensity of
the transmission lamp.
4. Open/close the shutter for transmission.
5. Light on/light off/choose the intensity of
the fluorescent lamp.
6. Open/close the shutter for fluorescence.
7. Choose the objective.
8. Change the filter bloc for fluorescence or
choose the ANALYSER position for DIC.
9. Choose the condenser prism for DIC
illumination.
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STATIF PRESENTATION
On the left side :
1. Focus knob
2. No fonction
3. No function
4. Optovar 1x
5. Previous fluorescence filter
6. Next fluorescence filter
On the right side :
1. Focus knob
1. Set the objective at the lowest position
to install your sample.
2. Set the objective at its working
position.
3. No function
4. Switch from the objective of high
magnification to a lower one.
5. Switch from the objective of low
magnification to a higher one.
6. Open/close the shutter of transmitted light.
7. Open/close the shutter of fluo lamp.
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ACQUIRE ONE OR SEVERAL STAININGS
1. Choose the ACQUISITION tab.
2. Tick SHOW ALL TOOLS.
3. In the LASER toolbox activate the 561
laser if you need it (Power On).
4. Open SMART SETUP.
5. In DYE select the different dyes and their
respective color.
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6. Several methods are available :
-FASTEST : allows a simultaneous acquisition ; it is the fastest method but the cross talk from one
color to the next channel could be important.
-BEST SIGNAL : each channel is acquired separately. It is the slowest method but it efficiently avoids
the Cross talk phenomenon.
-BEST COMPROMISE : compromise between speed and reduction of Cross talk
Example : blue and red channels are acquired simultaneously, then the green one is acquired alone.
-LINEAR UNMIXING : use spectral capacity of the system to separate simultaneously the different
dyes. First, you need to acquire sample stained with only one color.
Tricks : These modes are a help to start your configuration. The software does not always make the
smartest choice . You have to check by yourself and then make some modifications.

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7. In the LIGHT PATH toolbox, each TRACK
represents a sequence of one or several
colors.
8. Add or remove sequences by clicking on +/-
9. Adapt wavelength detection by moving the
window for each channel.
10. Add or remove channels with +/- for each
sequence.
11. If possible select the same dichroic for
each sequence, in order to speed up the
change from one sequence to the other.
If you don't need to use a dichroic for an
acquisition, you have to choose the
« Plate » filter.
12. Activate the 405 dichroic for each
sequence even if you don't use it.
13. Tick T-PMT to acquire images in
transmission in one of the sequences.
14.
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14. In CHANNELS toolbox, adjust the pinhole
at 1 AU (Airy unit) for each channel in
order to get the best resolution to signal
ratio.
15. Adjust the GAIN (MASTER) at 550 for each
channel except for the T-PMT.
16. Acquire in LIVE.
17. Adjust the laser power for each channel.
18. You can increase the (MASTER) GAIN to
decrease the laser power but the signal to
noise ratio will decrease.
19. Don't increase the DIGITAL GAIN except if
the GAIN (MASTER) is really high.
20. Adjust the DIGITAL OFFSET to improve the
image by increasing the signal to noise
ratio.
21. To make all the adjustments, it is
recommanded to use the « Range
Indicator » LUT.
In this mode, saturated pixels are red and
black pixels are blue.
22.
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22. In ACQUISITION MODE toolbox choose the
resolution (be careful of the sampling) see
p12.
23. Move in Z to find the plane of interest.
24. Choose the scan speed (faster it is, worse
would be the signal to noise ratio).
25. Average images (AVERAGING) if the signal
to noise ratio is not satisfying.
If the sample is fixed the Image mode is
more adapted. If it is a living sample the
Line mode is preferable. (Mean method is
recommanded).
26. The bidirectional mode allows to increase
the speed by a factor of two but it must be
well corrected on a high contrasted
sample. Phase adjustment (Corr X) is
important.
27. Zoom in (be careful of photobleaching and
sampling, see p12).
28. If you need, move your zoom zone
representing your field of view.
29. If you need , rotate your image.
30. You can do the same by moving, reducing,
rotating the square.
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31. You can zoom directly on your region of interest : stop the LIVE then click on CROP under the
image. A square appears on the image. The blue line represents the top of the final image. You can
move, rotate, enlarge or reduce the square. Then click on LIVE or SNAP.
32. Save your configuration.
33. Click on SNAP to acquire your image.
34. You can reuse the image parameters
acquired previously by selecting the
image then by clicking on REUSE.
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SAMPLING (Image resolution)
In order to get an optimal resolution for your images, the image voxel size must be equal to the half of the
objective resolution (Nyquist criterion). On a light microscope, the lateral resolution (in XY) is better than
the axial resolution (in Z).
Lateral resolution:
Choose the pixel size by modifying
1. the zoom : higher the zoom is, smaller is the
pixel size of your image (page 10-11).
2. Set the image frame size (number of pixels
which compose your image).
3. To choose automatically the optimal
resolution depending on the objective that
you use and the zoom, click on OPTIMAL.
It is not necessary to have pixels smaller than the
optimal resolution (oversampling).
However you can undersample your image in order to increase the acquisition speed and decrease the
photobleaching.
Axial resolution:
The axial resolution is inversely proportional to the
pinhole size. To get the maximum resolution with your
objective, you have to adjust the pinhole at 1 Airy Unit
size (click on 1AU in CHANNELS toolbox).
4. To get the optimal sampling in Z, according to
the pinhole size, click on SMALLEST.
5. To acquire with a bigger interval enter your value
manually in INTERVAL.
If you don't need to have an optimal resolution, you can
acquire with a bigger interval in Z in order to increase the
acquisition speed and reduce photobleaching.
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ACQUIRE A Z STACK
1. Proceed in the same manner as in the ACQUIRE ONE
OR SEVERAL STAININGS section and adjust the
parameters in the brightest plane.
2. Tick Z-STACK to make the toolbox appears in the
MULTIDIMENTIONAL ACQUISITION menu.
Two methods :
If you know about your sample thickess
3. Choose the CENTER tab
4. Make the focus on the center of the sample then
click on CENTER.
If you don't know about your sample thickness
5. Choose the FIRST/LAST tab
6. Make the focus on the bottom of your sample then
click on SET FIRST
7. Make the focus on the top of your sample then click
on SET LAST.
8. Choose the step between two slides by ticking
INTERVAL then by writing the interval in µm.
9. You can click on SMALLEST to choose automatically
the optimal resolution according to the pinhole size
(beforehand click on 1AU in the CHANNELS toolbox).
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10. For colocalisation acquisition, click on MATCH
PINHOLE in order to adjust automatically pinholes size
to get the same voxels size in all channels.
11. To adjust the acquisition sequence, in LIGHT PATH go
to SWITCH TRACK EVERY and choose Z-STACK to change
the channel after the acquisition of the entire stack.
Otherwise, choose FRAME to acquire all channels at
each plane in Z.
12. Click on « Start Experiment » to start the acquisition.
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ACQUIRE A TIME SERIES
1. Proceed in the same manner as in the
ACQUIRE ONE OR SEVERAL STAININGS section
and adjust the parameters in the brightest plane.
2. Tick TIME SERIES to make the toolbox
appears in the MULTIDIMENTIONAL ACQUISITION
menu.
3. Choose the number of cycle and the interval
between each time point.
4. Click on START EXPERIMENT to start the
acquisition.
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ACQUIRE A MOSAIC IMAGE
1. Proceed in the same manner as in the
ACQUIRE ONE OR SEVERAL STAININGS
section and adjust the parameters in the
brightest plane.
2. Tick TILE SCAN to make the toolbox appears
in the MULTIDIMENTIONAL ACQUISITION
menu.
3. There are several options in TILE SCAN
mode. Go to CENTERED GRID if you want
that your current position is considered as
the center of your mosaic.
4. Choose the number of lines and columns.
5. Let the OVERLAP at 10%.
6. Tick BI-DIRECTIONAL to acquire faster.
7. Tick ONLINE STICHING and let the
THRESHOLD at 0.10. Except if you make time
lapse tile scan imaging or multiple positions
tilescan imaging.
8. You can have an overview of your mosaic by
clicking on SCAN OVERVIEW IMAGE. You can
choose an objective and a zoom different
from the final acquisition (be careful when
you change objectives from dry to
immersion or the contrary).
9. Click on START EXPERIMENT to start the acquisition.
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10. To make a mosaic including different fields of
interest, go to BOUNDING GRID option.
11. Find fields of interest in LIVE and save their
coordinates by clicking on ADD. To remove a
position, select the coordinates on the list and
click on REMOVE. To remove all, click on
REMOVE ALL.
12. The size of your final mosaic is shown.
13. To make a mosaic including different fields of
interest without empty zones at borders, go to
CONVEX HULL option.
14. The process is exactly the same as in BOUNDING
GRID option.
15. The shape of your mosaic is shown.
16. Click on START EXPERIMENT to start the
acquisition.
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ACQUIRE MULTIPLE STAGE POSITIONS
1. Proceed in the same manner as in the
ACQUIRE ONE OR SEVERAL STAININGS section
and adjust the parameters in the brightest
plane.
2. Tick POSITIONS to make the toolbox appears
in the MULTIDIMENTIONAL ACQUISITION
menu.
3. Find the position of interest. Then in
POSITION LIST tab, click on ADD.
Repeat this process for each position.
4. To acquire a multiple well plate, go to
SAMPLE CARRIER.
5. Click on PROPERTIES and enter the
parameters of your multiple well plate.
6. Click on CALIBRATE to take these parameters
into account.
7. Select wells of interest with SELECT, SELECT
ALL buttons or CLEAR ALL.
8. Tick OBJECTIVE LOWERED WHEN MOVING
STAGE if you want the objective lowers
between each position. (For oil immersion
objectives).
9. Click on START EXPERIMENT to start the
acquisition.
10. Another solution is to localize several fields of
interest and acquire a fast mosaic in low
resolution. Then save each positions of
interest on the mosaic by clicking on
POSITIONS. Their coordinates are saved in the
POSITION LIST. You can start the acquisition
but untick TILE SCAN before.
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VISUALIZATION OF YOUR ACQUIRED IMAGES
Under the image you can find a panel where you can select channels you want to see on the screen.
1. Tick the name (white on blue) of
channels you want to see in the
image. Be careful, if all channels
are unticked no image is displayed.
2. Full screen zoom.
3. Native zoom (image pixel = screen
pixel).
4. Zoom in / Zoom out a zone.
5. Select Z position.
6. Select time position.
7. See a position.
8. Tick SINGLE CHANNEL to see channels separately.
9. Tick RANGE INDICATOR to use the LUT which allows you to avoid saturation.
10. See a merge of all channels.
11. See all channels separately.
12. See all the image gallery in function of time, z or wavelength.
13. Orthogonal view in XZ and YZ.
14. Cut in 3D.
15. 3D representation.
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