Mims Reference Manual Volume 1.2

MIMS Reference
Manual v1.2
Updated Jan 2008
National Resource for Imaging Mass Spectrometry

BWH HMS Boston
© 2007 National Resource for Imaging Mass Spectrometry

Table of Contents MIMS Reference Manual v1.2
Chapter 1: Tool Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1
A. Description of Tool Bar . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2
B. General Tips for Using NanoSIMS Software . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3
Chapter 2: Tuning Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4
A. Trolley Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6
B. Additional Controls . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8
C. Submenus . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10
1. Reset Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 12
2. Detector Calibration . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3. Define Analysis Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 15
4. Mass Table Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16
5. Bar Graph Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19
6. Energy Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
7. Beam Stability Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
8. PHD Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 29
9. Tools Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32
10. HMR Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
11. Sec. Ion Beam Menu. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
12. RTI Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
Chapter 3: Holder Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 44
A. Main Holder Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
B. Edit Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 49
C. Points Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
D. Crater Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
Chapter 4: Source Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 56
A. Main Source Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57
Chapter 5: Preset Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
A. Main Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61
B. File Management . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 63
C. File Management - Display . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 64
D. Ion Optics Parameter Sets . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65
E. L1 Toggle Switch . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67

F. File List . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
Chapter 6:Analysis Method Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

A. Selection . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70
B. File Manager . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 72
C. Depth Profile . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 73
D. Line Scan . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 75
E. Isotopes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 76
F. Image Acquisition . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 78
G. Grain Mode . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
H. Batch Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 82
I. Chain Analysis . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 83
Chapter 7: Analysis Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 86
A. Main Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 87
B. Results Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 90
C. Display Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 91
MIMS Reference Manual v1.2 i

D. Analytical Parameters . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 93
Chapter 8: Image Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94
A. Image Processing Control Board . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 95
B. Image - 2D Visualization Tool . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96
C. 2D Processing . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 98
D. 3D Processing - First Plane . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100
Chapter 9: Curve Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 101
A. Main Curve Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102
Chapter 10: Setup Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 103
A. Holder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104
B. Tuning . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106
C. Keyboard . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 108
D. Hardware . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 110
E. Slit & Diaphragm . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 112
F. Detector . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 114
G. B Field . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 116
H. Directories . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 117
I. Sources. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 118
Chapter 11: Vacuum Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 119
A. Automatic Control Panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 120
B. Manual control panel . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 123
C. Vacuum recorder . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126
Chapter 12:Miscellaneous Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 127
A. Miscellaneous Main Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128
B. Tools. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 129
C. Periodic Table . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 130
MIMS Reference Manual v1.2 ii

Chapter 1: Tool Bar
MIMS Reference Manual v1.2 1

Chapter 1: Tool Bar
A. Description of Tool Bar

The Tool Bar is the main panel for the NanoSIMS instrument. It allows the
user to open the control panels that address different aspects of the operation of the
instrument. Multiple panels can be open at the same time. A green square in the
icon indicates that the sub menu is already open.
The following menus will be discussed with their sub-menus in the following
chapters:
CCD: This button opens a window on one of the displays of the
MIMS SPARC that shows the image from the CCD camera at the
sample stage. This image can be used to select new regions on a
chip for analysis, or to move between chips if the lay-out of the
sample holder has not been saved..
Tuning: Allows the user to adjust the focus, mass selection, detec-
tor parameters and other variable settings and gives access to sub
windows that are needed to monitor the effects of these adjustment,
such as real time imaging and count rates.
Holder: Controls the positioning of the sample holder. This

includes the positioning in the x- and y- axis necessary for center-
ing of the sample, but also the movement of the entire sample stage
into the positions for inspection by the CCD camera and for mea-
surements of the primary ion current at the sample plane (FCO).
Sources: Selects and controls the primary ion source. This button
accesses a menu that allows for the selection of different primary
ion sources (if installed), as well as maintenance.
Preset: Accesses a list of saved parameter files for the settings of

the instrument. It also allows the editing and the creation of new
parameter sets.
Analysis Definition: Sets up various analytical methods, such as

imaging spectrometry, depth profiling, but also the batch mode of
the instrument that allows for automatic acquisition of a series of
experiments.

Chapter 1: Tool Bar
Analysis: Sets the parameters for a given experiment, such as file

names, etc. Also starts the data acquisition
Curve: Determines layout for multiple curves from multiple sub-

programs. This part of the program suite is not yet fully imple-
mented.
Setup. Controls instrument parameters such as slit widths, etc.
Vacuum. Monitors and controls the function of the vacuum sys-

tem.
Miscellaneous. Periodic table with isotope lists and other small

programs.This part of the program suite in not yet fully imple-
mented.
B. General Tips for Using NanoSIMS Software

• Whenever you enter input, i.e. a string, a numerical value, etc., always hit the enter key to ensure
the value has been stored
• For certain windows, you can only type in them if the top bar is blue. To activate a window in this
way, click on the top of the frame at the edge.
• For other windows, click on the edge.

Chapter 2: Tuning Menu

Chapter 2: Tuning
A. Trolley Panel
Tuning mode
Detector use
B. Ion optics
Trolley
positions
C. Submenus
Figure 2-1: View of Main Tuning Menu.

Chapter 2: Tuning
A. Trolley Panel
Count rate
Radius settings
Selected ion
Deflector plate
tuning
Detector tuning
Figure 2-2: View of Trolley Panel
Menu Details: Trolley Panel

Count rate or counts per integration period. The
counter will blank out if the ion current becomes too
high. This does not protect the actual electron multiplier
tube! To enlarge the count display to full screen (for tun-
ing, etc.), click on “thermometer” bar. Cumulative count
mode can be selected in Tuning mode window

Chapter 2: Tuning
Radius. Can be set numerically at the input line, or by

clicking on the arrow buttons of the slider. The numbers
below the slider indicate the range of the trolley in ques-
tion.
Mass. The mass of the ions detected by this channel is

given as a function of the B-field, the E-fields and the
radius set above. This mass is precise, but not necessarily
accurate. dM sets the amu range within which a ion is
recognized.
If you type a number, the trolley will move to that mass,

i.e. if you type 12, it will move to where carbon is
Symbol. Identification of the detected ion, based on
determined mass and acceptable deviation. The list of
these ions can be edited with the Symbol sub menu
If the mass value shows up in red, it needs to be adjusted.

When the value is in agreement, it will show in blue.
Deflector. Fine tuning adjustments for the detected ion
species at the detector level can be entered either as
deflector voltage, effective change of the radius or differ-
ence of the mass. The deflector potential necessary to
detect a specific ion is determined in the HMR (high
mass resolution) tuning process.
Focal potential. Controls the focusing of the selected
secondary ion beam into the electron multiplier. Change
slit accesses the detector entry slit menu.
Adjust. Click on box to apply changes; re-confirm entry

by clicking on Valid (French for Enter) or cancel.

Chapter 2: Tuning
B. Additional Controls
Tuning mode
Detector use
Ion optics
Trolley positions
Figure 2-3: View of Additional Controls Within Tuning Menu.
Menu Details: Tuning Mode

Multi Collection. Uses the electron multipliers after the
magnetic sector for detection. This setting is used to tune
the imaging aspects of the NanoSIMS.
???
???
Detector Use
Multi Collection. Uses multiplier tubes after the mass
spectrometer stage (Shown is the selected state for this
button).
Faraday Cups. Use of Faraday cups to detect total ion
current. The options are FCp to detect the primary ion
current at the end of the primary column, FCo to detect
the primary ion current at the sample stage and TIC to
measure the total secondary ion current prior to analysis
in the mass spectrometer stage.
???

Chapter 2: Tuning
Scanning Mode. Tuning can be done with a static pri-

mary ion beam, or with in scanning mode, where differ-
ent parts of the sample are exposed to the primary ions.
The latter is preferable to prevent the burning of holes in
the sample.
Integration Time. Dwell time per data point - set in
HMR tuning window etc.
Cnt / Cnt/s. Counting mode for ions - counts per integra-

tion time interval or counting rate as a measure for the ion
current.
NMR. Indicates state of the NMR feed-back control that
regulates the magnetic field strength
Ion Optics
Magnetic Field. Sets magnetic field strength in the mag-
netic sector of the mass spectrometer stage and thus
determine the radii of the secondary ion trajectories.
Enter field strengths numerically in Gauss
Magnetic Field. Alternative input for magnetic field
strength in Gauss. Minimum and maximum for the field
strength are given.
Center Beam. Centers secondary ion beam maximum in
detector if the tuning sub-modes are used.
Beam Off/On. Controls the primary ion beam. Make

sure that the beam is off while setting up any tuning
mode. A static beam can damage samples - defocus or
turn on scanning mode before turning on the beam.

Chapter 2: Tuning
C. Submenus
Figure 2-4: View of Bottom of Tuning Panel, Containing Buttons for Submenus.
Menu Details: Submenus

Reset/Setup Menu. Controls the positioning of the elec-
tron multiplier trolleys in the magnetic sector
Detector Calibration Menu. Similar in function to the

HMR Menu. Used to balance detector sensitivities.
Define Analysis File. Handles ion optics field parame-

ters. Can be used to save or read the values as parameter
sets.
Mass Table. Handles ion optics geometry parameters
such as trolley position and masses detected. Can be used
to save or read the values as parameter sets
Bar Graph. Allows the NanoSIMS to be used like a clas-
sical ES/MS system with fixed detector(s) and a scanning
B-field for mass analysis
Energy. Controls filtering of the secondary ion beam
according to kinetic energy in the electrostatic sector
SS100
Beam Stability. Records primary or secondary ion cur-
rent over time
PHD. (Pulse Height Distribution) . Scans electron mul-

tiplier voltage of the secondary ion detectors. Corrects for
aging and is used to optimize the S/N ratio of individual
detectors
Tools. Tunes the various lenses and deflection plates in
the optical path.

Chapter 2: Tuning
HMR. (High Mass Resolution) Allows for the fine tun-

ing of the selectivity of the detectors behind the mass
spectrometer stage by adjusting the potential of their
deflector plates..
Secondary Ion Beam. Controls the position of the sec-
ondary ion beam in the horizontal and vertical plane
prior to entering the mass spectrometer stage.
Real Time Imaging. Allows to observe effect of changes
in the ion optics on the actual scan in real time. used for
focusing, etc.
Check. ???

Chapter 2: Tuning
1. Reset Menu
Figure 2-5: View of Reset Submenu.
Menu Details: Tuning/Reset Menu

Moves trolleys back to the reset position
Readjusts the trolley position.

Chapter 2: Tuning
2. Detector Calibration
a) Setup window
Figure 2-6: View of Setup Window
Menu Details: Setup Window

Chapter 2: Tuning
b) Display Window
Line used to
select
deflection
voltage.
Figure 2-7: View of Setup Display Window
Menu Details: Display Window
The line in Figure 2-7 indicates the deflection voltage. You move the line to change the
deflection voltage. When you put your mouse over the window, a new line appears,
which you can move back and forth and place in any location. Currently the line is set
to select for just 14N. If you moved it to the right in the middle of the other plateau,
you d be choosing just 12C.

Chapter 2: Tuning
3. Define Analysis Menu
Figure 2-8: View of Define Analysis Menu.
Menu Details: Define Analysis

Print File. Prints out listing of the contents of the para-
meter file
Load. Retrieves saved parameter sets
Save as.. Writes current parameters to named file

Chapter 2: Tuning
4. Mass Table Menu

In Fig. 2-9, choosing the button ‘Trolley Install’ brings up the menu shown in (b). You select
trolley 1,2,3, or 4, and window (b) will give you a list of allowable positions.
Using the ‘Adjust radius’ button (which brings up panel ‘c’), does not result in mechanical
movement. The software just reorients itself to make sure it’s in agreement with the physics.
a) Mass Table - Edit Mass
b) Mass Table - Assign Trolleys c) Mass Table - Place Trolleys
Figure 2-9: View of Main Mass Table Menu with Three Panels Shown for Edit Mass (a), Assign
Trolleys (b), and Place Trolleys (c).

Chapter 2: Tuning
Menu Details: Mass Table Menu

a) Mass Table - Edit Masses
File list. List of existing files for combinations of mag-
netic field strengths, radii and isotope masses. Can be
selected by clicking on entries
New. Starts new blank file, using the current magnetic

field strength.
Delete. Deletes selected parameter set.
Discard edits. Returns parameters to initial, saved state

from any edits that have been made.
Save. Opens menu to write new parameter list to a file.
Print. Sends current parameters to print file
Close. Closes Mass Table menu.
Magnetic Field. Enter magnetic field strength for current

data set.
Fix Radius. Enter radius for selected isotope
Symbol. Symbol for detected ion - Applies to all the win-

dows during this analysis
A note about Magnetic Field, Fix Radius, and Symbol: these three parameters are inter-
related. You determine one parameter by setting the other two. For example, if you
input the magnetic field and the symbol, the appropriate radius will be automatically
calculated.

Chapter 2: Tuning
Mass Table/Real.
Field Install. Apply entered field strength to the magnet.

Large changes can lead to a loss of the NMR lock. Plus,
hysteresis and induction can also make transitions a bit
rocky.
Remove Mass. Delete high-lighted entry from mass table
Periodic Table. Accesses sub-menu with a periodic table

of the isotopes and an editable list of polyatomic ions.
B) Mass Table - Assign Trolleys

Magnetic Field Strength. Has been set in panel A)
Radius. Can be assigned. In this case the fixed Faraday

cup FCs had been selected, so the option is grayed out.
Select a trolley. Assigns a specific detector to a given

isotope under the chosen physical conditions (Field, etc.)
Mode. Fixes the position of a trolley or lets it float to

accommodate other restrains (Not really a choice in the
case of FCs).
C) Mass Table - Place Trolleys

Chapter 2: Tuning
5. Bar Graph Menu
a) Bar Graph Conditions
Figure 2-10: View of Bar Graph Conditions Menu

Chapter 2: Tuning
Menu Details: Bar Graph Conditions

Detector. Select detector used for the acquisition of the
spectrum
Start B Field. Sets starting point for B-field scan.
End B Field. Sets end point for B-field scan.
Bfield step. B field increment for scan - linked to num-

ber of steps.
Number of steps. Number of steps - linked to increment

size.
Mass resolution. ?????
Count time. Acquisition time per time point.
Waiting time. Equilibration time after move to next field

strength. Depends on step size. This interval can be com-
puted by the program.
Beam Blanking. Turns beam off during move from one
field strength to the other. Blurs spectrum if OFF.
Show Curve. Opens Display window for the effect of the

B-field on the count rates at the selected detector.

Chapter 2: Tuning
b) Bar Graph Display Window
Figure 2-11: View of Bar Graph Display Window.
Menu Details: Bar Graph Display

Display Units. Displays scanning results as secondary
ion current or as counts per acquisition period. Also
changes X-axis to mass units ????
Y-axis scale. Sets y-axis to either log or linear.
X-axis range. Lower and upper limit for x-axis
Y-axis range. Lower and upper limit for y-axis

Chapter 2: Tuning
6. Energy Menu
a) Energy Tuning
Figure 2-12: View of Energy Tuning Window.
Menu Details: Energy Tuning - Conditions

The electrostatic sector of a double focusing mass spectrometer selects the ions by
kinetic energy, regardless of mass. Energy tuning optimizes the voltage applied to the
electrostatic sector SS100 to send the center of the secondary ion beam kinetic energy
distribution into the magnetic sector.

Chapter 2: Tuning
Detector. Selects one or more of the electron multipliers

behind the magnetic sector to measure the specific sec-
ondary ion currents.
Voltage step. Increment for the voltage scan of SS100.
Points number. Number of increment steps during the

scan.
Count time. Acquisition time per scan point.
CL (V). Center line voltage. Automatically detected

maximum for the voltage scan. Can be written to the
parameter file by clicking on Apply CL.
Selected Value. User selected value for the potential of
SS100. This is done by clicking with the mouse in the
display window. Clicking on Apply writes the value to
the parameter file.
Show Curve. Opens display window for the energy scan.

Chapter 2: Tuning
b) Energy Display
Figure 2-13: View of Energy Display Window.
Menu Details: Energy Tuning - Display

After the scan the program selects automatically the peak maximum and passes the
sample offset value to the main panel as CL. Alternatively, the user can mark a different
peak with the mouse and apply this value as a correction to the potential of the electro-
static sector.
X-axis range. Lower and upper limit for x-axis

Chapter 2: Tuning
Y-axis range. Lower and upper limit for y-axis
Y-axis scale. Sets y-axis to either log or linear

Chapter 2: Tuning
7. Beam Stability Menu

a) Beam Stability Conditions
Primary beam is scanning over

a preset area, rather than burning
a hole in one spot.Static vs. Scan
is set in the main tuning window
Detection mode selects either

Faraday cups for the primary ions
or EM detectors for secondary
ions
Electron multiplier tubes after

mass spectrometer stage
Faraday cups in the primary

column and behind the sample stage
Start/Stop buttons greyed out since

no detector has been selected yet
Starts statistical analysis of the

beam stability after the acquisition
is completed
Figure 2-14: View of Beam Stability Conditions Menu.
Menu Details: a) Beam Stability Conditions

Scanning Mode. Indicates that the primary beam will be
scanned across the sample. Set in the main Tuning panel.

Chapter 2: Tuning
TIC/MC. Selects detectors used - either Faraday cups for

total ion current or electron multiplier dynodes for sec-
ondary ion counts after the mass spectrometer stage.
Detectors. Selects the EM detector used for the beam
stability measurements (as stability of secondary ion gen-
eration)
Faraday Cup. Selects position in w
Point number. Number of time points at which the beam

intensity is determined
Counting time.For scanning mode: Time per pixel dur-
ing the acquisition of one scan at a given time point.
Total time. Duration over which the beam intensity is
recorded
Start/Stop/Abort. Start: Starts beam stability recording.
Stop: Ends acquisition early, saves data. Abort: Stops
acquisition, discards data.
Show results. opens window with statistical analysis of

the beam stability
Show Curve. Opens Beam Stability Display

Chapter 2: Tuning
b) Beam Stability Display
Scanning mode with raster set

to 0 is the equivalent of a static
beam!
Acquisition time per

scanned frame.
Figure 2-15: The Beam Stability Display Window.
Menu Details: b) Beam Stability Display

Display Units. Either as counts per second (Cnt/s) or as
counts per scanned field (Cnt)
x-Axis. x-axis range
y-Axis. y-axis range
Log/Lin. Format of the y-axis (logarithmic or linear)

Chapter 2: Tuning
8. PHD Menu
a) PHD Conditions
Figure 2-16: View of the PHD Conditions Window.
Menu Details: a) PHD Conditions

Detector Selection. Selects detector for threshold adjust-
ment
Start Voltage. Starting point for threshold voltage scan.
Voltage Step. Voltage increment for threshold scan.
Points number. Number of data points for the scan.

Chapter 2: Tuning
Count Time. Acquisition time for each scanned point.

Show Curve. Opens PHD Display
Selected Value. Grayed out until completion of scan.

After using the mouse in the PHD display to select the
optimal voltage, the value is transferred to this line.
Apply. Applies selected voltage to the detector.

Chapter 2: Tuning
b) PHD Display
In Figure 2-17, move the line to select the threshold voltage. You change the voltage of the
actual detector to shut out noise. The line should always be at the vertex of the curve, as shown in this
example.
Figure 2-17: View of PHD Display Window.

Chapter 2: Tuning
9. Tools Menu
a) Tuning Tools Conditions
Lens to be tuned
Detection mode - defines mostly

where the effects of the tuning is
observed.
Progress bar
Value is transfered from display

window after being user-selected
Figure 2-18:View of Tuning Tools Menu.
Menu Details: a) Tuning Tools Conditions

Parameter. Selects lens, etc. that will be tuned

Chapter 2: Tuning
Detection mode. Selects detector for the observation of

the effects of tuning.
Detector. EM detectors used for detection via multi col-
lection after the mass spectrometer stage. Multiple detec-
tors can be used.
Faraday Cup. Faraday cups used for measurement of the
primary ion current.
Start Voltage. Starting point for tuning scan.
Voltage Step. Voltage increment for tuning scan.
Points number. Number of steps in the scan
Count time. Acquisition time per increment.

Show Curve. Opens Tools Display
Selected Value. Grayed out until completion of scan.

After using the mouse in the PHD display to select the
optimal voltage, the value is transferred to this line.
Apply. Applies selected voltage to the selected element.

Chapter 2: Tuning
b) Tools Display
Multiple EM detectors were

selected to observe the
effect of tuning on the
multi-collection stage.
Optimize tuning for all
4 collectors.
Figure 2-19: Tools Display Window.
Menu Details: b) Tools Display

Display Units. Either as counts per second (Cnt/s) or as
counts per scanned field (Cnt)

Chapter 2: Tuning
10. HMR Menu

a) High Mass Resolution Scan - Conditions
High Mass Resolution scans are done

after the mass spectrometer stage;
therefore only these detectors are
options.
X-Deflection, deflection voltage and

mass are used interchangeably in this
sub menu.
Figure 2-20: The High Mass Resolution (HMR) Scan Menu.

Chapter 2: Tuning
Menu Details: a) High Mass Resolution Scan - Conditions

Detectors. Select the detector used for tuning. Only one
detector can be tuned at a time.
Start voltage.Initial potential of the deflector plates in
front of the EM.
Voltage step. Increment size for the scan
Points number. Number of steps for the scan.
Count time. Acquisition time per point of measurement.

L10-90. Distance over which the signal rises from 10%

of the maximum to 90%, expressed in um. Serves as a
measure of the quality of the left shoulder of the spec-
trum.
L9-95. Distance over which the signal goes from 5% to
95% of the maximum.
L50. ????
CL. Center line - Automatically determined maximum of

the HMR spectrum
Apply L50 in setup.???
Selected Voltage. Deflection voltage selected in display

window with mouse (yellow line). Important for the dis-
tinction between isobars such as 12C15N and 13C14N.
Center Line Voltage. Deflection voltage to center maxi-
mum on detector
Apply. Transfers selected voltage to deflector potential

settings.

Chapter 2: Tuning
Apply CL. Transfers voltage settings to center maximum

on the detector to deflector potential settings.
b) HMR Display
Figure 2-21:View of HMR Display Window. Moving the bar sets the voltage of the deflector or lens
that you re checking.

Chapter 2: Tuning
11. Sec. Ion Beam Menu
a) Secondary Ion Beam - Conditions
Scan has not been run yet - some

options are grayed out or N/A.
Figure 2-22: View of Secondary Ion Beam Conditions
Menu Details: a) Secondary Ion Beam - Conditions

Detector. Selects detector used to monitor the quality of
the secondary ion beam after the mass spectrometer
stage.

Chapter 2: Tuning
Plane. Toggles between horizontal (Cy) and vertical (C?)

alignment of the secondary ion beam.
Start voltage.Initial potential of the deflector plates in

front of the EM.
Voltage step. Increment size for the scan
Points number. Number of steps for the scan.
Count time. Acquisition time per point of measurement.

Show Curve. Opens display window.
L50 (V): ???
CL (V): Focuses signal maximum into the selected

detector.
Apply CL. Applies potential CL(V) to detector plates to

center the signal peak in the detector.
Selected Voltage (V). Alternative voltage selected in the

displayed curve of the secondary ion beam scan.
Apply. Applies the selected potential from above to the

deflector plates.
Save to Def Analysis. Writes values to Def Analysis file.

Chapter 2: Tuning
b) Secondary Ion Beam - Display
Figure 2-23:Secondary Ion Beam Display Window.
Menu Details: b) Secondary Ion Beam - Display


Chapter 2: Tuning
12. RTI Menu

a) Real Time Imaging - Conditions
Scanning field (265x256 max) and

offset from center via range and
starting point
Detection mode for secondary

ions - Total ions or mass-filtered
Physical dimension of scanned

field
Parameters carried over from

trolley set-up
Data from RTI scans are not

saved as a file - Stop/Abort choice.
Figure 2-24: View of Real Time Imaging (RTI) Menu.
Menu Details: a) Real Time Imaging - Conditions

Counting Time/pixel. Acquisition time per pixel. has to
be balanced between signal intensity and scan rate.
NXMax. Right limit for scanned range

Chapter 2: Tuning
Width. Number of scanned points in the horizontal.
NXLow. Left limit for scanned range.
NYMax. Upper limit for scanned range
Height. Number of scanned points in the vertical
NYLow. Lower limit for scanned range
TIC/MC. Detection of either total (TIC) or mass-filtered

secondary ions.
Detector. Selection of up to two detectors in multi-col-

lection mode.
Scale. Linear or log(10) scale for counts per pixel repre-

sentation in the real time scan.
Raster. Physical dimension of scanned field. This setting

determines the magnification of the final image.
Init. Transfers the settings for the scanned field to the

instrument.
Full scale. Counts per pixel for maximal signal in repre-

sentation of the real time scan.
Offset. Lower cut-off for representation of counts in real

time scan.
Symbol. Label for the detected ion. Carried over from

set-up panel.
a.m.u. Nominal mass of the detected isotope
Radius. Position of the trolley.
EM/FC. Detector type - selected in the set-up menu,

either the moveable electron multipliers or the Faraday
cup behind the mass spectrometer stage.

Chapter 2: Tuning
Start/Stop/Close. Starts and stops the real time imaging

scan, and closes the panel.

Chapter 3: Holder Menu

A. Main Holder Menu
1. Mapping of
points of mea- Alternate holders:
surement
2. Positioning of
sample holder
BIOLOGY
3. Map of the sam-
ple holder in the
sample chamber
GEOLOGY
4. Position of the primary
beam
5. Sample stage
movement
Figure 3-1: Display Window of Holder Menu. To bring up this window, click on the top edge of the
frame.

Menu Details: Main Holder Menu

1. Mapping of points of measurement
Accesses the EDIT SAMPLE HOLDER sub-menu with

sample holder layouts files and editing tools for such files
Brings up the holder list
Saves a position after sputtering with primary beam
Positioning of the sample holder in the load position

(ready for measurement) or unload position (ready for
removal of the holder from the sample chamber
2. Positioning of the sample holder

Moves sample holder out of the way so that primary ion
current can be measured at the object plane via the Fara-
day cup FCo
Moves sample holder in position for SIMS analysis
Moves sample holder in position for inspection through

the CCD camera

Toggles settings of the holder panel between locked and

un-locked stage
???
Toggles position coordinates between absolute and rela-

tive
3. Map of the sample holder in the sample chamber
Map of the sample holder in the instrument. The black

area depicts the regions masked off by internal blinds.
The white circle is the outline of the sample holder. The
pink circles represent the slots in the sample holder with
the Si chips. These outlines do not limit the positioning of
the sample.
Saved points appear as squares, while the current field of
view is marked by a red circle.
4. Position of the Primary Beam

Actual position of the center of the current field of view
5. Sample stage movement

Set new center for the field of view. Click on Move.. to
move sample stage to this point
Speed for the X/Y stage

Move sample stage in pre-defined increments (see button

below). The effect is instantaneous.
The arrows refer to the apparent movement of the sample

stage - clicking on the right button will move the struc-
tures in the center of the field of view to the right.
?????
Adjusts the increments by which the stage is moved
???

B. Edit Menu
Figure 3-2: Edit Menu.

Menu Details: Holder Menu - Edit Menu

????
????
Sample name - can be edited
Date of the generation of the file.
????
Delete and undelete entries in the map of the sample

holder

C. Points Menu
Figure 3-3:View of Points Menu within Holder Menu.

Menu Details: Holder Menu - Points Menu
To use this menu, Analysis needs to be selected.
Clears all points.
Sorts list of points by date, name, or filter.
This updates the position (in prior software versions,

you had to close the holder and reopen).
Show
The Filter field allows you to see points from one

chip at a time. In the example to the left, only points
from chip 14 will be shown. The format of the field
is *XX-* where XX is the chip number (i.e. *14-*
for chip 14 or *08-* for chip 8.
Enter a name for your points in the Point field.

Automatic numbering has been implemented so that
when you enter a prefix in the Point field, the soft-
ware will automatically label, number, and incre-
ment each successive point you take. In the example
in Figure 3-3, the prefix in the Point field is 14-
path , so the points taken were automatically named
14-path_001 , 14-path_002 , etc.
Date shows the date the point was last modified.

Move the arrows to select the X and Y positions.
Prints the entire stage list.
Click on this to move to the location chosen
This saves your information.

* a note on saving names: saving names can by
tricky - be sure that when you re saving it, it has the
name you want it to have.
This allows you to correct the position of a point
already saved. You keep the name of the point, but
change the coordinates.
Allows you to delete a single point.

D. Crater Menu
Scrolls through list of File management

entries
Coordinates of
selected crater
Figure 3-4:View of Crater Menu within Holder Menu.

Menu Details: Holder Menu - Crater Menu

Scroll settings
Scrolls through list of crater coordinates
File management
Print data for current crater
Moves stage to the position of the selected crater
Delete file entry for selected crater or delete all entries in

file list
Coordinates
Editable comment, file name of the original acquisition
experiment, and the date of the experiment
Access to different crater entries in the file list; either by

their x- and y-coordinates, or by their file number

Chapter 4: Source Menu

A. Main Source Menu
Figure: 4-1:View of Source Menu. This is an example of a window that requires that the top bar be
blue before you can type in it.
Menu Details: Main Source Menu

Filename. Parameter file for a given source.
Cs/Duo. Toggles between the Cesium carbonate source

and the oxygen duoplasmatron as the source for primary
ions.
Polarity. Set for the charge of the primary ion - positive

for cesium cations, negative for oxygen anions.
Ionizer. Ionizer current. Be sure to hit enter after typing

this value.
Reservoir. Reservoir current. Be sure to hit enter after

typing this value.

HV. High voltage potential of the primary column. Be

sure to hit enter after typing this value.
State. State of the selected primary ion source.
Stop. Shuts down primary source. When you click this

you will be prompted to enter a delay. To shut down right
away, enter 0. To shut down at a later time, enter the
delay in hours and minutes. After this, another window
will ask you if you want to restart. If you answer yes to
this, you will be prompted to enter another delay in hours
and minutes.
Start. Takes selected source through start-up procedure.
Recycling. Regenerates the source if necessary.
File List. Opens the Sources File List with sets of param-
eter files for the primary ion sources (see Figure 4-2).
Real Measure. ????
Figure: 4-2:Window that appears after clicking File List .

Figure: 4-3: Window that appears when you stop/start machine. Enter the delay time in hours and
minutes; if you want to stop/start right away, enter 0.
Menu Details: Source File List

Lists parameter files for the available primary ion sources.

Chapter 5: Preset Menu

A. Main Panel
Changes can only be

made by the superuser
Ion Optics Parameter

set (current)
Detector parameter set

(current)
Figure 5-1:The Main Panel of the Preset Menu. In this window the top bar must be blue in order to
type in it.
Menu Details: Main Panel of Preset Menu

Opens file management panel.
Saves parameter set
Same as “save”
Creates new parameter set.
Shows parameter files currently used.
Opens html document with all parameters

Ion optics settings. Also referred to as either “Global” or

as “Primary”. This inputs all values in the file into the
keyboard.
List of ion optics settings
Detector settings. Also referred to as “Secondary”. This

inputs all values in the file into the keyboard.
List of detector settings.

B. File Management
Search criteria for parameter sets Information from file header

of selected file
Files that were found in search
(click to select)
Selection of parameter sub-sets to be

loaded
Figure 5-2: File Management Menu of Preset Menu.
Menu Details: File Management

Sections - Primary Parameters for ion optics
Sections - Secondary Parameters for detectors
Sections - NEG Parameters for electron gun
Mode - Import/Merge
Sends html file of parameter sets to web browser.

C. File Management - Display
Figure 5-3: Picture of File Management Display Window
Menu Details: Management - Parameter Display

D. Ion Optics Parameter Sets
Figure 5-4: Ion Optics Parameter Sets Menu.
Menu Details: Ion Optics Parameter Sets

Edit Allows parameter-by-parameter adjustments of a given
set.
Calib For whichever set is selected, clicking this button takes
the current machine conditions and puts them into
selected files
Valid Inputs the set on the buttons into the machine.
Define Allows you to select which lenses/deflectors should be
included in a certain set.
Label Allows you to give the set a name. Note: to complete this
operation you must click ‘Label’ and then click the set
you want, even if you already have that set selected.
TMP

Edit Submenu
Figure 5-5: Edit Submenu
Menu Details: Ion Optics Parameter Sets - Edit

Valid You input a single value by clicking ‘Valid’.

E. Use of the Preset L1=7000V Toggle Switch for High Spatial Resolution Analysis
To obtain the highest spatial resolution analysis (or smallest Cs Beam diameter), the voltage
on lens L1 needs to be brought from the normal operating value of 0 volts up to a value of
7000 V.
It is not advisable to simply use the thumbwheel to ramp up the L1 voltage as the Cs beam
current will go through a maximum around 3000V. Even a brief exposure to this high Cs
current can damage a sample, in particular if it is an ultrathin/EM section.
The toggle switch will change the L1 voltage from 0 to 7000V. It will also change the values
of Cox, C0y, C1x, C1y to the optimum values corresponding to L1=7000V.
To use the toggle switch, click on the “Preset” button on the NanoSIMS toolbar on the right
of the screen.
When you open the preset menu, a window will open with six rectangular boxes (below).
The top box will be titled “Large Current”. If you click on the rectangular box entitled
“G0_080103”, it will change the L1 voltage to 7000V and also the Cox, C0y, C1x, C1y values.
To switch back to the condition where L1 = 0V, simply click on the rectangular box again.
67
MIMS Reference Manual v1.2

F. File List
Figure 5-6: Snapshot of File List Window

FFF
Menu Details: Preset Menu - File List
Shows source of parameters for ion optics, detectors and electron gun.

Chapter 6:Analysis Method
Menu
69

Chapter 6: Analysis Method Menu
A. Selection
Figure 6-1: Snapshot of Selection Menu.
Menu Details: Analysis Method Menu - Selection

Path This shows the default path. In the directory structure,
you can only go two levels below the path that is shown.
You can change the default path (thereby using more than
two subdirectories) by going to the setup menu; see the
section “H. Directories” on page 116.
Select Brings up File Manager (shown in Figure 6-2)
DEPTH PROFILE Drills a hole into the sample and records composition at
different depths
LINE SCAN Elemental analysis along a line
ISOTOPES Get an isotope ratio from a selected point on a sample.
IMAGE ACQUISITION Imaging mass spectrometry
70

GRAIN MODE Batch analysis

CHAINED ANALYSIS
71

B. File Manager
List of method files
Figure 6-2: File Manager Menu within Analysis Method Menu
Menu Details: Analysis Method Menu - File Manager

Experience Experiment name. This applies to the first sub-level of
the current path.
Method This is where all info for that session will be saved, and is
in the second sub-level of the current path.
Valid Enter
Date / Name Sorting order for method files
72

C. Depth Profile
Figure 6-3: Menus for Depth Profile.
Menu Details: Analysis Method Menu - Depth Profile

Records counts on selected detectors while the primary ion beam erodes material at a single point
over time.
Ct/px: Acquisition time per point
Total time for primary beam exposure
Number of data points during the total analy-

sis time.
73

Initial exposure to ensure steady-state condi-

tions during data acquisition.
The Load button on the lefthand menu of

Figure 6-3 brings up a list of files taken for a
particular type of analysis. The menu brought
up by pressing Load is shown below in Fig-
ure 6-4.
Figure 6-4:Menu for loading a file.
74

D. Line Scan
Figure 6-5: Menus for Line Scan.
Menu Details: Analysis Method Menu - Line Scan

Total analysis time Total time for analysis - a function of the number of
points and the acquisition time.
X step X increment for each step
Y step Y increment for each step
Number of steps
Pre-sputtering Initial exposure to ensure steady-state conditions during
data acquisition.
Ct/pt Acquisition time per point
Offset ???
75

E. Isotopes
Ratios button
b.
a.
c.
Figure 6-6: Menus for Isotopes Menu within Analysis Method Menu. Clicking on the ‘Ratios’ button
in panel ‘b’ brings up panel ‘c’.
76

Menu Details: Analysis Method Menu - Isotopes

Ratios Clicking on this button brings up the ‘Ratios’ panel
shown in Figure 6-6. You select the trolleys you want in
order to specify isotope ratios. For example, if 12C is on
trolley 1 and 13C is on trolley 2, to specify the ratio 13C/
12C you would want the ratio 2 / 1. The key sequence to
type this is: 2, enter, 1, enter.
Block number Number of data blocks
Meas. per block Number of data points per block
Rejection at (sigma) Data quality criterion per block
Pre-sputtering Initial exposure to ensure steady-state conditions during
data acquisition.
Ct/pt Acquisition time per point
offset ???
77

F. Image Acquisition
Species Symbol
Figure 6-7: Image Acquisition Menus within Analysis Method.
78

Menu Details: Analysis Method Menu - Image Acquisition

The working frame/scanning frame feature allows you to
take a quick, lower-resolution image of a larger area (the
working frame), and then take a higher-resolution image
of a smaller area (the scanning frame) within the work-
ing frame.
First, take a two-minute image in MIMS. Then go to

ISee and use the image_transfer procedure to break the
2-minute image into its four masses and ratios. Select an
area of interest in ISee and record the X,Y address of the
top left pixel.
Then return to the MIMS software and enter this coordi-

nate next to Start Col and Start Row in Figure 6-7.
The X coordinate should go in Start Col , and Y in
Start Row . You can now launch MIMS acquisition to
take an image of the scanning frame.
IMPORTANT: For a given image size in the scanning

frame, the size of the original working frame image must
be double (i.e. for a 256 x 256 pixel scanning frame
image, the original working frame image would be 512 x
512 pixels).
This is a graphical illustration of the scanning and work-
ing frames described above.
If the species symbol here doesn’t show up, this means

that the radius needs adjusting. Check for this by going
to the tuning menu and observing if the mass is shown in
red (see Figure 2-2 and text on page 7). If it’s red, you
can do one of two things:
(1) Change the mass range
(2) Adjust the radius. This is the better option. When
the radius has been properly adjusted it will show up in
blue in the tuning menu.
79

Ct/px: Acquisition time per point
Number of repeat images of a field
Physical size of field of view. Also shown after applica-

tion of correction factors
80

G. Grain Mode
Figure 6-8: Grain Mode Windows.
Menu Details: Analysis Method Menu - Grain Mode

Meas. number Number of repeat images of a field
Raster size Physical size of field of view. Also shown after applica-
tion of correction factors
NXmax, NYmax Maximal size of image raster. Limited by instrument
Xlow, Ylow Starting points for scan based on current field size and
position
Width, Height Dimension of scanned field
Ct/px Acquisition time per point
Offset ???
81

H. Batch Analysis
Menu Details: Analysis Method Menu -- Batch Analysis
82

I. Chain Analysis
Figure 6-9:Chain Analysis Menu
Menu Details: Analysis Method Menu -- Chained Analysis
83

Edit MC changes the measuring conditions.
Very important: before saving, insert the file

name. Then press Save at the top left corner.
Load brings up the menu in the lower half of

Figure 6-9. Choose the file of interest (which
will have the extension .cha). Then hit
Load , which will close the Load window
and return you to the main chained analysis
screen.
Deletes all sample info in analysis list above.
Deletes only the highlighted sample in the

analysis list.
Adds an analysis at the location you are at.

This button adds the item above the high-
lighted position.
Uses the conditions of the loaded file for a
run at the current X, Y position.
Creates a run at a new X, Y position.
Types of Chained Analysis

This is the simplest type of chained analysis.
You perform analysis at the position where
you are currently at.
GoTo: This allows you to move a certain dX

and dY from the position you are at. You
enter values next to dX and dY, and a number
next to Nb: . Increasing Nb by X will move
the analysis X number of times (each time by
the prescribed dX and dY you have entered).
Analysis moves in a straight line.
84

Snake: The snake option completes an S

shaped path. You enter values for dX and dY;
Analysis will start at the initial point, move
dY, dX, then -dY. If you increase the number,
Nb: above one, the path will be repeated. A
simple path with Nb=2 would look something
like this:
(Nb = 1)
(Nb = 2)
Loop: This option will complete a rectangular

loop. You enter values for dX and dY, then
the analysis will move dX, -dY, -dX, and dY
to return to the original location.
This option lets you repeat a single path any

number of times. You enter values for dX
and dY, the beam will move to that location,
and then automatically return -dX and -dY to
the original position. Enter a value next to
Nb to repeat the path as many times as you
want.
For this analysis, you enter an X coordinate
and a Y coordinate, and the beam will move
to that one position to perform analysis.
85

Chapter 7: Analysis Menu
86

A. Main Menu
Figure 7-1: View of Main Analysis Menu.
87

Menu Details: Analysis Menu - Main Window
Quit from acquisition menu.
Real time display of count rates or count ratios. Opens

menu “Analysis/Display”
Directory path for the saved file
File name (can be edited)
Start data acquisition
Stop data acquisition, save data up to this point
88

Abort data acquisition
Estimated duration of the experiment
Opens Control sub-menu
Gives a drop-down list of parameters.
Opens multi collection sub menu
89

B. Results Menu
Figure 7-2: View of Results Menu. You can scroll down this page by using the scroll bar on the right.
90

C. Display Menu
Figure 7-3: View of Analysis Display Window.
Menu Details: Analysis - Display Window

Sends image of the countrate curve to lpr
Toggles Y-scale of the curve from total counts to count

rate or ratios
91

Selects log scale or linear scale for Y-axis
Scales X-axis to values entered as X max and X min
Doubles the range of the X axis from the set values
92

D. Analytical Parameters
Figure 7-4: View of Analytical Parameters Window.
93

Chapter 8: Image Menu
94

A. Image Processing Control Board
Figure 8-1: View of Image Processing Control Board
Menu Details: Image Processing Control Board
2D Visualization tool
2D image processing
First 2D plane of a 3D data set
Second 2D plane of a 3D data set
Color encoding method for data presentation
Selects color model for data encoding
95

B. Image - 2D Visualization Tool
Figure 8-2: View of 2D Visualization Window.
Menu Details: 2D Visualization

Opens data files
Scale image data
Select image from a table of images currently open
Zoom in or out of image

96

Print out of the image
97

C. 2D Processing
Figure 8-3: View of 2D Processing Screen
Menu Details: 2D Processing

Brings up file list, and you select from which files to cre-
ate images.
98

Allows you to switch between base-10 log and natural

log (ln).
Allows you to set up grids of pictures. The first number

you select tells you how many images you can show; in
the example at the left, 16 images would be displayed.
2D Processing Submenu: Image Computer
Figure 8-4: Window brought up by pressing ‘Compute’ on 2D Processing Menu
Menu Details: 2D Processing - Image Computer
99

D. 3D Processing - First Plane
100

Chapter 9: Curve Menu
101

Chapter 9: Curve Menu
A. Main Curve Menu
Figure 9-1: View of Curve Menu.
Menu Details: Curve Menu

Not yet implemented in the CAMECA NanoSIMS software.
102

Chapter 10: Setup Menu
103

A. Holder
Figure 10-1:View of the ‘Holder’ Tab on Setup Menu.
Menu Details: Setup - Holder Tab

Synoptic Offset ??
SIMS-CCD Offset Correction factor to align CCD image and SIMS image
during the definition of reference points
FCo Position of object Faraday cup in the holder. The sample
holder moves into this position during primary ion counts
at the FCo position.
Analysis sample Standard position for sample to be analyzed.
104

Standard sample Position for the reference sample.

FCo Voltage Potential difference between the object Faraday cup and
the listed lenses.
CCD Field of view (um) Linear dimension of the image shown by the CCD cam-
era.
105

B. Tuning
Figure 10-2: View of the ‘Tuning’ Tab on Setup Menu
Menu Details: Setup - Tuning

Active Detectors. Detectors available for this instrument
Trolley Parameters. Selects a specific trolley to set the

parameters.
Step Move Basic increment for moves of the trolley.

Offset Radius ???
Reset Radius Start position for trolley after reset.
106

dR/dV Effect of deflector potential in HMR scans, etc.

Page Move Batch increment for trolley move
Slope Similar to Step move setting
Secondary Ion Beam ????
107

C. Keyboard
Figure 10-3: View of ‘Keyboard’ Tab on Setup Menu.
Menu Details: Setup - Keyboard

Sample Voltage Prop.
EOW Std.
Propagation
FCp
L1 Std
Cx Std
108

SE FC
Raster
B1
B2X
B2Y
B3
Field (um)
Field DAC
Coef
LF4
LF4 (DAC)
TIC
Polarity
LF2
LF3
SS100 Int
SS100 Ext
CV
109

D. Hardware
List of installed options
Alternative ion sources
Figure 10-4: View of ‘Hardware’ Tab on Setup Menu.
Menu Details: Setup - Holder Tab

Accessories
Total Ion Current EM Detector for secondary ions prior to mass filtering
Sec. Elec. Detector ???
Electron Gun Can be used to prevent build-up of static charges due to
exposure of the sample to primary cations.
Large Detector Fixed EM detector after the magnetic sector
Wien Filter ???
110

FCs Plates Deflector plates for Faraday cup after magnetic sector
C7
Options
Source Type of ion sources in the primary column - Cesium car-
bide and oxygen duoplasmatron, or only a cesium carbide
source
Secondary ???
Slits
Selects exit slits for detectors after the mass spectrometer
stage.
Selects size for exit slits
111

E. Slit & Diaphragm
Figure 10-5: View of ‘Slit & Diaphragm’ Tab on Setup Menu
Menu Details: Setup - Slit and Diaphragm Tab

These settings define the dimensions of the slits and diaphragms at the settings.
Diaphragms (circular openings)
D Duo Duoplasmatron diaphragm - only needed with oxygen
source.
D0 Diaphragm in primary column to shape the primary ion
beam
D1 Diaphragm in the objective column. Effects the resolu-
tion and the depth of field of the final image.
112

Slits
Entrance Entrance slit. Shapes the beam between the electrostatic
and magnetic sectors.
Aperture Aperture slit. Shapes beam prior to entry into the mass
spectrometer.
Exit Exit slit. Limits mass range that can enter the mass detec-
tors.
113

F. Detector
Figure 10-6: View of ‘Detector’ Tab on Setup Menu.
Menu Details: Setup - Detector

Electron Multiplier
Selects detector for setup.
Security Secondary ion current that triggers shut down of the

detector to prevent burn-out. This is not implemented on
our machine
Yield Efficiency of the detector. This can be important for
quantitative analysis.
114

Background The background varies as the detector ages. Use PHD

scans to minimize background counts.
Dead Time Recovery time of the detector after an event.
Photo Multiplier (Not installed in this example)
DAC Maximum ???? Shouldn t this be an ADC?
Security Shut-down to prevent damage to detector.
Faraday Cup - Primary
Auto Range Off or On - Ion current is sued to adjust the sensitivity of
the ampere meter.
Polarity + or -. Adjust depending on primary ions used.
Range Background Sets expected level of background counts
Faraday Cup - Object
Auto Range Off or On - Ion current is sued to adjust the sensitivity of
the ampere meter.
Range Background Sets expected level of background counts
Faraday Cup - Secondary (Not installed in this example)
Background Sets expected level of background.
115

G. B Field
(Truncated)
Figure 10-7: View of ‘B Field’ Tab on Setup Menu
Menu Details: Setup - B Field

Waiting Time Computed
NMR Lock/ Unlock Magnetic field feed-back loop using nuclear magnetic
resonance as a detector
Hall Hall effect probe for B-field measurement.
Offset
Slope
dB0
t0 Time constant for measurements
116

H. Directories
(Truncated)
Figure 10-8: View of ‘Directories’ Tab on Setup Menu
Menu Details: Setup - Directories

User directory This is where you set up the default directory. Change
the default directory if you need access to more than two
levels of subdirectories (see page 69 for a description of
this issue).
117

I. Sources
(Truncated)
Figure 10-9: View of ‘Sources’ Tab on Setup Menu.
Menu Details: Setup - Sources

Sets ramp-up and ramp-down rates for the cesium source, as well as the sequence of
events during start-up and shut-down
Increasing Rate (Start-up)
Ionizer Ramp-up rate of the ionizer current during start-up
Reservoir Ramp-up rate of the reservoir current during start-up
Decreasing Rate (Shut-down)
Ionizer Ramp-down rate of the ionizer current during start-up
Reservoir Ramp-down rate of the reservoir current during start-up
Waiting Time (scheduled events)
Start Reservoir Delay for reservoir start-up to ensure that the ionizer cap
is already heated by the time cesium atoms are emitted
Stop Ionizer Delay for ionizer shut-down to ensure that the ionizer cap
is still heated as long as cesium atoms are emitted from
the reservoir
118

Chapter 11: Vacuum Menu
119

A. Automatic Control Panel
Vacuum pressure in Torr Status of air locks

Status of Status of
valves pumps
Figure 11-1: View of Automatic Control Panel
120

Menu Details: Vacuum Auto Panel

Controls the baking of the different compartments of the
NanoSIMS (Primary column, secondary column and
multi-collection compartment, selected by checking the
respective boxes).
The duration of the heat treatment can also be set in
increments of hours.
The instrument keeps a log of past heat treatments.
Shows the high voltage status (Green=ON!) of the

source, the ion multiplier tubes???, the primary and sec-
ondary columns and the sample stage)
Status bar of the instrument, showing the positions of the

loading rods, the status of pneumatics, electronics and
communication systems, as well as the frequency with
which the sensors are queried.
Quits vacuum menu
????
121

Automatic mode. This allows you to do the venting/

pumping process automatically.
Toggle switch between auto and manual mode. Also

opens the vacuum recorder window
Read status of all queried sensors immediately
122

B. Manual control panel

b)
Vacuum pressure in Torr Status of air locks

Status of Status of
valves pumps
Figure 11-2: View of Vacuum Manual Control Panel
123

Menu Details: Vacuum Manual Panel

Sets status of the ion pumps IP1 (analysis chamber), IP2
(central column) and IP3 (sample holder carrousel). Tog-
gles the pumps between “Protect” and “Start” and “Stop”.
Sets status for the turbo pumps TP1 (air lock), TP3 (multi
collection chamber) and TP5 (source column) as well as
the primary pump PM. Toggles between “START” and
“STOP?”
Sets status for vacuum gauges to either “ON” or “OFF”
Sets baking status for the three main compartments of the

instrument.
124

Sets status for sublimation pump SP, installed as a second

stage to IP1
Controls four valves; click on the buttons to open or

close. For the valves not listed to the left, you can manu-
ally control them from the manual control panel (Figure
11-2) by clicking on them to toggle between open and
close.
High voltage activation for the Cs source, the primary

and secondary column ion optics and the sample stage.
LMI is optional.
Status bar - same as for the Vacuum Auto panel.
????
Initializes lines????
SP authorization?
Toggle switch between manual and auto panel. Also

opens the vacuum recorder window
125

C. Vacuum recorder
Figure 11-3: Vacuum Recorder Window.
Menu Details: Vacuum Recorder
126

Chapter 12:Miscellaneous
Menu
127

Chapter 12: Miscellaneous Menu
A. Miscellaneous Main Menu
Figure 12-1: View of Miscellaneous Menu
Menu Details: Miscellaneous Main Menu

???
???
???
Tools. Simple parameter files for hardware
Periodic Table. Shows periodic table with information

about isotopes, abundance, physical parameters, etc.
128

B. Tools
Figure 12-2: View of Miscellaneous Tools Menu
Menu Details: Miscellaneous - Tools

Update Reads all parameters in machine. Gives applied voltage,
measured voltage, and the difference.
129

C. Periodic Table
Select element of interest

by clicking on tile.
Submenus
Figure 12-3: View of Periodic Table under Miscellaneous Features.
Menu Details: Miscellaneous - Periodic Table

Element info. Displays a list of isotopes of an element as
well as physiochemical parameters.
Isotopes. Bargraph-type spectrum of isotopes of the

selected element.
Interferences. Not yet implemented.
130

Periodic Table Submenu: Element Info
Figure 12-4: Element Submenu within Periodic Table Feature.
Menu Details: Miscellaneous - Periodic Table - Element Info
131

Periodic Table Submenu: Interference
Figure 12-5: View of Interference Submenu Within Periodic Table Menu.
Menu Details: Miscellaneous - Periodic Table - Interference

Not yet implemented
132

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MIMS Reference

National Resource for Imaging Mass Spectrometry

© 2007 National Resource for Imaging Mass Spectrometry

Chapter 6:Analysis Method Menu . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 69

MIMS Reference Manual v1.2 i

MIMS Reference Manual v1.2 ii

© 2005 National Resource for Imaging Mass Spectrometry

MIMS Reference Manual v1.2 1

A. Description of Tool Bar

Holder: Controls the positioning of the sample holder. This

Preset: Accesses a list of saved parameter files for the settings of

Analysis Definition: Sets up various analytical methods, such as

MIMS Reference Manual v1.2 2

Analysis: Sets the parameters for a given experiment, such as file

Curve: Determines layout for multiple curves from multiple sub-

Setup. Controls instrument parameters such as slit widths, etc.

Vacuum. Monitors and controls the function of the vacuum sys-

Miscellaneous. Periodic table with isotope lists and other small

B. General Tips for Using NanoSIMS Software

MIMS Reference Manual v1.2 3

© 2005 National Resource for Imaging Mass Spectrometry

MIMS Reference Manual v1.2 4

MIMS Reference Manual v1.2 5

Figure 2-2: View of Trolley Panel

Menu Details: Trolley Panel

MIMS Reference Manual v1.2 6

Radius. Can be set numerically at the input line, or by

Mass. The mass of the ions detected by this channel is

If you type a number, the trolley will move to that mass,

If the mass value shows up in red, it needs to be adjusted.

Adjust. Click on box to apply changes; re-confirm entry

MIMS Reference Manual v1.2 7

Figure 2-3: View of Additional Controls Within Tuning Menu.

Menu Details: Tuning Mode

MIMS Reference Manual v1.2 8

Scanning Mode. Tuning can be done with a static pri-

Cnt / Cnt/s. Counting mode for ions - counts per integra-

Beam Off/On. Controls the primary ion beam. Make

MIMS Reference Manual v1.2 9

Menu Details: Submenus

Detector Calibration Menu. Similar in function to the

Define Analysis File. Handles ion optics field parame-

PHD. (Pulse Height Distribution) . Scans electron mul-

MIMS Reference Manual v1.2 10

HMR. (High Mass Resolution) Allows for the fine tun-

MIMS Reference Manual v1.2 11

Figure 2-5: View of Reset Submenu.

Menu Details: Tuning/Reset Menu

Readjusts the trolley position.

MIMS Reference Manual v1.2 12

Figure 2-6: View of Setup Window

Menu Details: Setup Window

MIMS Reference Manual v1.2 13

Figure 2-7: View of Setup Display Window

Menu Details: Display Window

MIMS Reference Manual v1.2 14

3. Define Analysis Menu

Figure 2-8: View of Define Analysis Menu.

Menu Details: Define Analysis

Load. Retrieves saved parameter sets

Save as.. Writes current parameters to named file

MIMS Reference Manual v1.2 15

4. Mass Table Menu