Hardware Guide iXon Ultra Version 1.1 rev Jan 2013 andor.
iXon Ultra Table of Contents TABLE OF CONTENTS SAFETY AND WARNINGS INFORMATION 12 SAFETY AND WARNING SYMBOLS 13 MANUAL HANDLING 13 SHIPPING AND STORAGE PRECAUTIONS 13 SECTION 1: INTRODUCTION TO IXON ULTRA HARDWARE 14 1.1 TECHNICAL SUPPORT 14 Europe 14 USA 14 Asia-Pacific 14 China 14 1.2 DISCLAIMER 15 1.3 TRADEMARKS AND PATENT INFORMATION 15 1.4 COMPONENTS 16 1.4.1 Camera description 17 1.4.2 Camera Power Supply Unit 18 1.4.3 Software 18 Version 1.
iXon Ultra Table of Contents 1.5 SPECIFICATIONS 19 1.6 ACCESSORIES 19 1.7 SAFETY PRECAUTIONS AND MAINTENANCE 20 1.7.1 Care of the camera 20 1.7.2 Regular checks 21 1.7.3 Annual electrical safety checks 21 1.7.4 Replacement parts 21 1.7.5 Fuse replacement 21 1.7.6 Working with electronics 22 1.7.7 Condensation 22 1.7.8 Dew Point graph 23 1.7.9 EM Gain ageing 24 1.7.10 Minimizing particulate contamination Version 1.
iXon Ultra Table of Contents SECTION 2: INSTALLATION 26 2.1 INSTALLING THE HARDWARE 26 2.1.1 26 2.2 PC requirements INSTALLING ANDOR SOLIS SOFTWARE - WINDOWS O/S (XP/VISTA/SEVEN) 27 2.3 NEW HARDWARE WIZARD 30 2.4 CONNECTORS 32 2.5 WATER PIPE CONNECTORS 33 2.6 MOUNTING POSTS 34 2.7 COOLING 35 2.8 STARTUP DIALOG 36 Version 1.
iXon Ultra Table of Contents SECTION 3: FEATURES AND FUNCTIONALITY 37 3.1 EMCCD OPERATION 37 3.1.1 Structure of an EMCCD 37 3.1.2 EM Gain and Read Noise 39 3.1.3 EM Gain ON vs EM Gain OFF 40 3.1.4 Multiplicative Noise Factor and Photon Counting 42 3.1.5 EM Gain dependence and stability 44 3.1.6 RealGainTM : Real and Linear gain 45 3.1.7 EM Gain Ageing: What causes it and how is it countered? 46 3.1.8 Gain and signal restrictions 47 3.1.9 EMCALTM 47 3.2 3.3 COOLING 48 3.2.
iXon Ultra Table of Contents 3.3.6 3.4 Binning and Sub Image options 55 ACQUISITION OPTIONS 57 3.4.1 57 Capture Sequence in Frame Transfer (FT) Mode 3.4.1.1 Points to consider when using FT Mode 3.4.2 58 Capture Sequence in Non-Frame Transfer Mode (NFT) with an FT EMCCD 59 3.4.2.1 Points to note about using an FT EMCCD as a standard EMCCD 60 3.4.3 3.5 Capture Sequence for Fast Kinetics with an FT EMCCD 61 3.4.3.1 Points to consider when using Fast Kinetics mode 61 3.4.
iXon Ultra Table of Contents 3.5.3.2 External (FK) 75 3.5.3.3 External Start (FK) 76 3.6 SHUTTERING 77 3.7 COUNT CONVERT 78 3.8 OPTACQUIRE 79 3.8.1 80 3.9 OptAcquire modes PUSHING FRAME RATES WITH CROPPED SENSOR MODE 81 3.9.1 82 Cropped Sensor Mode Frame Rates 3.10 ADVANCED PHOTON COUNTING IN EMCCDS 3.10.1 Photon Counting by Post-Processing 3.11 SPURIOUS NOISE FILTER Version 1.
iXon Ultra Table of Contents SECTION 4: HARDWARE 87 4.1 EMCCD TECHNOLOGY 87 4.1.1 What is an Electron Multiplying CCD? 87 4.1.2 Does EMCCD technology eliminate Read Out Noise? 87 4.1.3 How sensitive are EMCCDs? 87 4.1.4 What applications are EMCCDs suitable for? 88 4.1.5 What is Andor Technology's experience with EMCCDs? 88 4.2 EMCCD SENSOR 89 4.3 VACUUM HOUSING 90 4.3.1 91 Thermoelectric cooler 4.4 USB 2.0 INTERFACE 92 4.5 OUTGASSING 93 4.6 EXTERNAL I/O 93 4.
iXon Ultra Table of Contents SECTION 5: TROUBLESHOOTING 95 5.1 UNIT DOES NOT SWITCH ON 95 5.2 SUPPORT DEVICE NOT RECOGNISED WHEN PLUGGED INTO PC 95 5.3 TEMPERATURE TRIP ALARM SOUNDS (CONTINUOUS TONE) 95 5.4 CAMERA HIGH FIFO FILL ALARM 96 5.5 USE OF MULTIPLE HIGH SPEED USB 2.0 I/O ON ONE CAMERA 96 Version 1.
iXon Ultra Section Title APPENDIX 98 A.1 GLOSSARY 98 A.1.1 READOUT SEQUENCE OF AN EMCCD 98 A.1.2 ACCUMULATION 99 A.1.3 ACQUISITION 99 A.1.4 A/D CONVERSION 99 A.1.5 BACKGROUND 99 A.1.6 BINNING 99 A.1.7 COUNTS 99 A.1.8 DARK SIGNAL 99 A.1.9 DETECTION LIMIT 100 A.1.10 EXPOSURE TIME 100 A.1.11 FRAME TRANSFER 100 A.1.12 NOISE 101 A.1.12.1 Pixel Noise 101 A.1.12.1.1 Readout Noise 101 A.1.12.1.2 Shot Noise 101 A.1.12.1.2.A Shot Noise from the signal 101 A.1.12.1.2.
iXon Ultra Section Title A.1.16 SCANS (KEEP CLEAN AND ACQUIRED) 103 A.1.17 SHIFT REGISTER 103 A.1.18 SIGNAL TO NOISE RATIO 103 B MECHANICAL DIMENSIONS 104 C DECLARATION OF CONFORMITY 105 D HARDWARE AND SOFTWARE WARRANTY SERVICE 107 D.1 Service Description 107 D.2 Access to Service 107 D.3 Hardware Remediation 108 D.4 Software Remediation 109 E THE WASTE ELECTRONIC AND ELECTRICAL EQUIPMENT REGULATIONS 2006 (WEEE) 109 Version 1.
iXon Ultra Safety and Warnings Information SAFETY AND WARNINGS INFORMATION PLEASE READ THIS INFORMATION FIRST 1. To ensure correct and safe operation of this product, please read this guide before use and keep it in a safe place for future reference. 2. If the equipment is used in a manner not specified by Andor, the protection provided by the equipment may be impaired. 3.
iXon Ultra About the Andor iXon Ultra SAFETY AND WARNINGS SYMBOLS The following are explanations of the symbols found on this product: This product has been tested to the requirements of CAN/CSA-C22.2 No. 61010-1, 2nd edition, including Amendment 1, or a later version of the same standard incorporating the same level of testing requirements The iXon Ultra camera head requires a Direct Current (DC) supply.
iXon Ultra Introduction to iXon Ultra Hardware SECTION 1 - INTRODUCTION TO IXON ULTRA HARDWARE Thank you for choosing the Andor iXon Ultra. You are now in possession of a revolutionary new Electron Multiplying Charge Coupled Device (EMCCD), designed for the most challenging low-light imaging applications. This manual contains useful information and advice to ensure you get the optimum performance from your new system.
iXon Ultra Introduction to iXon Ultra Hardware 1.2 - DISCLAIMER The information contained herein is provided "as is" without warranty, condition or representation of any kind, either express, implied, statutory or otherwise, including but not limited to, any warranty of merchantability, noninfringement or fitness for a particular purpose.
iXon Ultra Introduction to iXon Ultra Hardware 1.
iXon Ultra Introduction to iXon Ultra Hardware 1.4.1 - Camera description The iXon Ultra camera is shown below. The camera has evolved from the iXon and iXon3 systems, with the introduction of a USB 2.0 interface instead of the previous proprietary interface and PCI card. The camera builds on the strengths of the iXon3 including the high performance vacuum assembly and much of the camera triggering and control logic.
iXon Ultra Introduction to iXon Ultra Hardware 1.4.2 - Camera Power Supply Unit The iXon Ultra system is designed to be powered from an SW4189 external PSU (Andor P/N PS-90) as shown in Figure 2. This requires an AC mains input between 100-240 V, 47-63 Hz and a maximum supply current of 1.6 A. The output of the SW4189 is 12 V DC at 9 A maximum. However the maximum camera power consumption is 12 V at 6 A = 72 Watts. The SW4189 PSU is fitted with an IEC connector for the electrical supply input.
iXon Ultra Introduction to iXon Ultra Hardware 1.5 - SPECIFICATIONS PARAMETER SPECIFICATION Power supply ratings 100 - 240 V, 47 - 63 Hz, 1.6 A Location to be used Indoor use only Altitude Up to 2000 m Operating temperature range 0°C to 30°C Storage temperature -20°C to +55°C Operating relative humidity < 70% non-condensing Overvoltage category CAT II Pollution degree 2 Ingress protection rating IP20 Cooling water flow rate > 0.75 litre/minute Control interface USB 2.
iXon Ultra Introduction to iXon Ultra Hardware 1.7 - SAFETY PRECAUTIONS AND MAINTENANCE 1.7.1 - Care of the camera WARNINGS: 1. The camera is a precision scientific instrument containing fragile components. Always handle with the care necessary for such instruments. 2. There are no user serviceable parts inside the camera. If the head is opened the warranty will be void. 3. The camera should be mounted so that the mains supply can be easily disconnected.
iXon Ultra Introduction to iXon Ultra Hardware 1.7.2 - Regular checks The state of the product should be checked regularly, especially the following: • The integrity of the enclosure • Any water hoses used • The AC/DC External Power Supply • The mains cable WARNING: Do not use equipment that is damaged. 1.7.3 - Annual electrical safety checks It is advisable to check the integrity of the insulation and protective earth of the product on an annual basis, e.g. U.K.
iXon Ultra Introduction to iXon Ultra Hardware 1.7.6 - Working with electronics The computer equipment that is to be used to operate the iXon Ultra should be fitted with appropriate surge/EMI/RFI protection on all power lines. Dedicated power lines or line isolation may be required for some extremely noisy sites. Appropriate static control procedures should be used during the installation of the system. Attention should be given to grounding.
iXon Ultra Introduction to iXon Ultra Hardware 1.7.8 - Dew Point graph The relationship between Relative Humidity and Dew Point at varying Ambient Temperature is shown in Figure 3. This can be used to calculate the minimum temperature the cooling water should be set to.
iXon Ultra Introduction to iXon Ultra Hardware 1.7.9 - EM Gain ageing It has been observed that some EMCCD sensors, more notably in cameras that incorporate L3Vision sensors from e2v, are susceptible to EM Gain fall-off over a period of time. This ageing effect applies to any EMCCD camera manufacturer that incorporates L3Vision sensors into their cameras. The Andor iXon Ultra 897 model uses an L3Vision sensor.
iXon Ultra Introduction to iXon Ultra Hardware 1.7.10 - Minimizing particulate contamination It is important that particulate contamination of the exterior of the camera window is kept to a minimum, such that images are kept free of ‘shadowing’ particles directly in the optical path. The iXon Ultra range comes equipped with an internal C-mount shutter.
iXon Ultra Installation SECTION 2: INSTALLATION 2.1 - INSTALLING THE HARDWARE 2.1.1- PC requirements Install the camera Software before first connecting the camera – this will ensure that USB drivers are available when required. There are no restrictions on the order in which components are connected. It is best to allow a few seconds from camera power on (using the button or a mains switch) to starting Solis in order for the camera to be recognised by the PC. • 3 GHz Quad Core or 2.
iXon Ultra Installation 2.2 - INSTALLING ANDOR SOLIS SOFTWARE - WINDOWS O/S(XP/VISTA/SEVEN) 1. Terminate and exit any programmes that are running on the PC. 2. Insert the Andor CD. The InstallShield Wizard now starts. If it does not start automatically, run the file setup.exe directly from the CD then follow the on-screen prompts e.g.: 3. Click Next > and the following dialog box appears: 4.
iXon Ultra Installation 5. Select iXon Ultra, then click Next> and the following dialog box appears: 6. Click Next > (alternatively, click on Browse…, choose your own shortcut destination then click Next >). 7. Select (or de-select) the additional tasks to be performed during the set-up, then click Next>: Version 1.
iXon Ultra Installation 8. Click Install to continue with the installation (or click
iXon Ultra Installation 2.3 - NEW HARDWARE WIZARD When the first iXon Ultra camera is connected to a PC for the first time, the Found New Hardware Wizard screen will appear, e.g.: 1. Select the ‘No, not this time only’ option then click Next> and the following screen appears: 2. Select the ‘Install from a list or specified location (Advanced)’ option then click Next>. The following screen appears: 3.
iXon Ultra Installation 4. The installation wizard runs, e.g.: 5. When hardware installation is complete, the following screen appears: 6. Click the Finish button to complete the installation. NOTE: If the camera is connected to a different USB port, steps 1 – 6 will have to be repeated on the first connection only. This is a feature of how Windows deals with the USB interface. On the first startup of Solis, you may be required to direct the software to the iXon Ultra drivers.
iXon Ultra Installation 2.4 - CONNECTORS Figure 4: iXon Ultra connectors The Power connection is for the Power Supply Unit (PSU) described in Section 1.4.2 on page 18. Note the connector has a locking action. The USB should be connected to the PC with the supplied USB 2.0 cable – this type (with cable ferrite) was used during EMC testing. An alternative cable with locking adaptor is available. The iXon Ultra is supplied with an ACZ-03463 cable for the external I/O connector.
iXon Ultra Installation 2.5 - WATER PIPE CONNECTORS Two barbed coolant hose inserts are supplied as standard with the iXon Ultra camera, suitable for connection to 6 mm (0.25”) internal diameter soft PVC tubing / hose. The recommended tubing should have 10 mm (0.4”) outside diameter, i.e. a wall thickness of 2 mm (0.08”). Alternative hose dimensions and materials should be thoroughly tested to ensure a leak tight seal is achieved with the barbed inserts.
iXon Ultra Installation 2.6 - MOUNTING POSTS • Mounting posts can be fitted on all four sides of the camera. These can be used to mount the camera if the C-Mount is not used, or to mount accessories. NOTE: A bag containing two Ø1/2" x 80 mm long x 1/4-20 UNC posts is included with all kits. • There are 4 pairs of holes for the mounting posts, each with 2.0" spacing. Figure 6: Mounting post installation Version 1.
iXon Ultra Installation 2.7 - COOLING Cooling of a CCD or EMCCD sensor allows efficient reduction of dark current and unwanted silicon matrix ‘hot defects’ contributions.
iXon Ultra Installation 2.8 - START-UP DIALOG On start-up of the Solis software a dialog will appear, offering a selection of cameras currently connected to your PC, e.g.: Highlight the Andor iXon Ultra camera and click OK to continue with the selected camera. Version 1.
iXon Ultra , Features and Functionality SECTION 3 - FEATURES AND FUNCTIONALITY 3.1 - EMCCD OPERATION 3.1.1 - Structure of an EMCCD Advances in sensor technology have led to the development of a new generation of ultra-sensitive, low-light Electron Multiplying Charged Coupled Devices (EMCCDs). At the heart of your iXon Ultra camera is the latest EMCCD, a revolutionary technology, capable of single photon detection.
iXon Ultra Features and Functionality During an acquisition using a conventional Frame Transfer CCD (FT CCD), the image area is exposed to light and an image is captured. This image, in the form of an electronic charge, is then automatically shifted downwards behind the masked region of the chip before being read out. To read out the sensor, charge is moved vertically into the readout register, and then horizontally from the readout register into the output node of the amplifier.
iXon Ultra , Features and Functionality 3.1.2 - EM Gain & Read Noise As explained in Section 3.1.1, EMCCD sensors allow the detected signal to be amplified on the actual sensor itself before being readout through the output amplifier and digitized by the Analog to Digital (A/D) converter. The reason that this on-chip-multiplication process gives such a significant improvement in low-light detection is that it negates the effect of any electronic noise that may be generated by the read out electronics.
iXon Ultra Features & Functionality 3.1.3 - EM Gain ON vs EM Gain OFF Signal to Noise (S/N) plots derived from the specifications of the back-illuminated iXon Ultra EMCCDs (Figure 9), read out at 10MHz for a photon wavelength at which the Quantum Efficiency (QE) of the sensor is assumed to be 90%. Such plots are very useful to gauge at what signal intensity it becomes appropriate to use EM Gain to increase S/N.
iXon Ultra , Features and Functionality S/N plots derived from the specifications of the back-illuminated iXon Ultra EMCCDs at 1MHz (slower frame rate operation) read out either with EM Gain ON or, alternatively, through the conventional amplifier (i.e. standard CCD operation) are shown in Figure 10. Again, this plot assumes a photon wavelength at which the QE of the sensor is 90%. This figure applies specifically to models where the user has the choice of either EMCCD or conventional amplifiers.
iXon Ultra , Features and Functionality 3.1.4 - Multiplicative Noise Factor and Photon Counting It is impossible to determine the exact gain a detected signal charge traversing the EM Gain register will acquire, due to the stochastic nature of the processes which produce EM Gain. However, it is possible to calculate the probability distribution function of output charge for a given input charge.
iXon Ultra , Features and Functionality Figure 11: Signal intensity profile Within the framework of less than 1 electron falling on a pixel in a single exposure, the EMCCD can be used in Photon Counting Mode. In this mode, a threshold is set above the ordinary amplifier readout and all events are counted as single photons. In this mode, with a suitably high gain, a high percentage (>90%) of the incident photons can be counted without being affected by the Noise Factor effect. Version 1.
iXon Ultra Features & Functionality 3.1.5 - EM Gain dependence and stability EM Gain is a function of the EM voltage and of the sensor operating temperature. When the user applies gain through the software, it is the EM voltage in the gain register that is varied. As can be seen from Figure 12 below, the dependence of EM Gain on EM voltage is sharp (note the logarithmic scale).
iXon Ultra , Features and Functionality 3.1.6 - RealGainTM: Real and Linear gain Andor has successfully converted the relationship between EM Gain and the EM clock voltage setting into a linear one through a detailed analysis of the complex EM voltage dependence. The actual EM Gain can therefore be selected directly from a linear scale displayed in software. In effect one can select the best gain to overcome noise and maximize dynamic range.
iXon Ultra , Features and Functionality 3.1.7 - EM Gain Ageing: What causes it and how is it countered? As already noted in Section 3.1.5, EMCCD sensors can suffer from EM Gain ageing. This is the phenomenon whereby the EM Gain falls off over a period of time, when operating at the same clock voltage and cooling temperature.
iXon Ultra , Features and Functionality 3.1.8 - Gain and signal restrictions Part of the measures taken to prevent premature ageing of the sensor has been to use temperature compensated real gain limits, coupled with signal intensity feedback (after EM amplification). This ensures that the user is unable to apply excessive gain and/or signal, any more than is necessary to render the read noise floor negligible for a given signal intensity and readout speed.
iXon Ultra , Features and Functionality 3.2 - COOLING The EMCCD sensor is cooled using a Thermoelectric (TE) cooler. TE coolers are small, electrically powered devices with no moving parts, making them reliable and convenient. A TE cooler is actually a heat pump, i.e. it achieves a temperature difference by transferring heat from its “cold side” (the EMCCD sensor) to its “hot side” (the built-in heat sink).
iXon Ultra , Features and Functionality NOTE: The OptAcquire “Fastest Frame Rate” setting in Solis uses the fastest vertical shift speed and maximum vertical clock amplitude boost. This limits the minimum EMCCD cooling achievable. 3.2.3 Heatsink “hot side“ temperature As detailed in Section 3.2, the minimum sensor cooling depends on the temperature of the heat sink. The maximum EMCCD cooling will be achieved when the “hot side” is the coldest possible. This is usually achieved with water cooling.
iXon Ultra , Features and Functionality 3.3.1 - Sensor Pre-amp options An EMCCD sensor can have a much larger dynamic range than can be faithfully reproduced with the Analogue/ Digital converters and signal processing circuitry currently available on the market. To overcome this shortcoming, and to access the range of signals from the smallest to the largest, as well as to optimize the camera performance, it is necessary to allow different pre-amplifier gain settings.
iXon Ultra , Features and Functionality Andor recommends using the default highest value pre-amp setting (e.g. Gain3 setting of the iXon Ultra 897E giving ~ 4 e-/count @ 10MHz) for most low-light applications. Most genuinely low-light applications are not limited by well capacity, as long as sensible EM Gain settings are applied (we recommend not exceeding x500 EM Gain, except for single photon counting experiments).
iXon Ultra , Features and Functionality 3.3.2 - Variable Horizontal Readout Rate The Horizontal Readout Rate defines the rate at which pixels are read from the shift register. The faster the horizontal readout rate the higher the frame rate that can be achieved. The ability to change the pixel readout speed is important in order to achieve the maximum flexibility of camera operation, particularly in terms of dynamic range.
iXon Ultra , Features and Functionality 3.3.4 - Output amplifier selection The iXon Ultra camera incorporates dual output amplifiers, an electron multiplying output amplifier and a conventional output amplifier.
iXon Ultra , Features and Functionality 3.3.5 - Baseline Optimization 3.3.5.1 - Baseline Clamp When acquiring data, small changes in the ambient temperature and/or in the heat generation of the driving electronics within the camera may cause some drift in the baseline level. This is most often observed during long kinetic series. The iXon Ultra series employs a Baseline Clamp technique that holds the baseline to a predetermined level.
iXon Ultra , Features and Functionality 3.3.6 - Binning and Sub Image options Binning is a process that allows charge from two or more pixels to be combined on the EMCCD-chip prior to readout. Summing charge on the EMCCD, and doing a single readout, gives better noise performance than reading out several pixels and then summing them in computer memory. This is because each movement of the charge through the readout amplifier contributes to the noise.
iXon Ultra , Features and Functionality Figure 17: Vertical and Horizontal binning of two rows Step 1 Charge is built up on the sensor. Step 2 Charge in the frame is shifted vertically by one row, so that the bottom row of charge moves down into the shift register. Step 3 Charge in the frame is shifted vertically by a further row, so that the next row of charge moves down into the shift register, which now contains charge from two rows - i.e. the charge is vertically binned.
iXon Ultra , Features and Functionality 3.4 - ACQUISITION OPTIONS 3.4.1 - Capture Sequence in Frame Transfer (FT) Mode A number of acquisition modes are available for the iXon Ultra range to best suit your experimental demands. In Frame Transfer (FT) acquisition mode, the iXon Ultra can deliver its fastest performance whilst maintaining optimal Signal to Noise.
iXon Ultra , Features and Functionality 3.4.1.1 - Points to consider when using FT Mode • In this mode, there are no Keep Clean Cycles between images during an accumulation or kinetics series as they are not necessary. • This mode gives the fastest way to continually take images; however, the minimum exposure time is restricted to the time taken to read out the image from the Storage area.
iXon Ultra , Features and Functionality 3.4.2 - Capture Sequence in Non-Frame Transfer Mode (NFT) with an FT EMCCD It is also possible to operate an FT EMCCD in a Non-Frame Transfer (NFT) mode. In this mode of operation, an FT EMCCD acts much like a standard CCD. The capture sequence for this mode is illustrated here: Figure 19: Capture sequence (NFT mode) Step 1 Both Image and Storage areas of the EMCCD are fully cleared out.
iXon Ultra , Features and Functionality 3.4.2.1 - Points to note about using an FT EMCCD as a standard EMCCD • The exposure time, accumulation cycle time and the kinetic cycle time are independent. • The minimum exposure time is not related to the time taken to read out the image. • As the captured image is quickly shifted into the Storage area, even in NFT mode, the system can still be used without a mechanical shutter.
iXon Ultra , Features and Functionality 3.4.3 - Capture Sequence for Fast Kinetics (FK) with an FT EMCCD Fast Kinetics (FK) is a special readout mode that uses the actual EMCCD as a temporary storage medium and allows an extremely fast sequence of images to be captured. The capture sequence is illustrated here: Figure 20: Capture sequence (Fast Kinetics mode) Step 1 Both the Image and Storage areas of the EMCCD are fully cleaned (the Keep Clean Cycle).
iXon Ultra , Features and Functionality 3.4.4 - Keep Clean Cycles iXon Ultra cameras have a range of different Keep Clean Cycles that are run depending on the actual model and the state the camera is in. The first Keep Clean Cycle to be discussed is the one that runs while the camera is in an idle state, i.e. waiting for the PC to tell it to start an acquisition sequence. We will then look at the Keep Clean Cycle running during an internal trigger kinetics series sequence.
iXon Ultra , Features and Functionality The second type of Keep Clean Cycle is executed between individual scans in a kinetic series, and is relevant to NonFrame Transfer Mode combined with either Internal or Software Trigger. It is called the Internal Keep Clean Cycle. When the user configures a kinetics series acquisition, as well as defining the exposure time and the readout mode, they also define the number of scans to capture and the time between the scans.
iXon Ultra , Features and Functionality The third Keep Clean is the External Keep Clean Cycle. This cycle uses a different sequence of horizontal and vertical clocking, as it must be able to respond to external events extremely rapidly but at the same time keep the Image area of the sensor charge free. As can be seen from the figure below, the External Keep Clean Cycle consists of a continuous cycle of one vertical shift, both Image and Storage, followed by one horizontal shift.
iXon Ultra , Features and Functionality 3.5 - TRIGGERING OPTIONS The iXon Ultra camera has several different triggering modes. These include Internal, External (and Fast External), External Start, External Exposure and Software Trigger. Note also that many of these features require iCam technology within the camera, fuller details of which can be viewed through www.andor.
iXon Ultra , Features and Functionality 3.5.1 - Triggering options in Frame Transfer (FT) mode 3.5.1.1 - Internal Triggering (FT) This is the simplest mode of operation, in that the camera determines when the exposure happens. By monitoring the Fire output, the user can determine exactly when the camera is “exposing”. When the camera is idle, it is running the Idle Keep Clean Cycle described previously.
iXon Ultra , Features and Functionality 3.5.1.2 - External Triggering (FT) When the camera is idle, it runs the Idle Keep Clean Cycle described previously. On receipt of the Start command from the PC, the camera goes into its External Keep Clean Cycle. This cycle consists of one vertical followed by one horizontal shift, repeated continuously. The camera repeats this cycle X times, where X is the number of image rows on the sensor, before it accepts any External Trigger events.
iXon Ultra , Features and Functionality Since all iXon Ultra cameras have iCam technology, the rising edge of the external trigger can occur before the end of the previous read out, provided that the falling edge of the Fire pulse occurs after the readout has completed, i.e. the External Trigger is only accepted up to the ‘User Defined Delay Period’ before the end of the readout.
iXon Ultra , Features and Functionality 3.5.1.3 - External Exposure (FT) This mode is distinct from the triggering modes discussed previously, in that the exposure period is fully controlled by the width of the external trigger pulse. The exposure period starts on the positive edge and concludes on the negative edge. As illustrated in the timing diagrams below, the positive edge can occur either after the previous image has been completely read out, or while it is still being read.
iXon Ultra , Features and Functionality 3.5.2 - Triggering options in Non-Frame Transfer (NFT) mode 3.5.2.1 - Internal (NFT) When the camera is idle, i.e. not actively capturing images, it is repeatedly running the Idle Keep Clean Cycle. When the Start command is received from the PC, the camera will complete the current Keep Clean Cycle, and then perform sufficient vertical shifts to ensure the Image and Storage regions are completely free of charge.
iXon Ultra , Features and Functionality 3.5.2.2 - External & Fast External (NFT) In External Trigger modes, once an acquisition has been started, the camera is placed into the special clearing cycle called “External Trigger Keep Clean’, which was discussed previously. As can be seen from the figure below, the External Keep Clean Cycle runs continuously until the first external trigger event is detected; at which point the current cycle series will complete before the exposure phase starts.
iXon Ultra , Features and Functionality 3.5.2.3 - External Exposure (NFT) This mode is distinct from the triggering modes discussed previously, in that the exposure period is fully controlled by the width of the external trigger pulse. The exposure period starts on the positive edge and concludes on the negative edge. The exposure is physically ended by shifting the Image area into the Storage area. The Storage area is then readout in the normal manner.
iXon Ultra , Features and Functionality 3.5.2.4 - Software trigger (NFT) This mode is particularly useful when the user needs to control other equipment between each exposure and does not know in advance how long such control will take, or if the time taken changes randomly. With Software Trigger, the camera and software are in a high state of readiness and can react extremely quickly to a trigger event issued via software.
iXon Ultra , Features and Functionality 3.5.3 - Trigger options in Fast Kinetics (FK) mode 3.5.3.1 - Internal (FK) As Fast Kinetics uses both the Image and Storage areas as temporary storage areas, the number of options available is quite limited. The simplest mode is again Internal Trigger and, as with the internal trigger modes described previously, the system determines when the acquisition begins and then uses the exposure time defined by the user.
iXon Ultra , Features and Functionality 3.5.3.2 - External (FK) In External Trigger mode, a trigger pulse is required to start each scan in the series. The rising edge of the trigger defines the trigger event. The user can delay the start of the vertical shifting relative to the trigger event. After the delay has elapsed, the number of rows (as specified by the user) are vertically shifted. The system then waits for the next trigger to start the next scan.
iXon Ultra , Features and Functionality 3.5.3.3 - External Start (FK) External Start trigger mode is a combination of External and Internal Trigger. At the start of the capture process, the camera is running the External Keep Clean Cycle waiting for a trigger pulse to be applied to the External Trigger input. On receiving the trigger the exposure starts. The exposure period is defined by the user.
iXon Ultra , Features and Functionality 3.6 - SHUTTERING The iXon Ultra camera is supplied with a built in bi-stable shutter. This bi-stable shutter requires no power to maintain the open or closed state - so it is well suited to long exposures. The bi-stable shutter also has a longer theoretical life because of the lower energy levels used. The shutter is intended for taking background images and protecting the camera from excessive light and dust.
iXon Ultra , Features and Functionality 3.7 - COUNT CONVERT One of the distinctive features of the iXon Ultra is the capability to quantitatively capture and present data in units of electrons or photons; the conversion applied either in real time or as a post-conversion step. Photons that are incident on pixels of an array detector are captured and converted to electrons. During a given exposure time, the signal in electrons that is collected in each pixel is proportional to the signal intensity.
iXon Ultra , Features and Functionality 3.8 - OPTACQUIRE OptAcquire is a unique control interface, whereby a user can conveniently choose from a predetermined list of setup configurations, each designed to optimize the camera for different experimental acquisition types, thus removing complexity from the extremely adaptable control architecture of the iXon Ultra.
iXon Ultra , Features and Functionality 3.8.1 - OptAcquire modes Pre-defined OptAcquire modes include: Sensitivity and Speed (EM Amplifier) Optimized for capturing weak signal at fast frame rates with single photon sensitivity. Suited to the majority of EMCCD applications. Dynamic Range and Speed (EM Amplifier) Configured to deliver optimal dynamic range at moderately fast frame rates. Moderate EM Gain applied.
iXon Ultra , Features and Functionality 3.
iXon Ultra , Features and Functionality 3.9.1 - Cropped Sensor Mode Frame Rates In biological imaging, Cropped Sensor Mode can be successfully used to enhance performance, and throughput, in super-resolution ‘nanoscopic’ applications including STORM and PALMIRA. Imaging frame rates exceeding 1,000/s can be achieved with a sufficiently small crop area.
iXon Ultra , Features and Functionality 3.10 - ADVANCED PHOTON COUNTING IN EMCCDS Photon Counting in EMCCDs is a way to overcome the multiplicative noise associated with the amplification process, thereby increasing the signal to noise ratio by a factor of root 2 (and doubling the effective quantum efficiency of the EMCCD). Only EMCCDs with low noise floor can perform photon counting. The approach can be further enhanced through innovative ways to post process kinetic data.
iXon Ultra , Features and Functionality To successfully photon count with EMCCDs, there has to be a significantly higher probability of seeing a ‘photon spike’ than of seeing a dark current / CIC ‘noise spike’. The lower the contribution of this ‘spurious’ noise source to a single exposure within the accumulated series, the lower the detection limit of photon counting and the cleaner the overall image will be, as demonstrated in Figure 37 below: Figure 37: ‘Photon Counting’ vs.
iXon Ultra , Features and Functionality 3.10.1 - Photon Counting by Post-Processing As a post-processing analysis, the user holds the flexibility to ‘trial and error’ photon counting a pre-recorded kinetic series, trading-off temporal resolution vs SNR by choosing how many images should contribute to each photon counted accumulated image. For example, a series of 1,000 images could be broken down into groups of 20 photon counted images, yielding 50 time points.
iXon Ultra , Features and Functionality 3.11 - SPURIOUS NOISE FILTER It can be desirable to optionally filter spurious EM-amplified background events to give as ‘black’ a background as possible, eradicating any remaining ‘salt and pepper’ noise. It is important to utilize noise selection and filter algorithms that are intelligent enough to accomplish this task without impacting the integrity of the signal itself.
iXon Ultra Hardware SECTION 4: HARDWARE 4.1 - EMCCD TECHNOLOGY 4.1.1 - What is an Electron Multiplying CCD? Current trends in photonics are placing unprecedented demands on detector technology to perform at significantly greater levels of sensitivity and / or speed. Electron Multiplying Charge Coupled Device (EMCCD) technology has been designed to respond to this growing need and, in turn, is opening up new avenues of novel experimental design.
iXon Ultra Hardware 4.1.4 - What applications are EMCCDs suitable for? EMCCD based detectors have been designed for the most demanding of low-light, dynamic applications. These detectors have redefined the sensitivity expectations of scientific grade cameras, with a detection limit as low as single photons.
iXon Ultra Hardware 4.2 - EMCCD SENSOR The EMCCD sensor is the core enabling technology of the system. Everything else in the camera has been designed to extract the absolute best operational performance from this sensor. All EMCCD sensors in the iXon Ultra range have a frame transfer architecture. The frame-transfer EMCCD uses a two-part sensor in which one-half of the array is used as a storage region and is protected from light by a light-tight mask.
iXon Ultra Hardware 4.3 - VACUUM HOUSING Unless protected, cooled CCD sensors will condense moisture, hydrocarbons and other gas contaminants that will attack the CCD surface. If that happens, CCD performance will decline proportionally and will eventually fail. Fortunately, the integrity of the sensor can be preserved by housing it in a protective enclosure.
iXon Ultra Hardware 4.3.1 - Thermoelectric cooler The iXon Ultra range makes use of a four-stage Peltier cooling assembly, which utilizes the thermoelectric effect to rapidly cool the sensor down to the stable operating temperature. TE coolers have a cold end (in contact with the sensor) and a hot end. Heat must be efficiently dissipated from the TE cooler for effective cooling of the sensor.
iXon Ultra Hardware 4.4 – USB 2.0 INTERFACE USB 2.0 is a convenient interface standard for use with a Scientific camera, as it is designed to be “plug and play” and is available on all modern PCs, including Laptops and tablet PCs. Most modern desktop PCs will be able to support at least two iXon Ultras running at full Frame rate.
iXon Ultra Hardware 4.5 - OUTGASSING Outgassing is the release of a gas trapped in a material. It is a problem encountered in high-vacuum applications. Materials not normally considered absorbent can release enough molecules to contaminate the vacuum and cause damage to optical sensors, window coatings, etc. Even metals and glasses can release gases from cracks or impurities but sealants, lubricants and adhesives are the most common cause.
iXon Ultra Hardware 4.7 - SIGNAL DIAGRAMS iXon Ultra Input & Output Timing Hardware Figure 42: External Trigger External Trigger Input (at connector) • VIH (High level input voltage, minimum) = 2.2V • VIL (Low level input voltage, maximum) = 0.
iXon Ultra Troubleshooting SECTION 5: TROUBLESHOOTING 5.1 - UNIT DOES NOT SWITCH ON • Check power cord is plugged in and connected correctly to mains supply • If applicable, replace fuse in the supplied mains cable as detailed in Section 1.7.5 on page 21 • If the unit still does not switch on after the checks above have been carried out, contact Andor Technical Support 5.
iXon Ultra Troubleshooting 5.4 - CAMERA HIGH FIFO FILL ALARM On some systems, it has been observed that a camera will stop acquiring after approximately 1 - 10 seconds. When this occurs it has always been caused by insufficient USB bandwidth. The camera includes a buffer (FIFO) to overcome any short term bandwidth reductions, however, sustained insufficient bandwidth will always cause the buffer to overflow – regardless of what size of buffer is used.
iXon Ultra Troubleshooting To map each port, use a High Bandwidth device such as a modern USB memory stick. High bandwidth devices will only appear in an EHC section, as shown below, where one can see the USB mass storage device under “Enhanced Host Controller - 3A6A”. There is a second EHC called 3A6C. Test each physical port by placing the USB memory stick into it and record which EHC it is connected to.
iXon Ultra Appendix A.1 - GLOSSARY This glossary provides an overview of the concepts and terminology used in Andor’s EMCCD technology. A.1.1 - Readout sequence of an EMCCD In the course of readout, charge is moved vertically into the shift register then horizontally from the shift register into the output node of the amplifier.
iXon Ultra Appendix A.1.2 - Accumulation Accumulation is the process by which data that have been acquired from a number of similar scans are added together in computer memory. This results in improved signal to noise ratio. A.1.3 - Acquisition An Acquisition is taken to be the complete data capture process. A.1.4 - A/D Conversion Charge from the EMCCD is initially read as an analogue signal, ranging from zero to the saturation value.
iXon Ultra Appendix A.1.9 - Detection Limit The Detection Limit is a measure of the smallest signal that can be detected in a single readout. The smallest signal is defined as the signal whose level is equal to the noise accompanying that signal, i.e. a Signal to Noise ratio (S/N) of unity. Sources of noise are as shown hereunder: • Shot noise of the signal itself • Shot noise of any dark signal • Readout noise If the signal is small, we can ignore its shot noise.
iXon Ultra Appendix A.1.12 - NOISE A.1.12.1 - Pixel Noise The Pixel Noise is the variation in the pixel’s charge level when exposed to a constant signal flux over a significantly valid period of read levels. The pixel noise is normally expressed as the value of the Root Mean Square (rms) of these variations. NOTE: The rms value is approximately x 4 to x 6 smaller than the peak to peak variations in the level values read from the pixel.
iXon Ultra Appendix A.1.12.1.3 - Calculation of Total Pixel Noise The total pixel noise is not simply the sum of the three main noise components (readout noise, shot noise from the dark signal and shot noise from the signal). Rather, the rms gives a reasonable approximation - thus: total = sqrt (readnoise² + darkshot² + sigshot²) where: • total is the pixel noise • readnoise is the readout noise • darkshot is the shot noise of the dark signal • sigshot is the shot noise of the signal A.1.12.
iXon Ultra Appendix A.1.16 - Scans (Keep Clean and Acquired) The EMCCD is continually being “scanned” to prevent its becoming saturated with dark current (see Appendix A.1.8 on page 99). • If the scan is being used simply to “clean” the EMCCD (i.e.
iXon Ultra Appendix B - MECHANICAL DIMENSIONS Version 1.
iXon Ultra Appendix C - DECLARATION OF CONFORMITY Version 1.
iXon Ultra Appendix Version 1.
iXon Ultra Appendix D - HARDWARE AND SOFTWARE WARRANTY SERVICE D.1 - SERVICE DESCRIPTION D.1.1 The Andor Repair service provides a repair and return service for defective products supplied by Andor under a supply contract. Using this service, the original ,defective part sent in by the Customer will be, where possible, returned after repair or will be replaced. Any warranty obligation contained in an Andor supply contract will be carried out in accordance with this Repair Service. D.1.
iXon Ultra Appendix D.3 - Hardware Remediation D.3.1 If the issue cannot be resolved remotely and a fault has been diagnosed, a Return Materials Authorization (“RMA”) number will be issued. This RMA number will be valid for 30 days from the date of issue. An RMA number must be obtained from Andor prior to the return of any material. The RMA number must appear clearly on the outside of the shipping container and on return paperwork included inside the package. D.3.
iXon Ultra Appendix D.4 - Software Remediation D.4.1 During Warranty Customers have access to the Service Desk at www.andor.com/contact_us/support_request to report product defects. A Customer who has purchased their product via a reseller or third party and who believes they have a software warranty defect should in the first instance contact a representative of their seller’s product support team. D.4.2 Where as a result of the process described in 1.3.
