The Risø software suite

The Risø Reader is supported by full-featured set of programs both for operating the reader and processing the measurement data. Roughly the software can be grouped into these functional types:

• software that interacts directly with the Reader hardware
  • Sequence Editor
  • Control program
  • software embedded in the Controller box and the DASH
• main tool for general data analysis and equivalent dose estimation
  • Analyst
• more specialised tools for e.g. preprocessing and extracting ROI curves from multidimensional data
  • Viewer+
  • Viewer
  • PTanalyse
  • RLanalyse
  • XRFanalyse
• utilitities, typically only used on recommendation from Risø for a specific installation and purpose
  • CorrSGbin
  • DTcorrChange
• 3rd party drivers and programs needed by some attachements, like
  • XRF
  • Sample camera
  • Photon timer
  • EMCCD
  • Spectrometer

Some guiding principles underlie all the software:

• Comprehensive documentation is available in user manuals and online help files.
• Together with the documentation a large and diverse set of example data makes it possible to learn how to operate the software.
• Data export features are available at all relevant places in the programs. This means that you are not limited to perform data analysis and visualisations in the programs provided by Risø, only. Examples of other tools routinely used are: Origin, Matlab, Excel or R (e.g. with the Luminescence package). At all stages of processing data can be exported in standard file formats like CSV or BIN. You can directly access or export:
  • the raw data (e.g. PMT curves or EMCCD images)
  • preprocessed data (e.g. EMCCD images with cosmic ray noise removed)
  • ROI extracted data (e.g. POSL curves from photon timer data)
  • the data underlying the graphs shown in the programs (e.g. a large data set that has been binned to make the size manageable)
  • intermediate results in an analysis process, e.g. integral or normalised values
  • the final analysis results as summaries  including statistical information
• Flexible graphing. Most of the graphs shown in the programs can be customised in many ways, e.g. zooming, scrolling, editing of text labels, etc. It is also possible to compare data by plotting multiple curves in the same graph.
• Installation is made easy by utilising an installer program. The software will only run in a Windows environment which can be an emulated one on a Mac. A typical installation requires minimal IT knowledge. Even the installation of 3rd party drivers and programs is handled by the main Risø installer. There are three main choices for the installation type:
  • Typical - essentially only the Sequence Editor and Analyst for a basic Reader configuration. This is also the option to use for an office PC that will be used to prepare sequences and analyse results.
  • All - all programs, utilities and 3rd party software. This is only recommended for demonstration purposes. On a lab PC connected to the Reader you should only install what is required by using the Custom option.
  • Custom - use this option if the reader has attachments that requires extra drivers or specialised analysis software.

Sequence Editor

Despite the name, enabling editing of sequence files is actually only one half of the responsibilities of the Sequence Editor program, the other half is executing the sequences at runtime.

Editing sequences

Sequence files are edited in a spreadsheet-like environment that has proven itself to be very convinient while still allowing the user to control all the details of the measurements. Each cell can hold a single command that can be executed for any position on the sample wheel. Many of the commands are highly configurable with many parameters. But dedicated and consistent dialog boxes for each command provide help to the user in the form of input validation, context-sensitive help, graphical representations, etc.

The types of luminescence measurement methods directly supported by commands includes:

• TL
• OSL/IRSL/BLSL
• LM-OSL
• POSL including photon timer data acquisition
• Single grain OSL
• Single grain LM-OSL
• TOL
• RL
• XRF

A special user-defined command allows nonstandard or experimental measurements to be constructed by the end-user. Please, see the section on Controller software below.

Other types of non-data collecting instructions specified in sequence cells are: irradiation, illumination, preheating, pausing and taking sample pictures.

Sequence editing can be done on an office PC that is disconnected from the reader. This is made possible by describing the reader configuration in settings files that can be copied between PCs.

+ nitrogen, vacuum

+ time estimation

+ graphs while recording

Running sequences

During runtime the sequence editor controls and acquires measurement data from a long list of equipment. Most of this is done in cooperation with software embedded in the Controller box but some equipment is controlled directly from the PC - typically through a USB connection). The main units, that are controlled by software, are:

• In the base reader
  • the sample wheel and sample lift
  • sample heating
  • vacuum and nitrogen flow
• In the DASH
  • detector changer
  • filter changer
  • stimulation light sources: blue/green/IR LEDs, external (e.g. violet laser)
  • EMCCD focusing
• Irradiation source
  • beta
  • alpha
  • x-ray
• Detectors
  • PMT
  • EMCCD camera (USB )
  • Spectrometer (2 USB)
• Other attachments
  • The single grain box
  • XRF (2 USB)
  • Sample camera (USB)

The Controller software

Normally you do not care about the software running inside devices. But the Controller software has a published interface to the outside world that makes it very valuable on its own right ...

The Sequence Editor connects to reader hardware, sample camera, spectrometer and XRF by USB or in the case of the EMCCD camera, photon timer via PC plugin cards.

Programmable circuitry (CPLD) and hardware timers gives fast and exact timing of all stimulation and measurement events in a command.

SeqEd is responsible for … but a substantial part of the software responsible for executing a sequence is embedded in the Controller box. Here it can take advantage of direct access to purpose-designed hardware and interrupt timers for fast and …. (above).

Control without using the SeqEd: serial protocol, from LabVIEW or any programming language that allows communication on the serial port.

Some of the internal routines of the SeqEd is made available for custom scripting (inside SeqEd low-level or user-defined commands), e.g. wait for the reader to be idle, check error status, fetch and save PMT data, etc.

High-level and low-level commands:
IN TLMSLL.CMD file the high-level commands are defined in terms of the Controller low-level commands and the SeqEd low-level commands. The high-level command ‘User-defined’ (incl. dialogbox with parameters) together with the USERMSLL.CMD makes it possible for the end-user to define custom high-level commands. Typically you will copy and modify one of the predefined high-level commands from TLMSLL.CMD. Comprehensive documentation in the form of tutorials and detailed description of all the high-level and low-level commands makes customisation of commands possible for non-programmers also.

Analyst

The Analyst program is the intellectual property of Geoff Duller, Aberystwyth University.

Too feature-rich to do any justice here, excellent manual and eng. her. It is safe to say that one of the best ways to get started with equivalent dose determination is to use the resources authered by Geoff Duller and downloadable from http://users.aber.ac.uk/ggd/.

1. Read the summary "Luminescence Dating".
2. Read the Analyst manual.
3. Experiment with the Analyst program on the accompanying example data.

Supports the .SEC file in a sequence view. Can also be used to select records for analysis.

Flexible display of any of the data in a BIN file: record fields and curves, even EMCCD images.

Also supports the data external to the BIN file from newer Risø attachments: EMCCD camera and spectrometer.

A big part of Analyst is preparing data for analysis: Copy/paste/move (combining BIN files from different runs of measurements), Select (with criteria), Edit and Block edit

BIN file format

Analyst is always kept in sync with the Sequence Editor via the shared BIN file format. A BIN file contains a list of records where a record corresponds to a data acquisition command in the Sequence Editor. one of the reasons for the .SEC file (some SeqEd cells are not reflected in the BIN file e.g.)  calculates and stores values for Analyst (time between irr. and meas.)  Types of fields in a record:  

• Bin file records
  • cut/copy/paste between and inside files
  • merge files
  • new ‘handcoded’ records even of curve values
  • selection for analysis based on criteria
• Bin file record fields
  • View in main window (easy customisation of display) + sequence view
  • Edit, block edit
  • Flexi plot
• Bin file curves
  • Individual curve data incl. view point values
  • Plot multiple data
  • Normalisation of decay curves for for comparing the shapes of the curves (and also used in analysis procedures)
  • background subtraction
  • Integration of channels
• Analysis
  • curve fitting of dose response curve (multiple methods) with error calculation
  • batch processing with best practice rules (acceptance criteria) built-in
  • equivalent dose determination (Multiple Aliquot De (both regeneration and additive dose methods), )
  • g-values for anomalous fading

Viewer+

Used for preprocessing (cleaning and ROI curve extraction) of EMCCD and spectrometer data.

As much as possible the recorded data from measurements are stored in the BIN file, but some attachments (spect, emccd, photon timer) produces multidimensional data that does not fir into  the exclusivelely curve type binary data of the BIN file. These are stored externally to the BIN file in subfolders.

Viewer

The Viewer program is the original measurement data visualisation and analysis program. It predates Analyst which has almost completely superseded it. The only reason that the Viewer program has not been completely deprecated is that allows a BIN file to be constructed completely by hand. You can add records and specify the individual points of curve data. This feature can be used to construct data for testing analysis routines in e.g. Analyst or R with the Luminescence package.

The Control program

Mainly used by technicians during installation and for trouble-shooting:

• operate different hardware components individually
• controller software upgrade
• calibration
• reading of error status
  setting of Controller parameters/configuration

but can be useful for others to perform simple and isolated tests of the different parts of the Reader (e.g. sample lift, sample wheel positioning, detector and filter changer, stimulation light on/off)

PTanalyse

• Postprocessing of the timestamped log files of photon arrival times from the photon timer attachment
• 3D surface plots
• binning in multiple dimensions
• POSL curve, interval extraction, graphing and exporting (BIN/TXT)
• Photon arrival time distribution, interval extraction, graphing and exporting (BIN/TXT)

Photon timer recording is an extension of normal POSL measurement. The detection time of each individual photon is recorded in a file with a proprietary format. The first task for the PTanalyse software is to read these files and make the contents available for analysis in standard software like Excel. Because of the very high resolution of photon timer (e.g. 250 ps) binning is needed to get the data scaled down to a size that is manageable for plotting and analysis. This plot from PTanalyse shows the result of binning:

<image>

Time in this plot is progressing first from left to right and then from back to front. The total measurement time is 200 s which has been binned into 50 channels of 4 s each with a binning factor of 18200. The parameters for the pulse stimulation light source for this measurement were on-time = 20 us and off-time = 200 us. The pulse period of 220 us has been binned into 134 bins of 1.64 us each with a binning factor of 16384 (2^14)

You can also change the axes to display time instead of bin numbers:

<image>

Once you have found a suitable binning setting using the surface plot, you can export the underlying data to a CSV file or you can continue in PTanalyse to extract ROI curves with the POSL curve and Photon arrival time distribution functions.

The POSL curve feature allows you to see the PMT counts decay curve in up to five intervals defined in the pulse stimulation period.

<POSL image>

This figure shows two curves for the intervals 25-29 us and 25-29 us. The stimulation pulse was on from 0 to 20 us in the entire pulse stimulation period od 220 us. This is a more flexible alternative to gating of the PMT signal with the POSL command and Pulsed OSL attachment without the photon counter hardware.

The Photon arrival time distribution feature is slicing the POSL surface plot in the other dimension compared to the POSL curve feature.

<PATD image>

The figure shows how the profile of the arrival time distribution within the stimulation pulse period has changed through the first 10 secs of the total measurement time of 200 s.

RLanalyse

The RLanalyse program is used in connection with the BIN files produced by the RL attachment. It will make a curve fitting between to measurements: one for the natural signal and one for the bleached signal. Basically it calculates how many seconds the natural decay curve should be shifted to align with a section of the bleached decay curve.

The RL signal is already recorded as a normal PMT count decay curve in the BIN file by the Seq Ed, so there is no need for conversion, or any other preprocessing. The only purpose for the RLanalyse program is to …

XRFanalyse

The XRFanalyse is used to analyse spectrums recorded by the XRF attachment in BIN files. The main analysis result is a ternary diagram showing the composition of feldspar samples.

The DTCorrChange utility program

Dead time for PMT is the time after each pulse where the system is not able to detect another pulse. Statistical methods can be used to derive a formula for correcting the measured count. The Sequence Editor has dead time correction builtin (enabled in the System Options dialogbox). The dead time value in ns is measured by Risø and can be entered in the System Options dialog box. If you do not want to use dead time correction in the Sequence Editor (for one thing, you lose the original count values from the PMT). DTCorrChange is a stand-alone utility that can add or remove dead time correction from all the records in a BIN file. You should enter the dead time value supplied by Risø measured specifically for your PMT.

The dead time correction formula is explained in the Sequence Editor manual. Here is a table showing the effect of dead time correction using this formula for four different dead time values.

The CorrSGbin utility program

If you have been advised by Risø to correct single grain BIN files for beta source non-uniformity you should use the CorrSGbin program together with a CSV file containing a correction matrix supplied by Risø based on analysis of a GAF film exposure.