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PicoQuant PicoHarp 300 User Manual And Technical Data

Time-correlated single photon counting system and picosecond event timer with usb interface
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PicoHarp 300
Picosecond Histogram
Accumulating Real-time Processor
Time–Correlated
Single Photon Counting System and
Picosecond Event Timer
with USB Interface
User's Manual and Technical Data
Software Version 3.0.0.3 - October 2015

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Summary of Contents for PicoQuant PicoHarp 300

  • Page 1 PicoHarp 300 Picosecond Histogram Accumulating Real-time Processor Time–Correlated Single Photon Counting System and Picosecond Event Timer with USB Interface User's Manual and Technical Data Software Version 3.0.0.3 - October 2015...

  • Page 2: Table Of Contents

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Table of Contents 1. Introduction..............................2. Primer on Time-Correlated Single Photon Counting................5 3. Hardware and Software Installation....................... 3.1. General Installation Notes – Read This First..................13 3.2. Software Installation.......................... 3.3. Device Installation..........................3.4. Installation Troubleshooting.......................
  • Page 3 8.2.1. Interactive Histogram Mode File Format..................61 8.2.2. TTTR Mode File Format......................8.3. Technical Data........................... 8.3.1. Common Specifications......................8.3.2. Router / Control Port Connectors....................65 8.3.2.1. PicoHarp 300 Hardware Version 1.0.................65 8.3.2.2. PicoHarp 300 Hardware Version 2.0.................67 8.4. Using the PicoHarp Software under Linux..................70 Page 3...

  • Page 4: Introduction

    The PicoHarp 300E is a leaner variant targeting cost sensitive applications where some functionality is not required. The features that distinguish the PicoHarp 300 from the 300E model are support for routing de- vices for simultaneous measurements with several detectors and interfacing with external hardware via TTL marker signals.

  • Page 5: Primer On Time-Correlated Single Photon Counting

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 2. Primer on Time-Correlated Single Photon Counting In order to make use of a powerful analysis tool such as time-resolved fluorescence spectroscopy, one must record the time dependent intensity profile of the emitted light. While in principle, one could attempt to record the time decay profile of the signal from a single excitation-emission cycle, there are practical problems to prevent such a simple solution in most cases.
  • Page 6 50 to 500 kcps, newer integrated TCSPC boards can reach peak rates of several Mcps. With the PicoHarp 300, average count rates of 5 Mcps and peak rates up to 10 Mcps can be collected.
  • Page 7 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Timing Resolution The most critical component in terms of timing resolution in TCSPC measurements will usually be the detec- tor. However, as opposed to analog transient recording, the time resolution of TCSPC is not limited by the analog impulse response of the detector.
  • Page 8 MCPs can achieve timing uncertainties as low as 25 ps. Microchannel plates are in this respect an excellent match for the PicoHarp 300 but they are limited in permitted count rate and provide lower sensi- tivity towards the red end of the spectrum compared to suitably optimized APDs.
  • Page 9 Time to Digital Converter (TDC). These circuits allow not only picosecond timing but can also extend the measurable time span to virtually any length by means of digital counters. The PicoHarp 300 does not use one such circuit but two. They independently work on each input channel and provide picosecond arrival times that then can be processed further, with a lot more options than in conventional TCSPC systems.
  • Page 10 CFD at one of the inputs. The PicoHarp 300 is revolutionary in this respect, as it allows to work in forward start stop mode, even with fast lasers. This is facilitated by two design features: 1.
  • Page 11 (small negative pulses of typically –10 to –50 mV) is fed to the TCSPC electronics via a preamplifier (e.g. PAM 102 from PicoQuant). This gives pulses of –100 to –500 mV. Cabling is double shielded 50 Ω coax cable. If the detector is a SPAD module with TTL output (e.g. SPCM-AQR from Perkin Elmer or successor models from Excelitas) then an inverter/attenuator (SIA 400) must be inserted.
  • Page 12 Dead-time optimized time-correlated photon counting instrument with synchronized, independent timing channels. Review of Scientific Instruments, Vol.78, 033106 (2007) 6. Bibliography listing all publications with work based on PicoQuant instruments http://www.picoquant.com/scientific/references 7. Bibliography of publications of work using the PicoHarp 300 http://www.picoquant.com/products/category/tcspc-and-time-tagging-modules/picoharp-300-stand-...

  • Page 13: Hardware And Software Installation

    Version 3.0.0.3 of the PicoHarp 300 software is a bugfix release providing a firmware fix for all measurement modes resolving randomly and rarely occuring system errors. Version 3.0.0.2 of the PicoHarp 300 software was primarily a bugfix version but also provided a few new fea- tures:...
  • Page 14 License and Copyright Notice With this product you have purchased a license to use the PicoHarp 300 software on a single PC. You have not purchased any other rights to the software itself. The software is protected by copyright and intellectual property laws.

  • Page 15: Software Installation

    In this case you can unzip this file to a temporary hard disk location of your choice and run setup from there. In order to use the PicoHarp software with the PicoHarp 300 hardware, a suitable device driver must be in- stalled.

  • Page 16: Device Installation

    TTL marker signals. The reduced functionality is physically evident through the presence of two multi-pin connectors at the PicoHarp 300 front panel that are not present at the 300E model. If these connectors are present, do not connect anything other than dedicated hardware to these connectors. They are provided for hardware expansion (notably routing and experiment control) and must not be used otherwise.

  • Page 17: Installation Troubleshooting

    After completion of the software setup, the PicoHarp device should be listed in the Windows Device Man- ager under the class PicoQuant USB Devices. Right click My Computer > left click Properties > Device Man- ager to check if the device is free of conflicts and/or if the device driver is installed correctly. Under Pico- Quant USB Devices look for a device named PicoHarp 300 and inspect its Properties.

  • Page 18: Software Overview

    This allows you to use the software without the PicoHarp hardware, e.g. to view or print files on another computer. If the PicoHarp 300 is correctly installed and there are still hardware related errors, you can use the Win- dows device manager for troubleshooting (see section 3.4). If problems cannot be resolved, see section 7 on Problems, Tips &...
  • Page 19 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 In the top center of the display area a title line is shown. This can be double-clicked to edit the title. When editing the title, note that only the first line will appear in the display. The remaining lines are meant to be used as a file comment.

  • Page 20: The Toolbar

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 4.3. The Toolbar The toolbar is displayed across the top of the PicoHarp main window, by default this is below the menu bar. The toolbar provides quick mouse access to frequently used commands and tools. Note that some buttons may be grayed out (disabled) dependent on the installed software components and/or the state of the hard - ware.

  • Page 21: The Control Panel

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 4.4. The Control Panel The PicoHarp control panel is a dialog box for setting the parameters for hardware adjustment and data ac - quisition. It is implemented as a ‘non–modal’ dialog box, i.e. it does not have to be closed before the main window can continue.

  • Page 22: The Axis Panel

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 4.5. The Axis Panel The axis settings panel is a dialog box for setting the axis range for the histogram display in the main win - dow. It is implemented as a ‘non-modal’ dialog box, i.e. it does not have to be closed before the main window can continue.

  • Page 23: The Trace Mapping Dialog

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 4.6. The Trace Mapping Dialog The PicoHarp software can measure histograms in up to 512 memory blocks. Out of these up to 8 curves can be displayed. The Trace Mapping dialog is used to select the curves to display. It also allows to view curve details and cleanup.

  • Page 24: Specific Measurement Tasks

    In order to acquire any data, the two input channels Channel 0 (usually sync) and Channel 1 (usually photon detector) of the PicoHarp 300 must be set to match their electrical input signals. The PicoHarp input chan- nels are designed identically. Both are designed as a Constant Fraction Discriminator (CFD). They can han- dle an input pulse (negative going) peak range from 0 to −1 V for regular operation.
  • Page 25 Setting Up the Channel 1 Input As noted before, the PicoHarp 300 input channels are designed electrically identical, both with a CFD. They can handle an input voltage range of 0 to −1 V. Some SPAD detectors deliver TTL signals (positive pulses of ≈3 V) and must therefore be connected through a pulse inverter with attenuation (PicoQuant SIA 400).
  • Page 26 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 If you cannot get a stable sync rate reading of expected figures, there may be several reasons: there is no proper sync signal (voltage, polarity, pulse width, frequency) ● the Channel 0 CFD level setting is inappropriate ●...

  • Page 27: Setting Up And Running Interactive Measurements

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 5.2. Setting up and Running Interactive Measurements If you are running TCSPC measurements for the first time we strongly recommend you read our TechNote on TCSPC first (see online help or your distribution media). This will help you getting started much quicker.

  • Page 28: Routed Measurements

    TCSPC electronics. The PicoHarp 300 (but not the low cost model PicoHarp 300E) supports routing of up to four detectors. De- tectors with TTL output can be routed through the router module PHR 402. Up to four SPAD detectors with NIM output (usually PDM series from Micro Photon Devices, Italy) can be routed through the PHR 403 router.
  • Page 29 Note that the router acts as a multiplexer, so that the operation is only ‘quasi’ parallel. In particular, the four channels must share the channel 1 input of the PicoHarp 300, so that the total count rate cannot exceed that permitted by the PicoHarp channel.

  • Page 30: Using The Phr 800 Router

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 TTTR mode measurements (see section 5.4 on Time-Tagged Mode Measurements) always implicitly provide routing information if a router is used. The routing information from the PHR 40x is represented by two bits in each TTTR record, allowing the distinction of up to four routing channels.

  • Page 31: Time-Tagged Mode Measurements

    T2 Mode In T2 mode both signal inputs of the PicoHarp 300 are functionally identical. There is no dedication of input channel 0 to a sync signal. Usually both inputs are used to connect photon detectors. The events from both channels are recorded independently and treated equally.
  • Page 32 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 coming events. Even if the average read rate of the host PC is limited, bursts with much higher rate can be recorded for some time. Only if the average count rate over a long period of time exceeds the readout speed of the PC, a FIFO overrun can occur.
  • Page 33 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 age count rate. The PicoHarp software installation CD contains demo programs showing how T3 mode files can be read by custom software. The implementation of custom measurement programs requires the Pico- Harp programming library, which is available for purchase as a separate option.
  • Page 34 PicoHarp 300 can contain markers for synchronization information derived from an imaging device, e.g. a scan controller. For this purpose the control ports of the PicoHarp 300 provide three TTL inputs for synchronization signals (in addition to those for routing). Note that the low cost model PicoHarp 300E does not have this feature.
  • Page 35 Note that T2 and T3 mode files cannot be distinguished by their file extension. They both get stored as *.ptu . However, you can use the PicoQuant File Info shell extension that will be installed by the PicoHarp software setup to inspect individual header items of a *.ptu or *.phu file. This includes the measurement mode.

  • Page 36: Tttr Measurements With Real-Time Correlation

    Integrating mode and do not press reset during the measurement. If you need the correlation results you should save them here. If you need to perform further or more thorough FCS anal- ysis on the collected data you can use the SymphoTime software from PicoQuant. Page 36...
  • Page 37 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 On the right hand side there are controls for the axis ranges of the correlator display. Note that they affect only the display. Collected data is always complete, independent from the axis settings. In contrast, the se- lection box subsmpl has an effect on the correlator results.

  • Page 38: Time-Resolved Spectra

    Note that some monochromators can only be controlled through dedicated stepper motor hardware from PicoQuant or the monochromator supplier. Usually these are installed as part of a complete PicoQuant spectrometer. Please contact PicoQuant for details.
  • Page 39 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Monochromator Initialization Before use, the monochromator must be initialized. This means, it has to seek its mechanical reference posi- tion (typically determined by a micro switch). Physical calibration values are kept in a monochromator con - figuration file (monochromator.cfg) which is generated by the system supplier at the time of delivery.
  • Page 40 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 If there is a large difference between the current monochromator position and the position entered, the movement will take some time. If you wish to interrupt this process, press the Stop button. The monochro- mator immediately will slow down and stop.
  • Page 41 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 At the beginning of each TRES run, the active curve (block) will be set to 0, or to 1 if no IRF is collected. All curves that were previously collected and not saved to a file will be overwritten with new data. During a TRES run, the currently collected data will always be shown as Trace 0 (dark blue), even though the block (Trace) number is actually incremented at each wavelength step.
  • Page 42 OpenGL version 1.5 or higher. Speedy handling of large data files requires sufficient memory. Further data analysis may need to be performed by dedicated software, either custom programs or specialized solutions available from PicoQuant. Page 42...

  • Page 43: Controls And Commands Reference

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 6. Controls and Commands Reference 6.1. Main Window The Title Bar The title bar is located along the top of a window. To move the window, drag the title bar. Note: You can also move dialog boxes by dragging their title bars.

  • Page 44: Toolbar

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Panel Meters At the bottom of the main window there is a set of panel meters. The meters showing units of cps (counts per second) in their title are rate meters. The leftmost rate meter shows the sync input rate. The next meter shows the channel input rate.
  • Page 45 Notably these are: Display rate (0.1 to 1 s), Draw mode (lines, stairs), Prompt overwrite (warning be- fore overwriting existing data) and TTTR Marker Edges. The control connector of the PicoHarp 300 provides TTL inputs for synchronization signals. The markers can be recorded at the rising or falling edge of the cor - responding TTL signal.

  • Page 46: Control Panel

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 6.3. Control Panel Input Channel 0 - Zero Cross edit box and spin control Here the zero cross level of the Constant Fraction Discriminator (CFD) for the Channel 0 (sync) input can be set.
  • Page 47 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Resolution edit box and spin control Use this set of input controls to specify the acquisition resolution. Units are picoseconds (ps). Possible choices are the base resolution (4 ps) and binary multiples of this resolution (8, 16, 32, ... 512 ps). Type the desired resolution value (ps) as an integer in the edit box and press <Enter>.

  • Page 48: Axis Panel

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Restart check box If this box is ticked (checked) the measurement will automatically restart after the acquisition time has elapsed. Toggle the current setting with a mouse click. The setting is without effect in TRES mode.

  • Page 49: Trace Mapping Dialog

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Time Axis Maximum edit box and spin control Here the end of the displayed time axis can be set. Units are nanoseconds (ns). Type the value as an integer in the edit box and press <Enter>. Alternatively use the spin control (next to it) to increment or decrement the current value.

  • Page 50: Menus

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 6.6. Menus 6.6.1. File Menu The File menu offers the following commands: Opens a new data file, clears all histogram data and restores default settings.. Open Opens an existing histogram file. Save Saves a histogram file.
  • Page 51 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Save command Use this command to save the current histogram data to its current name and directory. When you save a histogram for the first time, PicoHarp displays the Save As… dialog box so you can name your file. This command is unavailable if a measurement is running.
  • Page 52 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Print Preview command Use this command to display the layout as it would appear when printed. The main window will be replaced with a print preview window in which one or two pages will be displayed in their printed format. The print pre - view toolbar offers you options to view either one or two pages at a time;...

  • Page 53: Edit Menu

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 6.6.2. Edit Menu This menu offers the following commands: Copy command Copies the currently displayed curves in ASCII format to the clipboard. This can be used to export histogram data to spreadsheet or data analysis software, e.g. the FluoFit Global Fluorescence Decay Fit Software.

  • Page 54: Help Menu

    Visit Website Opens www.picoquant.com in your browser. Visit User Forum Opens the website of the PicoQuant user forum. Request Support Provides support details and access to the support website. About PicoHarp… Displays version information of the PicoHarp software. Note: Online help (context help) on most functions, dialogs, control items etc. is available via the <F1> key.
  • Page 55 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Help Search command This command opens a browser offering a means of a full text search on words or word groups over the whole online help volume. You can enter more specific search pattern, using the operators "AND", "OR", "NEAR"...

  • Page 56: Title And Comment Editor

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 6.7. Title and Comment Editor You can use this dialog to edit the file title/comment. It can be opened via double-click on the title, via the File menu or via the Print Preview Toolbar. The text you enter here will be stored in the data file. The first line will be displayed as the file title over the histogram display area.

  • Page 57: Problems, Tips & Tricks

    USB Interface In order to deliver maximum throughput, the PicoHarp 300 uses high speed USB 2.0 bulk transfers. This is why the PicoHarp must rely on having a working USB 2.0 host interface. USB 3.0 host ports will also work.
  • Page 58 Bug Reports and Support The PicoHarp 300 system has gone through extensive testing and years of iterative improvement. Neverthe - less, it is a pretty complex product and we would like to offer you our support in any case of problems with the system.

  • Page 59: Appendix

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 8. Appendix 8.1. Warnings When the PicoHarp software is running with functional hardware it continuously collects informa- tion about the input signals and the current acquisition settings. If these settings together with the input rates indicate possible errors, the software will indicate this by means of a warning icon.
  • Page 60 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Warning Histo Mode T2 Mode T3 Mode WARNING_INP1_RATE_TOO_HIGH If you have selected T2 mode then this warning means the pulse rate at input channel 1 is higher than 5 MHz. The measurement will inevitably lead to a FiFo overrun. There are rare measurement scenarios where this condition is expected and the warning can be disabled.

  • Page 61: Data File Formats

    300 data files still carry a format version number, which is now called content version and currently has the string value “3.0”. In order to identify a PicoHarp 300 data file as a file created by and to be used by the na- tive PicoHarp software there is a tag assured content which begins with the string “PicoHarp 300“.

  • Page 62: Tttr Mode File Format

    The setup data in the file header which is similar to that in standard interactive mode files. In order to identify a PicoHarp 300 data file as a file created by and to be used by the native PicoHarp software, a pro- gram reading in these files can read the tag assured content which begins with the string “PicoHarp 300“.

  • Page 63: Technical Data

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 8.3. Technical Data 8.3.1. Common Specifications All information given here is reliable to our best knowledge. However, no responsibility is assumed for possi- ble inaccuracies or omissions. Specifications and external appearance are subject to change without notice.
  • Page 64 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Operating Enviroments Ambient temperature 15°C … 35°C 59°F … 95°F Required warm–up period ≥ 20 min Bus interface USB rev. 2.0 Recommended PC specs CPU clock ≥ 1 GHz ≥ 1 GB Operating system Windows 7⁄...

  • Page 65: Router / Control Port Connectors

    PicoHarp 300 Hardware Version 1.0 The figure below shows the pin layout of the PicoHarp 300 router/control ports as of PicoHarp 300 hardware rev. 1.0. There is a 15-pin male sub-D connector labeled 'RT'. This is the connector primarily for the PHR 402/403 routers.
  • Page 66 All other pins are used for communication with dedicated accessories (PHR 40x routers etc.) and must not be connected otherwise. Appropriate cables are available from PicoQuant. CTRL Connector While the RT connector is primarily for the connection of routers, the larger female 26 pin connector labeled 'CTRL' is for generic control signals such as markers in TTTR mode.

  • Page 67: Picoharp 300 Hardware Version 2.0

    PicoQuant for a tailored solution. The figure below shows the pin layout of the PicoHarp 300 router/control ports as of PicoHarp hardware rev. 2.0. There is a 15-pin male sub-D connector labeled 'RT'. This is the connector primarily for the PHR 402/403 routers.
  • Page 68 All other pins are used for communication with dedicated accessories (PHR 40x routers etc.) and must not be connected otherwise. Appropriate cables are available from PicoQuant. CTRL Connector While the RT connector is primarily for the connection of legacy routers, the larger DVI-I connector labeled 'CTRL' is for connecting the PHR 800 router.
  • Page 69 PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 Pins C1 through C4 accept TTL compatible synchronization signals that will be recorded as markers in TTTR mode (See section 5.4). The pins are internally pulled down, so that they are inactive when left unconnected.

  • Page 70: Using The Picoharp Software Under Linux

    PicoQuant GmbH PicoHarp 300 software v. 3.0.0.3 8.4. Using the PicoHarp Software under Linux The PicoHarp software can also be used under Linux. This requires that Wine is installed (see http://www.winehq.org). We have successfully tested with Wine 1.7.11 and 1.7.51. You can run the regular software setup as explained in section 3.2.
  • Page 71 50-udev.rules. Don't change this file as it could be overwritten when you upgrade udev. Instead, put your custom rule for the PicoHarp in a separate file. The contents of this file for the handling of the PicoHarp 300 should be: ATTR{idVendor}=="0d0e", ATTR{idProduct}=="0003", MODE="666"...

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