Zeiss LSM 510 inverted confocal manual

Zeiss LSM 510 inverted confocal manual
Power Up
Turn on the mercury lamp (if required)
Logon to ASADMIN
Open the Software
Double-click the 510 icon on the desktop, the LSM switchboard appears . . .
Make sure Scan New Images is selected.
("Use Existing Images" is an off-line
emulation mode)
Click on Start Expert in the Switchboard.
And the software looks like this. . .
Finding Your Specimen in the Eyepieces
The objectives, fluorescent filters, condenser, neutral density filters, and field diaphragm on the Axio
Observer stand are motorized and can be controlled in the software via the Acquire>Micro submenu
or the LCD touchscreen. You may want to find and view your specimen under transmitted light or
fluorescence, or both.
When you've located something you'd like to confocal, click the LSM button on the software panel.
Acquiring a confocal image
Turn On the Lasers
Select Acquire>Laser submenu will open the "Laser Control" window with a list of available lasers.
Colour of
Examples of
Deep blue
458 477
488 514
Green (Cyan
and Yellow)
GFP, Alexa 488,
Alexa 568, TRITC,
Alexa 594, texas
red, mCherry
Alexa 633, CY5
Turn on only the laser(s) you need to excite the fluorophores in your sample.
To turn on the Argon laser, click standby to warm it up. After the initial warm-up period, the on button
will appear allowing the laser to be fully activated. Set the output intensity to an appropriate level - 40%
is a good starting point.
To turn on any of the other lasers, simply click the appropriate "On" buttons - no warm-up is required
for ignition.
We try to minimize the number of times a laser is turned on or off - if somebody will use the laser within
2 hours leave it on (Argon laser in standby). Check the reservation schedule to see the laser usage
scheduled before and after your session. Turn off any lasers you don't need that may have been left on
for you by the previous user, as long as anyone scheduled after you won't use them within 2 hours of
your imaging session.
Choose a configuration
A filter configuration for the particular fluorophores you are using can be loaded via the "Configuration
Control" window. Open it by selecting the Acquire>Config submenu.
1. Single- or multi-track? Single Track mode is for single channel imaging or simultaneous excitation
of multiple channels; in Multi Track mode the laser scans multiple channels sequentially, which can be
useful when bleedthrough is a problem. Select whichever is appropriate for your imaging needs.
2. Apply preset configuration The saved configuration button on the right side of the "Configuration
Control" window opens the "Track Configurations" window with many popular combinations.
Capture an image: Scan control
Acquire>Scan opens the "Scan Control" window - the main dialog box for acquiring images. There are
several adjustments to make to get a good image. Each adjustment may effect the other settings so
some interation in the process is required.
Adjustments under the channels tab . . .
1. Adjust % laser transmission(s) in the Excitation panel at the bottom of the window. Doing so sets the
% laser power let through by the AOTF.
2. Set the pinhole diameter with the Pinhole slider scale. The smaller the pinhole, the thinner the
optical slice will be and the less light will be collected. A pinhole set to 1 Airy unit (click the 1 button) will
have optimal resolution. However, you will probably need to adjust this according to your sample's
fluorescence, using larger Airy values for dim samples. For multi-fluorophore imaging, it is usually
advisable to set the pinholes for each channel to produce equivalently thick optical slices.
3. Press "Find" to acquire a preliminary image using automatic setting of gain. An image display
window will open and the output of the scan will be displayed. If you are performing multi-channel
imaging, select Split XY button in the "Image" window's Display toolbar.
4. Click the Fast XY button and while the laser is scanning, use the XY Stage Controller and adjust
the fine focus on the microscope body. Clicking "Stop" in the Scan Control window will turn off the
Fast XY continuous scanning (minimize bleaching when you can).
The preliminary image, whether too dim or too bright, usually needs to be optimized. The PMTs need
to be adjusted according to the fluorescence intensity of the sample.
5. Select each channel separately by clicking on the corresponding coloured button.
6. The range indicator display is helpful for setting the gain and offset. Select Palette in the image
window's Select toolbar. From the Color Palette List, select "Range Indicator". In this palette, pixels
with intensity of 0 are blue and pixels with intensity of 255 (for 8 bit images) are displayed red.
7. Start Fast XY and set the Detector Gain until no more than a few % of your stained areas has red
pixels. Move the Amplifier Offset until the background is a mixture of blue and black pixels. (Always
leave the amplifier gain as 1). Make these adjustments for each channel.
8. Reset the Palette to "No Palette".
Adjustments under the mode tab . . .
Most of these will be fine as the default values. Averaging is the most important thing to adjust.
512*512 pixels is good for most imaging, choose other pixel sizes in the "image size" sub-panel
Under Speed, the default scan speed (when not zoomed in) is 9. Reducing the scan speed can improve
a noisy image; faster scan speeds are used to find regions of interest (like during the Fast XY function)
or when photobleaching of the sample is a concern.
Under Pixel Depth, Scan Direction & Scan Average, select your images to be 8 bit (256 gray levels) or
12 bit (4096 gray levels). Select the Scan Direction to be unidirectional or bidirectional. Unidirectional is
typically used, bidirectional scanning can be handy in live imaging since it cuts the scan time in half (but
may require phase adjustment).
To set the averaging for your final image, choose between line averaging, using the mean intensity
of 1,2,4,8, or 16 scans.
The amount of averaging necessary to obtain a good image depends on the signal to noise ratio of
your sample image. Low contrast images will require more averaging but be aware that this could
cause photobleaching. You can determine the amount of averaging necessary to yield the best image
of your sample empirically. As a rough guide, averaging should be set to 100th the gain value, meaning
most samples will require averaging of 4 or 8.
The zoom and scan field rotation can be set in the Zoom, Rotation, & Offset panel (Offset here refers
to fine XY movement of the scan area). You may find it more convenient to use the crop function in the
"Image" window Crop Your Image (optional)
This function is a true optical zoom performed upon image acquisition - the laser will scan a userdefined region of interest and display the scan data in the designated frame size (512x512, etc). It is a
convenient way of setting the zoom, rotation and offset displayed under the Mode tab.
Press "Crop" from the Image window display toolbar. A crop box appears in the current image window,
which can be moved, rotated and resized with the mouse.
Pressing "single" will rescan with the modified zoom etc settings
(Pressing the "reset" button in the mode panel is useful for undoing all these changes, ready for the
next sample.)
Images are overwritten so save as you
go along
Images are saved as .lsm files within a .mdb
database. Images can be exported as TIFFs
Click the "Save" icon on the bottom right of the image
If you don't have a database already, you need to
create one
Make sure you are saving images to the correct
Name the image and press save
Users should generally save their images either to their
own user folder on the \\Bio-lemming\Confocal fileserver or
directly to a USB memory drive. Any images saved on the
hard-drives are unsafe and are subject to deletion
WITHOUT WARNING. The Imaging Suite anteroom (4226
FFSC) has a PC workstation with both a USB port and a
DVD writer that can be used for transferring data off the
network to portable storage devices.
To collect a series of images at different points along the z-axis the settings can be inputted in two
ways: Z Sectioning or Mark First/Last.
Z-sectioning - takes x slices at a particular z interval
Mark first/last - set the top and bottom of your sample and select either the interval or number of
slices (the other is calculated for you)
Both of the methods described here assume that the user has optimized and set all imaging
parameters, including pinhole size, detector gain/offset, scan time and averaging described above.
Mark First/Last Method
1. Select Z Stack at the top of the "Scan Control" window - doing this will activate the Z Settings panel.
2. Determine the start and end points of the Z stack. (Z sectioning is performed moving into the
specimen, away from the coverslip.) To find the starting point for the Z stack perform a Fast XY scan
and focus toward the coverslip (rotate fine focus knob toward you) until you reach the point at which
you'd like to begin the Z stack. Stop the Fast XY scanning.
3. Click Mark First in the Mark First/Last tab in the Z Settings panel.
4.Start another Fast XY scan and turn the fine focus knob away from you focusing down through your
specimen until you reach the point at which you'd like to end the Z stack. Stop the Fast XY scanning.
5. Click Mark Last to set the end point of the stack.
6. Assuming you have already adjusted your pinholes as described in "Acquire Menu: Collect An XY
Section", look up the optimal z interval thickness by clicking Z Slice at the top of the Z Settings
box. This will open the "Optimal Slice" window.
7. Optimal z interval thickness for the objective currently in use will be displayed in this
window. Clicking Optimal Interval in the lower left corner of the window will set the z interval of your z
stack to the recommended thickness.
8. Start will begin scanning of the z stack. Settings last entered in the Channels and Mode panels will
be applied to this z stack collection.
9. The collected z stack is temporarily stored in the computer's memory. To permanently store the
stack, use Save or Save As in the image display window to save it to a database.
Z Sectioning Method
1. This method assumes the user has prior knowledge of the specimen's thickness and/or is willing to
guesstimate thickness. Select Z Stack at the top in the "Scan Control" window - doing this will activate
the Z Settings panel.
2. Click on the Z Sectioning tab and select Keep Interval. This will keep the z slice size constant, even
if you later decide to change the Num Slices or the upper and lower limits in your stack.
3.Type in the desired interval for your z stack in the Interval (um) field of the Z Sectioning tab. If
necessary, look up the optimal z interval thickness by clicking Z Slice at the top of the Z Settings
box. This will open the "Optimal Slice" window. Assuming you have already adjusted your pinholes as
described in "Acquire Menu: Collect An XY Section", your optimal z interval thickness for the objective
currently in use will be displayed in this window. Clicking Optimal Interval in the lower left corner of the
window will set the z interval of your z stack to the recommended thickness.
4. The Num Slices will be calculated automatically based on the chosen interval input.
5. Designate your current focal position (if you're in focus, you're probably somewhere near the middle
of the specimen) in the Current Slice field.
6. Clicking Start will begin scanning of the z stack. Settings last entered in the Channels and Mode
panels will be used to collect this z stack collection.
7. The collected z stack is temporarily stored in the computer's memory. To permanently store the
stack, use Save or Save As in the image display window to save it to a database.
Time series
The Time Series is a versatile software function that is useful in a variety of situations - from collecting
single confocal images or entire z stacks over time to more sophisticated applications such as FRAP. If
desired, a delay between the beginning of one scan process to the beginning of the next can be set. It
is important to note that Time Series works at only one location on the slide. To apply the Time Series
function to multiple stage locations, you will have to use the Multitime macro.
The following instructions are for applying a basic Time Series. It is assumed that the user has
optimized and set all imaging parameters beforehand (pinhole size, detector gain/offset, scan time,
averaging, and if desired, z stack). Refer to previous sections for more details on adjusting these
1. Select the Acquire>Time Series submenu.
2. In the Start Series panel, choose between a Manual start or a timed start via Time. Most users want
a manual start. If a timed start is desired, enter a start time in the Time (h:m:s) field. The time series
will start when the set time is reached according to the computer's clock.
3. In the End Series panel, enter the number of time points desired in the Number field if a Manual end
is selected. For a timed end point, depress Time and enter the end time in the Time (h:m:s) field.
In determining an experiment's length and the number of time points needed it is important to consider
the scan time and averaging settings (see the Speed section of the Mode panel in "Scan
Control"). Both parameters influence how long it takes the laser to clear the scan field and thereby
define the minimum time between time points.
4. The next panel you encounter will be either Time Interval or Time Delay, depending on the settings
of your Time Series register (see Options--> Settings). Time Delay is defined as the end of one scan
process to the beginning of the next, while Time Interval is the time between the beginning of one scan
process to the beginning of the next. Either panel, Time Interval or Time Delay, permits time series
scan parameters to be activated or changed from experiment to experiment.
You may load & Apply previously saved time series settings using the pulldown menu in either of these
panels. Or you may choose to manually enter scan parameters into the Time and Unit fields. If you
foresee performing other experiments with identical time scan settings, you should Store your manually
entered settings to the dropdown list for easy reference in the future.
5. Click Start T in the right-hand side of the "Time Series" window to start your time series.
6. The collected time series is temporarily stored in the computer's memory. To permanently store the
series, use Save or Save As in the image display window to save it to a database.
Ending your session
Remove your sample from the stage and clean any oil objectives you used. Please let us know of any
problems, the Report Problem form at http://microscopy.duke.edu/problem.html is quick to use.
Check the on-line reservation schedule to see if/when the next reservation is scheduled:
If someone else is scheduled to use the microscope within 2 hours...
Put the Argon laser into standby and turn off any lasers that won't be used by the next person,
leaving on hte ones indicated on the booking calendar
Exit the software
Select the "Log Off" command from the Start menu of the desktop and leave the system on.
Sign the logbook
If you are the last scheduled session of the day or for more than 2 hours...
Turn off all the lasers in the Acquire>laser box and exit the software
Select "Shut down computer" command in the Start menu of the desktop. The computer and
monitors will power down automatically.
Turn off the Components switch
Turn of the PC/system switch
Turn of the arc lamp
Sign the logbook
Image Processing & Analysis
Scalebars & Measurements
A scale bar, measurements (e.g. angle, area, line) and/or text can easily be drawn onto an image
that has already been collected using the Overlay option in the image display window. You are
encouraged to explore the drawing buttons in the Overlay toolbar - creating a scalebar on your
image is described here.
1. Click Overlay in the Select toolbar of an open image window.
2. Select the desired scalebar thickness from the line width option buttons appearing half way down
the Overlay image window submenu.
3. Click on the desired color of your scale bar from the color selection at the bottom of the Overlay
4. Click 1um in the Overlay submenu, then click in the vicinity of the image where you wish the
scalebar to be drawn.
5. Drag the mouse over some distance on the image until the resulting scalebar registers your
desired value. Release the mouse button to draw this scalebar overlay on the image.
6. Use Save or Save As in the image window to save it to a database.
3-D stack display options
Some users will find it helpful to assess their time or z-stack data by animating it.
1. Select Anim from the Select toolbar of a stack's "Image" window. The "Animate" window will open
and the stack will immediately be animated.
2. Speed 1 and Speed 2 in the bottom section of the "Animate" window allow the user to control the
speed of the animation.
3. To further control the animation, use the function buttons in the top section of this window to
animate forward and/or in reverse, stop, fast forward, and fast back through a stack. + and - will
animate the stack in forward or reverse by whatever increment you choose in the Increment slider
in the bottom section of this window.
4. The Increment slider reduces the number of slices included in the animation to every nth slice as
Stack slices are organized in rows and presented in the order in which they were generated inside
the image window. A 2-dimensional gallery of z-stacks over time can also be generated. Each slice's
z-data (um) and/or temporal interval can easily be displayed in every tile of the gallery. Z- or tgalleries can be saved as an image in a database for quick future reference. Additionally, a subset
of images within a stack can be selected and stored for later use (e.g. to create a 3-D projection).
1. Click Gallery in the Display toolbar of the image window. A gallery of the entire stack is
automatically generated and the Gallery toolbar becomes available in the image window. Click Save
if you want to save the gallery to your database for quick future reference. Otherwise, a gallery view
can always be generated from the stack at a later time.
2. For z-stacks taken over a time series, refer to the Gallery menu to select the format in which you'd
like the gallery be displayed - Z , Time , or entire z-stacks over time, Z + Time .
3. To have the stack data (z distance or time interval) displayed in every tile of the gallery, click Data
in the Gallery toolbar. Use the color selection button (located below Data ) to ascribe a color of your
choice to the gallery data display.
4. To separate a subset of images from the full image gallery, select Subset in the Gallery
toolbar. Here, define new start and end points of the series using the Start Slice and End Slice
sliders/data fields, or enter a value in the Every n-th Slice field if you would rather create a subset of
every n-th slice of your choosing.
3-D Projection
The Projection function can render a single projection or a series of calculated projections at set
angle increments around the X, Y, or Z axis. The user can choose between manipulating aspects of
the projection's transparency or creating a projection that has maximum intensity.
The "Transparent" projection method decreases the brightness of each file in the projected stack to
reveal structure in subsequent layers that would otherwise be hidden. The "Maximum" projection
method takes the intensity values of individual pixels in all sections and collapses them into one
single illuminated image. The "Maximum" method is chosen when the maximum pixel intensity is
desired to be represented in the projection.
Creating a maximum projection is described here. These instructions assume that an image stack is
open and therefore available for projection.
1. Select 3D View> Projection from the main menu. The Projection window will open.
2. Select the stack to be projected in the Source panel of this window.
Only stacks and images that are currently open are available for selection in the Source pulldown
3. To create an en face (straight-on) projection of all slices in the z-axis, select the Y radiobutton in
the Projection panel. Leave the First Angle set to 0 degrees, enter 1 in the Number Projections
field, and set the Difference Angle field to 0 degrees.
4. In the Transparency tab, select the Maximum radiobutton.
5. Generate the projection by clicking Apply located in the upper right corner of the Projection
6. If a sequence of projections at set angles has been created, it may be animated or viewed in a
gallery via the Select and Display toolbars of the image window.
Exporting Files to .tif Format
Files can be exported in a couple of different ways - via the batch export macro, which allows the
simultaneous export of multiple database items or the Export of Images function, which allows the
export of individual database items - be they single confocal sections or a stack. The Export of
Images method is described here.
1. Open your database and load (open) the file you would like to export.
2. Select File >Export from the main menu. The "Export Images and Data" window will open.
3. In the Save In field, designate to which drive or directory the exported data should be saved.
4. Enter a name for the exported image or series of images in the File name field.
5. In the Save as type field, select the image format into which the file should be exported.
When selecting an image format, pay heed to whether you are exporting a single confocal image or
a series (stack) of confocal images. Various image formats are supported (e.g. .bmp, .jpg), we
recommend TIF (.tif) format as it is lossless and widely usable.
For multi-channel images, you have the option of exporting individual color channels of data in
monochrome (grayscale) if Raw data single or Raw data series image type is chosen.
6. Click Save.
When a z- or time stack file is exported, each stack slice is stored as an individual TIF image with
a 3-digit numbered suffix appended to the designated file name.
Assigning Macros To Buttons In Macro Control
1. Open the software and click Macro main menu item.
2. Select Macro that now appears in the bottom right corner of the main menu toolbar. This opens
the Macro Control window.
3. Click on the Assign Macro to Button panel.
4. Indicate which button you want the new macro assigned (Button1, Button2, Button3, etc) from the
drop down menu in the Button field.
5. Name the new button in the Text field.
6. Click the ... button beside the Project field to link a macro of your choice to the newly created
button. An Open window appears. All macro programs can be found in the C:AIM\Macros folder.
7. Find the macro file that you want to load. Select this file and click on Ok in the Open window.
8. Select the macro name from the drop down menu of the Macros field.
9. Hit Apply and the macro you selected should be assigned to the button you designated in step
4. In a moment, the specified button will appear in the Macro toolbar.
Deleting A Macro From A Button In Macro Control
1. Working under the Macro main menu item, select Macro that appears in the bottom right corner of
the main menu toolbar. This opens the Macro Control window.
2. Click on the Assign Macro to Button panel.
3. Choose which button you want to disassociate from its macro in the drop down menu in the
Button field.
4. Press Delete to delete the linking of the macro program to the button. The specified button should
then ghost out to a blank n.n format.
Initializing User Software Settings - Running Registry Files
1. Logon to the system using your ASADMIN user name and password.
2. Run all the registry files in the folder on the desktop:
Double-click each of the files, after each file, you should see a dialog box confirming the registry
has been successfully updated. Click "OK" to these messages.
You will need to rerun LSM-Macros.reg whenever you want to use a newly installed macro (e.g.
newer version of multitime).
3. Start the LSM510 software as normal - "Scan New Image" & "Start Expert Mode"
4. In the Options menu, click the Settings submenu. Make the following settings in the different
tabbed sections of this submenu.
Program Start:
- Select the configuration you wish the software to load by default every time you log on.
- Un-select "don't show logo"
- Select the third radio button - at "Create Database" automatically create a subdirectory with
the same name as specified database and create dataset image files in that subdirectory.
Temporary Files:
"Use RAM" is fine unless you're doing time lapse, then you may want to set a temporary
location, e.g. to your server directory:
h:ASADMIN\Bio-lemming\Confocal\lab name\user name or use "Save To Disk"
Set location of files; click "User Default Path" to use your default directory defined by your user
Check all but objective