Operating Procedures: JEOL JSM

Operating Procedures: JEOL JSM- 6010PLUS/LA Analytical Scanning
Electron Microscope
Purpose and Scope:
This document describes the procedures and policies for using the MSE JEOL SEM 6010. The scope of
this document is to establish user procedures. Instrument maintenance and repair are outside the scope of
this document.
The department Lab manager maintains this document. The Lab Manager is responsible for general
maintenance and for arranging repair when necessary. If you feel that the instrument is in need of repair
or is not operating correctly, please notify the Lab Manager immediately. The Lab Manger will operate
the instruments according to the procedures set down in this document and will provide instruction and
training to users within the department. Users are responsible for using the instrument described
according to these procedures. These procedures assume that the user has had at least one training
The MSE Lab Manager will do all first and last training sessions, with the last training session being the
‘drivers test’. Occasionally the Lab Assistant will be on hand for the practice session(s) in between.
Users are NOT to train other people. Users found training other people will have their access revoked.
SEM training includes 3 training sessions. The first session will be an instrument demonstration and up
to two (2) students can attend at a time. MSE specimen will be used for training. Sample preparation
procedures for the trainee’s specimens are discussed during this session.
The second session will be a practice session for one student with supervision. Students can bring their
own specimen at this time as long as it has been prepared properly. If additional practice sessions are
needed as determined by the student or MSE Lab Manager /Lab Assistant, they will be scheduled at the
end of the session.
The last session will be the Drivers test that includes a short written test. Students will demonstrate their
competence in operating the microscope. Users are required to have their own samples ready by the
driver’s test. If students do not pass this test, they will be given the opportunity to come back for another
training session. The student CANNOT take the Drivers test after taking a practice session on the same
day. After passing the Drivers test users will be issued a license to operate the instrument. The checklist
for the driver’s test is included at the end of this document.
Since SEM operation is only reinforced by repetition, it is recommended that the student have his/her own
specimens to work on immediately after passing the Drivers test. The MSE Lab Manage will have
discretion on when is the appropriate time to start training. Students will need to be recertified by the
MSE Lab Manager after 3 months or more of inactivity on this instrument.
Access and use:
The MSE JEOL SEM was purchased with Student Technology Fee’s. Please be sure to read department
policies regarding the use of STF purchased equipment. This funding project is focused on providing
quality SEM and EDS to undergraduates who cannot gain access to the other instruments on campus.
These students will always have first priority to training and access.
This is a very delicate, sensitive and costly instrument and will require extra care when operating it. In
light of this, after hours use will not be available at this time. The scope will be available Monday –
Friday 9am – 6pm. Users who have access to these labs for other instruments who violate the
hours policy will lose access to the labs.
Users can save their data to a lab network share computer. The SEM computer is to operate the
instrument only. It is not connected to the internet and USB drives are not allowed. There is software on
the computer available to save pictures and spectra and users may use that to put together their results, but
further analysis must be done on users own time. This will ensure that the instrument is available to the
most number of users.
Once training is complete users can sign-up for up to 2 hours per session unless other arrangements have
been made. Users who try to reserve 2 hour increments multiple times a day or throughout the week will
have their reservations cancelled.
USERS MUST USE GLOVES: This instrument is a high vacuum system. Finger oils, dirt, etc. can
compromise the vacuum and dirty the chamber. Users MUST wear gloves when handling any part of the
instruments, samples, or sample holders. When doing other things, like typing please remove the gloves.
Gloves are provided.
Features and Specifications:
Basic specifications are:
Resolution: 4.0nm (at 20kV)
Resolution in LV Mode: 5.0nm
Magnification: 8X to 300,000X (5X possible)
Accelerating Voltage: 500V to 20kV
There is not a motorized stage or internal camera for position control. EDS is available in high and low
vacuum modes. (EDS training is a separate process). Please note that the resolutions stated may not be
the same for all materials. Most materials can be imaged in the SEM except for materials that are wet or
that may outgas hazardous or corrosive gasses. Whenever possible samples should have a conductive
coating. This will reduce deposits on the filament and extend the life of the detectors.
MSE has a number of standard sample holders available for students to use. Non-student users must
supply their own sample preparation materials and holders but the holders must be of the correct type.
Please see the Lab Manager for more information. Specimen preparation materials may be purchased
from Electron Microscopy Sciences: https://www.emsdiasum.com/microscopy/.
From MSE 313 Junior Lab Manual:
A scanning electron microscope (SEM) uses electrons as a probe just like an optical microscope uses light
as a probe. The interaction of electrons with the object under investigation is utilized in imaging and
chemical analysis and forms the subject of scanning electron microscopy. High resolution and large depth
of focus coupled with X-ray chemical analysis makes it one of the most versatile instruments for
microscopic examination and analysis of materials.
The interaction of a primary electron beam with a specimen leads to the generation of secondary electrons
(SE), backscattered electrons (BSE), Auger electrons (AE), X-rays, cathode luminescence and other
phenomena. The different types of electrons and energy quanta, mentioned above, arise from different
depths of the material and provide microscopic information about the material.
The other feature of scanning electron microscopy is resolving power, which is the smallest detail that a
microscope can resolve, or "see". The resolving power of electron microscopes is orders of magnitude
better than that of an optical microscope because the wavelength of the probing beam is orders of
magnitude smaller. The resolving power of a microscope is inversely proportional to the wave length of
the radiation or particles constituting the probe. Since electrons have much lower wavelengths than light,
it is possible to resolve finer details of specimens using SEM. The depth of focus of a SEM is much
higher than an optical microscope. Depth of focus is defined as the ability of a microscope to bring the
features of an object at different depths into focus.
Optical vs. Electron Microscopy
The attractive feature of optical microscopy is that it is so easy: samples can be analyzed in air or water,
the images are in natural color with magnifications of up to one hundred to one thousand times, and
modern semiconductor electronics with charge-coupled devices (CCD) allow image processing.
The optical microscope should dominate the field but it doesn't. The scanning electron microscope
(SEM) is the microscope of choice because of its depth of focus and resolving capability. Examination of
Fig. 1 shows a striking contrast between an A) optical and B) SEM viewgraph of a radiolarian at the same
Figure 1. (Taken from J.I. Goldstein et al., eds., Scanning Electron Microscopy and X-Ray Microanalysis,
(Plenum Press,NY,1980).)
In the optical micrograph taken at high resolution only a section of the radiolarian is in sharp focus. In
the SEM image the whole specimen is in focus.
For the optical microscope, the depth of focus is the distance above and below the image plane over
which the image appears in focus. As the magnification increases in the optical microscope the depth of
focus decreases.
The three-dimensional appearance of the specimen image in (b) is a direct result of the large depth of field
of the SEM. It is the large depth of field in the SEM that is the most attractive feature of the SEM. This
field arises because of the method in which the data is obtained with a fine electron beam scanned over
the surface and with the detected secondary electrons forming an image on the "TV"-like monitor.
The limit on what size specimen can be resolved -- irrespective of instrument type -- is set by the
wavelength. The wavelength of the visible light used in optical microscopes is between 400 and 700
nanometers (nm). The resolving powers of high-quality light microscopes are limited by the wavelength
of imaging light to about 200 nanometers (0.2 microns). Scanning electron microscopy uses electrons
with energies of a few thousand electron volts (eV), energies a thousand times greater than that of visible
light (2 to 3 eV). The wavelength is given by equation 1 below.
 = h / momentum
where h is Planck's constant. For 3600 electron-volt electrons, the wavelength is 0.02 nanometers. The
resolving powers of ordinary electron microscopes is 1 nm (above the limit because construction details
determine resolving power), a value which can be pushed to 0.1 nm.
Depth of focus and resolving power draws one to the SEM, and operating maintenance as well as vacuum
requirements drives one away. Electrons are lightweight (1/1836 the mass of the proton) and are
scattered or absorbed in air. The sample chamber of a SEM must be a vacuum, which limits the sample
size to a few centimeters on edge. Electrons carry charge (e = 1.6 x 10-19 Coulomb) so samples must be
covered with a conductive coating if they are non-conductive (most ceramics and polymers). Finally, the
SEM is capital intensive, e.g., expensive, requires maintenance and laboratory space.
Basic Operating Procedures:
Please be sure to read this document in full before taking the Driver’s test.
The SEM Chamber operates in high vacuum (10 -4 – 100 Pa) so users should observe high vacuum
protocols. Users must always wear gloves when handling anything that will be in the chamber. When
users finish loading (or unloading) a specimen their gloves should be removed. Remove gloves when
handling items that do not go in the chamber because oil and dirt on fingers are transferred to the doors,
keyboards, vacuum control buttons, etc. and then to the surface of the gloves, rendering the gloves
Specimen preparation materials like carbon tape and specimen stubs can be purchased from a number of
vendors. MSE maintains these supplies for undergraduates only. All other users must supply their own.
Ideally users will have their samples prepared before coming to the lab. Users must have their own
prepared sample for the driver’s test. Users are encouraged to have their own ‘kits’ so they know that
their materials are uncontaminated. However, there are tweezers, gloves, a ruler and other necessary tools
for imaging.
The SEM computer is for operating the SEM ONLY. Do not install software of any kind, or attempt to
uninstall software. Do not input a usb drive or a dvd into the computer. All data is saved to a shared
folder and can be retrieved from the network share computer in the lab. There is also a log file that must
be filled out.
1. Turn on the computer monitor. The JEOL software (In Touch Scope) should be open and
running. A dialog indicating that the system is in Eco mode should be up. Select the cancel
2. Check the following:
a. N2 gas pressure
b. EVAC is on
c. HT (beam) is off
d. Start time has been entered in the log.
e. Take care not to fall on or bump the instrument. It is mounted on rubber feet to reduce
vibrations. The turbo pump is attached just below the instrument and if it gets tilted
enough it can damage the pump.
3. There is a N2 gas tank connected to the instrument. It would be prudent to check that the tank is
still full. Do not make any adjustments to the pressure.
Sample (specimen) preparation:
A wide range of types of specimen can be imaged in this SEM due to the low vacuum setting.
However, certain types of materials must never be placed in the instrument:
Wet samples – either from water, or a solvent
Samples that outgas water vapor (porous materials) or corrosive or toxic gases.
Specimen that are not conductive may be imaged in the low vacuum mode, however, if they
can be coated they should be. Images will be better and the chamber will stay cleaner. If
you need information about conductive coating, please contact Hanson Fong
(hfong@uw.edu) or Tuesday Kuykendall (tuesday@uw.edu)
Regardless of the type of material, all specimen should be kept in an evacuated desiccator or
drying oven (50 C +) for 24 hours before loading in the chamber. Users must gain
permission before putting anything in the desiccator or drying oven in MUE 167.
Specimen are mounted on the surface of a stub with 2-sided carbon tape. Do not use any
other kind of tape. Specimen MUST be mounted in the standard sample holders (figure 2).
Specimen should never be mounted directly on the specimen stage.
Figure 2: Sample preparation tools
There are a variety of mounts available. Specimen can be mounted on one stub or 4. Odd
shaped specimen or specimen with a diameter greater than 10 mm (but less than 32 mm) may
be mounted on the large stub. Samples should not be over 10 mm tall. Sample surfaces
should be as flat as possible.
If there are 2 – 4 specimen then use the 4 stub holder. However, it is important that all of the
specimen are the same height. If you are unsure of how to prepare and load your specimen
please stop and ask.
4. Select and hold in the ‘Vent’ button on the vacuum mode control until it flashes (figure 3).
Figure 3 Front panel Vacuum Control: NEVER TURN THE KEY
5. About 10 seconds before the chamber is fully vented a dialog (figure 4) will pop up on the
computer monitor asking for the height of the specimen above the specimen holder. Enter the
height. DO NOT proceed if you’re not sure or have forgotten how to measure the height.
Figure 4: Dialog pop-up just before chamber is fully vented.
6. VERY GENTLY check that the specimen stage door is ready to open. It should slide forward
very easily. If it doesn’t wait a few more seconds.
7. Load your mounted specimen. The holders have a dovetail slide (Figure 5) on the bottom that fits
over the raised circle in the center of the stage. There is a straight edge on the stage and the
holder for orientation. Make sure you load in such a way that your hand does not go into the
a. When changing out multiple samples please evacuate the chamber between changes.
Never leave the chamber open it the room any longer than it takes to load or unload a
Figure 5 Side and bottom of specimen holder showing the dovetail slide.
8. Adjust the stage position using the XY knobs and note the specimen position and height.
9. Raise the Z- axis. For the MSE sample holders the top of the holder is in the same plane as the
working distance of 10 mm when the Z axis is set to 10 mm. If the specimen is flush with the
holder then move the Z-axis of the stage up to 10 - 11 mm. If the stub/specimen assembly is
above the top of the sample holder then measure the specimen from the top of the sample holder
to the highest point of the specimen. Add the measured value to 10 mm and that is the highest the
Z axis should ever go. Z-axis is NOT working distance. Think of the adjustment of the z-axis as
moving up and down under the detector.
Figure 6: Manual Controls
10. When the sample is in place gently push the stage door back in – WATCH the stage as it moves
back in place to see where it is with respect to the detector. If your specimen or any other part
hits the detector it will cause catastrophic damage! The highest point on the surface of your
sample must be 10 mm below the detector.
Figure 7: Open stage and Objective
11. Press and hold the EVAC button on the vacuum control until it starts flashing. It will take about
1 minute to evacuate to a pressure that is safe for the beam. Be sure to wait for the green “Off”
icon on the software before proceeding.
1. The JEOL software should always be on and open. There are three main sections (Figure 8).
Navigate between the three sections using the left/right arrow keys in the center.
Figure 8: Software user interface
2. Users may adjust the parameters by selecting them from the bottom of the screen.
3. When the chamber has evacuated to a safe pressure the on/off/wait button (upper RH side) will be
green and off. Wait an additional 5 minutes then press the button to turn on the beam.
4. If there is no image, press the ACB (Auto contrast and brightness). An image should appear. If
the magnification is at 30X you will see the round outline of the objective. Increase the
magnification to 100X.
5. You may make a small adjustment in the Z-axis by manually raising the stage. Do this with great
care! Do not exceed the 10 mm plus offset established earlier. Once you are satisfied that the Z
axis is in the correct position increase the magnification.
6. It is usually preferable to get a focused image at a higher magnification then lower the
magnification for imaging.
7. A step – by – step guide is available.
8. There are a number of automatic features in the software that are not used since we don’t have a
motorized stage or a camera. Some of the operations selections on the main page are not used
because they cause unexpected behavior – using them runs the risk of having the beam turn on or
the chamber venting when the user is finished. (see figure 8, crossed out buttons).
9. The SEM comes equipped with a traditional operation keyboard (figure 9):
Figure 9: Operations Keyboard
10. At very high magnifications its usually more advantageous to use the manual knobs for
Magnification and focus (5), stigmatism (4), and contrast and brightness (7).
11. In addition to the auto-processing in the software, there is a AF, AS, and ACB (6) on the
keyboard as well. Scan speed can be selected here as well (3). Scan 1 and 2 are fast scans and
resolution isn’t very good but it’s easier to see any adjustments or movements.
12. Stigma may also need to be adjusted. Users will have an opportunity to practice this. The only
way to learn how to obtain an ideal image is to practice.
13. Scan 3 is much slower but the image is better. Scan 4 and Photo both acquire the image to be
saved. This freezes the image.
14. Select scan 2 or 3 to unfreeze the image.
Getting the best image and obtaining valid spectroscopy data takes practice and is often material/sample
Shut down procedures:
1. Turn off the beam.
2. Press and hold the vent button until it flashes. When the height offset dialog pops up close it
(unless you are installing a new sample then follow start-up).
3. If you are finished, make sure to close the height input dialog. If it is left on it can cause the
software to freeze.
4. Open the chamber door.
5. Lower the stage
6. Turn the stage so that your hand enters from the side.
7. Remove the sample holder. (with gloved hand) and carefully remove your sample. NEVER leave
a sample in the chamber.
8. Close the chamber door and press the EVAC button until it flashes. NEVER leave the chamber
9. Please leave the area clean for the next user.
• Never leave the chamber vented
• Minimize the amount of time the chamber door is open.
SEI - Secondary electron image
BSE – Backscattered Electrons
kV – Energy of incident beam
WD – working distance
SS – Spot Size
For an in-depth treatment of SEM and the theories of operation please read:
Goldstein, Joseph et.al; Scanning Electron Microscopy and X-Ray Microanalysis, 3rd edition,
Springer Science, 2003 ISBN: 978-0-306-47292-3
Certification Checklist for STF-JEOL 6010 SEM
User Name:_______________________________________
Tested by:_________________________________________
Test Specimen:_______________________NOTE: User must have their own sample for certification.
User filled out the user log on the work share computer
Policies are read and understood
Sample is properly prepared - it is not wet, corrosive or a hazardous material.
Start-up procedures are followed.
Sample specimen is properly mounted.
Sample specimen height measured and noted.
Specimen height offset has been entered in height record in computer
User can correctly load specimen onto stage.
User understands the relationship between working distance and specimen height
User turns Z axis up or down using the correct scale
User is able to correct stigmatism.
User is able to record an image at 20000X using spheres sample within 30 minutes of
turning on beam. (Or maximum quality image of their own material)
User follows shut down procedures
Sample specimen/holder is properly extracted from chamber.
Chamber contamination is minimized throughout user interaction.
SEM work area is cleaned up
User knows how to save and retrieve images and data.
User completed the written portion of the Drivers test.
User has signed contract
For Beginners - Step by Step Start-up: Please read all steps before you begin.
1. Check that there is nitrogen.
2. Check that the computer is signed on – if not, contact Tuesday, Hanson, or Tatyana.
3. Wear Gloves.
4. Prepare the sample and load in in the provided sample holder. Keep everything that will go into
the chamber on a clean surface, like the white pad next to the instrument.
5. Measure the offset height. This is the height of everything (sample, stub, etc.) above the surface
of the holder.
6. Make a ‘map’ of the arrangement and orientation of the samples in the holder.
7. Vent the chamber.
8. Enter the offset in the dialog.
9. Open the chamber door. You must always open the chamber door BEFORE adjusting the Z –
10. Make sure that the stage is oriented so that your hand enters from the side, not into the chamber.
11. Install the sample holder
12. Raise the Z-axis to the point that equals 10mm + your offset. Use the scale on the right. (a
camera is coming soon.)
13. Slowly push in the chamber door until it is almost closed.
14. With your eye at the level of the top of your sample, check the distance from it to the detector.
15. Make sure it is 10mm or more from the bottom of the detector.
16. Push in the chamber door. Gently.
17. Press the ‘evac’ button until it starts blinking.
Minimize the amount of time the chamber door is open. Do not vent until your sample is ready to
Suggestions for obtaining an image:
1. Let the chamber evacuate for 5 minutes after the HT light goes green.
2. Start with scan parameters: 10kV, SS30mm, 50X and scan mode 2
3. Find an area of good contrast (light and dark) and center it by moving the x and y micrometers.
4. Switch to scan 1 and center again.
5. Increase magnification just before losing contrast.
6. Focus coarse mode.
7. Increase magnification again, again in an area of high contrast.
8. Focus in fine mode.
9. Adjust the x and y stigma - do this one plane at a time.
10. Focus again in fine mode
11. Continue increasing magnitude and focusing until you can no longer get good resolution.
12. Try fine focus in the Scan 3 mode.
13. Reduce magnification for imaging.
• It is necessary to repeat these steps whenever voltage, spot size, or working distance is changed.
• Scan mode 3 allows for a more careful focusing at higher magnifications.
• The auto focus and auto stigma do not work very well at magnifications of about 1000X and
• For focus, x, and y stigma. Try to find an edge with good contrast – turn all the way to the left,
then back to the right for each plane until you maximize the image. This takes practice.
Step by Step Shut down:
10. Turn off the beam
11. Press and hold the vent button until it flashes. When the height offset dialog pops up close it
(unless you are installing a new sample then follow start-up).
12. If you are finished, make sure to close the height input dialog. If it is left on, it can cause the
software to freeze.
13. Open the chamber door.
14. Lower the stage
15. Turn the stage so that your hand enters from the side.
16. Remove the sample holder. (with gloved hand) and carefully remove your sample. NEVER leave
a sample in the chamber.
17. Close the chamber door and press the EVAC button until it flashes.
18. Please leave the area clean for the next user.
NEVER leave the chamber vented.
Minimize the amount of time the chamber door is open.
MSE User Facility Contract
•I certify that I have completed Instrument training and taken the written and hands on drivers test.
•I acknowledge that I have received lab safety training – am aware of safety resources – and understand PPE.
•I understand that this certification is good for up to 90 days past the last time I use the instrument or 1 year, which ever comes
•I will always sign up on the resource scheduler.
•I will always sign the user log.
•I will not use the instrument after hours until I have been certified to do so.
•I will NOT train other users – even if that user plans to schedule formal training.
•I will NOT give other users my access.
•I will only use the instruments for my research and will direct others who want measurements done to the Lab Manger.
•I will keep the lab clean. I will leave it as I found it.
•I will always ask before using any new equipment, I will never use equipment I have not been trained for.
•I will not insert any kind of external media (dvd, usb, etc.) into the instrument.
•I will NOT remove any item from the lab except what I bring into it.
•I will treat the equipment with respect – I understand that only the Lab Manager is qualified to calibrate, repair, or reset the
instruments. (including changing out fixtures on the UV-Vis, FTIR, etc.)
•I will treat other experiments with respect.
•I will always ask if I don’t know.
•I will use Best Lab Practices and observe all safety rules.
•I understand that violation of these rules will result in loss of access.
Print Name________________________________________
PI or Advisor________________________
Title or Class________________________
Date: _________________
Email address_______________________