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Research Technologies Branch

Biological Imaging Section

Protocols: Leica TCS-NT/SP1 Confocal Microscope​

Startup Procedure

  1. If you are going to use the UV laser, this must be turned on first to prevent any possible damage to other pieces of equipment. To turn on the laser: Flip circuit breaker on the power supply to the on position and allow a few moments for the cooling system to start. Turn key to on position and wait for fan to start. After a few minutes a squeal will be heard, which is the ignition of the UV laser. Now it is safe to proceed to the next step. Be sure the power level control is turned clockwise above 0 such that the current limit light is off after ignition. This level will need to be increased before scanning by rotating the power level control knob .5 turns clockwise (to a 7 or 8 o'clock position). Don't forget to turn on the nitrogen supply to the air table. The tank is located in the hallway and labeled "confocal air table." Do not adjust the regulator pressure, just open the tank valve. The tank is the second one from the right.
  2. Switch on epifluorescence lamp power supply (on left beside microscope table). This should start almost immediately.
  3. Switch on lasers (two large boxes on right beneath bench). First switch on power and cooling fans by pressing red switches to the on positions. Wait a minute or so, then switch keys to on position. The key must be switched momentarily beyond on to start the laser. Switch on both lasers if you need 488nm and 568nm, and only 1 if you only need one wavelength. The laser labeled Ar supplies 488 (FITC) and 458nm, while the laser labeled Kr supplies 568nm (Rhodamine, Texas Red).
  4. Switch on both monitors.
  5. Switch on microscope. The switch is on the left side near the front. This must be switched on before starting the Leica LCS software.
  6. Switch on the scan control electronics. This is a red switch immediately beneath the bench on the right hand side.
  7. If you need 633 nm excitation (CY5), switch on the HeNe laser. This is the key switch right next to the scan electronics switch.
  8. Switch on the computer with the large button on the right at the top. This is the white box to the left of the two lasers beneath the bench. Allow the computer to complete its boot sequence.

Using the Leica Software (Version 2.1227)

To use this software you must have a local account set up on the confocal computer. If you do not have one, please see Juraj Kabat or Owen Schwartz.

  1. Log on to the computer with your usual network name and password, but be sure the domain is set to the local domain NIAIDCONFOCAL.
  2. On the Windows desktop click the red and yellow Leica icon with the name "Leica confocal." A dialog box will appear listing your name. Click start to begin loading the software. The software will take a long time to initialize (several minutes).
  3. The Leica desktop will appear.
  4. Once the main menu has opened, click beam to bring up the detector/laser control dialog box. Select a method from the Leica list or from the user list at the bottom. Double-click the method to load.
  5. At the lower right of the menu monitor click the folder button and select a control panel template. Normally the one to select is Control Panel - Username
  6. Be sure to click lens and enter the correct objective before beginning to scan. The microscope turret will automatically move to the correct position once this information is entered.
  7. Click on the frame average button and be sure to enter 4 (the default is 1). A setting of 4 is good for most frame averaging operations.
  8. A scan speed of medium is recommended for most normal operations. This is the default setting.
  9. Click pinhole --> airy 1 to select the standard pinhole for the objective you have chosen.
  10. If you are using UV excitation, click "UV lens" and confirm the correct UV compensation lens is selected for the objective you are using.
  11. Select mode and choose the appropriate mode for your experiment. If you are doing time series work, xyt or xyzt must be selected, otherwise the time functions will be grayed out.
  12. Adjust the AOTF sliders to get reasonable brightness using the least amount of power. To protect your samples, it is far better to use higher PMT gain (700-900 v) than to increase laser power. Typical AOTF settings are Ar 15%, Kr 30%, HeNe 15%. The UV laser is limited to the discreet steps of 12.5%, 25%, 50%, and 100% transmission. Minimization of cross talk also should be considered when setting laser power.

File Saving Procedures

The confocal software saves files in a database system, with a file extension .lei. There also is a .txt file saved to allow you to view the file parameters from outside the Leica software.

  1. Files can only be saved from "single scan" or "series" modes. "Continuous" is only for viewing the image on screen and setting the parameters. Once the parameters are set, click single scan to collect a frame averaged image.
  2. Click on the image name "Image XX" which appears in the database window. The image name will become highlighted and a dialog box will form around the name. Type the new file name then enter. If the dialog box does not form, click a second time. Alternately, you can follow instructions 3 and 4 below.
  3. Right click on the highlighted image name, then Rename. A dialog box will appear around the name, and the new name can be entered.
  4. After the first image has been collected and named, the database can now be named and saved. Highlight a file, or the database name, then click Save in the buttons above the database window. You can now name the confocal session (called an experiment by Leica) with either a date or another name. Be sure that the location for saving is correct. The blank in the dialog box is labeled file name, but is in actual fact the name of the folder you are creating for the session's experiment. Be sure that the location for saving is correct. The experiment should be saved in D:\users\username\experiment. Be sure it is not being saved in C:\temp (a system default for the first use). Note: you are naming the file called experiment.lei, not the line above called "experiments."
  5. Once you have named the database file you can resume collecting images. Continue to name your files by right clicking and naming through Rename. Warning: These named files are not actually saved. They are stored in RAM until you save them. Should the system crash, all of these files will be lost. Therefore, you should click "save" every few files to ensure that the data is written to the hard drive.
  6. Files saved in the Leica database system are directly readable in Imaris or in Photoshop. However, each channel of your images will be saved as a separate file. Imaris will re-associate these separate channels.
  7. File movements: Although you are logged into the local machine, and not the network, there is no need for a new login to transfer data to your area. Go to Run, type \\Niaid-file1\Username$ --> Enter. The next dialog box will request your username and password. Be sure you enter your username as "niaid\username," and your normal network password, then enter. You will now get a box showing your network directory. You also can open "my computer," D --> Users --> Username, and then copy and paste.
Saving the Overlay Image for Later Viewing in Photoshop
  1. Open the confocal file.
  2. Select tiled.
  3. Click "OVL" to turn on the overlay box. Note there are two forms of overlay—a fast "or" format or a true color. Choose the form you want, normally Fast for fluorescence merges, and True Color for merges with DIC.
  4. If the file is a z series, project the file or select the appropriate plane of section.
  5. Right click inside the overlay image and select send to --> experiment --> selection raw.
  6. A file will appear in the database window as "Overlay000." The file size should be 769K (24-bit color file).
  7. Right click the filename and then rename the file to match the original data.

Shutdown Procedure

  1. UV laser: On the UV laser, turn the knob counterclockwise but not all the way down. Be sure that the current limit light does not come on (if it does, you have gone too far). Allow the laser to run at this level for 3 minutes, then turn off the keyswitch.

    Visible lasers: Turn down the laser power with the black power control knobs on the front of each laser box. On the Kr and Ar lasers turn the knob fully counterclockwise. Allow the lasers to run at low power for 3 minutes, then turn of the keyswitch (counterclockwise). For the Cy5 (633) laser just turn off the key. This is located beneath the table adjacent to the scan control electronics powerswitch.
  2. Allow the lasers (including UV) to cool for 10 minutes with the key off, but the fan running, before switching off the red power switches. THIS STEP IS CRITICAL! (During this 10 minute cooldown period, you can proceed with the rest of the shutdown procedure.)
  3. Exit LCS software.
  4. Turn off the Hg lamp (epifluorescence) with the switch on the white box on the left side of the microscope table.
  5. Turn off the scan control electronics (red switch beneath table on right side).
  6. Turn off the microscope (left side at bottom).
  7. Exit Windows NT (start --> shutdown --> shut down computer).
  8. When the dialog box "It is now safe to turn off the computer" appears, press the red button to turn off the computer.
  9. Turn off monitors.
  10. Turn off the power to the lasers: On the Kr and Ar lasers, switch off the red power switch. On the UV laser, switch off circuit breaker.
  11. Shut off N2 to floating table (in hallway), middle tank. Do not adjust the regulator pressure. Close the tank valve on the N2 tank (clockwise).

Correct Use of the DMIRBE Microscope Program

The Leica DMIRBE microscope uses its own internal program to control the objective turret and focus motor. All of the objectives, Wollaston prisms, and phase rings have been programmed in already. Please do not change these settings.

All of the objectives to be used in the confocal imaging mode are oil immersion objectives and have short working distances. Place a small drop of oil on the objective before putting your slide on the stage. Different brands of immersion oil are not miscible and will cause serious imaging problems if mixed. If in doubt, be sure and clean your slides of any old immersion oil before starting.

The basic controls you will need to use the microscope are as follows:
  1. The two buttons on the right hand side of the microscope control the movement of the objective turret up and down. When pressed simultaneously, these switch the focus motor to the coarse focus function.
  2. The two buttons on the left hand side of the microscope control the choice of objective. The upper button moves to the next highest power objective, the lower button to the next lowest. If either of the buttons is depressed longer, an objective can be skipped in either direction. If you have not set the upper and lower limits for the objective turret, DO NOT PRESS EITHER BUTTON! This can cause the turret to rotate without lowering the objective.
  3. Setting the upper and lower turret movement limits: Place a slide on the stage—coverslip side down. Lower the objective turret 3 – 4 mm below the slide using the lower button on the right side. Press the lower limit button "0" on the front of the microscope and hold it until "del?" appears. Release the button, and press again and hold until "Set?" appears. Release the button. A 0 should appear in the microscope control window now. Slowly raise the objective using the upper button on the right hand side of the microscope until the immersion oil just makes contact with the slide. Now gently raise the objective using the focus knob until the sample comes into focus. Press the upper limit set button on the front of the microscope and hold until "Del?" appears. Release the button. Press and hold the button once again until "Set?" appears, then release. A Ð symbol should appear in the microscope control window, and the display should say "0um." This will set the upper limit for the raise/lower controls.
  4. With the exception of the 10x and 20x objectives, all require immersion oil. In order to put oil onto the objective, you can rotate the objective turret gently by hand or use the "learn" button. Pressing the learn button once will cause the objective turret to rotate and present the objective you were using at the rightmost position. Apply the immersion oil to the objective, press "learn" once again, and the objective will return to its initial position.
To switch between epifluorescence and confocal scanning
  1. Close the epifluorescence shutter with the slider on the left hand side of the microscope.
  2. Rotate epifluorescence filter wheel to the "scan" position.
  3. Rotate magnification wheel to "scan."
  4. Pull out slider to open confocal port.
  5. If necessary, switch brightfield light source control from view to scan.
  6. Be sure Wollaston prism wheel is set to blank position. The DIC prisms will cause the confocal fluorescence images to be much less sharp.
To collect DIC images through the confocal
  1. Be sure to have the illumination control knob switched to "scan."
  2. Rotate the Wollaston prism wheel to the appropriate position for the objective you are using. This will be indicated in the window on the front of the microscope. Match the letter in the second position to the letter specified by the objective.
  3. Be sure the Wollaston prism selected on the condenser filter wheel is the correct one for the objective you are using.
  4. On the main control window, turn on the transmitted light detector.
  5. Switch one of the buttons on the panelbox to PMTT (PMT transmitted). (I suggest using the pinhole control knob because this on is seldom used.)
  6. Turn off the fluorescence detectors so that the images collected will be single channel.
  7. While scanning move the Wollaston prism slightly to vary the amount of "shear" in the image of the specimen.
  8. Adjust the "PMTT" and "Black level" controls to yield a nice image.
  9. Save the image using "Save As."
Saving the overlay image for later viewing in Photoshop
  1. Open the confocal file.
  2. Select tiled.
  3. Select overlay.
  4. If the file is a z series, project the file or select the appropriate plane of section.
  5. Select single to display the overlay alone.
  6. Select save selected to save the overlay as a file. This file can only be saved as a scanner file, but since this is a single channel file, it will open in Photoshop without any difficulty. The file size should be 769K (24 bit color file).
Note for Photoshop users

If you are planning to open and adjust your images in Adobe Photoshop, the following initial procedures are recommended:

  1. Click Image --> Mode and be sure it is set to RGB color.
  2. Click Image --> Image size and set the resolution to 300 dpi. Before doing this, be sure the resample box is ticked, as well as the constrain proportions box.
  3. Set image size to 4 x 4 (or 5 x 5) to reduce the file sizes slightly.

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Last Updated April 05, 2007