a flexible labview™-based data acquisition and analysis system for scanning microscopy

7
A flexible LabVIEWä-based data acquisition and analysis system for scanning microscopy Daniel H. Morse a, * , Arlyn J. Antolak a , Graham S. Bench b , Mark L. Roberts b a Sandia National Laboratories, Livermore CA 94551, USA b Lawrence Livermore National Laboratory, Livermore CA 94551, USA Abstract A new data analysis system has been developed with computer-controlled beam and sample positioning, video sample imaging, multiple large solid angle detectors for X-rays and gamma-rays, and surface barrier detectors for charged particles. The system uses the LabVIEWä programming language allowing it to be easily ported between dierent computer operating systems. In the present configuration, digital signal processors are directly interfaced to a SCSI CAMAC controller. However, the modular software design permits the substitution of other hardware with LabVIEW-supported drivers. On-line displays of histogram and two-dimensional elemental map images provide a user- friendly data acquisition interface. Subregions of the two-dimensional maps may be selected interactively for detailed analysis or for subsequent scanning. O-line data processing of archived data currently yields elemental maps, analyzed spectra and reconstructions of tomographic data. Ó 1999 Published by Elsevier Science B.V. All rights reserved. Keywords: Acquisition; Scan; Microprobe; Microscopy 1. Introduction A new nuclear microprobe, designed principally for rapid particle-induced X-ray emission (PIXE) analysis of individual particles on environmental samples, has been jointly constructed by Sandia National Laboratories and Lawrence Livermore National Laboratory [1,2]. A unique feature of this system is the very large solid angle (>1 sr), pro- vided by four 200 mm 2 IGLET_detectors – two located in front of the sample and two behind. Environmental filter samples are typically scanned with a 10 lm · 10 lm, 50 nA, 3 MeV proton beam. Rapid scan rates (>1000 pixels/s) and large scan areas (> 10 mm 2 ) reduce damage to the sample. The combination of large solid angle and relatively high beam current permits rapid location and classification of particles based on the presence of counts in specified X-ray peaks. Heavy elements whose characteristic X-ray energies lie well above the bremsstrahlung peak can be identified with only a few counts per pixel. A list of pixels sus- pected of containing particles-of-interest can be generated by specifying an X-ray energy and a threshold. The region may then be rescanned at a lower current, dwelling only on the selected pixels Nuclear Instruments and Methods in Physics Research B 158 (1999) 146–152 www.elsevier.nl/locate/nimb * Corresponding author. Fax: +1-925-294-3231; e-mail: [email protected] 0168-583X/99/$ - see front matter Ó 1999 Published by Elsevier Science B.V. All rights reserved. PII: S 0 1 6 8 - 5 8 3 X ( 9 9 ) 0 0 5 0 7 - 8

Upload: daniel-h-morse

Post on 16-Sep-2016

220 views

Category:

Documents


0 download

TRANSCRIPT

Page 1: A flexible LabVIEW™-based data acquisition and analysis system for scanning microscopy

A ¯exible LabVIEWä-based data acquisition and analysis systemfor scanning microscopy

Daniel H. Morse a,*, Arlyn J. Antolak a, Graham S. Bench b, Mark L. Roberts b

a Sandia National Laboratories, Livermore CA 94551, USAb Lawrence Livermore National Laboratory, Livermore CA 94551, USA

Abstract

A new data analysis system has been developed with computer-controlled beam and sample positioning, video

sample imaging, multiple large solid angle detectors for X-rays and gamma-rays, and surface barrier detectors for

charged particles. The system uses the LabVIEWä programming language allowing it to be easily ported between

di�erent computer operating systems. In the present con®guration, digital signal processors are directly interfaced to a

SCSI CAMAC controller. However, the modular software design permits the substitution of other hardware with

LabVIEW-supported drivers. On-line displays of histogram and two-dimensional elemental map images provide a user-

friendly data acquisition interface. Subregions of the two-dimensional maps may be selected interactively for detailed

analysis or for subsequent scanning. O�-line data processing of archived data currently yields elemental maps, analyzed

spectra and reconstructions of tomographic data. Ó 1999 Published by Elsevier Science B.V. All rights reserved.

Keywords: Acquisition; Scan; Microprobe; Microscopy

1. Introduction

A new nuclear microprobe, designed principallyfor rapid particle-induced X-ray emission (PIXE)analysis of individual particles on environmentalsamples, has been jointly constructed by SandiaNational Laboratories and Lawrence LivermoreNational Laboratory [1,2]. A unique feature of thissystem is the very large solid angle (>1 sr), pro-vided by four 200 mm2 IGLET_detectors ± twolocated in front of the sample and two behind.

Environmental ®lter samples are typically scannedwith a 10 lm ´ 10 lm, 50 nA, 3 MeV proton beam.Rapid scan rates (>1000 pixels/s) and large scanareas (> 10 mm2) reduce damage to the sample.The combination of large solid angle and relativelyhigh beam current permits rapid location andclassi®cation of particles based on the presence ofcounts in speci®ed X-ray peaks. Heavy elementswhose characteristic X-ray energies lie well abovethe bremsstrahlung peak can be identi®ed withonly a few counts per pixel. A list of pixels sus-pected of containing particles-of-interest can begenerated by specifying an X-ray energy and athreshold. The region may then be rescanned at alower current, dwelling only on the selected pixels

Nuclear Instruments and Methods in Physics Research B 158 (1999) 146±152

www.elsevier.nl/locate/nimb

* Corresponding author. Fax: +1-925-294-3231; e-mail:

[email protected]

0168-583X/99/$ - see front matter Ó 1999 Published by Elsevier Science B.V. All rights reserved.

PII: S 0 1 6 8 - 5 8 3 X ( 9 9 ) 0 0 5 0 7 - 8

Page 2: A flexible LabVIEW™-based data acquisition and analysis system for scanning microscopy

to provide better statistics in a shorter time. Thedata acquisition system also supports Rutherfordbackscattering spectroscopy (RBS), scanningtransmission ion microscopy (STIM) and ionmicrotomography (IMT) analyses [3].

Although other software systems were takeninto consideration [4±6], we developed our ownsoftware for the following reasons. First, many ofour experiments are very specialized in nature andhave speci®c performance requirements. We alsowanted to have ¯exibility in choosing the hard-ware. Finally, our previous software [7], written inC on a Sun computer, would have required signi-®cant modi®cation. We looked for a solution thatwas less tedious than programming in C, relativelyplatform independent, and adaptable to changes inexperimental demands or hardware. With thesefactors in mind, we based the data acquisitionsystem on the National Instruments graphicallyoriented programming language, G, more com-monly known as LabVIEW. LabVIEW is a well-established language that is supported on UNIX,Windows and Macintosh operating systems and isreadily ported between platforms. As a high levelgraphics-oriented language, LabVIEW has built-ingraphics displays and other graphical objects, suchas switches, numerical displays and text panels.Additionally, LabVIEW includes a library ofmathematical subroutines and other utilities, in-cluding a growing library of drivers for manykinds of hardware. Other advantages are its in-herent modularity, in that each subroutine iswritten and tested as a stand-alone program, andthat it supports multiple tasking.

2. Hardware

Although we originally intended to use analogADCs, we eventually chose to purchase a unitmanufactured by X-ray Instruments (XIA) whichcontains four sets of ampli®ers and digital ADCspackaged in a single-width CAMAC module. Ac-cording to the manufacturer, the digital ADCshave nearly half the dead time of an equivalentanalog system. The cost per ADC was also lowercompared to the analog system we considered(<$3000 in US dollars for each ADC and ampli®er

pair). A LabVIEW driver was supplied by XIA toprovide software control of all hardware parame-ters as well as list mode data acquisition. Themodule also contained a built-in counter thatcould be used to output a pixel number for eachpulse height measurement. We later discoveredseveral limitations of the XIA module. First, thereare no hardware gate inputs; gating must be donethrough software. Second, data acquisition mustbe stopped periodically to transfer the 16 k ADCdata bu�er to the computer. This is not a seriousproblem except at extremely high count rates, sinceit only increases the dead time by a few percent.Third, optimizing the 15 or so parameters for eachADC can be very tedious, since each parametermust be adjusted by editing its value in a text ®leand then collecting a spectrum. Once the param-eters are set, however, they seem to be stable. Fi-nally, there are no ``busy'' outputs for the ADCs.With our previous system, we used the ADC``busy'' output to gate the output pulses from ourcurrent integrator before sending them to the dwelltime counter in the scanning system. The resultwas a direct measurement of live-time correctedcharge, so that, allowing for some statistical vari-ation, each pixel received the same charge. Al-though the module returns an average live time foreach data bu�er, pixels with higher count rates willhave more dead time and, therefore, fewer countsthan expected. As long as the dead time is low orrelatively constant the error can be tolerated.

Fig. 1 shows a schematic representation of thedata acquisition hardware. Pulse height and pixellocation data are read from the XIA module over ahigh-speed Jorway model 73A SCSII crate con-troller, capable of transferring data at the speed ofthe CAMAC bus. The sample stage, manufacturedby Newport, uses vacuum compatible dc motorsand a linear optical encoder with closed loopfeedback to provide 1 lm positioning accuracy. Amulti-function PCI bus I/O card from NationalInstruments supplies all the other counters andDAC outputs needed for the scanning system. APCI video board was included to store images ofthe sample through any of the three video micro-scopes mounted in the chamber. All the hardwareinterfaces selected were supplied with LabVIEWdrivers.

D.H. Morse et al. / Nucl. Instr. and Meth. in Phys. Res. B 158 (1999) 146±152 147

Page 3: A flexible LabVIEW™-based data acquisition and analysis system for scanning microscopy

3. Scanning

One of six scanning modes can be selected. (1)Single-spot analysis is the simplest case with noscanning at all. (2) Rectangular two-dimensionalscanning allows the selection of scan size, pixelsize, scan center position, number of scans, anddwell time from a pop-up menu. In addition, ascan interlace ratio may be speci®ed, so that ad-jacent lines are not scanned sequentially, therebyreducing beam damage to the sample. (3) Me-chanical rastering (not yet implemented) may beselected to raster the sample instead of the beamfor scanning large areas at the expense of scanspeed. (4) Tomographic scanning is the same asrectangular scanning except that the sample isrotated after each pass. (5) Mask scanning movesthe beam sequentially to pixels located in a region-of-interest as speci®ed in a mask array. The maskis normally generated by taking a quick scan of arectangular area, then automatically selecting onlythose pixels whose counts in a speci®ed energyrange exceed a speci®ed threshold. The mask re-gion may be enlarged slightly by passing it throughan algorithm that includes all pixels bordering theoriginal mask region. (6) Finally, as an aid in

focusing, a single pair of horizontal and verticallines may be scanned across a grid or similar high-contrast target. A plot of signal intensity versusposition in each axis is updated continuously toprovide rapid feedback to the operator.

Beam positioning is accomplished simply bygenerating a sequential list of X and Y coordinatesand then passing the array to a LabVIEW driversupplied with the I/O board. In our hardwarecon®guration, the outputs of the DACs are cou-pled to high speed, high voltage ampli®ers with a®xed gain of 1000 (manufactured by Trek) whichare connected to electrostatic de¯ection plates. Thedwell time at each pixel is determined by a pro-grammable divide-by-n counter that can be drivenby current integrator pulses, clock pulses or ADCevents. For thin targets, charge is collected in a 37mm diameter by a 150 mm deep stainless steelFaraday cup, lined with graphite on the bottom toreduce the X-ray background in the chamber. Thecup is ®tted with an electron suppression ring at itsentrance. However, we ®nd no signi®cant changein beam current with the suppression voltage on oro�, indicating that very few secondary electronsare entering or leaving the cup even without sup-pression.

Fig. 1. A schematic representation of the principal hardware and signal connections of our data acquisition and scanning system.

148 D.H. Morse et al. / Nucl. Instr. and Meth. in Phys. Res. B 158 (1999) 146±152

Page 4: A flexible LabVIEW™-based data acquisition and analysis system for scanning microscopy

4. Data displays

LabVIEW o�ers a wide selection of graphicalobjects (controls and indicators) that can bedragged onto control panels as shown in Fig. 2.Each object placed on the front panel automati-cally appears as a symbol on a second ``wiringdiagram'' window where its inputs and outputs areconnected to other program elements. For exam-ple, an X±Y plot of a histogram can be imple-mented simply by dragging an icon onto the frontpanel and connecting the histogram array to thecorresponding symbol on the wiring diagram. In asimilar manner, PIXE map data can be displayedby connecting a 2D array to an intensity plot. Aplot representing the ratio of two elements can bedisplayed by selecting any two maps. Other X±Yplots can be displayed to show the sums of rows

and columns of a selected map. All the plots exceptthe histogram are displayed on separate pop-upwindows to avoid clutter on the main screen. Thefunction and appearance of any LabVIEW displaycan be set by the program or modi®ed interactivelythrough pop-up menus. For example, it is possibleto interactively change the maximum or minimumvalue on any scale, to select a logarithmic or lineardisplay, to pan or zoom the display window, or toread the value of any pixel in a map by positioninga cursor. Windows may be printed at any timeeither interactively or by program control.

5. Data processing and storage

After initializing the hardware, we initialize theLabVIEW global variables by reading a parameter

Fig. 2. A screen-captured image of the data acquisition system front panel partially obscured by two pop-up windows. One window is

a map of copper X-rays and the other represents the sum of the map values in Y for each pixel in X. The sample is a copper grid with

bars spaced at 12.5 lm used for tests of spatial resolution.

D.H. Morse et al. / Nucl. Instr. and Meth. in Phys. Res. B 158 (1999) 146±152 149

Page 5: A flexible LabVIEW™-based data acquisition and analysis system for scanning microscopy

®le from a speci®ed previous data set (by default thelast data set). Next, we wait for the user to modifyany parameters and press the start button. The scanis de®ned by four arrays: two to indicate the se-quence of X and Y scanning voltages, and two toindicate corresponding X and Y coordinates in themap display. The scanning DACs and dwell timecounter are loaded and enabled to begin scanningwith no further software control. Each time thedwell-time counter counts down to 0 it triggers thenext DAC output and also triggers a pixel counterin the XIA module. At this point two separateprocessing loops are initiated using the multi-tasking capability of LabVIEW ± one functionreads data from the ADC while the other processes

data. The XIA module is programmed to set aCAMAC LAM signal when any of the four 16kbu�ers (one for each ADC) is half full. The moduleis polled every 0.1 s, and data transfer is begunwhen the bu�er is more than half full or when 3 shave elapsed. Because the XIA module uses thesame microprocessor for data processing andtransfer, data acquisition is interrupted and thedwell time counter is gated o� during the actualdata transfer. Data is stored temporarily in a Lab-VIEW array set up as a circular bu�er until it can beprocessed. If the bu�er becomes full, data acquisi-tion will be interrupted until space is available. Fi-nally, after the scan is completed or manuallyterminated, a detailed parameter ®le is written.

Fig. 3. Cross-section of a super-conducting wire made for the proposed ITER reactor. The stranded Nb±Sn core is sheathed in a thin

layer of tantalum and a thicker layer of copper. These scans were collected in LabVIEW and analyzed o�-line with the Ion Micro-

Analysis Package (IMAP). The scan area is 0.55 mm ´ 0.55 mm, and the pixel size is 3.5 lm ´ 3.5 lm.

150 D.H. Morse et al. / Nucl. Instr. and Meth. in Phys. Res. B 158 (1999) 146±152

Page 6: A flexible LabVIEW™-based data acquisition and analysis system for scanning microscopy

The collected data are stored in three formatsin every experiment. First, an image of the listdata in each bu�er is appended to a disk ®le eachtime data are read. Second, a histogram is accu-mulated and displayed for each ADC and storedat the end of the acquisition period. Finally, maparrays are updated according to a list of pre-de-termined energy regions. A cube ®le (a ®le con-taining a sequence of histograms corresponding toeach pixel in a two-dimensional scan) is notsaved, because cube arrays can be excessivelylarge. Cube ®les or additional map ®les can begenerated and displayed, if needed, by post-pro-cessing the image ®le with LabVIEW routinesthat are similar to the data acquisition program.More quantitative o�-line analysis is performedusing the Ion Micro-Analysis Package (IMAP)which has recently been ported from UNIX to theMacintosh [8,9]. Fig. 3 shows an example of ele-mental maps generated by IMAP from PIXE datacollected by scanning the cross-section of astranded superconducting wire.

6. Performance

The detector resolution of the IGLET-X de-tector measured with the XIA module set for aGaussian time constant of 8 ls was 155 eV at 5.9keV and 1000 counts/s. The resolution measuredunder similar conditions with an analog systemwas nearly identical. We tested the throughput ofthe data acquisition system at high count ratessuitable for semi-quantitative measurementsneeded for locating particles on a large area ®lter.The maximum count rate per detector with a 2 lssecond Gaussian ®ltering time constant was about20 000 counts/s. Even at the highest rates, theresolution was better than 210 eV and the pile-upfor a spectrum with one dominant peak (alumi-num) was less than 1.5%. Our 266 MHz PowerPCdata acquisition computer was able to acquire,display and store data even at this rate (>60 kHzfrom three channels) without over-running its databu�er. We also tested the scanning system at ratesas high as 5000 pixels/s, the maximum clockingfrequency of our current integrator. Signi®cantlyfaster scanning frequencies are certainly possible,

limited mainly by the settling time of the DAC andscanning ampli®ers.

7. Conclusion

The data acquisition system we have developedsupports a wide selection of scanning, on-line datadisplay and processing options at data rates inexcess of 60 000 randomly occurring pulses persecond and can run on Windows, Macintosh orUNIX platforms. Because of the growing libraryof LabVIEW drivers, the modularity of programdesign, and the ability to test each module inde-pendently, the data acquisition system could easilybe adapted to other hardware or other data pro-cessing requirements. (Modi®cation of the soft-ware requires the purchase of a LabVIEWdevelopment license for about $2000 US.) Futureplans are to incorporate additional post-process-ing software, complete the mechanical scanningcapability, and possibly to implement analogADCs for other systems.

Acknowledgements

This work performed under the auspices of theUS Department of Energy under Sandia NationalLaboratories contract DE-AC04-94AL85000 andLawrence Livermore National Laboratory con-tract W-7405-ENG-48.

References

[1] A.J. Antolak, D.H. Morse, G.S. Bench, D.W. Heikkinen,

M.L. Roberts, E. Sideras-Haddad, Nucl. Instr. and Meth. B

130 (1997) 211.

[2] M.L. Roberts, P.G. Grant, G.S. Bench, T.A. Brown, B.R.

Frantz, D.H. Morse, A.J. Antolak, these proceedings

(ICNMTA-6), Nucl. Instr. and Meth. B 158 (1999) 24.

[3] D.H. Morse, A.J. Antolak, G.S. Bench, D.W. Heikkinen,

M.L. Roberts, E. Sideras-Haddad, Nucl. Instr. and Meth. B

130 (1997) 740.

[4] G.W. Grime, M. Dawson, Nucl. Instr. and Meth. B 104

(1995) 107.

[5] G.R. Moloney, P.M. Obrien, A. Saint, L. Witham, A.

Sakalleriou, A. Bettiol, G.J.F. Legge, Nucl. Instr. and Meth.

B 104 (1995) 114.

D.H. Morse et al. / Nucl. Instr. and Meth. in Phys. Res. B 158 (1999) 146±152 151

Page 7: A flexible LabVIEW™-based data acquisition and analysis system for scanning microscopy

[6] M. Elfman, P. Kristiansson, K. Malmqvist, J. Pallon, A.

Sjoland, R. Utui, C. Yang, Nucl. Instr. and Meth. B 130

(1997) 123.

[7] D.H. Morse, Nucl. Instr. and Meth. B 85 (1994) 693.

[8] A.J. Antolak, G.S. Bench, Nucl. Instr. and Meth. B 90

(1994) 596.

[9] A.J. Antolak, G.S. Bench, M.L. Hildner, D.H. Morse,

Nucl. Instr. and Meth. B 85 (1994) 597.

152 D.H. Morse et al. / Nucl. Instr. and Meth. in Phys. Res. B 158 (1999) 146±152