eTraining Introduction

Specimen Preparation

Leica Ultracut UCT



Hitachi S-4700 FE-SEM

Hitachi FB-2000A FIB


Veeco Dim 3000 AFM

Fluorescence Microscopes


Safety Procedures

Knob TweakingOperational

Initial Settings

When you get on the SEM do not assume that all the controls are where they should be. The stage may have been left in the wrong position, the EDS detector may have been left cranked in, or the aperture may have been left in the highest setting.

Always check the conditions before you begin, using the Brief Operating Instruction sheet found in the lab.

See also Knob Tweaking under General Lab Safety in Support.

Caution with overall sample height

The size of your specimen is constrained by specimen chamber dimensions. There must be adequate space between the top of the specimen and the bottom of the objective lens. If your specimen is too tall and you decrease the working distance, there is a risk of hitting the lens, or worse, the ED detector. See the section below for additional information concerning detector damage. You will always use 39 mm working distance for X-ray analysis.

Oversaturating the filament

When saturating the filament, increase the current slowly and pay careful attention to the waveform on the viewing CRT to be sure that you are not over saturating it. We often mark the filament saturation with a pencil—but do not rely on the pencil mark made by previous users! The saturation level will have changed since it was last used and it is best to find it on your own. View the filament saturation method in the SEM Start Up Technique video in JEOL JSM-6400 SEM.

Detector damage (EDS)

Always check the stage position before moving the EDS detector into the specimen chamber. Be sure that your specimen is positioned at the 39 mm working distance position so that the detector does not crash into it the specimen. Repair costs for damaged detectors are approximately $15,000. We do not want you or your advisor to be responsible for this expensive repair. For the same reasons retract the detector before removing the specimen.

Exchange Rod

The sample holder is attached to the exchange rod, which is inserted into the specimen chamber during the loading process. Never over-tighten the specimen rod to the holder—it only needs to be snug. If you over-tighten the rod it may be impossible for you to remove it later. If this occurs, contact lab personnel. NOTE: the grease used to lubricate the rod is toxic; therefore, DO NOT TOUCH THE EXCHANGE ROD ITSELF!

Specimen dropped in the chamber.

When loading your specimen into the chamber, make sure that you feel some friction when it slides onto the stage. Sometimes users think the sample holder is on the stage when it is really just on the edge of it, or they overshoot it by lifting their exchange rod over the SEM stage. If the holder is not locked into the stage and you remove the rod, your specimen will drop into the chamber. If this happens contact lab personnel for assistance.


The chamber vacuum is lost during specimen loading.

When removing the specimen, sometimes the exchange rod does not match up with the holder and you have to press the rod up or down. When you apply torque to the rod, though, it may pull the plexiglass away from the opening, resulting in a vacuum leak. Vacuum leaks can be avoided by applying little or no torque to the rod and also by holding the plexiglass in place when sliding the specimen into place. If the chamber vacuum is lost, call lab personnel.


General safety

Liquid Nitrogen

See also Properties of LN2 under General Lab Safety in Support.

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