JEOL 1010 User manual

Version 2017-01-19 for GI use
How to use the Jeol 1010 TEM of GI (Liesbeth own GI version)
1.Load the specimen
Load a grid into the rod holder: USE ONLY THE TOP POSITION (blue arrow),
Specimen selection on 1 (The rear one is only a reserve one- Spec sel 2). Use the
white wing key with a feather tail (red arrow) to insert the slit over the cover: grab the
cover with the red dots oriented in the long axis, turn a quarter and gently open it.
Insert the grid specimen up. Close the cover and remove the wing key. (Check that all
covers are closed before inserting the rod in the goniometer. Be careful to not lose
the wing key and put it back in its hole on the standard.
If not already done, rotate the tilt of the insertion chamber (goniometer) to the zero
position (scale to be read in the scale on the left side) by releasing the lock h(lift it

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slightly). When ready, close this lock (lift hdown to vertical position).
Align the pin of the grid holder with the slot (line above pointing to the slot) in the
goniometer. Gently press the grid rod straight into the opening. To make contact
press the rod cylinder (metal color in ours) with a flat hand palm: a green light lights
(line).
Wait until the green light goes off.
Without delay but slowly turn the rod one quarter clock-wise and slowly guide it into
the heart of the column. Do not release the holder until the rod is fully inserted.

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2. Viewing specimen, acquiring images
right panel, left panel and central base of the column with xy navigation


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Press the HT knob 1under the plastic cover (it lights up) and check that the green
light is ready. Beam current (3) rises to 040. Press the FIL knob 2on. Also here a
green ready light goes up and the current 3rises from 40 until about 60µA.
Open the iTEM software (click on icon on desktop)
Press Intelligent exposure (pink cross)
Start imaging at low magnification. For magnification below 800x press the “LOW
MAG” knob in the Magnification Selector panel. The lower diaphragm handle fshould
be switched to the right. For still low magnifications, but above 800x, use MAG 1 and
turn diaphragm fto the left. To modify the magnification factor, use switch 4. MAG 2
is for pre-set magnifications. (If possible, use standard magnification steps to better
compare images).
XY navigation with 14 and 15
Spread the bundle as evenly as possible just over the field of view using the
brightness knob 12.
Use the Shift 10 and Shift 13 knobs (right and left panel) to center the bundle. (make
the bundle small to better judge the center. In general, when brightness needs to be
dimmed, it is recommended to use the domain that can be reached by turning the
know clockwise
Focus using 5, 6, 7. Option 16x (5) is for a very coarse focusing. It can be employed
with both the macro (6coarse) and micrometer (fine 7) knob. Without 16x a finer
tuning can be achieved. (In summary, there are four grades of focusing)
To further improve the focusing, use the wobbler function x and y (8and 9) and focus
until the image is stable on the screen

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In case the alignment of the microscope is lost, which will for example become
evident because the beam has an oval shape (astigmatism), the original settings can
be recalled. Ask assistance. [Note for assistants: to the hardware keyboard (the one
going along with the small monitor), press ESC to make sure to start with a clean line
and type: ufc o 1 (which is ufc in small letters, space, letter o , not zero, in small font,
space and then 1). Press Enter. ]
To acquire an image, press on the right camera icon of intelligent exposure. The
entire gray levels displayed on the histogram are automatically recorded. However,
the brightness settings should be adjusted in such a way that the histogram is
centered and as broad as possible so that many gray levels are recorded, but also
the exposure time should be as short as possible, in order to prevent vibrations to
bias the image quality. Note that there is a slight difference in eveness ofillumination
for direct vision under the column or through the camera (use brightness to
compensate).
In case automatic balancing of the
camera is not suitable, for example
because the interesting parts in the
specimen are very dark or very bright,
one can apply (automatic, fixed scale or
manual) exposure on a Region of
Interest around these part (click the
green screen icon within the Intelligent
exposure pop-up window and drag a
ROI). Manual exposure, manual
minimum and maximum setting and
manual gamma adjustment is also possible. Ask Geert-Jan for the various options.
For saving images, enter the correct magnification (mag x can be read on the small
hardware monitor) and image name in the own folder (D:>Users> path). Scale bars
are automatically burned into the image. (Cancel the second pop-up screen). Images
can be uploaded to a server at the end of a session.
To finish a session, go back to small magnification (lower diaphragm handle to the
right). Finish after having taken one picture to allow the charge on the chip of the
camera to be withdrawn and switch of the filament 2.
To unload the specimen holder, always check first (once again) that the FILAMENT
IS OUT (!). Gently pull the rod to the final stop. Turn one quarter anti-clockwise.
Release the rod by holding one finger against the goniometer to counter the vacuum
sucking in a controlled manner and pull the rod out. If you are the last user of the day,
switch also the HT 1out. Exit the program.
Place the grid rod holder on the standard and release the grid cover with the wing
key. Allow the grid to fall on a clean piece of paper and lift it with tweezers to set it
back in the grid box. Close the cover and secure the wing key in its cavity.
HALIGNMENT JEOL 1010 TEM (GI)
HOW TO CHECK THE SATURATION OF THE TEM FILAMENT?
1. Start the High Tension (HT) and the filament (Fil)

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2. Remove the upper and the lower condenser diaphragms by switching the level
c to the right
3. Go up and down with brightness (12). Adjust over and underfocus. If the A well
centered filament gives a centered beam position swings, adjust the centering with the
screws shift 10 and shift 13

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4. If the filament (hairpin) becomes visible, VERY SLIGHTLY adjust the filament
knob (under the brownish cover on the right panel) by turning it in clockwise direction
until the pin shadow disappears.
5. Close the brownish lid
6. Spread the beam with brightness
7. Reinsert the upper diaphragm c and the lower diaphragm.
HOW TO ADJUST THE UPPER/CONDENSER DIAPHRAGM?
1. Switch HT and Fil on
Go to LOW MAG and spread the beam.
2. The upper diaphragm should be directed to the left (like always during
operation, except filament adjustment)
NOTE: USERS SHOULD NEVER TOUCH THIS DIAPHRAGM, AND BACKUPPER ONLY
AFTER HAVING BEEN FULLY TRAINED.
3. Find one edge of the diaphragm by gently turning screw a clockwise (in)

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4. Turn screw a counter-clockwise until the other edge is found. Do this while
counting the number of turns, to know where the center is.
5. Use screw b (first completely in until stop. Be careful not to … to prevent the
diaphragm to fall into the column ???
6.
FRESNEL FRINGES ADJUSTMENT
1. Insert a carbon test grid (ASK Geert-Jan). Put HT and Fil on.
2. Go to low magnification to search a nice piece of membrane
3. Low mag with level f directed to the left
4. Check astigmatism by defocussing a little bit (knob 7)

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5. If Fresnel fringes appear in the holes of the carbon grid as lateral shadows,
instead of a well-centered rings, adjust the center with screw xx and yy
6.
Explanations-Theory
http://www.uiowa.edu/~cmrf/methodology/tem/tem_pg3.html
To optimize imaging in the TEM a beam alignment should be performed prior to use. A
tool for this alignment is a holey grid. A holey grid is a TEM grid support coated with a
thin plastic film and a stabilizing carbon layer. It is manufactured to contain small
round holes useful in alignment of the TEM. The holes in the grid create Fresnel fringes
when the electron beam diffracts around the edges as the electrons come together at
overfocus. The edge of the hole appears to have bands or fringes.

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The final image is viewed by projection onto a phosphorescent screen which gives off
photons when irradiated by the electron beam. A film camera is located beneath the
phosphorescent screen. The screen is raised in order to expose a special
photographic film with a thicker emulsion layer than light film. An alternative to
photographic film is digital capture with a computer digitizing and archiving (CCD)
camera.
The operator is responsible for adjusting variable bias, recognition of aberrations,
image drift, photography, specimen contrast, resolution, even illumination, and filling
the anticontaminators with liquid nitrogen before using the TEM.
Instrument maintenance that requires staff or company repair are filament saturation,
filament exchange, aperture cleaning or replacement, specimen holder cleaning,
vacuum pump maintenance, and viewing screen.
The theoretical resolution described by Abbe for the light microscope can be modified
and applied to the TEM by using DeBroglie's formula. DeBroglie stated that the
wavelength of an electron beam is a function of the accelerating voltage used. By
increasing the accelerating voltage, a shorter wavelength is obtained. The shorter
wavelength is applied to Abbe's equation and the increased resolution can be
calculated. Typical accelerating voltages for a biological TEM range up to 125,000
Volts.
Abbe's equation: r = 0.612 x l
sin a
r = resolution
l = wavelength (nm)
a = angle of incoming beam
Resolution is defined as the distance at which two points or objects can be
distinguished. Therefore as r approaches zero we say that the resolution is
increased.
DeBroglie's formula:
l = h/mv
h = Plank's constant
(6.626 x 10 –23 ergs/ sec)
m = mass of the electron
v = electron velocity
DeBroglie's formula states that if the accelerating voltage is increased, electron
velocity will increase as will resolution.
As in the light microscope several factors detract from this number. Spherical
aberration is also present in the TEM as electrons passing through the periphery of the
lens are refracted more than those passing along the axis. All the electrons will
therefore not reach a common focal point. To reduce spherical aberration, an aperture
is used to eliminate some of the periphery electrons.
a.

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a.
b.
One would not normally expect chromatic aberration to be a problem in an electron
microscope, but, electromagnetic radiation of different energies converge at different
focal planes. This is essentially the same problem as the chromatic aberration
observed in the light microscope. To correct for chromatic aberration, increase
accelerating voltage, improve the vacuum and/or use a thinner specimen.
An astigmation occurs when a lens field is not symmetrical in strength, but weaker in
one plane than another. Astigmation can be caused by imperfect polepiece boring,
non-homogenous blending of polepiece materials, or by dirt on the polepieces,
apertures, and/or specimen holders. A stigmator can be used to apply a correcting
field of the appropriate strength in the proper direction to counteract the asymmetry.
Stigmators are located in the objective and condenser lenses.

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Although diffraction can be useful, diffraction of electron waves around the aperture
openings can interfere with the initial wave front. The results are an unclear or out-of-
focused image. It is important to create a balance between reduction of spherical
aberration and diffraction by selecting an appropriate sized aperture.
How to align the TEM? [For assistants only!!]
Insert a holy grid in the TEM like described here above.
Go to Mag1 (lower diaphragm handle f to the left) , Magnification minimal to LOW
(switch 4 to the left). 800x
Do not forget to spread the bundle with the brightness knob.
Alignment procedure step A:
Switch handle f of the lower diaphragm to the right
Close the beam as much as possible and use the shift knobs left end right to center
the spot right on the small dot on the phosphor plate.
Spread the bundle with the brightness knob
Center the position of the spread bundle using the lateral and front knobs of the upper
diaphragm this time. (Note, upper handle is directed to the left)
Repeat above four steps if necessary (iteration) Additional tip Geert-Jan: adapt the
magnification so that the edge of the bundle respect to the opening on the phosphor
plate is optimal to view the centering.
When ready, switch back the lower handle f to the left.
Press the Diff (diffraction) button on the right panel.
Make a bright narrow pin spot and center the surrounding halo using the leftand right
DEF knobs
When ready, spread bundle and press Mag1 again. Dif goes out.
Click on COND STIG in the left panel. Turn the brightness knob left and right. The
shape of the bundle should remain round. If it is elliptical, correct for this with the Def
knobs left and right. When ready, press COND STIG again.

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To correct for astigmatism, still using the holy grid, search for a small hole at high
magnification (e.g. 100000x).

Apply underfocus: Fresnel rings appear (see arrows here above). Apply just enough
defocus so that the rim appears only just a little bit in one axis.
Switch on the OBJ STIG (objective stigmator on the left panel) and using DEF left
and right, for big steps use the 16x knob on the left panel between Brightness and
Def. Apply iterations until the rim is central respect to the hole.
When ready OBJ STIG off. Focus. And check with the wobbler that not shift occurs.
BUGS TROUBLE SHOOTING
When the switch function between camera and direct eye vision is lost, check that 2x
enabled is chosen in Image> Configure input> macro
When the vacuum is lost during insertion of the rod, switch off with the key under the
door left front wing just below the table surface, and switch on again. It takes about
20min before the vacuum is restored. The progress can be followed on the small
monitor (page down of the second keyboard to browse menus)

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
If the manual switch camera has been touched use one acquire round to reopen the
camera.
There are in principle two positions for two single grids on the holder. Each position
can be found by switching SPEC SEL (left –bottom of the column). However, as a
routine, only the position (1) is used.
When a very bright spot that can not be moved is present in the mid of the screen,
follow:
- Switch off filament and HT
- Open the left door under the front side of the table
- Switch off Lens power and wait a few seconds
- Open the Lens power switch to ON again

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- HT and FIL on again
Bugs