Hitachi HT7800 User manual

1
Hitachi HT7800 user guide
System overview column page 2
Control panel overview page 3
Start up / shut down routine page 4
Holder - Sample mounting page 5
Inserting and removing sample holder page 6
The process of exchanging samples page 7
Software overview page 8
How to start your imaging page 9
Adjusting image display and camera capture page 10
Camera capture parameters page 11 - 12
Save file setting page 13 -14
How to use autofocus page 15
Beam cross over page 16
Beam shift horizontal page 17
Auto multiple frames (AMF) page 18
Column mode operation page 19
Common nomenclature explained page 20
Troubleshooting page 21 - 24

Power switch panel
2
EMERGENCY OFF switch
(should be used in case
of an emergency like
water leakage or fire
exposure). Special
procedure must be
followed for switching
on the system again).
EVAC power switch
(evacuation system).
Do not touch!
COL power switch
(high voltage,
lenses, deflection
system)
Goniometer switch panel
Sample holder
Condenser aperture
Objective aperture
(automized)
Cold fingers –only
used when needed

3
Control panel overview
Turn right for
lower
magnification
Ctrl brightness
and work on
the right side of
the crossover
BH (beam horizontal)
used for aligning
beam (with X and Y)
to the center of your
screen
Wobbler is used
to adjust for
eucentric height
or focus
Focus knob,
switch above
switches
between
fine/coarse
Resets
lenses (use if
you get lost)
to go back to
start
Turns off the
filament and HV
Switch between Screen
and Main camera
Goes to live mode
Auto focus
Captures and
saves image

Start up routine
1. If the COL power is off, turn it ON
2. Turn on the computer and log in with password: mic77cim
3. Start the software. An initial screen will appear, and each control unit will be
executed. This window will automatically close, and the main control window
will be loaded.
4. Turn on the HV (normally we use 100kV) and wait until it reached 100kV (5 min).
This is a good time to prepare the holder with your samples (see page 5).
5. Insert the holder with your sample(s) (see page 6).
6. Turn on Filament and wait for it to stabilize ~ 30.3V (5 min).
The beam should turn on automatically as soon as the
holder is in PARK position. Do not change the Beam µA!
Shut down routine
1. Go to the Screen camera (press F1).
2. Press holder RESET (stage operation window)!
3. Remove your samples holder. Place holder in the stand
and remove the grids. Insert holder and follow the
evac procedure to fully insert the holder.
4. Turn off “HV on” from the control panel.
5. Close the HT7800 software.
6. Shut down the computer (start menu + shut down).
7. Leave COL power ON (we turn it off during vacations).
8. Sign the logbook.
Breaks?
Turn off beam or place sample holder i PARK position if you need a 5 min break
Turn off filament if you need a lunch break 4
1
3
6
2
4
4
1
7

Mounting the sample is a delicate process and the sample holder needs to be handled with
great care. Please be especially careful to only load completely dry samples.
•The holder should have been left inside the column (without evac) away from dust.
Remove holder.
•Place the holder carefully in the stand. Make sure to never touch the area above the o-
ring. Place the silicon cylinder in position. Using the coarse tweezers, carefully lift the
metal lid. The MS2 holder can fit up to three samples at a time.
•Carefully place each grid inside the slot and make sure to note down the sample
position.
•Carefully close the top lid to secure the grids in position either with tweezers or by
pulling the silicon cylinder. Make sure there is no dust or excess of grease on the o-ring.
Holder - Sample mounting
5
1
2
3
Slits to facilitate the
removal of grids
To open, lift the metal lid Place samples in slots
Pull the silicon cylinder to close the metal lid

6
Inserting and removing sample holder
•Remove the sample holder from its stand. Insert the holder carefully and align the pin with
the opening in the goniometer. Push until it stops.
•Set the goniometer switch to “evac” (the evacuation of the prechamber starts).
•Wait for the beeping sound and the light to turn green.
•Gently rotate the holder towards the right, gently hold back when it is being sucked into
park position.
•Turn the holder to the left and let it go all the way in.
•The beam should now turn on automatically (if not, click on “beam”).
•To remove the sample holder, remember to do a “reset holder” in the software first.
•Pull the holder, turn right and when you reach the end, continue pulling out.
•Turn left and stop once you see the pin.
•Turn the switch to “air” and wait 5 sec before pulling out the holder.
•Once you have removed your grids from the holder, place it back into the opening (you
don’t need to evac and insert the holder).
Insert
holder
and press
Evac, wait
for sound
(20 sec)
Turn holder
to the right,
holder will be
sucked in.
Holder is now in
PARK position,
beam turns on.
INSERTING
Press Air,
wait for
5 sec
Turn holder
to the left.
Pull the holder
and turn it to
the right. Continue
pulling the
holder.
Remember to reset Holder
REMOVING

7
The process of exchanging samples
1. Switch over to the screen camera (press F1).
2. Go down in magnification.
3. Click holder reset in the stage operation
window.
4. Remove the holder by following the guidelines
(more info on page 6).
5. Place holder in it’s stand and carefully open top
lid and remove your samples. Place new grids in
the holder and close the lid (with tweezers or by
pulling the silicon cylinder).
6. Insert holder by following the guidelines (more
info on page 6).
7. The beam should come on automatically after
you have inserted the sample holder. If not, turn
on the beam.
2
3
1
5
6

Information about magnification, kV,
filament V and vacuum condition Turning On/Off HV,
filament V and beam bias.
You will create a “whole” grid view here
and “click and start” to automatically
navigate to specific region.
Camera control (switch between
screen/main, autofocus and saving).
Histogram for chip exposure will show up
here –very useful.
You can adjust “live” camera exposure here as well as
black/white and gamma levels. The “R” will refresh
and “auto LUT” will automate the lookup table.
8
Software overview

How to start your imaging
Insert your sample holder and perform a beam shift horizontal alignment (page 17).
1. Open the Stage operation window.
2. Select the field mode you want to use (HC=high contrast, magnifies up to 200.000
or HR=higher resolution, magnification between 200-600.000).
3. Select the correct holder and specific holder position your want to image.
4. Open the camera operation mode.
5. Magnify to 5-6K. Focus you image by using the wobbler and carefully adjusting the
eucentric height with the screw.
5
4
3
1
6
9
2

Adjusting image display and camera capture
The camera exposure and gain can be
changed for the live mode. “R” is to reset.
The camera display, white/black values and
gamma can be changed. If “Auto LUT” is checked,
the values change automatically.
•Increase the brightness in order to place the
spectra in the middle of the window (A).
•Set the standard averaging to 4-6 images and set
the capture exposure between 200-800 ms (B).
•Set the capture gain (C) to 2-6 (under “image”
window).
A
10
B
D
C
•Find your preferred “capture parameter” (D).
“Maximize” is imaging the whole camera chip
dimension. Default is very useful. Set 1 will
give more contrast (dedicated to HUS). Set 2
and 3 can be set up by any user.
A
To acquire images with high quality use the MAIN camera!

11
Camera capture parameters (MAIN camera)
Capture exposure: increasing the exposure time will give
less noise and a smoother image with more details. If the
exposure is too long, you might experience unsharp image
due to drift. Try using between 300-600 ms.
Standard averaging/drift correction: averaging will result
in a less grainy image. Too many averaging might result in
unsharp images due to drift.
Try using 3-5 “standard averaging”. If drifting, try using
“drift correction”.
600 ms , no ave 600 ms, 8 ave 600 ms, 20 ave
150 ms 600 ms 900 ms

12
Capture gain (dB):
Range between 0-20, default is 0
For normal samples, we use capture gain 0.
In the example under you can see that gain
8 gave an overexposed image.
It can be a bit challenging to define the
capture gain especially if you leave the live
gain very high.
Turn off “set run after save” if you want to
see the histogram of the captured image.
600 ms , 4 ave, gain 4 600 ms, 4 ave, gain 8
“Effect of save”: if you check sharpness or/and median filter, these will
be processed and saved in your image. This is a postprocessing action.
Sharpening 25 Sharpening 50 Sharpening 100
Median inactive Median 4
Median filter will remove noise
and sharpening will make edges
more defined.
Camera capture parameters (MAIN camera)

•Define the save file settings inside the camera operation window, under file.
•To acquire an image, click “save” button on the control panel.
The image should now be automatically saved.
Save file setting
This option should always be checked in order to protect
the camera chips from long exposure of the frozen
image. Once you have acquired an image, it will
automatically be saved and the frame will go back to live.
For automatic saving of images,
reset the counter to 1 between
users or grids (it’s up to you).
Create a folder with your name
under pictures/users save here/
Define the format. If you select
jpeg, you will decrease the image
quality.
13

14
Save file setting continues…
You can investigate your image in the Hitachi
EMP-EX software –this is optional
The acquired image will show up in the
Thumbnail window. Double click the image to
open it up in Hitachi EMIP-EX software. Here you
can make measurements and change contrast on
the image if needed.
You can also open multiple images and place them next each other to compare.

15
How to use autofocus
The autofocus works by searching for contrast changes in the middle of the image (10% of
the center). If the signal is low there or structures are missing, autofocus will fail.
Solution: Move your sample in order to place something with more contrast in the middle
of the image.

•The brightness knob controls the beam. By turning
the knob to either direction, you will spread the beam
or center the beam into a spot.
•For optimal focus condition, you need to be on the
right side of the crossover, ie you increase the light
(the beam gets smaller) by turning the brightness
wheel anti-clock.
Beam cross over
Brightness knob movement
Beam intensity
16

17
Beam shift horizontal
Why do we need to shift the beam?
- To get optimal resolution, contrast and
enough light.
If you notice that a shadow sneaks into your
image, it’s most probably because the beam
is not in the centered.
Use the X and Y under alignment and shift
the beam to the center. It can be useful to
minimize the beam to find the center.
Once in the center, open the beam to fill the
whole image with homogeneous light.

AMF –Auto multiple frames
It is possible to create up to 4x4 tile scan with
the Main camera using the AMP function.
•Open the Auto multiple frames (AMF) under
Function (A).
•Define where your images should be saved
under “quick save file setting” (B).
•Define the size of your panorama image (C).
•Define the starting position (D) and make
sure you are in the desired position.
•Define the movement method (ISF is
recommended (E). Run the “Get ISF
condition” (F). You only need to do this once
per magnification range.
•Make sure the overlap is set to 10-20% (it’s
highly dependent on the image details) (G).
•Click “start” (H) and watch the acquisition.
Images will be acquired with “maximized”
capture parameters.
•Click “run” to go back to live mode in order
to protect the camera.
B
E
C
F
D
G
A
18

19
Column mode operation
Brightness link should
be checked to
facilitate transition
between
magnification and
beam brightness.
Common users will not change these options.
Spot number/size
(1= smallest, 5= largest) The
smaller the spot, the more
light you get. Generally spot
size 3 is ok to use.

HV The system can operate from 0-120 kV. The higher the V, the “harder” the electrons
will hit your sample. For biological samples, try using kV between 60-100 kV.
Filament V The voltage is set by the technician when the filament is saturated (a process involved
in the filament mounting).
Beam µA This beam current reflects the “number” of electrons hitting the sample.
Condenser
aperture
0= it is out, 1= large, 5= smallest. We generally use size 2 for Lab6 filament, size 1 for
Tungsten filament.
Objective
aperture
0= it is out. Aperture 1 will give the largest contrast image. We are leaving it on size 2.
Spot size (1= smallest, 5= largest) The smaller the spot, the more light you get. Generally spot
size 3 is ok to use.
Magnification
crossover
A small magnetic lens comes into play and the beam shifts a bit. In HC field it happens
between 30-40K, while in HR between 50-60K
Beam µA The is the “amount” of electrons. 8 µA is default. Lower it for critical samples.
Changing µA will affect the beam alignment.
Lab6 Lanthanum Hexaboride Filament. It’s lifetime is about 1000 hours.
Screen camera This is the camera which looks down on the fluorescent screen. As the camera chip is
not hit directly by the beam, this camera can take a lot of light exposure. It is a 14 bit
camera with 1024 x 1024 pixels.
Xarosa camera This is the main camera and is mounted on the top-bottom. It is a 16 bit camera with
5120 x 4005 pixels.
HC field
High contrast mode. There is a mini lens which improved the contrast (will reduce a bit
the light). You can magnify up to 200K. This mode is generally used for most specimen.
HR field This is used for higher magnification and can reach 600K. When switching over to HR,
notice that the beam gets brighter.
Lens reset Pressing this button resets everything to morning setup. Use this if you “get lost”.
TMP Tubular Molecular Pump, a new and fast pumping system which will quickly remove
contamination from the column.
OS Object stigma. It can be adjusted when you notice that your beam is not circular any
more.
Eucentric You can focus the sample inside the goniometer instead of using the beam focus
mode. Adjusting eucentric height is crucial before tomography. It’s done at 3-5K.
AMF Automatic multiple fields. With Xarosa you can do 4x4 images. If you need larger
fields, you need to use “image navigation”. Images will always be acquired with
“maximize” capture parameter.
Resolution This system can give you 0,2 nm resolution at 100kV.
Common nomenclature explained
20