Tecnai 12 User Interface

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Table of Contents
1
2
3
4
5
6
7
8
9
Introduction.......................................................................................................................................... 3
1.1
Copyright and liability limitation ................................................................................................ 3
TEM Account Log................................................................................................................................ 4
2.1
Introduction............................................................................................................................... 4
2.2
The main window...................................................................................................................... 4
2.3
Overview................................................................................................................................... 5
Big Screen........................................................................................................................................... 6
3.1
Introduction............................................................................................................................... 6
3.2
General principles..................................................................................................................... 6
3.3
Popup menu ............................................................................................................................. 6
3.4
Display...................................................................................................................................... 7
3.5
Optics parameters .................................................................................................................... 7
3.6
Stage parameters ..................................................................................................................... 8
3.7
Various parameters .................................................................................................................. 8
3.8
Window position and size ......................................................................................................... 8
3.9
Help access .............................................................................................................................. 8
Exposure Log ...................................................................................................................................... 9
Image Search .................................................................................................................................... 10
5.1
Image Search Control Panel .................................................................................................. 10
5.1.1
Image shift and maximum deflection .................................................................................. 10
5.1.2
Image search controls......................................................................................................... 10
5.2
Image Search Calibrate.......................................................................................................... 11
5.3
Image Search Options............................................................................................................ 12
Preset Magnifications ........................................................................................................................ 13
Screen Saver..................................................................................................................................... 15
Serial Sections .................................................................................................................................. 16
8.1
Introduction............................................................................................................................. 16
8.2
Location .................................................................................................................................. 17
8.3
Section.................................................................................................................................... 17
8.4
Overview................................................................................................................................. 18
8.5
Menu....................................................................................................................................... 19
8.5.1
File menu ............................................................................................................................ 19
8.5.2
Setup menu......................................................................................................................... 19
8.5.3
Section menu ...................................................................................................................... 20
8.5.4
Location menu .................................................................................................................... 21
8.5.5
Display menu ...................................................................................................................... 21
8.5.6
Help menu........................................................................................................................... 22
8.6
Control options ....................................................................................................................... 22
8.7
Reference points .................................................................................................................... 22
8.7.1
Setting reference points for new data ................................................................................. 23
8.7.2
Redoing reference points for old data ................................................................................. 23
8.8
Section data display ............................................................................................................... 24
8.9
Select section ......................................................................................................................... 25
8.10
Location list............................................................................................................................. 26
8.11
Select location ........................................................................................................................ 26
Total Recall ....................................................................................................................................... 27
9.1
Total Recall Control Panel...................................................................................................... 27
9.2
Total Recall Reference Points ................................................................................................ 28
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9.3
Reference points .................................................................................................................... 29
9.3.1
Setting reference points for new data ................................................................................. 30
9.3.2
Redoing reference points for old data ................................................................................. 30
9.4
Total Recall File...................................................................................................................... 32
10
Vacuum Logger ............................................................................................................................. 33
10.1
Introduction............................................................................................................................. 33
10.2
General principles................................................................................................................... 33
10.2.1 On-line operation ................................................................................................................ 33
10.2.2 Off-line operation ................................................................................................................ 33
10.3
Program structure................................................................................................................... 33
10.4
How to run the logging software ............................................................................................. 33
10.5
Menu....................................................................................................................................... 34
10.5.1 File menu ............................................................................................................................ 34
10.5.2 Display menu ...................................................................................................................... 34
10.5.3 Log menu ............................................................................................................................ 34
10.5.4 Help menu........................................................................................................................... 34
10.6
Logging parameters................................................................................................................ 35
10.7
File.......................................................................................................................................... 35
10.8
Display.................................................................................................................................... 36
10.9
Print ........................................................................................................................................ 36
10.10 Display parameters................................................................................................................. 37
10.10.1
Display settings dialog..................................................................................................... 37
10.10.2
Log scale ......................................................................................................................... 37
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1 Introduction
This document is a collection of the documentation of the freeware available for the TEM microscope.
Before using the software, please refer to the copyright and liability limitation below.
1.1
Copyright and liability limitation
Please note:
• TEM Freeware is freeware and may be distributed and used freely.
• The copyright of the TEM Freeware lies with Mad Max Software.
• The creation of the TEM Freeware by Mad Max Software and distribution of the TEM Freeware by
the same or by FEI Company does not imply any future support of the software and future
compatibility with new versions of the TEM software.
• TEM is a registered trademark of FEI Company.
• The TEM Freeware is NOT a product of FEI Company. It is consequently NOT covered by any
warranties or support agreements between the user and FEI Company.
• Limited warranty: Mad Max Software expressly disclaims any warranty for the TEM Freeware. The
TEM Freeware and any related documentation is provided "as is" without warranty of any kind, either
express or implied, including, without limitation, the implied warranties or merchantability, fitness for a
particular purpose, or non-infringement. The entire risk arising out of use or performance of the TEM
Freeware remains with you.
• No liability for consequential damages. In no event shall Mad Max Software be liable for any
damages whatsoever (including, without limitation, damages for loss of business profits, business
interruption, loss of business information, or any other pecuniary loss) arising out of the use of or
inability to use this TEM Freeware, even if Mad Max Software has been advised of the possibility of
such damages.
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2 TEM Account Log
2.1
Introduction
The TEM Account Log software automatically monitors use of the TEM microscope, starting when you
log in to Windows and closing when you log off again. You cannot close the program but only minimize
it. The program will close automatically when you log off from Windows.
2.2
The main window
The window contains information about the current microscope session. The system assumes that you
will work with one or more project codes (up to 60 characters). The project codes normally used are
inserted in the drop-down list. The selection in the list is set automatically to your choice during the
previous microscope session.
Project codes can be added to the list by typing the code in the edit control to the right of the Add code
button. Press the Add code (which becomes enabled when values are entered) to enter the new code in
the list. The software checks against duplication of codes already present.
To delete project code(s) no longer needed, select the required code in the drop-down list, then press
the Delete code button.
Because the data are logged only when you log off from Windows, you cannot use more than one
project code during a session. If it is necessary to use more than project code, you must log off from
Windows after work under the first project code is finished (the data are then logged), then log on again
and use the other project code.
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Overview
You can get an overview of your microscope usage as logged. The overview is taken from the date given
(in the edit controls to the right of the Show overview button). Default setting is the first of the current
month.
The overview window contains two sets of data
On the left-hand side is a list of the individual entries. These entries are sorted initially on date, but they
can be sorted differently by pressing the button at the top of the column that is to be the criterion for the
sorting. Press the same button again and the sorting reverses its order (from e.g. a..z to z..a). On the
right-hand side is a display of the totals per project code (taken from the date defined in the main
window).
There is no printing function provided, but the totals can easily be copied over to Notepad. Click with the
right-hand mouse button in the right-hand text part and choose Select all, then Copy in the popup menu.
Then paste into Notepad.
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3 Big Screen
3.1
Introduction
Big Screen is an application that can be used to fill the 'data' space of the TEM User Interface (in case
there is no other useful information, like CCD or STEM images, to be found there), displaying a selection
of microscope settings with a large, easy-readable font, and with a user-selectable foreground (font) and
background color, to reduce ambient light from the monitor from interfering with TEM work at low lightlevel conditions.
3.2
General principles
An essential control for Big Screen is the right-mouse click (click with the right-hand mouse button). This
will bring up a popup menu with various controls for Big Screen.
The Big Screen window can contain up to three panels, one for Optics parameters, one for Stage
parameters and the third for Various parameters. These panels can be resized at will by dragging the
splitters between them to other positions. The parameters displayed are adjusted automatically, centered
horizontally in their panel and with equal spacing in the vertical direction. Big Screen does not check and
see if there is enough space available for displaying all labels. It is up to you to define the size of the
panels and size of the font to make sure the labels do not overlap and are visible.
In principle Big Screen can be run even if the TEM User Interface is not running. There is, however, little
point in doing so, since the Control Pads (with the buttons and knobs) are disabled when the TEM User
Interface is closed. If the TEM User Interface is closed, locking the Big Screen window to the 'data'
space has no effect (apart from making the window non-sizeable).
Big Screen will store and recall user's individual settings.
3.3
Popup menu
The popup menu (which appears when the right-hand mouse button is
clicked inside the Big Screen window) contains six categories of items that
control Big Screen:
• Display
• Optics parameters
• Stage parameters
• Various parameters
• Window position and size
• Help access
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Display
The display settings that can be chosen are the colors of foreground (font) and background and the
size and type of the font used for displaying the microscope parameters. The colors can be selected
by making the color selection bar visible. This bar will be displayed on the left-hand side of the Big
Screen window and contains the colors available. Two of the fields will contain labels, 'FG' and 'BG'
(foreground/font and background). To change the foreground color, click with the left-hand mouse
button in the color field required. To change the background color, click with the right-hand mouse
button in the color field required. You can also select the foreground color in the font selection
dialog.
The Select font item of the popup menu
brings up the Font selection dialog
wherein the type of font, size and color
can be selected. The font color is the
same thing as the foreground color.
3.5
Optics parameters
Five optics parameters can be selected for
display, magnification (or camera length),
microscope mode, spot size, intensity setting and
defocus value. If none of these values is
selected, the Optics panel will not be visible.
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Stage parameters
The stage parameters that can be selected for display are all relevant axes.
The b tilt axis is only displayed if a double-tilt holder is present. If stage
parameters is not selected, the Stage panel will not be visible.
3.7
Various parameters
Three plate-camera exposure parameters can be selected for display,
measured exposure time, exposure mode (auto or manual) and manual
exposure time. If none of these values is selected, the Various panel
will not be visible.
3.8
Window position and size
The Big Screen window can be locked to the 'data' space of the TEM User Interface (the empty space
left over by the user interface in its various display modes). If the display of the TEM User Interface is
changed and the Big Screen window is locked, the size of the Big Screen window is adjusted
automatically. When locked, the Big Screen window cannot be resized (though it can be moved around).
3.9
Help access
By selecting the Show help item of the popup menu (or pressing the F1 function key) the help file is
displayed.
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4 Exposure Log
The Exposure Log Control Panel allows definition of microscope
settings that will be stored to file when an exposure is made.
The Exposure Log is a text file with a series of microscope settings (dependent on definition by the user),
separated by tabs. Such files can easily be read in in spreadsheet programs like Microsoft Excel, which
will translate each tab into a new column (thus the settings are ordered into columns). At the beginning
of each session, the Exposure Log will write a line with 'Exposure log' followed by the date and time.
After that line follows a second line with a header, describing each item of a column. When the options
are changed, the header will be written again (otherwise the columns will not match up with the header
anymore). The starting line of the session may be the first line of the file, but data from multiple sessions
can be written to the same file (appended automatically).
Select File
When the Select File button is pressed, a standard Save As dialog is displayed in which a filename can
be defined. This filename is stored (for the particular user) at logoff and at next logon automatically
selected again. If the file exists, the new data will be appended to the file automatically (so old data do
not get overwritten). The button is yellow when a filename has been defined. When the button is still
gray, no data will be written to file.
Optics
On the Optics tab a number of settings related to the optics of the microscope can be selected.
Plate
On the Plate tab, a number of settings related to the plate camera can be stored such a exposure
number, exposure time and film text.
Stage
On the Stage tab, each axis of the CompuStage can be selected (individually) for storage.
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5 Image Search
5.1
Image Search Control Panel
The Image Search Control Panel provides the controls necessary
for the image-search method. With this method the image
movement with the track ball normally connected to the stage is
done with the image shift instead of the CompuStage, giving
faster and smoother image movement. Because of the limited
range of the image shift, the image search resets the image shift
as needed, with a compensating CompuStage shift motion to
keep the same field of view before and after the reset.
Note: Image Search only works in the HM magnification range (Mi and SA magnifications). When Image
Search is active and the magnification is changed to LM, the Activate button and Reset buttons become
disabled until the magnification range goes back to the HM range (it is not possible to reset the HM
image shift while the microscope is in LM).
5.1.1 Image shift and maximum deflection
There are two important settings during Image Search, the amplitudes of the image shift position and
that of the total deflection. The image shift is but one component active on the image shift deflection
coils, other components being the alignment values of the image shift (magnification) and diffraction
shift. The total value, given by the maximum deflection can never exceed 100%, even if the image shift
itself is less than that. The amplitude available for the image shift will depend on the microscope (and to
some extent the magnification). Reset the image shift before the total deflection amplitude reaches its
maximum.
5.1.2
Image search controls
Activate
To start using the Image Search, press the Activate button (it will become yellow). The control of the
track ball connected to the stage (which track ball is automatically detected by the software) is changed
to the Image Search. To revert to the standard situation, press the Activate button again (the button
becomes gray again).
When the Activate button is disabled, the Image Search calibrations have not been done.
Image shift position
The amplitude of the image shift is displayed by a progress bar.
Maximum deflection
The maximum deflection (the sum of all components working on the image shift deflection coils) is
displayed by a progress bar.
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Reset
To Reset the image shift with a compensating stage movement, press the Reset button. The Reset
button remains disabled until the image shift has reached more than 20% of the available image shift
range (below that the inaccuracies in the compensating stage movement are such that a reset does not
makes much sense).
Auto Reset
The reset can be done manually (by pressing the Reset button) or automatically (when the Auto Reset
checkbox is checked). When Auto Reset is active, the software will do a reset when the image shift
amplitude reaches the value for the Maximum deflection range given. When the reset is automatic, the
reset is preceded by a beep (PC sound signal). Another beep sounds when the procedure is finished.
Maximum deflection range
The maximum deflection range value determines the image shift amplitude at which an automatic reset
will be done.
Flap-out
The flap-out button leads to the Calibrate and Options tabs of the Image Search Control Panel.
5.2
Image Search Calibrate
The Calibrate tab of the Image Search Control Panel provides
the controls necessary for the calibration of the image-search
method. There are two things to be calibrated, the relation
between the image shift and the stage motion, and the direction
of the image shift as seen on the screen. The first determines the
accuracy of the compensating motion of the image shift with the
stage, while the second ensures that the direction of the image
motion is linked to the direction of the track ball movement.
Note: The Image Search method makes use of the image shift with compensated beam shift (a standard
feature of the TEM software). For this to work properly, the Image/Beam calibration procedure of the
Image HM-TEM alignment procedure must have been done. If the beam shifts away from the center of
the screen during image shift, this calibration has not been done properly.
Start
To start a calibration, select a procedure in the selection list and press the Start procedure.
Procedure selection
The two calibration procedures are selected in a drop-down list.
Instructions
Instructions during the calibration procedures will be displayed here.
OK
Pressing the OK button proceeds with the calibration procedure to the next step.
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Cancel
Pressing the Cancel button cancels the calibration procedure. The microscope returns to its starting
position.
5.3
Image Search Options
The Options tab of the Image Search Control Panel provides the
controls necessary for the setting the options of the imagesearch method.
CompuStage backlash correction
During a reset the compensating stage motion will contain a backlash correction motion (the stage is first
driven a certain distance further negative on X and Y before going to the required position). This
backlash correction makes the setting of the stage position more reliable and thus the compensation for
the image shift more accurate. Typical values for the backlash correction are between 5 and 20 um.
Reset under control pad button
The Reset function can also be activated by assigning the function of one of the user buttons L1..L3 and
R1..R3. Select the button to use in the drop-down list. The function is only active when Image Search is
active.
Exposure enabled/disabled while active
Because image quality is affected by strong off-axis image shifts, exposures should not be taken without
resetting the image shift to zero. In order to make sure this happens, you can choose on of two options:
• The exposure button is completely disabled while Image Search is active. In this case you have to
de-activate Image Search (which forces a reset) before you take an exposure.
• The Exposure button is enabled while Image Search is active. In this case Image Search catches the
pressing of the Exposure button and no immediate plate exposure takes place. Instead Image search
forces a reset and then releases the Exposure button for taking a plate exposure. A message to that
extent is displayed in the control panel.
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6 Preset Magnifications
The Preset Magnifications Control Panel provides rapid switching
between a number (up to six) of user-defined magnifications
through the user buttons (L1..L3, R1..R3) on the TEM Control
Pads. When a previously defined setting (consisting of
Magnification, Intensity setting and Spot size) are active, a press
of the associated user button switches the microscope to those
settings. The Preset Magnifications function thus assists in work
on the microscope where a fixed set of magnifications is used
repeatedly (as e.g. in diagnostic screening).
The operation is as follows:
• Press Active if the button is gray to activate Preset Magnifications.
• Decide which user button to use and check the check box for that user button.
• Press the associated Define button (which becomes yellow). The software asks to select the required
magnification, intensity setting and spot size.
• Press the Define button again (button goes back to normal). The settings are now defined.
• To go back to these settings, press the user button on the TEM Control Pad.
To redefine the settings under a user button:
• Press the required user button.
• Press the associated Define button (which becomes yellow again).
• Change the settings and press the Define button again.
Settings are user-specific and stored automatically when the TEM User Interface is closed and recalled
when it is re-opened. First-time users get the settings as defined by the Supervisor (Note: only
Supervisor, not Service or Factory), if available.
Note: Preset Magnifications requires TEM Scripting on the microscope.
Active button
The active button determines whether the Preset Magnifications are assigned to the user buttons. The
function is active when the button is yellow, inactive when it has the normal button color.
Automatic
When the Automatic check box is checked, the Preset Magnifications function automatically becomes
activated when the TEM User Interface is started (if not, it only becomes active once the Active button is
pressed).
User button check box
The check boxes determine whether a particular user button is used. To activate a user button, check
the box and define the settings. To deactivate, click on the check box to remove the check.
Magnifications
For active user buttons the magnifications used are displayed in a list to the right of the check boxes.
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Define buttons
The Define buttons allow definition of the microscope settings associated with a user button. For the
procedure, see above.
Instructions
The instructions field at the bottom will display instructions on how to proceed, or a status description or
error message.
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7 Screen Saver
The TEM Screen Saver can be used as an easy check on the status of an unattended microscope
(provided a user is logged on).
The TEM Screen Saver (called TEM Vacuum Saver in the Display Properties) acts as a normal screen
saver and has three modes of display:
1. There is no connection to the Tem server: the display states Not connected to TEM server and
draws red octagons.
2. There is a connection to the Tem server and the column valves are closed: the display states
Column valves closed and draws green balls.
3. There is a connection to the Tem server and the column valves are open: the display states Column
valves open and draws red octagons.
There is no automatic preview in the small “monitor” in the Display Properties, but the Preview button will
start a screen saver preview.
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8 Serial Sections
8.1
Introduction
The serial section software provides an automatic way of retrieving one or more locations within a series
of sections by driving the CompuStage to each location as directed by the user. The software is a
separate application that you can find in the Start menu under Programs\TEM
The serial section software assumes that the specimen contains a number of sections cut from a single
block. Each of the sections can be defined and the software can then determine equivalent locations for
each section. In this way a three-dimensional impression of the specimen can be obtained, e.g. by
recording images for a particular location in each section and combining all these images.
The method used by the software is as
follows. A first section must be defined by
moving each of the four corners of the
section (or specially applied marker points
near the corners such as laser-drilled
reference holes) with the specimen stage to
the screen center (at which point the
software will read the stage locations). The
four points must always be in a certain
sequence. The first two points define the
baseline. By definition, this is the bottom of
the cutting block which must be as
perpendicular as possible to the cutting
direction. The third point is one (the best
defined) of the corners at the top of the
section. Point four is used only for display
purposes and needs to be defined only for
the first section (its position is calculated for
all other sections).
From these data the software determines a number of variables for each section:
• the baseline rotation angle (the slope of the line through points 1 and 2)
• the baseline stretch factor (the ratio of the distances between points 1 and 2 in any section and that
in the first section). Although not critical for the performance of the software, under normal
circumstances the baseline stretch should be very close to 1.0
• the perpendicular stretch factor (the ratio of the projection of point 3 onto the baseline in any
section and the same projection in the first section). In practice this factor can vary quite a bit.
After a first section is defined, locations can be stored or other sections can be defined (locations can be
stored in any section and at any stage of using the software). For each subsequent section, the three
relevant corners (1 through 3) must defined as for the first section. Locations are stored by centering
them on the screen and selecting the relevant function (Location, Insert).
Once a sufficient set of data has been defined, the software can be instructed to move from section to
section (where it will go to equivalent locations for each section) or from location to location within each
section. Location-section combinations can be marked as visited to allow the operator to keep track of
what has been done (an unmarked location is shown as a red number, a marked one as a black number
on a green background). The software can display an overview of the visits status. Marking as visited
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can be automatic when the program is instructed to go to a location for a particular section or by active
selection by the operator. The choice between automatic or user marking is done under Control options.
Stored locations are either defined in the first section or, when the operator stores a location while on
another section, the stored location X,Y values are calculated back to the equivalent location in the first
section.
The location recalculation method works as follows:
1. determine the length of the projection of the location onto the baseline along the perpendicular and
the distance of the projection point on the baseline from point 1.
2. determine for the current section the point on the baseline, adjusted for the baseline rotation and
baseline stretch.
3. project the location from the point of the baseline along the perpendicular, adjusted for the
perpendicular stretch.
Note: The method used for calculating the point assumes that any change in location position is wholly
determined by a baseline stretch and a perpendicular stretch. The implication is that the cutting direction
must be nearly or wholly perpendicular to the baseline. If the stretching due to the cutting deviates
significantly from the perpendicular, the software will not work properly. This methodology has been
adopted on purpose because there is in the three or four corner points insufficient accuracy to
determine a variable cutting direction.
8.2
Location
A Stored location is any location at which the operator presses the Insert key or selects Insert from
Location menu. If use labels (see Control Options) is active, a dialog will appear asking the operator to
enter the label (a string with a maximum of 120 characters) for the location.
The number of stored locations that the program can handle is limited only by the amount of memory
available on the computer. However, the program will not mark locations visited for more than 64
locations (per section).
8.3
Section
A Section represents a piece of tissue on the specimen. Each section is defined by three corner points,
the first two defining the baseline (the bottom of the block where the knife hits first), the third one of the
upper corners (the best defined of the two).
The fourth corner is set only for the first section and is used only to allow display of the section shape on
the screen.
If a section is represented by a single X,Y value (e.g. under Show section or Goto
section), that value is the center of the section, defined as the X and Y values that lie
halfway between the lowest and highest values for all four corners.
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Overview
It can be difficult to keep track of which location in which section has been inspected or recorded. The
software therefore marks location-section combinations as visited (either automatically or by operator
selection).
Sections are plotted vertically, locations horizontally. Green section-location combinations have been
marked as visited. If the left-hand mouse button is double-clicked on any rectangle representing a
section-location combination, the program will bring up a dialog giving the information about the location
indicated. If the button Go there is pressed, the program will move the specimen stage to that sectionlocation combination (and mark the location as visited if automatic marking is switched on).
If the Print button is pressed in the Status overview dialog, the overview is printed. Note that the print-out
may spread over several pages if many locations have been stored.
The maximum number of locations for the program keeps track is having been visited is 64, the
maximum number of sections is 200.
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Menu
The menu contains six main items, File, Setup, Section, Location, Display and Help. Depending on the
current status of the program, some of the items may be grayed (inactive).
8.5.1 File menu
The File Menu provides the operations that are concerned with Data and Settings files as well as
Printing.
New specimen
Resets all series settings (section, location definitions, status) as currently defined
and makes ready for a new specimen.
Open
Opens an existing data file allowing continuing working with the specimen. To allow
accurate restoring of stage coordinates use reference points.
Save
Saves the currently defined series settings into a data file.
Save As
Same as Save but allowing change of file name.
Control options
Leads to control options dialog.
Default settings
Resets settings to default values for program.
Print Screen
Prints the graphical display.
Print List
Prints a complete list of all sections and all locations per section.
Printer setup
Leads to the Printer setup dialog (e.g. for selecting Landscape printing).
Exit
Exits the program.
8.5.2 Setup menu
In the Setup Menu, the operator defines reference points. It is also possible to move the stage to 0,0
before or during work on a specimen.
Reference points
Starts procedure for storing reference points (new file) or finding back old points
(stored data on old file).
Show rf. pt. data
After reference points from an old file have been found again, the program can
display the relation between old and new reference points, such as rotation angle
and relative shifts.
Stage to center
Moves the specimen stage to 0,0.
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8.5.3 Section menu
In the Section Menu, the functions concerning the sections are found.
Insert
Starts the procedure for defining a new section.
Delete
Presents a list of sections (as serial numbers plus the section center) from which one
or more sections can be selected for deletion. If a section is marked for deletion
accidentally, click again on the section and the highlight will be removed. If only one
section is defined as yet, that first section definition will be deleted.
Delete All
Deletes all sections currently defined.
Show section
Brings up an overview of all data concerning the current section (corner positions,
rotation angle, baseline and perpendicular stretch factors). Pressing the Go there
button instructs the program to move the stage to the section selected (either to the
currently active location or to the section center; the latter if no location has been
stored yet).
Goto section
Present a list of sections (as serial numbers plus the section center). If one of these
sections is selected and OK is pressed, the stage is moved to that section (either to
the currently active location or to the section center; the latter if no location has been
stored yet).
Next section
Move the stage to the next section (either to the currently active location or to the
section center; the latter if no location has been stored yet). The menu item is grayed
if no next section exists.
Previous section
Move the stage to the previous section (either to the currently active location or to
the section center; the latter if no location has been stored yet). The menu item is
grayed if no previous section exists.
Status overview
Displays an overview of section-location combinations visited.
Mark location
Marks a location as visited. The menu item is enabled only if User mark has been
selected under Control options.
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8.5.4 Location menu
The Location menu contains a number of functions that are related to the locations stored.
Note: A hidden function is present in the program if hyperlabels are (see under Control options): Clicking
with the left-hand mouse button on a stored location will bring up a dialog with data (X, Y, label) of the
stored location if such a location is near. Pressing the button Goto there will move the stage to the
location.
Insert
Inserts the current stage location in the stored list.
Delete
Presents a list of locations (as serial numbers plus the label) from which one or more
locations can be selected for deletion. If a location is marked for deletion
accidentally, click again on the location and the highlight will be removed.
Delete All
Deletes all stored locations.
Display list
Displays a list with all stored locations (X, Y, label) for the current section and allows
printing of the list.
Show number
Shows a list of stored locations (with number and label) for the current section,
allowing selection of one location for which the data (X,Y, label) will be shown. A
button Goto allows moving the stage to the stored location.
Goto number
Shows a list of stored locations (with number and label) for the current section,
allowing selection of one location where the stage will be moved.
8.5.5 Display menu
The Display Menu allows the operator to select the method of displaying the section and location data on
the monitor. The active selections are checked.
Current section
Displays the currently active section. The numbers of the current section and current
location are displayed top left. Locations are shown as red (not visited) or black on
green numbers (visited). A scale bar is shown at bottom right. If hyperlabels are used
(see Control options), it is possible to display the data of each location (X,Y position
and label) by clicking on it with the left-hand mouse button. If the button Goto is
pressed, the stage is moved to the location.
Overview
Displays an overview of all sections.
Whole specimen
Displays the sections in relation to the whole specimen.
For current
section:
Baseline
Displays the current section with the baseline horizontally on the monitor.
Screen
orientation
Displays the current section in its orientation as on the TEM microscope's viewing
screen for the currently active magnification.
Stage X,Y axes
Shows the current section with the stage X axis horizontal and the Y axis vertical.
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8.5.6 Help menu
Show
Brings up the Help file. Pressing the F1 function key is equivalent.
About
8.6
Brings up the program About box with version and copyright information.
Control options
Control options (under Setup menu) allow the operator to choose how to use the Serial Sections
software. The options are:
• Whether the grid used is a so-called relocatable grid (a grid with a special "ear" on one side that
allows it to be fitted into the single-tilt specimen holder of the CompuStage in only one way).
• Whether to use labels (a user-defined string) for stored locations.
• Whether to use hyperlabels. Hyperlabels are "hyperlinked" labels of the locations in a section. The
labels will flash blue when the cursor moves over them and when clicked will bring up a dialog with
information about the location with a button that allows a direct Goto to the location.
• Whether to mark locations as visited automatically when the program is instructed to move the stage
there (By visit) or whether the marking only takes places when the user selects Mark location in the
Section menu.
• The colors of the various items on the display: background, foreground (outline of sections and text
at top left), sections, locations and current stage location. The definition of these colors is through a
standard color definition dialog.
The display colors can also be changed by clicking on the display with the righthand mouse button, giving the popup menu where the relevant color can be
chosen.
8.7
Reference points
Reference points are locations on the specimen that are easily recognized and can be used as reference
when the specimen is removed from the specimen holder and later put back in again. By finding the
reference points again, the program can recalculate the old locations to new ones.
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Reference points should be located close to but not at the periphery of the specimen. Locations further
from the center increase the accuracy of relocation but if a reference point later lies outside the reach of
the stage, it is not possible to recalculate the old locations to new ones. Because specimens are often
shifted up to 0.2 mm when re-inserted into the specimen holder, keep the reference points less than 800
um away from the center.
Setting the reference points can be done at any stage of working with the Serial Section software (but
before the data are saved into a file, otherwise the reference points are not included in the file). When an
old file containing reference points is opened, the software will ask to redo the reference points
immediately. If the reference points are not redone at this stage, the software will display the stored
locations in their original configuration. It is then no longer possible to redo the reference points (unless
by reading in the file again).
8.7.1
Setting reference points for new data
During the procedure wherein new reference points are defined, the operator is asked
to drive the stage to 2 or 3 points that can be recognized. It is suggested to avoid
points that lie on the opposite side of the center as this will make it much more difficult
to decide later whether the specimen has been reloaded in the same way or upside
down. If at least two points are defined lying at an angle of about 120°, then it will be
easier to decide. Three points make recognition of an upside-down position of the
specimen even easier. If no third reference point is to be set, then simply press OK
while keeping the specimen stage at the same location as for point 2. The third point will then be
ignored.
8.7.2
Redoing reference points for old data
If an old file containing reference points is reopened, the software will suggest to go
through the procedure for relocating the old reference points. The software will show
the distribution of the old reference points and list the label of each point in turn. The
reference point locations will be updated with the new ones, once a reference point
has been found again.
During this procedure the software can assist in finding back the old reference points through the Assist
function. The Assist function will list a number of possibilities depending on which reference points must
be found again:
• move the specimen stage to the old location for point 1
• move the specimen stage in a circle, around 0,0 for point 1, around 1 for point 2, etc.
• calculate alternative locations for points 2 and 3 on the assumption that the specimen is upside down
After finding reference point 1, the software will calculate what the most likely new location is for
reference point 2 and ask if the stage must be driven there. The same is done for point 3 (if a third
reference point had been set originally).
For each reference point found back as well as the whole set of the reference points the software will go
through a number of consistency checks (distances between old points and new points comparable,
angles from the center of gravity of the old three-point triangle and old points and the center of gravity of
the new three-point triangle and new points comparable).
The software can handle rotation, shift and mounting upside down of the specimen. The software also
calculates a 'stretch' parameter that is related to the percentage difference in dimensions between old
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and new reference points. The software cannot however accommodate severe distortions due to
bending of the specimen, so some care should be taken to ensure the integrity of the specimen. The
various values can be displayed under Show ref. pt. data.
8.8
Section data display
The Section data display dialogs shows the data for the section selected.
These data consist of the X,Y positions of the four corners, the rotation angle of the baseline, and the
perpendicular and baseline stretch values.
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Select section
For selecting a section (a single section for go to or one or more sections for deleting) the software
brings up the Select section or Delete section dialog. The two dialogs are similar in operation, the main
differences being the text of the main button (OK or Delete) and the possibility of multiple section
selection (use Ctrl+Click or Shift+Click; Ctrl+Click on an already selected - that is, highlighted - section,
will remove the selection again).
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8.10 Location list
The Display list item of the Location menu displays a list with all stored locations (X, Y, label) for the
current section and allows printing of the list.
8.11 Select location
For selecting a location (a single location for go to or one or more locations for deleting) the software
brings up the Select location or Delete location dialog. The two dialogs are similar in operation, the main
differences being the text of the main button (OK or Delete) and the possibility of multiple location
selection (use Ctrl+Click or Shift+Click; Ctrl+Click on an already selected - that is, highlighted - location,
will remove the selection again).
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9 Total Recall
9.1
Total Recall Control Panel
The Total Recall Control Panel provides the means for storing specimen locations in such a way that
later the specimen can be re-inserted into the microscope and the locations easily found again. This is
achieved through the use of two or three reference points, which should be locations on the specimen
that are easily recognised. When the reference points are found again upon re-insertion of the specimen
holder, the software recalculates the original specimen locations, taking proper account of specimen
rotation, shift and mirror (the latter when the specimen is reloaded upside down). A prime application for
the Total Recall software is dual-axis tomography, where two separate tilt series are collected of the
image area, with a rotation of about 90° of the specimen in between. The combination of these two
series reduces the missing wedge to a (smaller) missing pyramid (and thus reduces the consequent
aretefacts). However, you can use the software in any other way you see fit.
Label
At the top of the control panel is an edit control wherein you can define the label used for the next
location added. When you enter no label, the software will automatically use the label "Location " plus a
serial number.
Add
Press Add to add the current stage position to the location list.
Location list
The location list contains all user-defined locations, shown by label and X,Y location. The stage locations
are displayed as rounded off micrometers values, but the software stores more accurate values of the
stage location.
Goto
If one of the locations in the list is highlighted (by clicking on it with the mouse), the Goto button is
enabled. Pressing the Goto button will have the software drive the stage to the indicated location. Goto's
are subject to the normal uncertainties in stage position (~500 nm for X and Y, no backlash correction is
done because the original storing of the locations is also done without backlash correction so any such
correction later on would be without benefit).
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Delete
If one of the locations in the list is highlighted (by clicking on it with the mouse), the Delete button is
enabled. Pressing the Delete button removes the selected location from the list.
Flap-out button
The flap-out button leads to the Reference points and File tabs of the Total Recall Control Panel.
9.2
Total Recall Reference Points
The Total Recall Reference Points tab provides the means for
defining and inspecting reference points.
Define
On a new specimen, the reference points are defined by pressing the Define button. The user will be
asked to center two or three reference points on the screen with the stage (if you use but two reference
points, keeping points two and three the same, the software will not be able to determine if the specimen
has been reloaded upside down). The software will display the X,Y locations and labels defined for the
reference points.
The manipulation of reference points from an existing file is started automatically when a file with
reference points is loaded (for further explanation see below).
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Show data
If an existing file has been reloaded and the reference points found again, the software will display the
X,Y locations and labels defined for the reference points. In addition, it is possible to compare some data
on the old and new reference points in a separate dialog that is called up by pressing the Show data
button.
The data listed are the old and new reference point positions, whether the specimen is upright (same
way as before) or upside down, the rotation angles calculated for the average and each individual
reference point set (old to new), the shift of the specimen, and the stretch between sets of reference
points (in principle all stretch factors should be very close to 1.0).
Reference points
The bottom part of the panel displays the X,Y locations and labels of the current reference points.
9.3
Reference points
Reference points are locations on the specimen that are easily recognized and can be used as reference
when the specimen is removed from the specimen holder and later put back in again. By finding the
reference points again, the program can recalculate the old locations to new ones.
Reference points should be located close to but not at the periphery of the specimen. Locations further
from the center increase the accuracy of relocation but if a reference point later lies outside the reach of
the stage, then it is not possible to recalculate the old locations to new ones. Because specimens are
often shifted up to 0.2 mm when re-inserted into the specimen holder, keep the reference points less
than 800 um away from the center.
Setting the reference points can be done at any stage of working with the software (but before the data
are saved into a file, otherwise the reference points are not included in the file). When an old file
containing reference points is opened, the software will ask to redo the reference points immediately. If
the reference points are not redone at this stage, the software will display the stored locations in their
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original configuration. It is then no longer possible to redo the reference points (unless by reading in the
file again).
9.3.1
Setting reference points for new data
During the procedure wherein new reference points are defined, the operator is asked
to drive the stage to 2 or 3 points that can be recognized. It is suggested to avoid
points that lie on the opposite side of the center as this will make it much more difficult
to decide later whether the specimen has been reloaded in the same way or upside
down. If at least two points are defined lying at an angle of about 120°, then it will be
easier to decide. Three points make recognition of an upside-down position of the
specimen even easier. If no third reference point is to be set, then simply press OK while keeping the
specimen stage at the same location as for point 2. The third point will then be ignored.
9.3.2
Redoing reference points for old data
If an old file containing reference points is reopened, the software will suggest to go
through the procedure for relocating the old reference points. The software will show
the distribution of the old reference points and list the label of each point in turn. The
reference point locations will be updated with the new ones, once a reference point
has been found again.
As a first step the software lists the old location for reference point 1 and you can have the software drive
the stage there (in case you expect the new point to be close to the old one).
During this procedure the software can assist in finding back the old reference points through the Assist
function. The Assist function will list a number of possibilities depending on which reference points must
be found again:
• move the specimen stage to the old location for point 1
• move the specimen stage in a circle, around 0,0 for point 1, around 1 for point 2, etc.
• calculate alternative locations for points 2 and 3 on the assumption that the specimen is upside down
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After finding reference point 1, the software will calculate what the most likely new location is for
reference point 2 and ask if the stage must be driven there. The same is done for point 3 (if a third
reference point had been set originally).
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For each reference point found back as well as the whole set of the reference points the software will go
through a number of consistency checks (distances between old points and new points comparable,
angles from the center of gravity of the old three-point triangle and old points and the center of gravity of
the new three-point triangle and new points comparable).
The software can handle rotation, shift and mounting upside down of the specimen. The software also
calculates a 'stretch' parameter that is related to the percentage difference in dimensions between old
and new reference points. The software cannot however accommodate severe distortions due to
bending of the specimen, so some care should be taken to ensure the integrity of the specimen.
9.4
Total Recall File
The Total Recall File tab contains three buttons which bring up
standard File dialogs for loading and saving data from and to file.
Total Recall files are text files with the extension .prf. You can in
principle open these files in Notepad but if you make changes it
is possible that Total Recall can no longer read the file.
Open
When the Open button is pressed, the Open file dialog comes up
where you can select a file for loading. When the loading is
finished and the file contains reference points, the procedure for
finding the reference points again is started.
Save
Once a filename has been defined, the Save button is enabled so you can simply save the data under
the same filename (to save under another filename use Save As).
Save As
When the Save As button is pressed the Save file dialog is brought up, allowing you to define a filename
to save the data.
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10 Vacuum Logger
10.1 Introduction
Vacuum Logger is a program for the TEM microscope that allows logging of vacuum pressures and the
high tension condition (disabled, off, on). The logging data are written to a file and, if selected by the
user, displayed graphically on the screen. The graph can be printed. Logging files can be read by the
program (on-line on the microscope as well as off-line) and displayed graphically. All data logged are in
Pascal. The program allows a maximum number of 10000 measurement cycles.
10.2 General principles
There are two modes of operation for Vacuum Logger, on-line and off-line. When starting, Vacuum
Logger will attempt to connect to the TEM microscope software. If it succeeds, it will continue with online operation. If it fails to connect to the TEM software, it will continue with off-line operation. In the latter
case, controls and menu items used for on-line operation will be removed or disabled.
10.2.1 On-line operation
With on-line operation you can:
• Log vacuum system pressures, high-tension status, and vacuum and gun events.
• Obtain a graphical display of selected parameters against time elapsed.
• Read Vacuum Logger files and display their contents graphically.
• Print the graphical display.
10.2.2 Off-line operation
With off-line operation you can:
• Read Vacuum Logger files and display their contents graphically.
• Print the graphical display.
10.3 Program structure
The program contains three elements for controlling the logging and graphical display, the program
menu, a panel directly underneath the menu for selection of logging parameters such as logging interval
and start/stop date and time, and a panel at the bottom for controlling which elements are displayed
graphically. The graphical display itself covers the area between the panels at the top and the bottom.
Vacuum Logger will store and recall user's individual settings.
10.4 How to run the logging software
Program Vacuum Logger is an application, not a service. This implies that you have to be logged in (to
Windows NT) to run the software and that the program will be closed (and thus log no further) when you
log out from Windows NT.
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10.5 Menu
The menu contains four main items, File, Display, Log and Help.
10.5.1 File menu
New
Defines a new name for the log file. For starting logging this is not strictly necessary
as Start always brings up the Save file dialog wherein the filename is defined. If New
file has been done, the Save file dialog will not be displayed when Start is pressed.
Open
Print
Opens an existing log file and displays the data graphically. Selecting Open always
stops any logging currently being done.
Prints the graphical display.
Printer setup
Leads to the Printer setup dialog (e.g. for selecting Landscape printing).
Exit
Exits the program.
10.5.2 Display menu
Settings
Brings up the Display settings dialog, which allows selection of all display
parameters.
Statusbar
Shows or hides the Statusbar wherein display parameters can be defined for
individual pressures or high tension.
Lock to data
space
The Vacuum Logger window can be locked to the 'data' space of the TEM User
Interface (the empty space left over by the user interface in its various display
modes). If the display of the TEM User Interface is changed and the Vacuum Logger
window is locked, the size of the Vacuum Logger window is adjusted automatically.
When locked, the Vacuum Logger window cannot be resized (though it can be
moved around).
10.5.3 Log menu
Start/stop
Starts or stops logging. If delayed action is on, the actual measurements will start
once the start date and time are past. Otherwise logging starts or stops immediately.
You cannot pause logging by start-stop-start, because the second start will require a
new filename (or, if you select the previous filename, the previous file is overwritten).
Delayed action
When checked, delayed action is on, otherwise it is off. After selecting delayed
action, you still have to start logging (but now you start the timer that looks if the start
date and time have passed).
10.5.4 Help menu
Show
Brings up this Help file. Pressing the F1 function key is equivalent.
About
Brings up the program About box with version and copyright information.
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10.6 Logging parameters
Logging can be done at selected intervals (1, 5, 10, 30 seconds, 1, 5, 10, 30, 60 minutes), selected from
the drop-down list in the panel underneath the menu.
Logging can be started and stopped manually or in delayed-action mode. In delayed-action mode the
panel contains additional controls for defining Start date and time and Stop date and time. The formatting
of date and time must be exactly as indicated (a maximum of two characters for the date, then month,
then year, all separated by hyphens; a maximum of two characters for the hour, then a colon, then two
characters for the minutes).
Note: It is possible that the 1 second interval is not totally stable and may result in the program hanging
(since the logging data are saved for each measurement the logging file will still be accessible).
Especially for larger series of measurements (>200 cycles) it is advised not to use the 1 second interval.
For this reason it is also not possible to display the vacuum pressures for the log interval of 1 second. If it
is necessary to log at 1 second intervals, first collect the log and then read in the log file to obtain a
display.
10.7 File
The logging file is a text file. The file starts with a header, which contains the start date and time and a
line displaying the names of all vacuum elements measured. The last item is the high tension status. The
individual measurements are separated by tabs, making it easy to read the file into spreadsheet
programs like Excel (read in as text file).
Below come lines of three different types:
• Measurement data. Each measurement is on a separate line, containing the date and time of the
measurement. The Event type (listed in the first column) is type 0. The data, separated by tabs, are
in Pascal unit, except for the high tension which is 0 (disabled), 1 (off) or 2 (on).
• Vacuum status events. These are events triggered by the vacuum system itself and received by the
program. These events can come in at any time (not at the specified measuring intervals) and are
logged under Event type 1.
• High tension events. These are events triggered by the high tension system itself and received by
the program. These events can come in at any time (not at the specified measuring intervals) and are
logged under Event type 2.
The data logged are always the complete data from the microscope, not just the elements selected for
display in the graph.
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10.8 Display
The central part of the Vacuum Logger window is reserved for a graphical display of the pressures and
high-tension status. The horizontal scale is the true time of the log (thus even if the logging interval is
changed during the acquisition, the values will still plot properly along the scale).
• For a display of a file read from disk, the horizontal scale stretches form the start time to the end
time.
• During logging, the horizontal scale will start at the start time, but the end of the scale is adjusted in
steps. Initially the program will choose an end value for the horizontal scale. Once the logging time
has exceeded that value, the scale will be expanded (typically by a factor 2). Since the display width
doesn't change, the display of the pressures will jump back halfway. In this way the graphs will
appear to 'grow' progressively to the right as logging proceeds, with stepwise adjustments when the
horizontal scale becomes too short.
Underneath the display are some parameters.
In the off-line case the top line lists the start time at far left. The corresponding value on the scale is the
absolute left-hand point (not a tick that may or may not be centered on the label). The far right right value
is the end time of the log and once again the corresponding value is the far right-hand point of the scale.
In the center is listed the interval represented by the tick marks. The tick marks are chosen such that
they represent unitary (whole) values. This means that the first tick mark in the figure below coincides
with the first unit value (1 hour) after the start time, in this case 2:00:00 PM (so not 1 hour after 1:21:21
PM). At the lower line is indicated the number of measurement cycles read from the log file.
In the on-line case the top line is the same as in the off-line case, showing the start and end times of the
scale and the tick mark value. The lower line now shows on the left how many measurement cycles have
been done, in the center when the next measurement will take place, and on the right the current system
time.
10.9 Print
The print from Vacuum Logger will be a close a match to the display with some modifications.
• The height and width of the print-out will be matched to the paper size (Portrait or Landscape)
available, while the ratio of height and width will be the same as the display.
• The background of the graph will be white. Light colors such as yellow are made somewhat darker
for better printing. It is advised to use a color printer, otherwise it may not be possible to distinguish
between multiple lines in the graph.
• The printed graph has a header listing the vacuum elements displayed with their scale value. These
labels are in the same colors as the lines and act as legend. If a pressure is displayed with log scale,
the label is followed by '(log )' with a number indicating the exponent of the value used for the base.
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Display parameters
Pressures and the high-tension status can be displayed graphically in the display of Vacuum Logger.
The display parameters are defined in the Statusbar underneath the display window.
The following controls are present in the Statusbar, from left to right:
• A drop-down list with the settings that can be displayed.
• A checkbox that determines whether a setting is displayed.
• A drop-down list box with a range of scaling factors (used as maximum display values), including
Default (set by the program to the maximum value found for the particular setting). All pressures are
scaled individually. The high-tension status is scaled from disabled (just above the base line) to off
(center) to on (just below the top).
• The value of the maximum of the particular setting. When Default is chosen, this is the maximum
value of the display scale.
• A checkbox to select between regular and log scaling.
• A drop-down list box with a selection of colors.
10.10.1 Display settings dialog
In addition to selection of display parameters in the Statusbar, it is also possible to bring up the Display
settings dialog, which contains controls for defining the display parameters for all pressures and high
tension together.
10.10.2 Log scale
Because of the large range available to the vacuum pressures (from air pressure to values in the range
of 10-6 Pascal), it can be difficult to display a pressure graphically such that fine detail as well as the
whole range is visible. Because of this, pressures can be displayed on a log scale.
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Since a log scale in principle can go to very small numbers, the minimum of the log scale is not 0 (as it is
for the regular scale). Instead the minimum of the log scale is the truncated exponent of the smallest
value of the particular pressure. For example, if the pressures range from 99.9 to 1.1, the truncated log
value of 1.1 = 0 will be minimum of the display scale. While a pressure ranging from 3.33e-2 to 1.2e-5 will
have as minimum the truncated log value of 1.2e-5 = -5. The maximum value is as defined by the user
(Default or one of the fixed values).
There is no fixed recipe for determining whether a log scale is useful or not, because it will depend on
the pressure range as well as the absolute values. If the pressure range is within a factor 10, a normal
scale is more useful. Similarly, a small pressure range can also lead to compression of the graph at the
top of the display, for example when there are a few values just inside a lower decade.
The figures above show an example of the effect of plotting a vacuum pressure on a log scale. The
regular scale (on the left) is dominated totally by the 'spike' of high pressure and the fine details of the
pressure changes are invisible (unless the scale is modified so the 'spike' goes far off the maximum
scale. In the log scale display on the right, the fine details are well visible while the 'spike' is still within
the whole vertical range.

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