Zeiss LSM 510 User manual

Quick Start
Zeiss LSM 510

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Table of Contents
1. START HARDWARE....................................................................................................................... 3
2. START SOFTWARE........................................................................................................................4
3. START LASERS.............................................................................................................................5
4. FIND THE SPECIMEN (AXIOPLAN 2).....................................................................................................6
4. FIND THE SPECIMEN (AXIOVERT 200M).................................................................................................7
5. CONFOCAL FILTER SET CONFIGURATION.................................................................................. 8
6. ACQUIRE PRELIMINARY CONFOCAL IMAGE...............................................................................9
7. OPTIMIZING THE SETTINGS........................................................................................................ 10
7.1. GETTING THE DISPLAY READY.................................................................................................... 10
7.2. SCAN CONTROL:CHANNELS WINDOW......................................................................................... 12
7.3. ACQUIRING YOUR FINAL IMAGE .................................................................................................. 15
8. SAVING YOUR FINAL IMAGE ...................................................................................................... 17
9. ACQUIRING A Z-SERIES.............................................................................................................. 18
10. ADVANCED OPTIONS............................................................................................................. 20
10.1. SINGLE-TRACK –SIMULTANEOUS ACQUISITION ............................................................................ 20
10.1.1. Getting the display ready............................................................................................. 20
10.1.2. Optimise settings.........................................................................................................20
10.2. Z-ATTENUATION COMPENSATION................................................................................................ 21
10.3. TRANSMITTED LIGHT IMAGE....................................................................................................... 22
10.4. FRAP................................................................................................................................... 23
11. SHUTTING DOWN THE SYSTEM............................................................................................. 25
11.1. TURN OFF LASERS................................................................................................................... 25
11.2. REMOVE SPECIMEN AND CLEAN MICROSCOPE.............................................................................. 25
11.3. EXIT THE SOFTWARE................................................................................................................ 25
11.4. POWER DOWN THE SYSTEM....................................................................................................... 25
12. OPENING YOUR IMAGES OFFLINE ........................................................................................ 26
12.1. ZEISS IMAGE BROWSER ............................................................................................................ 26
12.2. IMAGEJ ................................................................................................................................. 26

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1. Start Hardware
•Turn on the mercury short arc lamp light
switch.
Note: Whenever the mercury lamp is turned on,
it should be left on for at least 30 minutes. Once
the lamp has been turned off, it should not be
turned on again for 30 minutes.
•Remote control
•PC power
•IF REQUIRED: UV laser power (black switch in white
frame)
Do not touch the cooling unit; it has been set to
“automatic”.

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2. Start software
•Log on to Win2000 (you will be issued with a username and password during
training). Change your password now if you have not already done so.
•If you are using the UV laser, start this no before starting the LSM software.
•Double click the LSM 510 desktop icon.
•The Zeiss LSM 510 switchboard window will appear
•Make sure Scan New Images is
pressed and then click the Start
expert mode button. If Scan
New Images is not pressed, the
software will start but no initialize
the hardware.
•You will get an error message. Ignore it. It’s just
telling you the UV laser is not switched on. Contact
facility staff if you require the UV laser. Press
Cancel to close the window.

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3. Start Lasers
Click the Acquire button on the
toolbar. The lower toolbar will now
change to the Acquire sub-toolbar and
show the acquisition controls.
Click the Laser button.
Turn on the desired lasers
position: HeNe’s to ON, Argon
to Standby. When the Status
reads Ready, click the On
buttons.
Also turn OFF any lasers that
have been left on for you, but
you will not be using.
If the previous user has left the
lasers on for you, Argon and
Enterprise may already be in
standby mode and ready to be
tuned on.
When all the Status reads Ready, close the Laser Control window.

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4. Find the specimen (Axioplan 2)
The light path select,
focus knob
and stage
are manual controls. The rest of the microscope
is controlled by the software.
To set up the Axiovert microscope to locate your
specimen first move the light path selector to
VIS.
Move the correct objective in to place.
Do not use air-objectives after an
immersion objective without wiping the
immersion liquid (water or oil) from the
specimen and objective.
Brightfield, halogen light can be switched on and off HAL button
on the body of the microscope.
The intensity of brightfield light is most easily adjusted with the
Intensity control knob on the body of the microscope
Arc lamp light can be shuttered on and off by either the FL button
on the body of the microscope on the right hand-side.
The fluorescence filter block carousel can be switched back
and forward using the two buttons on the body of the microscope,
underneath the left hand focus
knob.
Once you have found your specimen, pull the light path
selector out to the LSM position. The microscope will
automatically change the filter-position and shutter the light
sources. If you fail to do this you will receive an error when you
try to acquire a confocal image.

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4. Find the specimen (Axiovert 200M)
•Change the microscope-light path to direct the emitted
fluorescence is sent to the eyepieces by clicking on the Eye
button in the LSM software toolbar.
•Move the correct objective into place using the Objective buttons on the
microscope button.
Do not use air-objectives after an immersion objective without
wiping the immersion liquid (water or oil) from the specimen
and objective.
•The arc-lamp light can be shuttered on
and off by the FL button on the
body of the microscope on the right
hand-side.
•Brightfield, halogen light can be
switched on and off HAL button on
the body of the microscope.
•The fluorescence filter block (a.k.a. reflector) carousel can be switched back and
forward using the two buttons marked Reflector on the body of the
microscope, behind the right hand focus knob.
•Once you have found your specimen, redirect the light-path to button in the
confocal by clicking the LSM button in the LSM software
The microscope will automatically change the filter-position and
shutter the light sources

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5. Confocal filter set configuration
Click the Config button (in the Acquire sub-toolbar).
To activate multi-tracking simply chose the
MultiTrack
button in the Configuration Control window.
Load the configuration that matches your
fluorophores (referred to as ‘tracks’) by clicking
the Config button.
•Click on the drop down box and select a desired configuration, apply then close.
If you cannot see the appropriate configuration for you fluorophores, contact
Facility staff.

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6. Acquire preliminary confocal image
Click the Scan button in the Acquire sub-toolbar
to open then Scan control window.
Click the Find
button and the computer will open a new image window and
calculate the approximate levels to generate a starting image.
You will see an image
looking something like
this (left).

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7. Optimizing the settings
Due to the sequential nature of ‘Multi-track’
acquisition optimizing the settings in this mode is
difficult. It is easier to set the imaging parameters
for each Track individually. You can do this by
switching off each track with the checkbox
along side it.
Turn off all but one channel now.
7.1. Getting the display ready
This current type of display does not allow fine tuning of the imaging parameters and
so needs to be adjusted.
Optimizing the confocal settings is best done with the image pseudo-colored to
highlight saturated and zero value pixels.
To do this, first click Palette on the image window tool bar and the Color Palette
window will open.
Click Range Indicator and close the window.
Now you will have an image where red represents the saturated pixels (i.e. =255) and
the blue represents the black pixels (i.e. zero).

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Your image window will now look like this.

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7.2. Scan control: Channels window
Click on the Channels button of the
Scan control window.
The active channel will appear here.
The settings below need to be adjusted
for each channel separately.
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1. Set Pinhole of each channel:
The pinhole diameter determines the thickness of the optical section – i.e. the axial
resolution. By increasing the pinhole diameter (and therefore optical section) you are
also increasing the amount of out of focus fluorescence being detected. Start with
each at the optimum (1 Airy Unit) by clicking the 1button.
This will give different Optical Slice values for each channel. Increase the pinholes
of the shorter wavelength channels to match the longest wavelength.
Do not go below 1 Airy unit – you will lose signal with no significant improvement
in axial resolution. Adjust the Pinhole for each channel so that they have the same
optical slice (typically the green channel will be ~ 1.1 Airy units).
2. Check focal plane
Click the Fast scan
button to start acquiring a high-speed, low quality image. Use this mode to focus up
and down through the specimen to get the desired focal plane.
=1.00

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You need to set the detector range to match the dimmest and brightest signal
from the specimen. Setting the detector incorrectly results in the loss of
information from the specimen.
3. Set Ampl. Offset – setting the ‘min’ signal
This should be set next, but may need re-setting later. While acquiring with the Fast
scan button, adjust the Amp. Offset so that only a few of the pixels in the background
of the image are blue. If you have a lot of blue colour in the background, move the slider
to the right.
4.Set Detector Gain and Excitation
power – setting the ‘max’ signal
The ‘max’ signal is set by adjusting the
detector gain and laser
transmission simultaneously. You
need to empirically work out the best
laser power settings – low laser power
causes less bleaching but requires the
detector gain to be set high; which
introduces noise.
Whist acquiring with the Fast scan button, adjust increase the Detector Gain so that
you get a bright image, but not too many red (saturated) pixels and not too much noise.
You may need to adjust the Ampl. Offset if you increase the Detector Gain a lot.
Around 600 is a good start. This should be set in conjunction with the excitation
intensity.
5. Set Ampl. Gain
Leave as 1 unless you have a very dim signal and nothing else works. This will amplify
noise as well as signal.

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A few red speckles; a few blue speckles
After you have set both channels, stop scanning by pressing the Stop
button in the Scan Control window. Your image will look like this (above).
Turn off the optimised channel in the
Configuration Control window.
Turn on the next channel and optimise
these settings for this channel.

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7.3. Acquiring your final image
Once you are satisfied that each channels detector is set optimally to the range of the
image, you can create your final image. Ensure that all Tracks are checked when
acquiring the final image.
Go to the Scan control window and click the Mode button.
Change the Frame size by clicking on the Optimal button (see Appendix 1 for an
explanation of this).
Noise can be reduced by averaging a
number of frames and slowing the scan
speed.
In the first instance, try the following values:
Mode: line
Method: mean
Number: 2
Scan speed: 6
Change the image Palette back to No Palette.
Click Palette
on the image window tool bar and the Color Palette window will open.
Click No Palette and close the window.

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Click on the
Single button in
the scan control
window to
collect your
final image
(bottom).
Click on the image window Info button. This will bring up a bar on the left of the image
window with the image information on it.

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8. Saving your final image
When you are satisfied with your image you need to save it to
your database. Images are saved to Databases. A database can be
single or multiple images or stacks.
Press Save as
in the image window and the Save Image and Parameter
window will open.
You can now chose to add your image to an existing database
(Open MDB button), or create a new database (New MDB button)
Name the file and include any other information in the description of
notes sections.
Do not select Compress file option.

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9. Acquiring a Z-series
Having set the system to acquire a satisfactory image, you can acquire a z-series. It may
be worthwhile changing the frame size to 512×512 to minimize file size and to speed
acquisition.
Click on the Z-Stack
button in the Scan control window.
Using Fast scan
mode to acquire a continuous image of the
specimen. Focus up and down with the
microscope focus wheel to ensure your
specimen is in the centre of the field of view
and the microscope is focused in the middle of
the specimen.
Stop acquisition.
You can now precisely define the middle and
depth of you z-series.
Ensure the Num Slices = 20 and the
Interval = 1 µm at this point to ensure the top
and bottom of the specimen is located.
Click the Range
button from the Scan control window – this
will generate a side view of you specimen.
This button is not available if the
MarkFirst/Last button is depressed.
(LEFT) The green line represents the
middle of your z-series. The upper red
line represents the top and the lower red
line the bottom of the z-series.
(RIGHT) Drag the green line to the
centre of the specimen and the red lines
to just outside the top and bottom of the
specimen.

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In the Scan control window, click the Z-
slice button to bring up the Optical Slice
dialog
Click the Optimal Interval
button. Check the optical section
for each channel is the same and close. If you optical
sections are different for each wavelength go to
Mode/Channels and adjust the Pinhole so that each
channel has the same optical section – around 1 Airy
unit, but one channel will have to be slightly larger.
Readjust the red lines that indicate the top and bottom of the specimen (Step 7 above).
Reduce the Frame Size also if possible to speed stack-acquisition.
To acquire your z-series stack click the Start button.
The system will begin
scanning the specimen.
You can check progress by
selecting Gallery button
on the image window
sidebar.

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10. Advanced Options
10.1. Single-Track – simultaneous acquisition
Multi-track can solve the problem of cross-talk. Typically this occurs with bleed
through of green fluorescence in to the red channel. Multi Track avoids this by acquiring
the fluorescent channels sequentially, not simultaneously as with Single Track
acquisition. In Multi Track mode the red channel detector is turned on, the green one
off. Then the red fluorophore is imaged.
The red channel detector is then turned off, the green one on and the green fluorophore
imaged. Any bleed through of fluorescence from the green fluorophore to the red detector
does not register.
This switching between tracks means that there is a delay between channels. Sometimes
this is unacceptable, in particular for live cell imaging where the cell can move between
channels creating artefacts. In this case Single track mode should be used.
•To load pre-designated configurations
click the Config button in the
Configuration control window.
10.1.1. Getting the display ready
For multi-label experiments, it is best to have both channels
displayed at once.
To do this:
In the Live image window’s Display side-bar, click the Split
xy button
This will make your image small so resize the image window
(usual Windows mouse-drag). Then click on the Zoom button to
bring up the Zoom sidebar and select Auto button.
10.1.2. Optimise settings
Unlike Sequential acquisition (Multi-Track), each channel is acquired simultaneously
during optimization – so be quick!
Refer to section 7.2 for instructions on how to optimize the channel settings.