0.9  Smooth Starts & Clean Finishes (Care of the Conventional Microscope)

Since a user who has just taken control of the microscope does not know in what configuration it was left, the following steps are offered as suggestions for a smooth start.

And most importantly, each user is a front-line soldier in the battle to keep the lenses in fine working order.

N.B. Numbers in parenthesis refer to the figure at http://confocal.med.unc.edu/wwwLeica/Operation/OP_dmirbe.html

First, follow the Brief Check List to turn on the electronics and TCS program (see Note 1, "Loss of focus", below).

Then, at first approach to the microscope, follow these three lists:

For protection of the microscope, verify that

If the conventional microscope is on, turn it off before you ignite the mercury arc lamp. The electro-magnetic surge could damage the microscope's controls, Leica informs us. The lamp's power supply is far enough away from the computer that you may turn it on even if the computer is on. Since the lamp has significant warm-up time, turn it on first thing.

Using the condenser height adjustment knob (5), the condenser can be lowered below the stage. If it is so lowered when you swing the transmitted illumination arm into working position, you could destroy both the condenser and your sample.

Most of the lenses are spring-loaded and retractable. To lock them in the retracted position, push in the end and turn clockwise. Unfortunately, the lenses are functional, but poorly so, even in the retracted position. If you should set up with a lens in this position and then change to a lens that is not retracted using the motor, the second lens may smash the stage. You may wish to examine the tip of the 40x lens to see the least worrisome damage that can be caused by such a maneuver. In general, the lenses should never be retracted.

Warning: The focus positions of the 20X, 40x and 100x lenses are higher than the focus position of the 10x lens by approx. 120 m m (+120 m m on the LCD) or less; if the LCD says the lens is higher than this (more positive than 120 m m) and you are still groping for focus, stop immediately, drop the stage and un-retract the lens or lenses. Start over.

For an irritation-free startup, verify that the

Located on the right hand side, about 6 inches above the condenser. If the white line is toward you, the light path is blocked. Turn the knob 90o clockwise.

Closing these diminishes the transmitted light intensity and you may see the field diaphragm if the lens in place is near focus. Improper settings here can lead you to say "The lamp isn't working."

Use HF position normally. 100 and 40 are for DIC. A sometimes useful dark field view can be obtained on the cheap by moving the condenser ring between click stop positions, and a previous user might have left it in that position.

Located on the right hand side, its action is to deflect the laser beams from the oculars and block off the oculars during scanning, all for your protection The lower rod has no function for the moment

If you are not using DIC, you want position "H" (for brightfield). Two other positions are identified as being for the 40x and 100x lenses, and the 4th is blank for now (equivalent to H).

The collars on the 100x, 40x and the 20x objectives are intended to give greater depth of focus by closing down a diaphragm. This reduces the N.A., however, and creams resolution. Use them with the diaphragm wide open (fully clockwise). The obvious effect of having the collar at any other position is decreased light. Warning: These collars, which can not be locked, are going to be a nuisance for high resolution users.


And do the following:

If you have examined the slide previously with an oil immersion lens, clean it off with alcohol (found in the confocal room). The presence of two different oils having different viscosities and possibly other properties, even though they have the same refractive index, leads to a very disconcerting overall background which renders the image essentially useless.

If you will be using transmitted light for anything more than just finding fluorescent samples, complete the Kohler illumination procedure (see Note 2 below).

Note that the electronic focus (3) will not move the lens higher than the set upper limit. This is a major lens protection feature and proper setting of the upper limit is crucial. The manual focus wheel (18) will go anywhere.

Distance is displayed on the LCD; lens retraction is indicated by negative numbers.


To clear the travel limits


To set travel limits

With the lens turret actually at the desired upper or lower limit position, push the corresponding button until SET? is displayed. Release the button and push again until the upward or downward pointing arrow reappears


Set the oculars to be parfocal with scanned images.

With each new element you want to image, your movement from the conventional microscope to scanning will be easiest if focus in the former puts you real close to focus in the latter. To do this, get an initial scan of your first sample, then return to the conventional microscope and adjust the oculars to give a sharply focused image.


For a clean finish (leave nothing but footprints, take nothing but memories)


Note 1: Loss of focus in going from the microscope to scanned images?

Think first about movements of the galvo stage rather than random focus drift in the microscope.

When the scan electronics are off or the TCS program is closed, the galvo stage is parked. The parked position is about 80 m m below the position during XY scans, which is also the "holding" position between scans. If you set up the microscope when the stage is parked, the stage will rise to the XY scan position when you start the scan and your first scanned image will be miles out of focus (you probably won't see any image at all). Solution: Turn on the scan electronics and activate the TCS program before setting up. If for some reason you have to turn on the scan electronics with the TCS program already loaded, move the stage to the "holding" position by doing one scan before anything else (no sample needed, the lasers don't even have to be on).


Note 2: Kohler illumination

All but the crudest uses of transmitted light require that the microscope be in the Kohler illumination configuration. For an optical explanation, see XXXXXX (in preparation). To set up the Leica properly, do the following:

7/28/97 final version (modified by m.c. 98-04-29, 99-06-01, 99-06-23, 00-08-22)