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SEM directions - DOC

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                               Controls on the ISI-SR-50 SEM

The complete operation manual is available in the lab. Be aware that it may talk about some
options that are not available on our instrument, and it does not cover the EDS or the EDS2004
digital imaging software at all.


Front lower panel: Three buttons for operating the vacuum system

OPER. – Press to pump down the column/chamber to operating vacuum
SHUT – Press to shut valves and isolate the vacuum system
AIR – Press to vent the column/chamber to air to exchange specimens

After pumping down the column with the OPER button and the green VACUUM LEVEL light
(front panel, main console) comes on, wait about three minutes before turning on the filament.

Before pressing the AIR button to vent the column, wait about three minutes after turning off the

Stage – the specimen rotate knob is on the front of the door. The Z and Tilt adjustments are the
large micrometer knobs above the door.

Movable Aperture – midway up the column. Check out the operation manual for complete

Top Front Panel

VARIABLE KV – leave off 99.9% of the time, and look in the operation manual for a
description of its operation.

gamma control – used to adjust contrast on specimens with extremely bright areas (perhaps due
to charging). In general leave off, complete description is in the operation manual.

SCAN ROTATION - Spins the beam (not the sample) – can be used to frame the image in the
                scanned area. Setting the angle to about 30° will make the stage x and y
                go up and down and right and left on the monitor, although the electron
                image shift not go exactly in x and y.

TILT CORRECTION - Stretches the image to correct foreshortening in the image of a tilted
                specimen. Not used a lot on anything except generally flat specimens, so
                mostly leave set to 0°.See JEOL pg. 26-27.

Top “Hidden” Panel

Lots of knobs, the majority of which should be left alone. All are described in the operation
manual. Do not fiddle with any knob or switch except for those marked with tape without
special dispensation, and if you do, put it back in the “normal” position.

Working left to right –
PHOTO RETURN – takes the SEM out of photo mode if you accidentally put it in photo mode
and don’t want to wait around.

DET HV – Turns the bias voltage to the Everhart-Thornley detector off and on. For whatever
reason, up is on (secondary electron mode), and down is off (back scattered electron mode).

GUN ALIGNMENT TILT (X and Y) – use to maximize the brightness of the image (maybe with
the wave form monitor) after saturating the filament or changing accelerating voltage or beam

EMISSION – On the upper right hand side of the “hidden” panel. Only mess with the manual
knob, not any of the three switches. Used to heat the filament to saturation.

Vacuum power control – three push buttons on the lower right hand side of the “hidden” panel.
All three should be lit. The DP (diffusion pump) button may be up (DP off, depends on how
often the machine has been run) when you come in. It must be down at least 20 minutes before
trying to operate the instrument.

MAIN FRONT PANEL – left to right

EMISSION / VACUUM METER and switch – switch as appropriate to monitor what you want.

VACUUM LEVEL light – Lights green when it is OK to turn on the high voltage and filament.

HV button – turns on the high voltage, only works when VACUUM LEVEL light is on.

HIGH VOLTAGE – used to select the accelerating voltage which is displayed on the LEDs

SCAN SPEED controls

       P2 and P1 buttons – used for photographs. If you push one by accident get the scans
       going again with the PHOTO RETURN button on the left of the top “hidden” panel.

       V1 button – slow video scan
       V2 button – tv mode video scan
       RED button – reduced video scan – adjust the size and position of the reduced area with
              the four knobs to the right (X and Y R REDuced position and size)
       WFM button – wave form monitor, used to monitor brightness, works best in V2 (TV)


         ZOOM knob (above) and range (below). Magnification is indicated on the LEDs.

IMAGE SHIFT knobs – x and y to move beam across image, works best at high magnification.

CONTRAST (AUTO contrast button is a waste of time, read the manual if you care to learn
          something pretty useless) - Controls the amplification of the photo multiplier tube
          and the contrast of the image. Use to set the contrast for digitally captured images
          in conjunction with reduced area scan and the CONTRAST/BRIGHTNESS

BRIGHTNESS – Controls the brightness of the image on the SEM monitor. Has no effect on
          the digitally captured image!

CH2 knob – not connected to anything. Use it for practice turning a knob!

FOCUS knobs – Coarse and Fine, as you would expect, and WORKING DISTANCE, which is
            really a VERY COARSE FOCUS.

STIGMATOR X-Y knobs- Use to get the beam round at high magnification (> ~ 8,000X). The
          best way to use these is to adjust the fine focus for the best image, then the X
          stigmator, the fine focus, the Y stigmator, and so on until you get the best image.
          Takes lots of practice and frustration. The MONI button seems to just put a cross
          on the monitor, I’m not really sure what it does.

AUTO BEAM SYSTEM knobs – the knob on the left (click stops) controls both beam current
         and focus, making life a bit easier. Counterclockwise is less beam current, better
         resolution, and noisier image, Clockwise is more beam current, brighter image,
         and less resolution. At the farthest clockwise position the control becomes
         completely manual using the knob on the right.

STAGE MOVEMENT – SPEED BUTTONS on top, arrow buttons below. Use the speed
         buttons to select the speed you want the stage to move (left buttons are faster,
         right buttons are slower), and the arrow keys to move the stage in direction you
         want to move. Easy, and you don’t have to worry about moving the stage too far,
         unless your specimen is really big!

                              Setting Contrast for a Digital Image

        Do the usual things in the EDS2004 software (set the pixel dimensions, frame averaging,
               and such), and frame and focus your image nicely in the SEM.
        Next, go into REDuced area mode and turn the X and Y reduced width knobs clockwise
               to make the reduced area as large as possible.
        Use the X and Y position knobs to move the scanned area over a representative part of
               your image.

       Adjust the BRIGHTNESS and CONTRAST knobs so that all the green
              Contrast/Brightness LEDs are lit, but neither of the red ones are lit. Changing the
              CONTRAST will change the number of lights lit, changing brightness will change
              where the LEDs are “centered.”
       Important: The brightness has no effect on the digital image, so what is really important is
              to have about 7 LEDs lit to use the full gray scale capturing capabilities of the
              digital system.

                    Normal operation procedures for ISI SR-50 SEM
Step 1 does not apply if the diffusion pump has been on for at least 20 minutes.
    1   If you come in and the diffusion pump is off (DP button on upper right of hidden panel is up and
        not lit), make sure the SHUT button on the column is pressed, then turn on the diffusion pump by
        pressing the DP button down.
               Start timing 20 minutes, but you can proceed as far as Step 7 while waiting.
    2   Make sure the chamber is tilted to about zero degrees.
    3   Push the AIR button on the column.
    4   After about 40 seconds you should be able to open the stage door (there is a latch on the left hand
        side of the door).
    5   Mount your sample however it needs to go. Refer to the operations manual if you have oddball
        sized specimens.
    6   Make sure there aren’t too many hairs on the o-ring around the door, then close it gently.
    7   Assuming the diffusion pump has been on for at least 20 minutes, push the OPER button on the
        column. The column will pump down.
               You can monitor the vacuum level on the EMISSION/VACUUM meter if the selector
                switch is in the down (Vacuum) position.
               When the meter gets to the green zone, and the green VACUUM LEVEL Led comes on
                wait for about three minutes before going on to step 8.
    8   Make sure the MANUAL EMISSION knob (top right of the “hidden top panel”) is all the way
        counter clockwise.
               Use the HIGH VOLTAGE knob to select the accelerating voltage you want on the HIGH
                VOLTAGE Led display.
               Turn on the accelerating voltage by pressing the HV button down.
               Set the AUTO BEAM SYSTEM knob to about 10 o’clock
               Set the BRIGHTNESS and CONTRAST knobs to about 12 – 2 o’clock
               Set the MAGNIFICATION to somewhere around 50 – the exact value is not at all
               Select the V2 scan speed and push down the WFM (wave form monitor) button. You
                can use other scan speeds, but they are a bit confusing.
    9   Saturate the filament by gently turning the MANUAL EMISSION knob clockwise.

                You should see the wave form go up, come down a bit, and finally go up to a stable
                 position where turning the MANUAL EMISSION knob further does not make a
                 significant change in the wave form.
                Turn the MANUAL EMISSION knob a bit counter clockwise until the wave form just
                 starts to go down.
                Turn the X and Y GUN TILT knobs (one at a time!) to maximize the wave form.
                        If you can’t maximize the wave form with the GUN TILT knobs
                                1. turn them both to 12 o’clock (red lines straight up)
                                2. Gently, no more than 1/8 turn at a time, turn the alignment knobs at the
                                   top of the column to maximize the waveform as best you can.
                                3. Touch up the final alignment with the GUN TILT knobs.
     REMEMBER that as the filament warms up and the gun area heats up things will move around, so
     you probably won’t get a perfectly stable alignment until the gun has been on at least 20 minutes.
     The message is don’t worry about alignment too much at first (but don’t oversaturate the
     filament!) – but check things before you take the perfect image!
         1   Gently turn the MANUAL EMISSION knob (top right of “hidden” panel) down
             (counterclockwise), and release the HV button.
                    Start a timer for about three minutes.
                    While you are waiting move the stage back to about 0° tilt.
                    Get more samples ready to go.
         2   After three minutes
                    Press the AIR button on the column
                    Wait about 40 seconds for the column to vent
                    Open the door
                    If you have more samples, load them, pump down and continue.
         3   If you are done.
                    Close the stage door
                    Push the OPER button
                    Wait until the green VACUUM LEVEL led comes on.
                    Push the SHUT button on the column.
         4   If no one is scheduled to use the SEM for the next “little while” – I know, if it “feels right” –
             probably a day or so, then turn off the diffusion pump (release the DP button), otherwise, you
             are done. Don’t panic about whether or not the DP switch is on or off, but do make sure the
                    SEM is left with a vacuum (green VACUUM LEVEL led is on) and
                    SEM is left in SHUT position

What does saturate mean? Basically you want the filament heated at the lowest level that gives you a
stable beam. The ideal saturation curve looks like 'a' and you want to set the filament heating so that you
are at the '*', but often the curve will look like 'b'. Operating at the '*' on 'b' is ok, but better gun alignment
will change the shape of the curve to the one shown in 'a.' Filament heating, the gun alignment, and the
shape of the saturation curve are related; change one and you change the other. A cold filament twists
and warps as it is heated, so you won't obtain good saturation until the filament has warmed up for 10
minutes or so.

                                     a                                                        b

                                               beam current
                                 *                                                       *

                                         fil amen t heat


1. Turn emission control fully counter clockwise and turn off operation switch.

2. Wait about 3 minutes for filament to cool.

3. Un-tilt the stage so it won't bang into the chamber when you open the door.

4. Depress red AIR button to admit air into the instrument. Venting takes about 45 seconds.

5. Release door latch and open door.

6. Exchange sample.

7. Close specimen chamber door and latch.

8. Depress blue OPERATE button. If the pump does not quiet down quickly press the door
   gently closed until a vacuum seal is formed. When the green light to the right of the
   REALLY COARSE FOCUS knob lights the machine is ready for operation, but wait another
   10 minutes or so before turning on operation switch.


When you are done, be sure to leave the SEM pumped down with the blue OPERATE
button depressed. It is OK to leave a sample in the SEM (but remember that the next user

                          Computer Stuff for Imaging with EDS2004
The blue box under the keyboard must be on for imaging or X-ray work.

The PC is hooked to a Windows network (GEOLOGY) which can be accessed from just about
everywhere on campus by either PCs or Macs. Printing to the laser printer in Room 155 is done
through the network, so you must be logged onto the network. You do this when you start or
restart the computer. The user name you should use is SEMUser, the password is sem (case
sensitive). Those of you on the Geology Department server can also log into Nugget and save
files there.

Once you are logged in use the Shortcut to EDS2004 to get EDS2004 running. When the
program starts you will probably want to select "New Image". After an image is open you can
adjust its resolution with the "Setup - Image" Menu. Be aware that 4K by 4K images are
beautiful, but will stop most computers dead. I generally use a 1K by 1K.

At this point the best thing to do is play with the program and look at the EDS2004 Help Files.
You can get started by pushing the Camera Icon to collect an image. Notice that the micron scale
bar will show up many many times, so you might want to use the EDS2004 scale bar after
calibrating it.

sem_users/2006 folder. This is the folder that you will be able to access via FTP
( for file transfers to your favorite computer. There is no limitation on
disk space, but please be somewhat careful and delete unwanted files as the image files are fairly
large. CAUTION: You can get to pretty much any file on the computer. Please don't mess with
other people’s files and make sure that any files you delete are your own. Also, while surfing the
web and listening to music through the computer is fine, please don’t download programs onto
the machine. Finally – Ken is not responsible for saving your files forever. They may hang
around, I won’t intentionally delete them, but no guarantees!

If you have more than four or five images open at the same time EDS2000 may well crash. Close
images you aren't using, and save early and often.

EDS2000 images are in a format called .IMX. These files cannot be used by an other program I
have found. To make image files that can be used in another program simply use the "Export As"
command, or you can use the “Batch Export.” I have found that the .TIF24 format is the most
stable. Be sure to use the "save annotations" option if you want the scale bar or labels you have
put onto the image saved. The TIF24 files are stored in RGB format. By running them through a
program such as Photoshop you can convert them to grayscale, and save 67% of the file space.

You can use Explorer or FTP (if someone figures out how to do it with FireFox let me know!) to
access the C: drive and copy the files to your favorite computer. Use the URL and start clicking on files to get the ones you want. For hard-core FTP
types, this is an anonymous account with no password.

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