Ul. Radzikowskiego 152, 31-342 Kraków, Poland.
Kraków, November 2000
Report No 1856/AP
CMB v. 1.1
Data Acquisition and Evaluation System
of the Cracow Nuclear Microprobe
J. Lekki, R. Hajduk, S. Lebed1, A. Potempa, T. Pieprzyca,
Institute of Applied Physics, Sumy, Ukraine
An overview of the Cracow nuclear microprobe together with its data acquisition and control
system is presented. Magnetic deflection was applied for beam scanning, while detector
signals acquisition is performed by the NIM / CAMAC modules under supervision of a
Windows operating system running on a PC equipped with the GPIB controller card. Total
spectra from every detector are accessible on–line during the measurement, while full
information about detected energy and beam position is stored to a disk file in the list mode to
allow off–line data analysis. System hardware and software setups together with software
operations and data formats used for information storing are described.
An overview of the Cracow Nuclear Microprobe
The microprobe in Cracow is based on a HVEC KN-3000 type Van de Graaff accelerator
with proton beam energy up to 3 MeV and energy stability of ∆E/E ≈ 10-3. The focusing elements
of the microprobe (two doublets of magnetic quadrupole lenses) were manufactured in the Micro
Analytical Research Centre (MARC, Melbourne, Australia). The scanning system operates with
the ferrite–cored magnetic coils of the Institute of Applied Physics (Sumy, Ukraine) design [1].
The focusing system (FS) of the operating microprobes (MP) with submicron resolution has
usually the total length l of more than 5 m. Compact versions (l < 4 m) of an optimized FS based
on a divided Russian quadruplet have a great promise for the next generation of MP [1]. The MP
with such FS is economical in space, easy to align and less sensitive to mechanical vibrations than
a long system. In particular, a large demand for such systems comes from biological laboratories,
where a vertical position of the MP is preferable. Due to its unique construction [2,3], the Cracow
microprobe is a very short one (l = 230 cm).
The MP is installed in a new experimental hall located to the right angle from the accelerator
compartment (Figure 1).
Figure 1. Layout of the Cracow MP unit. B1: dipole magnetic steerer; S1 and S2: entrance– and
exit–slit boxes, respectively; B2: analyzing magnet; B3: quadrupole doublet; B4: switching
magnet; S3: feedback slit; S4: object slit.
The ion beam from the accelerator is delivered to the object slit (S4) of the MP using a dipole
magnetic steerer (B1), a 900 double-focusing analyzing magnet (B2) with a bending radius of
240 mm and with a doublet of magnetic quadrupole lenses (B3). The beam-optical transport
system has been designed to minimize the degradation of the beam brightness due to chromatic
and spherical aberrations. The magnetic field of analyzing magnet is stabilized using a power
supply controlled with a Hall probe. A stability of the power supply of the magnet is of the order
of 10-5. The momentum spread of charged particles beam is stabilized by a feedback loop to the
corona discharge current from the Van de Graaff accelerator terminal. The error signal for the
feedback loop is taken from the beam current difference between left and right slit edges located
prior to the object slit of the MP. A switching magnet (B4) is located before the MP enabling the
use of the ion beam in standard experiments not requiring the micro-focusing optics.
The Institute is located close to a road with heavy car traffic, what requires careful precautions
against mechanical vibrations of the MP system. The MP setup is mounted therefore on a heavy
anti–vibrational concrete block 8 m long, put in a sand bath.
Figure 2 presents a schematic view of the MP beam line. A heavy table made of steel (1) is
fastened to the concrete block. A position of the table is adjustable using precise screws (2). The
elements of the MP line are mounted to the table using hard rubber attenuators. The ion beam line
and the target chamber of the MP are pumped down with a 100 l/s ion pump (3) and a turbomolecular pump (16) vibrationally decoupled from the setup using metal bellows and bunapren
elastic sleeves (17). The turbo-molecular pump can be switched off during the most sensitive
The MP is connected with elastic bellows to the accelerator ion beam system and separated with a
gate valve (4). Following the valve, a pair of tanatalum slit edges (5) is mounted using linear feedthrough micrometer screws. A difference of the beam current signals taken from the edges of the
slits is used as an error signal for the feedback loop of energy stabilization.
A water-cooled circular slit (6) is mounted in the same vacuum box. The slit assures that only a
central part of the beam can pass to the object slit (7). Following the experience of the MARC
group, a commercial diaphragm made for a scanning electron microscope is used as an object slit.
Several such diaphragms are mounted in a frame moved by a linear feed-through rod with a
micrometer screw. In the same way an angular collimator (8) is constructed. Two doublets of the
magnetic quadrupole lenses (9) are mounted on separate supports located after a box with the
angular collimator. A two-dimensional ferrite-cored scanning system (10) is mounted between the
last doublet of quadrupole lenses (9) and the target chamber (11). This new compact system
(3.5 cm long only) for each scanning direction is composed of two coils wound on circular lobes
of ferrite rings [1]. In the central part, where each pair of rings is glued together, a hole for the ion
beam tube is drilled. The magnetic field at the ion beam position is sufficient for a scan area of 0.5
x 0.5 mm2 at the target for 2.5 MeV protons with working distance of 15 cm. The scanning system
was developed and tested in IAP (Sumy, Ukraine). The deflecting field produced by the system
shows a high degree of uniformity.
In several positions along the ion beam tube, there are boxes (12) enabling the beam diagnosis.
Each box is equipped with a Faraday cup and a quartz or a BGO plate for the beam visualisation.
In particular, the box (13) is located at the expected position of the cross-over of the beam
between the doublets of quadrupole lenses. Each quartz plate for the beam spot visualisation is
observed by a CCD camera (14). At the end of the MP beam line a target chamber (11) is
mounted. The chamber is equipped with a rotatable x-y-z micromanipulator (18). At present, the
detector system consists of a channeltron for secondary electrons detection, a surface-barrier
detector for scattered ions and a Si(Li) detector (19) for PIXE measurements.
The x-y-z position of each element of the FS (the object slit, the angular collimator, the beam
monitoring boxes, the doublets of the quadrupole lenses, the target chamber) as well as angles of
its inclination with respect to the beam axis are adjustable by high precision screws (20). This
construction enables a step-by-step procedure of fine adjustments of the MP elements with the
proton beam and therefore it permits to find the best alignment with the maximum ion beam
Figure 2. Schematic drawing of the microprobe beam line
The more detailed description of MP construction and parameters can be found in references
Data acquisition system – hardware description
The hardware of CMB system consists of the three main parts:
• The magnetic beam deflection system based on fast power supplies (ES 030-10, 30 V, 10 A,
1.2 ms response, Delta Elektronika, Holland) controlled by a specialized GPIB module PSC–
44M, also from Delta Elektronika.
• GPIB controlled CAMAC crate and a NIM crate containing at least the following modules:
ADC, constant fraction discriminator and gate generator, scaler, clock and GPIB CAMAC
controller. In the present microprobe setup the data acquisition system consists of:
– ADC 4418/V SILENA, 8 inputs, 4096 channels
– CFD 584 ORTEC constant fraction discriminator,
– GG 8010 ORTEC gate generator,
– NIM–ECL–NIM translator model 82, CAEN,
– CC-625 ELLEK GPIB crate controller.
– clock (1MHz) and a quad scaler,
– timing (863) and spectroscopy (572) ORTEC amplifiers, single channel analyzers
and detector power supplies.
• Windows 98 PC microcomputer equipped with a GPIB card. The card is working as an
interface between PC and CAMAC crate controller and between the PC and the beam
deflection system.
Present setup allows to acquire the data simultaneously in multichannel and multiscaler
modes with the detector pulse energy and/or number of counts data correlated with beam
position information. The schematic diagram of electronic modules and their interconnections
is shown in the following figures:
Figure 3a. Main modules of the CMB data acquisition system.
As it is decribed in the microprobe overview, beam scanning is performed by magnetic
deflection. Because of the high inductivity of the deflecting coils, current changes cannot be
very rapid. Therefore, in present setup the minimal reasonable time of single pixel irradiation
is of about 10 ms. The useful (more or less linear) range of magnetic coils currents is limited
to 2.5 A, what corresponds to a beam deflection of about 0.5 mm.
Figure 3b. An overview of signal connections.
General concept of the software
The CMB data acquisition system was developed as a hybrid of the two programming
languages. The first one was the Tcl/Tk [4] VHL (very high–level) scripting language used
for user interface construction and for offline analysis. The second part, performing time
critical tasks was written in C/C++. Such approach allows for reasonable system performance
in parallel to the rapid software development and modification. All the graphic windows
shown in this paper and most of evaluation routines are written in Tcl/Tk. In the case of time
consuming calculations (some display operations, data extraction etc.) the Tcl/Tk
performance was enhanced using C language modules loaded as a DLL library into Tcl/Tk
scripts. The DLL library was prepared with the use of SWIG wrapper and interface generator
[5]. The separate executable responsible for CAMAC crate control, detectors and scalers
readouts and beam scanning, was written using Microsoft Visual C/C++ Development Studio.
Communication and data exchange between threads is assured by means of a shared memory.
It should be pointed out that the CMB is an open system, to which a new hardware (detectors,
CAMAC units) can be added easily with only a minor software updates.
Main CMB window
The principal window of the CMB data acquisition system is shown in the following figure:
Figure 4. CMB main window.
Main window has a standard structure with a menu bar at its top, a rectangular window for
spectrum display (with axes description) and several pushbuttons placed right to the spectrum
rectangle. Their functions are more or less self–descriptive and are listed below:
• Log10 / Lin : Y axis display mode setting.
• Zoom In : after defining the region of interest (ROI) it is possible to limit the displayed
spectrum only to ROI.
• Adjust XY : sets X and Y axis limits to values allowing for full spectrum display.
• Calibrate : allows for entering constant factors for energy spectrum calibration.
• Gaussian : Gaussian fit to a peak defined by ROI.
• Peak Info : Peak parameters – height, area, background, FWHM.
• FWXM : Full Width at X Maximum.
• Map ROI : provides visualization of surface distribution of particular element, defined by
the registered x–ray energy. To specify energy of interest the user must first define the
corresponding region of interest (ROI). This function usually deals with event files that must
be accessible for the system. More information on maps is given in next chapter.
• Clear : removes experiment from memory and clears display window.
• Detector : allows for specification which ADC (or scaler input) should be displayed in the
main window. This choice is enabled by launching a separate dialog window.
The top part of the CMB window displays some useful information about the displayed
spectrum. Starting from the left, the currently displayed spectrum description is shown. Next,
two numbers correspond to the current mouse position recalculated into channel number (or
corresponding energy value) and Y position. Instead of the Y position of the mouse the
current channel content may be displayed with the mouse left click. Finally, if the ROI is set,
the ROI limits and the ROI area of spectrum are displayed. The ROI limits may be set (and
reset) using the right mouse click (first and second clicks set the ROI, and the third one
performs ROI reset).
CMB menu system
CMB main menu consists of the following items: File, Display, Setup, Scanning, Analyse,
and Help. The following description covers all functions accessible for the user from the
♣ Menu File enables standard manipulation on data files like loading or saving them and
contains the following options:
• Open Experiment
• Merge Experiments
• Load Spectrum / Map
• Load Spectrum / New Window
• Save Experiment As…
• Save Spectrum / Map As…
• Exit
The above options are mostly self–descriptive. “Merge Experiments” item is provided to
allow to combine two separate experiments into a single one. Of course, all vital experiment
conditions (like pixels number or beam shift) must be the same for the combined spectra.
As it is reflected in the File structure, the data files are divided into three main cathegories:
A. Experiment contains full information about the performed measurement: total ADC
spectra1 registered by all detectors and the values of readouts of all counters used. All events
are stored in disk files providing off–line access to energy and beam position for every
registered detector pulse. This information is contained in three files:
• One ASCII file containing a header describing the experiment conditions followed by total
spectra of all active detectors and digital counters (scalers). The default extension of this file
is “.cme”, but in general the name and extension may be set freely.
• Two binary event files, one for ADC events and one for scalers readouts, containing the
same ASCII header as the ASCII file. The names of binary files are set by the CMB system
and are constructed as follows:
The term “total spectrum” is used to denote raw ADC spectra where detector pulses are not associated with the
beam position information.
– ADC events: ea_hh_mm.cmb, where “ea” is a fixed prefix, “.cmb” a fixed
extension, “hh” and “mm” denote the time of starting the measurement. Underscores are used
as separators.
– Scalers readouts: eq_hh_mm.cmb, where “eq” is also a fixed prefix and the rest of the file
name is constructed like in the case of ADC.
The structure of binary data record in an event file is as follows:
ADC events:
BYTE x position
BYTE y position
WORD channel number
BYTE detector number
Scaler readouts:
BYTE x position
BYTE x position
DWORD readout value
BYTE scaler number
Because of a large size of event files and the redundant structure the experiment files are
always compressed into a single archive during save operation. The archive name is the same
as the experiment file name plus the extension “.rar”.
B. Spectrum file contains a single total spectrum associated with a particular detector without
any positional information. Standard header describing the experiment conditions is added at
the file beginning. Such file contains only one spectrum and is provided mainly for easy
exporting/importing ASCII data to and from external programs.
C. Map file contains information limited to particular detector and energy range correlated
with the beam position. Maps allow for PIXE / PIGE or RBS studies of surface distribution of
elements. This data representation format may be constructed with the combined use of event
files and total ADC spectrum (the most straight-forward option) or by analyze of QS counters
spectra. Map is displayed using a color representation for number of counts in every pixel2
corresponding to the beam position.
Figure 5. An example of the elemental map window.
“Pixel” is used to here (and later) to represent the beam spot on a target and not the single pixel displayed on a
screen. A beam spot “pixel” of a map is represented by a square area of NxN screen pixels where N depends on
screen resolution, scan size and beam position step.
A map is “clickable”, i.e. pressing left mouse button over a map area displays the number of
counts corresponding to the mouse pointer position. The color scale of the map may be either
linear or logarithmic (see menu Display).
♣ Menu Display
This popup menu allows for change of the display mode, screen details and screen colors. The
acquired spectra may be displayed as a scatter graph, bars or a line. The color of most of the
display regions may be adjusted according to user’s preferences. It is also possible to section
the Y axis using the horizontal grid. Finally, the user may decide whether linear or
logarithmic color scale should be used for maps.
♣ Menu Setup
Main task of this item is to open a window providing the user input for defining the
measurement conditions used for microprobe experiment.
Figure 6. CMB setup window.
The adjustable parameters are as follows:
• Step size determines the beam position update single step in a range from 1 to 100 microns.
• Steps number × Step size product determines the scan area. The maximum value of Steps
number is 256. At present, due to the characteristics of the scanning coils, scan area is limited
• Pixel time represents the time when the beam is positioned at a particular spot on a sample
and detector pulses are acquired. At present, this time corresponds to beam position update
rate. In future, beam will be switched off during the position update and pixel time will
correspond only to a stable position of the beam on a target. Pixel time may be adjusted
between 1 ms and 5 sec.
• X Shift and Y Shift allow for horizontal and vertical adjustment of the beam position on
The lower part of Setup window describes the details of the acquisition system:
• ADC N and Quad Scaler N edit boxes correspond to position of these modules in a
CAMAC crate.
Not connected ADC and QS inputs should contain “nc” in their edit boxes.
Any other character string in an Input edit box means that this input is used and provides a
description of detector signals connected to this input.
Input 4 of the quad scaler is connected to a 10 kHz clock output (cf. Figure 3b). This provides
Edit boxes of X and Y corrections (linear and nonlinear) correspond to coefficients used to
calibrate and linearize the scanning system. Beam scanning is accomplished by changing the
magnetic filed which deflects the beam in X and Y directions. This is accomplished by
controlling the current delivered to two perpendicular magnetic coil pairs. In example, at
present coils parameters and the low X current (less than 0.5 A), the current change of 5 mA
causes beam deflection of about 1 micron.
The remaining edit boxes are self-descriptive. The difference between OK and OK & Save
buttons is that OK stores the actual parameters for the current session only, while OK & Save
writes them to initialization file. One should mention also the Test Mode checkbox which is
provided for allowing a convenient way of the system testing. When checked, it disables all
system hardware calls.
It is not practical to use a Setup window to change scanning parameters during normal work
of the system. While the coefficients like linear / nonlinear corrections or CAMAC blocks
positions will not change frequently, the other parameters like scan size or pixel time must
sometimes be adjusted many times during the measuring session. Therefore a separate panel
window is provided, launched automatically during program start (or accessible through menu
item Scanning / Control Center).
♣ Control Center window is shown on the following figure:
Figure 7. Scanning parameters window.
In the top left part of the window a map is
displayed which main task is to show a momentary
position of a beam during scanning and (optionally)
a secondary electrons image of the scanned area. In
the Figure 7 an example secondary electrons image
of calibration grid is displayed. The example image
shows severe nonlinearity of the beam deflecting
system and was used as a base of scanning system
linearization. Map is “clickable” – the topmost edit
box (XY Coordinates) displays the XY position and
Z readout (counts number) corresponding to a
position of mouse click.
Small edit boxes (read only) located to the right of
the map show the actual scan size, calculated time
of scanning corresponding to present settings and
the required number of beam passes through the
scanned area.
Horizontal sliders allow for easy adjustment of the
five main scanning parameters.
The lower part of the Control Center window is
occupied by ten buttons. Their functions are as
• Go Online – starts a time-critical application
cmb_w32.exe (written in C/C++ language)
responsible for beam scanning, detectors data
acquisition and online display. During cmb_w32
execution a new window is displayed (similar to main CMB window, but with much faster
• Special – starts the same cmb_w32.exe application but in specialized scanning mode
(foreseen for beam lithography).
• Set X/Y Position – set horizontal/vertical shift of the beam position on target. The function
is performed immediately after pressing the button. This function is not needed for normal
scanning as beam shifts (determined by X/Y Shift sliders) are applied automatically before
scan starts.
• Line Scan X/Y – operation similar to normal scanning mode (Go Online), but in this case
the scan is performed along the single horizontal or vertical line only.
• Scaler Map – displays the map obtained by correlating scaler readouts (usually the
registered secondary electrons number) with the position of the beam on target. The user
decides which scaler should be displayed.
• Set Defaults – re-reads the default scan parameters from the initialization file.
• Pass No – determines number of beam passes over the scanned surface needed for
completing the measurement. After setting the Pass No the acquisition time of experiment is
calculated and displayed.
• Acq. Time – sets the maximum acquisition time for a measurement. This value does not
affect other scan settings with the exclusion of Pass No which is automatically adjusted if
Minimal Acq. Time is determined by the product of Pixel Time × Pixels × Pixels.
♣ Menu Analyze
This menu position gives access to the following options:
• Experimental Data displays all of the scanning parameters of the experiment displayed
currently in the main window. This includes e.g. date and time of experiment, all scanning
parameters and corrections, detectors and scalers which were active during the measurement
and the names of event files.
• Normalize allows for easy spectrum normalization by simple channel contents
• Elemental Map provides visualization of surface distribution of particular element, defined
by the registered x-ray energy. To specify energy of interest the user must first define the
corresponding region of interest (ROI).
• QS –> Line and Map–> Line options are useful particularly for the test phase of
microbeam development and provide one–dimensional projection of the scaler or ROI map.
• Background subtraction allows for correction of the displayed map by removing the
calculated background.
[1] V.Khomenko, S.Lebed, S.Mordik, Nucl. Instrum. and Meth. B 130 (1997) 86.
[2] S.Lebed, M.Cholewa, Z.Cioch, B.Cleff, P.Golonka, D.M.Jamieson, G.J.F.Legge,
6àD]DUVNL$3RWHPSD&6DUQHFNL=6WDFKXUDNucl. Instr. and Meth., B 158 (1999) 44-47.
[3] S. Lebed, M.Cholewa, Z.Cioch, R.Hajduk -/HNNL $3RWHPSD =6WDFKXUD -6W\F]H B.Sulkio–&OHII 6àD]DUVNL 60DUDQGD &6DUQHFNL =6]NODU] 3URF RI ;;;,9 =DNRSDQH
School of Physics, eds. ($*|UOLFK$73 G]LZLDWU.UDNyZS
[4] Tcl/Tk version 8.3, http://www.scriptics.com
[5] SWIG version 1.1, http://www.swig.org
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