Home

A USER'S GUIDE TO

1. Exposure period Image areaclocks Storage area clocks Horizontal clocks External Trigger Fire output Start command External Keep clean running Image area shifted Horizontal clocks With global clear on 885 into storage area running Figure 33 External Trigger in non Frame Transfer mode NOTE There is no need to worry if the trigger occurs at the early phase of the keep clean cycle as the light signal will not be lost during the completion of the cycle since only one vertical shift will have occurred For pulsed light of very short duration of the order of one vertical shift the resultant image may appear to have shifted one row IXon3 SECTION 3 Page 57 p ANDOR TT eene FEATURES amp FUNCTIONALITY For the 885 range of cameras the Global Clear functionality is used to keep the image area free of charge prior to the external trigger pulse This reduces the pre trigger image smear which might be seen on other frame transfer sensors Also due to the iCam functionality of the 885 this feature can be used to allow the overlap of exposure and readout but still maintain a charge free sensor prior to the external trigger pulse see figure 34 below Idle keep clean External Keep clean Global clear used to cycle Waitingfor running i Cycle Time i keep Image area clear Start command i j Exposure period Exposure period Image area clocks Storage area clocks Horizontal
2. Page 53 AN DOR QA oreeeocoe FEATURES amp FUNCTIONALITY Since all X3 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 This enhanced trigger mode will result in a higher frame rate see figure 30 below External trigger cycle running while waiting Horizontal clocks for first trigger with Exposure period 1 Storage area read continue to run after global clear on 885 7 out phase readout completes X Global clear not active Exposure period 2 Exposure period 3 Image area clocks n i pq 0 7o X Storage area clocks Tal EUH BEE Horizontal clocks External trigger Fire output A Arm output Image area shifted First external trigger into storage area Falling edge of Fire pulse Arm signal active User settable must occur after read out is delay before readout complete completed User settable delay Second external trigger Figure 30 iCam enhanced External Trigger in Frame Transfer mode IXon3 SECTION 3 Page 54 lt ANDOR Se FEATURES amp FUNCTIONALITY 3 5 1 3 External Exposure FT External Exposure combined with Frame Transfer readout is available only on iXon 885 cameras It is not avai
3. the sensor to achieve faster frame rates and can also be used to reduce charge leakage into the image area when there is saturated signal in the frame transfer storage area e g when combining very short exposure with a slow readout speed e Horizontal readout speed Ranging between 10 MHz and 1MHz 10MHz for faster frame rates 1 MHz for best dynamic range e Pre amplifier gain Trading off reduced digitization noise versus accessing full pixel well depth e EM Conventional amplifier To choose between ultrasensitive EMCCD operation or traditional high dynamic range CCD operation the latter recommended for relatively brighter signals or when it is possible to apply long exposures to overcome read noise floor e Frame Transfer overlap Overlapped readout is used to achieve 100 duty cycle ideal for fastest frame rate measurements without switching exposure time between frames This mode should be deselected for time lapse experiments IXon3 SECTION 3 Page 66 p ANDOR Seen FEATURES amp FUNCTIONALITY Pre defined OptAcquire modes include Optimized for capturing weak signal at fast frame rates with Sensitivity amp Speed EM Amplifier single photon sensitivity Suited to the majority of EMCCD applications Dynamic Range amp Speed Configured to deliver optimal dynamic range at fast frame rates EM Amplifier Moderate EM gain applied For when it s all about speed Optimized for absolute fastest Fas
4. WU eem FEATURES amp FUNCTIONALITY OptAcquire is a unique control interface whereby a user can conveniently choose from a pre determined list of set up configurations each designed to optimise the camera for different experimental acquisition types thus removing complexity from the extremely adaptable control architecture of the iXon3 The control architecture of the iXon3 is extremely tuneable meaning the camera can be adapted and optimized for a wide variety of quantitative experimental requirements ranging from fast single photon counting through to slower scan 16 bit dynamic range measurements However successfully optimizing EMCCD technology is not a trivial exercise with various set up parameters directly influencing different camera performance characteristics OptAcquire has been designed as a unique interface whereby a user can choose from a pre determined list of nine camera set up configurations A variety of set up parameters are balanced behind the scenes through the OptAquire menu Furthermore advanced users may wish to create their own additional OptAcquire iXon3 control parameters include e EMGain This parameter has a direct bearing on both sensitivity and dynamic range e Vertical clock speed flexibility in this parameter is critical to optimizing the camera for lowest noise fastest speed minimal frame transfer smear or maximum pixel well depth e Vertical Clock Amplitude Can be employed to help over clock
5. e For low CIC Use the fastest vertical shift speed that still transfers charge correctly no image distortion without having to select excess vertical shift voltage amplitude e For maximum pixel well depth Use the slowest vertical shift speed which will give an increase in CIC e For maximum frame rate Use the fastest vertical shift speed and increase the vertical shift voltage amplitude to the minimum value that regains the full pixel well depth e To reduce vertical smearing during very short exposure use a faster vertical shift speed This vertical smearing is due to the fact that light is still falling on the image area during the short time taken to transfer the charge from the image area into the storage area If the actual exposure time is of a similar magnitude to this transfer time then as pixels are shifted vertically through brighter regions of the image they will collect extra charge which will manifest itself as vertical streaking NOTE For extremely short exposure times a fast external shutter or pulsed light source may be required e For short exposures e g 1ms with high signal count and DC illumination it may be necessary to increase the vertical clock voltage to ensure that the keep clean cycle can fully remove the extremely high saturated signal that may have accumulated during the sensor readout phase IXon3 SECTION 3 Page 38 p ANDOR A enm FEATURES amp FUNCTIONALITY 3 3 4 Output amplifier selection
6. modes selected These will be discussed later in this document Pattern repeated indefinitely Number of vertical clocks Number of horizontal clocks will depend on the number depends on the number of of rows on the sensor horizontal pixels mA yaa S Acquisition starts here Image amp storage vertical clocks Horizontal serial register clocks Software Start event Clocking pattern will depend on acquisition mode See timing diagramsthat follow A start event can occur any time during this period Figure 25 Idle Keep Clean Cycle IXon3 SECTION 3 Page 48 p ANDOR We onse FEATURES amp FUNCTIONALITY The second type of keep clean is executed between individual scans in a kinetic series and is relevant to Non Frame 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 During the time between individual scans the sensor must be kept free of charge to ensure the data captured is a true reflection of the light that fell on it during the exposure period The keep clean cycle run during this time is very similar to that described in the Idle Keep Clean Cycle on the previous page in that the cycle is one vertical followed by a series of horizontals In this mo
7. 59 3 5 2 4 Software trigger NFT 60 3 5 3 Trigger options in Fast Kinetics FK mode 61 3 5 3 1 Internal FK 61 3 5 3 2 External FK 62 3 5 3 3 External Start FK 63 IXon3 TABLE OF CONTENTS Page 4 ANDOR TABLE OF CONTENTS PAGE SECTION 3 continued 3 6 SHUTTERING 64 3 7 COUNT CONVERT 65 3 8 OptAcquire 66 3 8 1 OptAcquire modes 67 3 9 PUSHING FRAME RATES WITH CROPPED SENSOR MODE 68 3 9 1 Cropped Sensor Mode Frame Rates 69 3 10 ADVANCED PHOTON COUNTING IN EMCCDs 70 3 10 1 Photon Counting by Post Processing 72 iXon3 TABLE OF CONTENTS Page 5 ANDOR TABLE OF CONTENTS PAGE SECTION 4 HARDWARE 73 4 1 EMCCD TECHNOLOGY 73 4 1 1 What is an Electron Multiplying CCD 73 4 1 2 Does EMCCD technology eliminate Read Out Noise 73 4 1 3 How sensitive are EMCCDs 73 4 1 4 What applications are EMCCDs suitable for 74 4 1 5 What is Andor Technology s experience with EMCCDs 74 4 2 EMCCD SENSOR 75 4 3 VACUUM HOUSING 76 4 3 1 Thermoelectric cooler 77 4 4 OUTGASSING 78 4 5 CONTROLLER CARD PINOUTS 79 4 6 SMB SIGNAL DIAGRAMS 80 iXon3 TABLE OF CONTENTS Page 6 ANDOR TABLE OF CONTENTS PAGE APPENDIX 81 A1 1 GLOSSARY 81 A1 1 1 Readout sequence of an EMCCD 81 A1 1 2 Accumulation 82 A1 1 3 Acquisition 82 A1 1 4 A D Conversion 82 A1 1 5 Background 82 A1 1 6 Binning 82 A1 1 7 Counts 82 A1 1 8 Dark Signal 82 A1 1 9 Detection Limit 83
8. amp SCREWDRIVER 4 SHANK E Figure 10 Mounting post installation IXon3 SECTION 2 Page 21 ANDOR INSTALLATION During the start up sequence the operating system will detect the Andor PCI PCie controller card and a dialogue box will prompt you for the location of the device driver e Insert the CD containing the driver file With Andor Solis or iQ software this is located on the main application CD 3rd party software packages may supply a separate driver installation CD containing the Andor drivers Navigate to the Setup Information File atmcd inf e Select the device driver file and click OK e Restart the PC This completes the device driver installation e The Andor Technology PCI driver should now be shown in the Device Manager e g Device Manager olx File Action View Help t meae alga E E Andor m H Computer S Disk drives Display adapters db DVD CD ROM drives Human Interface Devices IDE ATA ATAPI controllers H Keyboards TD Mice and other pointing devices Monitors Network adapters X Ports COM amp LPT SW Processors 1 9 Sound video and game controllers System devices 2 Universal Serial Bus controllers 2 6 1 Installing Linux driver The Andor PCI PCle controller card device driver is compiled from source and installed automatically during installation of the Andor Linux SDK using the install_andor script 2 6 2 Software
9. 1 1 Internal 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 On receipt of the Start command from the PC the camera will complete the current keep clean cycle and then perform sufficient vertical shifts to ensure that the Image and Storage regions are completely free of charge The camera then starts its real exposure sequence for which the timing sequence is illustrated in the figure below The first thing to notice is that the FIRE output is high for much of the time This is because there are no keep cleans running between each acquisition and hence the exposure time starts on completion of the transfer of the Image area into the Storage area This also has the consequence that the exposure time and the cycle time are closely linked We have defined the exposure time as the time during which there are no vertical shifts occurring which also corresponds to the time during which the FIRE output will be high The other point to note is that the exposure time overlaps the read out of the image Idle keep clean cycle First image read out Waiting for Start occurs here command Exposure period Cycle time Image area clocks Storage area clocks Horizontal clocks Fire output Horizontal clocks continue
10. 7 Millennium Way 425 Sullivan Avenue Springvale Business Park Suite 3 Belfast South Windsor BT12 7AL CT 06074 Northern Ireland USA Tel 44 0 28 9023 7126 Tel 860 290 9211 Fax 44 0 28 9031 0792 Fax 860 290 9566 http Www andor com contact us support request http www andor com contact us support request Asia Pacific China Andor Technology Japan Andor Technology 7F Ichibancho Central Building Room 1116 22 1 Ichiban Cho Zhejiang Building Chiyoda Ku No 26 Tokyo 102 0082 An Zhen Xi Li Japan Section 3 Tel 81 3 3511 0659 Chaoyang District Fax 81 3 35110662 Beijing 100029 http Www andor com contact us support request China Tel 86 10 5129 4977 Fax 86 10 6445 5401 http Wwww andor com contact us support request The latest contact details for your local representative can be found on our website IXon3 SECTION 1 Page 8 ANDOR A INTRODUCTION 1 2 COMPONENTS The Andor iXon3 system comprises the following main items e Detector head hereinafter referred to as a Camera see figure 1 below e 20ff BNC SMB cables e User manuals on CD e Software disk SDK and or Solis if ordered e Andor Programmer guide to Andor Basic if ordered e Software Development Kit manual if SDK ordered e Camera specific performance booklet or sheet e ESD wrist strap NOTE This must be worn at all times when handling the PCI card e PCI PCle card CCI 22 CCI 23 or CCI 24 camera model dependent e PCI PCIe con
11. A number of the EMCCD sensors in the iXon3 range have dual output amplifiers an electron multiplying output amplifier and a conventional output amplifier This increases the versatility of the camera as the EM amplifier can be selected for fast imaging in low light conditions whilst the conventional amplifier can be selected where more light is available and a slower readout with its associated lower read noise and higher dynamic range is preferred Figure 20 below details schematically the readout structure on sensors with both output amplifiers present From this it can seen that when reading out through the EM amplifier accumulated charge will move to the right along the serial register and then into the EM gain register When the conventional output amplifier is selected the charge to be read out will move along the serial register to the left then be transferred directly into the conventional output amplifier This change in direction has the effect of producing mirror images when comparing raw data from the two output amplifiers Some software packages will automatically reverse the image orientation of one of the output amplifiers to allow direct comparison of images The user should consult their software manual to verify if this is the case Conventional output O EM output Figure 20 Sensor readout structure iXon3 SECTION 3 Page 39 p ANDOR WU emm FEATURES amp FUNCTIONALITY 3 3 5 1 Baseline Level and Basel
12. OFF 26 3 1 4 Multiplicative Noise Factor amp Photon Counting 28 3 1 5 EM Gain dependence and stability 30 3 1 6 RealGain Real and Linear gain 31 3 1 7 EM Gain Ageing What causes it and how is it countered 32 3 1 8 Gain amp signal restrictions 33 3 1 9 EMCAL 33 3 2 COOLING 34 3 2 1 Cooling options 34 3 2 2 Fan settings 34 3 3 SENSOR READOUT OPTIMIZATION 35 3 3 1 Sensor PreAmp options 36 3 3 2 Variable Horizontal Readout Rate 38 3 3 3 Variable Vertical Shift Speed 38 3 3 4 Output amplifier selection 39 3 3 5 Baseline Optimization 40 3 3 5 1 Baseline Level and Baseline Offset 40 3 3 5 2 Baseline Clamp 40 3 3 6 Binning and Sub Image options 41 3 4 ACQUISITION OPTIONS 43 3 4 1 Capture Sequence in Frame Transfer Mode 43 3 4 1 1 Points to consider when using FT Mode 44 3 4 2 Capture Sequence in Non Frame Transfer Mode with an FT CCD 45 3 4 2 1 Points to note about using an FT CCD as a standard CCD 46 3 4 3 Capture Sequence for Fast Kinetics with an FT CCD 47 3 4 3 1 Points to consider when using Fast Kinetics mode 47 3 4 4 Keep Clean Cycles 48 3 5 TRIGGERING OPTIONS 51 3 5 1 Triggering options in Frame Transfer FT mode 52 3 5 1 1 Internal FT 52 3 5 1 2 External FT 53 3 5 1 3 External Exposure FT 55 3 5 2 Triggering options in Non Frame Transfer NFT mode 56 3 5 2 1 Internal NFT 56 3 5 2 2 External amp Fast External NFT 57 3 5 2 3 External Exposure NFT
13. User selectable cropped sensor size highly intuitive software definition e The iXon3 is now available with the complementary OptoMask accessory which can be used to shield the region of the sensor outside of the cropped area If an experiment demands fast temporal resolution but cannot be constrained by the maximum storage size of the sensor as is the case for Fast Kinetics Mode of readout then it is possible to readout the iXon3 in Cropped Sensor Mode In this mode the user defines a sub array size from within the full image sensor area such that it encompasses the region of the image where change is rapidly occurring e g a calcium spark within a cell The sensor subsequently imagines that it is of this smaller defined array size achieved through software executing special readout patterns and reads out at a proportionally faster frame rate The smaller the defined array size the faster the frame rate achievable In order to use Cropped Sensor mode one has to ensure that no light is falling on the light sensitive area outside of the defined region Any light collected outside the cropped area could corrupt the images which were acquired in this mode For microscopy set ups this is now aided with an accessory called OptoMask available from Andor Cropped Sensor Mode has the end result of achieving a much faster frame rate than that obtainable in a conventional sub array ROI readout during which we would still have
14. already occurred prior to calibration and setting of the EM gain The explanation for this ageing effect is not fully understood but it is assumed that accelerating charge through the high electric fields is causing a tiny fraction of that charge to become permanently embedded in the insulator typically silicon dioxide between the EM electrode and the active silicon This slow build up of charge effectively reduces the field strength produced by the electrode The signal electrons therefore experience a lower accelerating potential which subsequently produces fewer secondary electrons from the impact ionisation process resulting in less electron multiplication and in effect a lower EM gain In order to minimise the effect of EM gain ageing it is recommended that the following guidelines are always adhered to e Do not use EM gains greater than necessary to overcome the read noise please refer to figure 13 on page 25 and figure 14 on page 26 A rule of thumb is that a gain of x4 or 5 the root mean square read noise accessible from the performance sheet is more than sufficient to render this noise source negligible In practice this can always be achieved with EM Gain of less than x300 often much less Pushing gain beyond this value would give little or no extra S N benefit and would only reduce dynamic range e Only select the extended EM gain scale of x 1000 when single photon counting and always ensure that the signal falling onto the sensor
15. amp Shutter SMB IXon3 SECTION 4 Page 80 ANDOR E APPENDIX APPENDIX A1 1 GLOSSARY If this is the first time you have used Andor s EMCCD the glossary that follows will help familiarize you with its design philosophy and some of its key terminology A1 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 The simple readout sequence illustrated below which corresponds to the default setting of the Full Resolution Image binning pattern allows data to be recorded for each individual element on the EMCCD chip Other binning patterns are achieved by summing charge in the shift register and or the output node prior to readout For further information on Binning please refer to pages 41 42 Readout sequence of an EMCCD only subset of pixels shown 1 Exposure to light causes a pattern of charge an electronic image to build up on the frame or Image Area of the EMCCD chip 2 Charge in the frame is shifted vertically by one row so that the bottom row of charge moves into the shift register 3 Charge in the shift register is moved horizontally by one pixel so that charge on the endmost pixel of the shift register is moved into the Gain register 4 Charge is shifted into the output node of the amplifier 5 The charge in the output node of the amplifier is passed to
16. 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 On completion of the exposure period the cameras performs the number of vertical shifts defined by the user and then again waits for the exposure period before the next set of vertical shifts This process is repeated until the number in the series has been captured at which point the read out starts The timing sequence is shown below and as before the Fire output envelopes the period when no vertical clocking is occurring You will also see there are no readout cycles or keep clean cycles running during the sequence hence the very fast kinetic cycle period but limited number of exposures in the series Number of vertical clocks Idle keep clean 7 depends on sub area height running with global clear on 885 l Image amp Storage area Horizontal clocks Fire output Number of repeats set Read phase Exposure time by series length Figure 37 Internal Trigger in Fast Kinetics mode iXon3 SECTION 3 Page 61 NDOR WC enm FEATURES amp 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 s
17. by Andor Technology in 2000 with the launch of our dedicated high end iXon platform of ultra sensitive cameras Essentially the EMCCD is an image sensor that is capable of detecting single photon events without an image intensifier achievable by way of a unique electron multiplying structure built into the chip EM gain can be increased to a degree It is readily adjustable in real time through the software where extremely weak signals may be detected above the read noise of the camera at any readout speed This is important because the traditional problem of combining sensitivity with speed in standard CCDs is that the two are mutually exclusive i e greater read noise detection limits result from faster pixel readout 4 1 2 Does EMCCD technology eliminate Read Out Noise System noise within modern silicon based detectors has two primary sources dark current noise and read noise The higher the noise floor on a detector the less able it is to read out the extremely weak signals associated with ultra low light imaging With thermoelectric cooling dark current noise can be reduced to negligible levels An EMCCDS ability to multiply weak signals above the detector s read noise floor by applying EM gain effectively eliminates read noise at any speed by reducing it to lt lt 1 e p s 4 1 3 How sensitive are EMCCDs Two parameters significantly influence detector sensitivity namely Quantum Efficiency QE and system noise QE is a
18. clocks External Trigger Fire output Start command Storage area read Horizontal clocks out phase running Image area shifted into storage area Figure 34 iCam enhanced External Trigger in non Frame Transfer mode 885 iXon3 SECTION 3 Page 58 p ANDOR ee FEATURES amp FUNCTIONALITY 3 5 2 3 External Exposure NFT External Exposure combined with Non Frame Transfer readout is available to all iXon3 cameras 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 On completion of the readout the external keep clean cycle is started again Idle keep clean cycle Waiting for pol Cycle Time Start command i j j Exposure period Exposure period Image area clocks Storage area clocks Horizontal clocks External Trigger Fire output TEN External Keep clean hifted running with global mage area shifte Horizontal clocks into storage area clear on 885 running Storage area read out phase Figure 35 External Exposure Trigger in Non Frame Transfer mode IXon3 SECTION 3 Page 59 lt ANDOR WO eem FEATURES amp FUNCTIONALITY 3 5 2 4 Software trigg
19. form as shot noise in that each noise type results in an increase in the variation of number of electrons that are read out of the sensor under constant uniform illumination IXon3 SECTION 3 Page 28 p ANDOR eee FEATURES amp FUNCTIONALITY Indeed multiplicative noise can be thought to contribute directly to the overall shot noise in that one should multiply the Shot Noise by the Noise Factor when calculating overall noise Simply put multiplicative noise does not in any way reduce the average signal intensity or reduce the number of photons that are detected it simply increases the degree of variation of the signal around the mean value in addition to the variation that already exists from the shot noise variation from pixel to pixel or from frame to frame This additional variation to the signal intensity is represented pictorially below in figure 15 as a signal intensity profile Shot Noise Variation Shot Noise Multiplicative Noise Variation Average Signal Intensity vh In the limit of when there is less than 1 electron falling on a pixel in a single exposure the EMCCD can be used Figure 15 Signal intensity profile 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 fraction of the incident photons 9096 can be counted without being affected by the Noise Factor effe
20. has to be a significantly higher probability of seeing a photon spike than 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 43 below A B C Standard EMCCD Image Photon Counting Photon Counting Low CIC Low CIC High CIC Standard EMCCD Image Photon Counting RO Signal to Noise 3 86 RO Signa to Noise 6 02 Figure 42 Photon Counting vs Standard EM on Imaging for very weak signals Images A B and C were recorded under identical illumination conditions identical exposure times and each with EM Gain set at x1000 The benefit of photon counting under conditions of low clock induced charge CIC is evident Images D and E are derived from a larger number of accumulated images to yield a greater measurable signal to noise ratio An identically positioned Region of Interest on each image was used to determine S N of 3 86 and 6 02 for standard and photon counted images respectively This factor improvement is in accord with the theory of Photon Counting circumventing the influence of multiplicative noise noise factor in EMCCD signals iXon3 SECTION 3 Page 71 p ANDOR MT FEATURES amp FUNCTIONALITY 3 10 1 Photon Counting by Post Processing As a post processing analysis the user hold
21. 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 As stated on the previous page the readout register is extended to include the multiplication gain register The amplification occurs in this register through the scheme highlighted below in figure 12 below When moving charge through a register there is a very tiny but finite probability that the charges being transferred can create additional charge by a process known as impact ionization Impact ionization occurs when a charge has sufficient energy to create another electron hole pair and hence a free electron charge in the conduction band can create another charge Hence amplification occurs To make this process viable EMCCD s tailor the process in two ways as follows 1 Firstly the probability of any one charge creating a secondary electron is increased by giving the initial electron charge more energy This is typically done by replacing one of the electrodes phases of this readout section with two electrodes The first is held at a fixed potential and the second is operated as normal except that much higher voltages are employed than are necessary for charge transfer alone The large electric field generated betw
22. is indeed within the regime of low numbers of photons per pixel e Turn the EM gain OFF when not in use e Try not to over saturate the EMCCD detector For simplicity and ease of use many of these guidelines have been uniquely woven into the iXon3 systems to make it difficult for the user to step outside of them and unwaringly cause accelerated sensor ageing This defence is two pronged and makes heavy use of Andor s linear and quantitative gain calibration scale RealGain described above IXon3 SECTION 3 Page 32 lt ANDOR Se FEATURES amp FUNCTIONALITY 3 1 8 Gain amp signal restrictions Part of the measures taken have been to invoke 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 Secondly when not actually acquiring data for example during keep clean cycles or when outside a selected sub image area Andor EMCCDs have been internally configured to prevent any unwanted signal entering the EM gain register Together these measures ensure that the rate of EM gain ageing is significantly reduced 3 1 9 EMCAL Andor have developed in the iXon3 a unique and patented method of user initiated EM gain self recalibration EMCAL This is available only in iXon3
23. 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 Left unchecked cooling performance would steadily degrade and therefore lead to increased dark current Furthermore resulting electrochemical reactions would eventually destroy the sensor IXon3 SECTION 4 Page 78 ANDOR ee HARDWARE 4 5 CONTROLLER CARD PINOUTS CONTROLLER CARD AUXILIARY CONNECTOR DESCRIPTION PIN NUMBERS 1 Aux In 1 2 Aux In 2 3 Aux In 3 4 2C DATA 5 Aux In 4 6 Aux Out 2 7 Aux Out 1 Aux Out 3 9 2C Clock 10 GROUND 11 Reserved 12 Reserved 12 Reserved 14 Aux Out 4 152 45V CONTROLLER CARD WARNING Pins 11 12 amp 13 are reserved These pins are NOT available for auxiliary use DO NOT make electrical connections to these pin locations when attaching external devices via the Controller Card Auxiliary Connector Port Doing so may cause damage to the Controller Card the Camera or your external device IXon3 SECTION 4 Page 79 ANDOR ee HARDWARE 4 6 SMB SIGNAL DIAGRAMS TTL amp CMOS compatible iXon3 family TTL Signal EX Trig SMB Figure 45 External Trigger SMB IXon3 camera Use 509 cable high impedance input gt 1KQ Drive both TTL amp CMOS unterminated input Figure 46 Fire SMB
24. of pixels shown Figure 21 Vertical amp Horizontal binning of two rows Charge is built up on the sensor Charge in the frame is shifted vertically by one row so that the bottom row of charge moves down into the shift register 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 Charge in the shift register is moved horizontally through the EM gain register if using the EM output amplifier until the first data pixel is just about to enter the output node of the amplifier Charge in the shift EM gain register is moved horizontally by one pixel so that charge on the endmost pixel of the shift register is transferred into the output node of the amplifier Charge in the shift register is again moved horizontally so that the output node of the amplifier now contains charge from two pixels of the shift register i e the charge has been horizontally binned The charge in the output node of the amplifier is passed to the analog to digital converter and is read out Steps 5 7 are repeated until the shift register is empty The process is repeated from Step 2 until the whole frame is read out IXon3 SECTION 3 Page 42 ANDOR iN FEATURES amp FUNCTIONALITY 3 4 ACQUISITION OPTIONS 3 4 1 Capture Sequence in Frame Transfer Mode A number of acquisition modes are
25. on a pixel of the CCD A1 1 8 Dark Signal Dark signal a charge usually expressed as a number of electrons is produced by the flow of dark current during the exposure time All CCDs produce a dark current an actual current that is measurable in typically tenths of milliamps per pixel The dark signal adds to your measured signal level and increases the amount of noise in the measured signal Since the dark signal varies with temperature it can cause background values to increase over time It also sets a limit on the useful exposure time Reducing the temperature of the CCD reduces dark signal typically for every 7 C that temperature falls dark signal halves CCD readout noise is low and so as not to compromise this by shot noise from the dark signal it is important to cool the detector to reduce the dark signal If you are using an exposure time of less than a few seconds cooling the detector below 0 C will generally remove most of the shot noise caused by dark signal IXon3 APPENDIX Page 82 ANDOR E APPENDIX A1 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 follows e Shot noise of the signal itself e Shot noise of any dark signal e Readout noise If the signal is small
26. produces Superpixels These consist of two or more individual pixels that are binned and read out as one large pixel Thus the whole CCD or a selected sub area becomes a matrix of Superpixels e g Superpixel 2 D Pixel RAR Matrix Sub area NOTE ONLY THE SUB AREA WILL BE DISPLAYED NOT THE AREA AROUND IT The horizontal and vertical binning parameters determine the dimensions of any superpixels created On the one hand superpixels result in a loss of spatial resolution when compared to single pixel readout but on the other hand they offer the advantage of summing data on chip prior to readout thereby producing a better signal to noise ratio and a higher frame rate All iXon3 models offer completely flexible binning patterns which are user selectable from software For the purpose of initial focusing and alignment of the camera or to increase the readout speed the user may wish to only readout a particular sub area of the CCD to produce a Sub Image When a sub image has been defined only data from the selected pixels will be digitized Data from the remaining pixels will be discarded The flexible configuration of the iXon3 allows the user to set the Sub Image area to any size and location on the CCD chip IXon3 SECTION 3 Page 41 ANDOR ndm FEATURES amp FUNCTIONALITY Step 1 Step 2 Step 3 Step 4 Step 5 Step 6 Step 7 Step 8 VERTICAL amp HORIZONTAL BINNING 2 X 2 SUPERPIXELS Only subset
27. systems in the field and a measured Mean Time Between Failure MTBF of 100 years that means it will take 100 years for half of them to fail Furthermore Andor s rigorous proprietary vacuum process is carried out in a Class 10 000 clean room this means less than 10 000 particles of less than 0 5 micron dimension per cubic meter The air is fully replenished every minute We welcome visitors to inspect our state of the art facility Y Sustained vacuum performance over many years operation proprietary process to minimize outgassing Y Benefit from a thoroughly proven solution UltraVac 10 years of shipping vacuum systems to the field and a negligible failure rate an MTBF of 100 years Y Performance improves because the temperature of the chip can be reduced significantly Better cooling down to 100 C with an enhanced thermoelectric Peltier design translates into substantially lower darkcurrent and fewer blemishes Y Such darkcurrent performance is particularly critical to EMCCD technology where even a single thermal electron is detected as a spurious noise spike Y Elimination of condensation and outgassing means that the system can also use only a single entrance window with antireflection coating you can believe the QE curve Y The permanent hermetic vacuum ensures that peak quantum efficiency and cooling will not degrade even after years of operation IXon3 SECTION 4 Page 76 ANDOR HARDWARE The iXon3
28. the analog to digital converter and is read out 6 Steps 3 and 4 are repeated until the shift register is emptied of charge 7 Theframe is shifted vertically again so that the next row of charge moves down into the shift register The process is repeated from Step 3 until the whole frame is read out IXon3 APPENDIX Page 81 ANDOR E APPENDIX A1 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 A1 1 3 Acquisition An Acquisition is taken to be the complete data capture process A1 1 4 A D Conversion Charge from the CCD is initially read as an analogue signal ranging from zero to the saturation value A D conversion changes the analogue signal to a binary digital number which can then be manipulated by the computer A1 1 5 Background Background is a data acquisition made in darkness It is made up of fixed pattern noise and any signal due to dark current A1 1 6 Binning Binning is a process that allows charge from two or more pixels to be combined on the EMCCD chip prior to readout A1 1 7 Counts Counts refer to the digitization by the A D conversion and are the basic unit in which data are displayed and processed Depending on the particular version of the detection device one count may for example be equated with a charge of 10 photoelectrons
29. to recommend this PreAmp setting even over the middle x2 4 PreAmp setting is that it implements an additional restriction as to how much charge is allowed to build up in the sensor This in turn will help minimize the rate of EM gain ageing please see page 31 for further details on measures against gain ageing However some applications can be very demanding of dynamic range and for those we recommend using a lower PreAmp setting such as x2 4 This will ensure the A D capacity is more closely matched to the well capacity of the gain register pixels thus affording maximum dynamic range Also as mentioned above to maximize the true dynamic range of the camera we recommend tuning the RealGain gain setting to a value close to the value of the readout noise at the selected readout speed e g if readout noise is 50 electrons 10 MHz set the EM gain to x50 for maximum dynamic range iXon3 SECTION 3 Page 37 lt ANDOR WU eem FEATURES amp 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 to achieve the maximum flexibility of camera operation particularly in terms of dynamic range Slower readout typically allows lower read noise and higher available dynamic range but at the expense
30. to vertically shift the unwanted rows The frame rate increase is achieved by not reading out i e discarding the unwanted pixels T Shift Register e d Q 41 To o Fon n n n o f n n n n n a Figure 41 Cropped Sensor Mode The active imaging area of the sensor is defined in a way that only a small section of the entire chip is used for imaging The remaining area has to be optically masked to prevent light leakage and charge spill over that would compromise the signal from the imaging area By cropping the sensor one achieves faster frame rates because the temporal resolution will be dictated by the time it requires to read out small section of the sensor iXon3 SECTION 3 Page 68 lt ANDOR WU noe FEATURES amp 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 1000 s can be achieved with sufficiently small crop area Series of measurements done on Andor iXon3 885 EMCCD camera have demonstrated that Cropped Sensor Mode in conjunction with binning has pushed the speed beyond 4000 frames per second The table below shows the Imaging frame rate potential of the Andor iXon3 885 EMCCD camera under conditions of Cropped Sensor Mode readout Array Size Binning 502x501 251x250 125x125 75x7
31. 0 for 6mm I D tubing Figure 8 iXon3 connectors There are six connections points on the iXon3 as shown in figure 8 above There are four industry standard SMB Sub Miniature B connectors details as follows e Fire please refer to pages 51 63 e Shutter see page 64 e Arm please refer to pages 51 63 e Ext Trig External Trigger Input please refer to pages 51 63 These are used to send receive Trigger and Fire signals The SMB outputs Fire amp Shutter are CMOS compatible amp series terminated at source i e in the camera head for a 50Q cable NOTES 1 The termination at the customer end should be high impedance gt 1KQ as an incorrect impedance match could cause errors with timing and triggering 2 The External Trigger Input SMB is TTL level amp CMOS compatible and has 470Q impedance 3 Signal diagrams of these connections can be found on page 79 There is an lC connection point and the pin outs for this are shown in Figure 9 below PIN FUNCTIO LEES lif IAN 1 IC DATA if amp ON UC j j 2 PC err Jj j N 3 5V 4 GROUND Figure 9 I C connection facing in with pin outs The connection for the 26 pin interface between the camera and the PCI controller card is made via an MDR 36 connector shown in figure 8 above The Cooler Power connection is for the Power Supply Block PSB described on page 11 IXon3 SECTION 2 Page 20 ANDOR INSTALLATION Two
32. 2006 Electromagnetic compatibility EMC Testing and measurement techniques Surge immunity test Criterion A e EN 61000 4 6 2009 Electromagnetic compatibility EMC Testing and measurement techniques Immunity to conducted disturbances induced by radio frequency fields Criterion A e EN 61000 4 11 2004 Electromagnetic compatibility EMC Testing and measurement techniques Voltage dips short interruptions and voltage variations immunity tests Criterion A Offices in oH go aiii Omsan MINI WORSE INA 18036091 2004 a China Co Reg No NI 22486 VAT No GB 517 1829 44 iXon3 APPENDIX Page 88 ANDOR eo APPENDIX EU Declaration of Conformity LVD Andor Technology plc hereby declares under its sole responsibility that the aforementioned equipment meets the requirements of EU Low Voltage Directive 2006 95 EC by means of conformity to the following harmonised standard e EN 61010 1 2001 Safety requirements for electrical equipment for measurement control and laboratory use Part 1 General requirements Additional EMC Standards This product also complies with the following e FCC 47 CFR 815 Subparts A and B 2005 Code of Federal Regulations Title 47 Telecommunications Part 15 Radiofrequency Devices Class B e EN 61000 3 2 2006 Electromagnetic compatibility EMC Limits Limits for harmonic current emissions equipment input current 3 16 A per phase DD ENV 50204 1996 Radiated electromagneti
33. 5 and are intending to discard these products at the end of their useful life Andor are happy to assist The cost for the collection treatment recycling recovery and sound environmental disposal of these goods at the end of its useful life has not been included in the price If you require help assistance regarding the disposal of this equipment please refer to our website or contact our sales team at which point instructions and a quotation can be provided A copy of the Company s WEEE Policy can be viewed at the Company website www andor com iXon3 APPENDIX Page 95
34. 5 32x32 1004x1 62 231 465 763 1704 13812 118 426 859 1401 2976 213 735 1474 2404 4746 361 1144 2341 3637 6757 EMCCD based adaptive optics for which smaller format EMCCD sensors are often used can benefit from cropped sensor readout Small area EMCCDs can already operate at gt 500 fps and can be flexibly optimized in cropped mode to exceed 2000 fps Use of cropped sensor mode opens new possibilities for very fast adaptive optics imaging enabling the users to reach into several thousands of frames per second There is also potential to use cropped EMCCDs for multi spectral fluorescence confocal scanning as an alternative to the arrays of PMTs that have traditionally been used in this approach The gt 90 quantum efficiency of the back illuminated sensor single photon sensitivity array architecture and rapid pixel readout speed can be exploited to markedly improve this approach The laser dwell time should be set to coincide with the time to expose and read out a short row of approx 32 pixels sufficient spectral channels to yield effective un mixing of several known emitting dyes resulting in a data cube of 512 x 512 x 32 spectral taking less than 1 second to generate There is a clear sensitivity advantage of EMCCD pixels over the usually employed PMT technology which is circa 5 fold in the blue green and up to tenfold in the red IXon3 SECTION 3 Page 69 p ANDOR ene FEATURES amp FUNCTIONALITY 3 10 ADVA
35. 6 Fax 44 28 9031 0792 Web www andor com ANDOR discover new ways of seeing Description of Equipment Andor Technology plc hereby confirms that the following product is manufactured in the United Kingdom and complies with the following EU Directives iXon Scientific Digital Camera DU DV 860 865 885 888 897 PCI Interface Cards CCI 22 23 and PCle Interface Card CCI 24 EU Declaration of Conformity EMC Andor Technology plc hereby declares under its sole responsibility that the aforementioned equipment meets the requirements of EU EMC Directive 2004 108 EC by means of conformity to the following harmonised standards e EN 61326 1 2006 Electrical equipment for measurement control and laboratory use EMC requirements Part 1 General requirements Class B e EN 55011 2007 Industrial scientific and medical ISM radio frequency equipment Electromagnetic disturbance characteristics Limits and methods of measurement Class B e EN 61000 4 2 2009 Electromagnetic compatibility EMC Testing and measurement techniques Electrostatic discharge immunity test Criterion A B e EN 61000 4 3 2006 Electromagnetic compatibility EMC Testing and measurement techniques Radiated radio frequency electromagnetic field immunity test Criterion A e EN 61000 4 4 2004 Electromagnetic compatibility EMC Testing and measurement techniques Electrical fast transient burst immunity test Criterion A B e EN 61000 4 5
36. A1 1 10 Exposure Time 83 A1 1 11 Frame Transfer 83 A1 1 12 Noise 84 A1 1 12 1 Pixel Noise 84 A1 1 12 1 1 Readout Noise 84 A1 1 12 2 Fixed Pattern Noise 84 A1 1 13 Quantum Efficiency Spectral Response 85 A1 1 14 Readout 85 A1 1 15 Saturation 85 A1 1 16 Scans Keep Clean amp Acquired 85 A1 1 17 Shift Register 85 A1 1 17 Shot Noise 86 A1 1 18 Signal To Noise Ratio 86 A1 2 MECHANICAL DIMENSIONS 87 A1 3 DECLARATION OF CONFORMITY 88 A1 4 TERMS amp CONDITIONS 90 A1 5 STANDARD WARRANTY AND WARRANTY SERVICES 91 A1 6 THE WASTE ELECTRONIC AND ELECTRICAL EQUIPMENT REGULATIONS 2006 WEEE 95 iXon3 TABLE OF CONTENTS Page 7 ANDOR p ANDO INTRODUCTION SECTION 1 INTRODUCTION TO iXon3 HARDWARE Thank you for choosing the Andor iXon3 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 If you have any questions regarding your iXon3 system please feel free to contact Andor directly or via your local representative or supplier You can find contact details below 1 1 TECHNICAL SUPPORT If you have any questions regarding the use of this equipment please contact the representative from whom your system was purchased or Europe USA Andor Technology Andor Technology
37. A1 1 12 Noise Noise is a complex topic the full exploration of which is beyond the scope of this glossary However noise may be broken down into two broad categories as follows 1 Pixel Noise 2 Fixed Pattern Noise A1 1 12 1 Pixel Noise Let us first attempt to define pixel noise Assume that a light signal is falling on a pixel of the CCD If the charge on the pixel is read and the read process is repeated many times the noise may be taken as the variation in the values read The Root Mean Square rms of these variations is often used to express a value for noise As a rule of thumb the rms is 4x to 6x smaller than the peak to peak variations in the count values read from the pixel Pixel noise has three main constituents e Readout noise e Shot noise from the dark signal e Shot noise from the light signal itself Shot noise cannot be removed because it is due to basic physical laws Most simply defined shot noise is the square root of the signal or dark signal measured in electrons A1 1 12 1 1 Readout Noise Readout noise which in our detectors is in any case low is due to the amplifier and electronics It is independent of dark signal and signal levels and is only very slightly dependent on temperature It is present on every read as a result of which it sets a limit on the best achievable noise performance Shot noise from the dark signal is dependent on the exposure time and is very dependent on the temperature sh
38. Customer Replacement with a new or refurbished part Andor will invoice the customer the full merchandise contracted customer price of the unit 1 5 9 Unless elsewhere agreed between the Customer and Andor this service does not include root cause analysis the provision of fault reports or lead time and performance metrics 1 6 Software Remediation 1 6 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 1 6 2 Where as a result of the process described in 1 3 2 above it is determined that the defect relates to software a trouble ticket will be logged in respect of the software issues observed 1 6 3 Under the warranty provisions of the supply contract we will not provide the customer with a guaranteed SLA service level agreement for their problem IXon3 APPENDIX Page 94 NDOR X TECHNOLOGY APPENDIX Where appropriate Andor has labelled its electronic products with the WEEE label crossed out wheelie bin to alert our customers that products bearing this label should not be disposed of in a landfill or with municipal waste If you have purchased Andor branded electrical or electronic products in the EU after August 13 200
39. E output will be high and there will be no vertical clocking However the horizontal register will keep running At the completion of the exposure time the FIRE pulse will go low and the Image area of the CCD will be shifted into the Storage area As the acquired signal is now safely placed in the masked off region of the CCD light still falling on the CCD will not contaminate the acquired image while it is being read out On completion of the readout the camera will perform the Internal keep clean cycle until the user specified cycle time has elapsed This process is continued until the complete series of acquisitions has taken place Idle keep clean cycle Waiting for Cycle Time Start command a o Exposure period Exposure period i lt gt Image area clocks Storage area clocks Horizontal clocks Fire output Start command Keep clean running Image area shifted Horizontal clocks into storage area Storage area read running out phase Figure 32 Internal Trigger in Non Frame Transfer mode IXon3 SECTION 3 Page 56 lt ANDOR es FEATURES amp FUNCTIONALITY 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
40. HARDWARE GUIDE p ANDOR www andor com Andor Technology plc 2011 Version 1 5 July 2011 ANDOR TABLE OF CONTENTS PAGE SECTION 1 INTRODUCTION TO IXON3 HARDWARE 8 1 1 TECHNICAL SUPPORT 8 1 2 COMPONENTS 9 1 2 1 Camera 9 1 2 2 Controller Cards 10 1 2 3 Controller Card Cables 10 1 2 4 Cooler Power Supply Block 11 1 2 5 Software 11 1 3 SAFETY PRECAUTIONS amp MAINTENANCE 12 1 3 1 Care of the camera 12 1 3 2 Environmental conditions 12 1 3 3 Regular checks 13 1 3 4 Annual electrical safety checks 13 1 3 5 Replacement parts 13 1 3 6 Fuse replacement 13 1 3 7 Overheating 13 1 3 8 Working with electronics 14 1 3 9 Condensation 14 1 3 10 Dew Point graph 15 1 3 11 EM Gain ageing 16 1 3 12 Minimizing particulate contamination 17 IXon3 TABLE OF CONTENTS Page 2 ANDOR TABLE OF CONTENTS PAGE SECTION 2 INSTALLATION 18 2 1 INSTALLING THE HARDWARE 18 2 1 1 PC requirements 18 2 2 CONNECTORS 20 2 3 WATER PIPE CONNECTORS 21 2 4 CONNECTING THE SYSTEM 21 2 5 MOUNTING POSTS 21 2 6 INSTALLING PCI PCle DRIVER WINDOWS O S 2000 XP VISTA 22 2 6 1 Installing Linux driver 22 2 6 2 Software installation 22 iXon3 TABLE OF CONTENTS Page 3 ANDOR TABLE OF CONTENTS PAGE SECTION 3 FEATURES amp FUNCTIONALITY 23 3 1 EMCCD OPERATION 23 3 1 1 Structure of an EMCCD 23 3 1 2 EM Gain amp Read Noise 25 3 1 3 EM Gain ON vs EM Gain
41. N plots derived from the specifications of the back illuminated iXon3 EMCCDS read out at 10MHz for a photon wavelength at which the Quantum Efficiency QE of the sensor is assumed to be 9096 Such plots are very useful to gauge at what signal intensity it becomes appropriate to use EM Gain to increase S N It is clear that at 10MHz readout one needs to encounter relatively intense signals of gt 2900 photons pixel before it becomes advantageous to operate with EM Gain off Note that the ideal curve represents a pure Signal to Shot Noise ratio and is shown for reference if the camera had no sources of noise this is what the curve would appear like Even with EM Gain turned on we encounter uniformly lower signal to noise than the ideal curve This is due to the influence of Multiplicative Noise which has the effect of increasing the shot noise by a factor of 4 2 or 1 41 100 eid 2900 photons 100 Photons pixel Assuming 9096 QE SIN ideal SIN 10MHz EM OFF SIN 10MHz EM ON 1000 10000 0 1 0 01 Figure 13 EM Gain ON vs EM Gain OFF signal to noise plots for back illuminated iXon3 EMCCDs at 10MHz readout speed applies to 897 860 and 888 models IXon3 SECTION 3 Page 26 p ANDOR We cm FEATURES amp FUNCTIONALITY Figure 14 below shows S N plots derived from the specifications of the back illuminated iXon3 EMCCDs at 1MHz slower frame rate operatio
42. NCED 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 The industry leading dark current and Clock Induced Charge CIC specification of the Andors back illuminated iXon3 897 model renders it uniquely suited to imaging by Photon Counting Photon Counting can only be successfully carried out with very weak signals because as the name suggests it involves counting only single photons per pixel If more than one photon falls on a pixel during the exposure an EMCCD or an ICCD for that matter cannot distinguish the resulting signal spike from that of a single photon event and thus the dynamic range of a single frame exposure is restricted to one photon Key Fact To successfully photon count with EMCCDs there has to be a significantly higher probability of seeing a photon spike than seeing a dark current CIC noise spike The iXon3 897 has the lowest dark current CIC performance on the market yielding both lower detection limits and higher contrast images Under such ultra low light conditions photon counting mode imaging carries the key benefit that it is a mean
43. Page 11 ANDOR S INTRODUCTION 1 3 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 In case of emergency the disconnecting device is the mains lead This will either be the mains lead connected to the product or in the case of a cabinet based system the mains lead to the cabinet 4 To prevent accidental internal damage to the camera objects small enough to enter the slots on the sides of camera should be placed well away from these slots 5 Ensure that a minimum clearance of approximately 100 mm 4 is maintained in front of all ventilation slots and the fan inlet Cooling performance cannot be guaranteed unless these criteria are observed 6 Only use a dry clean lint free cloth to clean all painted surfaces If necessary use a water diluted detergent to lightly dampen the cloth do not use Isopropyl alcohol solvents or aerosols 7T To clean the window remove loose particulate matter with an air blower If the component is still not clean it may be drag wiped using folded lint free clean soft white tissue dampened with pure methanol 8 If the equipment is used in a manner not stated by Andor t
44. Service 1 4 1 A Customer who has purchased their product via a reseller or third party and who believes they have a warranty defect should in the first instance contact a representative of their seller s product support team Customers who have bought products directly from Andor can access the Service Desk at www andor com contact us support request 1 4 2 The Customer should indicate that they are pursuing a warranty claim and specify the equipment type and the contract under which it was supplied The Service Desk representative will then work with the Customer to establish the nature of the defect and to determine whether the reported defect is one which meets the criteria under the supply contract for warranty remediation This process will comprise question and answer between Service Desk and Customer and the Service Desk operative may at their sole discretion ask the Customer to perform some basic diagnostic actions in relation to the problem item 1 5 Hardware Remediation 1 5 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 1 5 2 Following allocation of a RMA number by And
45. 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 In EMCCDs the signal in electrons is further multiplied in the EM gain register The average multiplication factor is selected in software from the RealGain scale It can be desirable to directly quantify signal intensity either in terms of electrons per pixel or in terms of incident photons per pixel However during the readout process array detectors must first convert the signal in electrons the multiplied signal in the case of EMCCDs into a voltage which is then digitized by an Analogue to Digital Converter ADC Each Analogue to Digital Unit ADU is presented as a count in the signal intensity scale each count corresponding to an exact number of electrons Furthermore the signal value in counts will sit on top of an electronic bias offset value In the iXon3 this baseline can be clamped at 100 counts Therefore in order to back calculate to the original signal in electrons electron to ADU conversion factor must be very accurately stored by the camera which varies depending on the pre amplifier gain selection chosen through software Calculation of the signal as absolute electrons a
46. any of these features require iCam technology within the camera fuller details of which can be viewed through www andor com e In Internal Trigger the camera determines the exact time when an exposure happens based on the acquisition settings entered by the user This is the most basic trigger mode and requires no external intervention In External Trigger once an acquisition has been started the camera is placed into a special cleaning cycle called External Keep Clean Cycle which ensures that charge build up on the CCD is kept to a minimum while waiting for the external trigger event The external keep clean consists of a continuous sequence of one vertical shift followed by one horizontal shift Once the External Trigger is received the current keep clean sequence is completed and the exposure phase initiated The exact nature of the acquisition will depend on the user settings and is explained in more detail in a subsequent section The external trigger is fed via the Ext Trig input on the camera head Fast External Trigger is for the most part identical to External Trigger It differs in only one key aspect In Fast external trigger the camera will not wait for a sufficient number of keep clean cycles to have been completed to ensure the image area is completely clean of charge before accepting an external trigger event but instead will allow a trigger event to immediately start the acquisition process As a result Fast External trigger allow
47. around the connectors where the water tubes are attached In such circumstances switch off the system and wipe the camera with a soft dry cloth It is likely there will already be condensation on the cooling block and cooling fins inside the camera Please also carry out the following actions e Setthe camera aside to dry for several hours before you attempt re use e Before re use blow dry gas through the cooling slits on the side of the camera to remove any residual moisture e Use warmer water or reduce the flow of water when you start using the device again IXon3 SECTION 1 Page 14 ANDOR er INTRODUCTION 1 3 10 Dew Point graph The graph in figure 7 below plots the relationship between Relative Humidity and Dew Point at varying ambient temperature This can be used to calculate the minimum temperature the cooling water should be set to Ambient Temperatures 200C 22C 24C 26 C 28 C 30 C 68 Humidity with 30 C Ambient Temperature 23 C Dew Point Relative Humidity Dew Point C Figure 7 Dew point graph For example when using an iXon3 897 you will need 10 C cooling water to guarantee performance down to 100 C In the relatively dry atmosphere of an air conditioned lab cooling water at 10 C should not present any problems However in humid conditions such as exist in some parts of the world condensation may occur resulting in damage to the head In such conditions you will have to u
48. available for the iXon3 range to best suit your experimental demands In Frame Transfer FT acquisition mode the iXon3 can deliver its fastest performance whilst maintaining optimal Signal to Noise It achieves this through simultaneously acquiring an image onto the image area whilst reading out the previous image from the masked frame storage area Thus there is no time wasted during the readout and the camera operates with what is known as a 100 duty cycle Step 1 Step 2 Step 3 Step 4 Step 5 Continuously Clean ccD Keep Clean Cycle n Mer rr eae 2 Step 3 Step 1 A 7 m m Step 4 Step 5 Figure 22 Capture sequence FT mode Both Image and Storage areas of the CCD are fully cleaned out This is known as a Keep Clean Cycle Keep Clean Cycles occur continuously to ensure that the camera is always ready to start an acquisition when required Further details of the keep clean cycle are given later On receipt of a Start acquisition command the CCD stops the Keep Clean Cycle This allows the image photoelectric charge to build up in the Image area of the CCD The CCD remains in this state until the exposure time has elapsed at which point the read out process starts The first phase of the readout process is to quickly shift the charge built up in the Image area into the Storage area The time required to move the charge into the Storage area is approximately calculated as follo
49. c field from digital radio telephones Immunity test Criterion A CE Mark CE Mark first applied to this product in the year 2004 Gary Wilmot Head of Engineering 1 December 2010 ANDOR discover new ways of seeing iXon3 APPENDIX Page 89 ANDOR e APPENDIX 1 In these Conditions BUYER means the person who accepts a quotation of the Seller for the sale of the Goods or whose order for the Goods is accepted by the Seller GOODS means the goods including any instalment of the goods or any parts for them which the Seller is to supply in accordance with these Conditions SELLER means Andor Technology plc CONDITIONS means the standard terms and conditions of sale set out in this document and unless the context otherwise requires includes any special terms and conditions agreed in writing between the Buyer and Seller CONTRACT means the contract for the purchase and sale of the Goods WRITING includes telex cable facsimile transmission and comparable means of communication 2 Any reference in these Conditions to any provision of a statute shall be construed as a reference to that provision as amended re enacted or extended at the relevant time 3 The headings in these Conditions are for convenience only and shall not affect their interpretation iXon3 APPENDIX Page 90 ANDOR X TECHNOLOGY APPENDIX 1 1 Introduction 1 1 1 This document describes the general Andor S
50. cally along a column from the Image area The slower the read out rate or the shorter the exposure time the greater the possibility of corruption To see why this is the case consider the following situation During a 100us exposure enough light has fallen on a pixel to register 10000 counts or 100 000 electrons assuming 10e count The image is then shifted into the Storage area To read out the image assuming 1000x1000 pixels it would take approximately 100ms at 10MHz readout rate This means that during the reading out of the image 10 million counts 10000 1000 will have been acquired into the pixel described above As a pixel saturates at approximately 160 000 electrons this means that the pixel will over saturated by 60 times All the excess charge has to go somewhere and spreads vertically along the CCD column As the clocks in the Image area are not actively shifting the charge the mobility of the charge will be low and you may not see any effect However when you consider that more than one pixel in any given column could be exposed to 10000 counts per 100us The chance of corrupting data is correspondingly increased Reducing the amount of light falling on the CCD outside of the exposure period and increasing the exposure time accordingly will reduce the possibility of data corruption iXon3 SECTION 3 Page 46 lt ANDOR NU ems FEATURES amp FUNCTIONALITY 3 4 3 Capture Sequence for Fast Kinetics with an FT CCD Fas
51. cameras that contain L3 vision sensors from E2V i e 897 and 888 models The 885 range of iXon3 cameras contain sensors from Texas Instruments that show negligible levels of gain ageing and thus the EMCAL function is not required Thus for the L3Vision based cameras even after exercising due care during usage and availing of the above internal restrictions the EM gain will gradually decrease over an extended period of time This reduction in EM gain can be rectified by using the EMCAL self recalibration process which is very easily initiated by the user Check on line for the latest EMCAL routine This process uses the iXon3 in built temperature compensated linear gain scales to reset the EM gain calibration to reflect the true values requested on the software scale in reality giving RealGain values and thus markedly prolonging the operational lifetime and quantitative reliability of the technology and circumventing the need to return to the factory for recalibration To the user this means optimal signal to noise ratio maximum dynamic range and prolonged system longevity 7 years Additional gain register voltage available 0 500 1000 1500 2000 2500 Days Operation 24 7 operation 30 frames sec x90 000 electrons per pixel through gain register 130 000 pixels illuminated Figure 19 Ageing profile of an Andor backlit EMCCD Test conditions 24 7 operation 30 frames sec x90 000 electrons per
52. connectors are fitted to the camera in order to allow water cooling pipes to be connected e g n A These can be connected to a water cooler or recirculator to improve cooling 2 4 CONNECTING THE SYSTEM Connect the elements of your system as follows 1 Wherever possible plug your PC into the mains outlet to ensure grounding but keep the power switched off 2 Connect the Camera to the Controller Card using the Cable provided It is important that this cable is securely fastened to provide a good grounding between the camera and Controller Card 3 Your system has been supplied with a PSB for cooling The PSB connects to the camera via a 2 1mm Jack plug and to the mains electricity supply with a standard plug for your location 4 There is only one socket on the camera that the PSB can be connected to and this is labeled Cooler Power please see figure 8 on page 20 5 For best performance the PSB should be plugged into the same power source as the computer 2 5 MOUNTING POSTS e Mounting posts can be fitted on three sides of the camera These can be used to mount the camera if the C Mount is not used and or to mount accessories NOTE A bag containing two 01 2 x 80mm long x 1 4 20 UNC posts is included with all kits e There are 3 pairs of holes for the mounting posts each with 2 0 spacing 1 REMOVE BLACK GROMMET 3 SCREW MOUNTING POST INTO EXPOSED HOLE 2 EASE OUT VERTICALLY 4 TIGHTEN USING MOUNTING POST HOLE
53. creases with temperature To make up this loss and maintain EM gain a larger EM electric field must be used at higher temperatures As can be seen from Figure 18 EM gains well in excess of x1000 can be achieved at low temperatures However it is not recommended that gains above x1000 be used because such high gains can cause significant ageing of the gain register see EM Gain Ageing on page 32 10000 1000 3 451 A43 100 Real EM Gain 434 2423 3 410 386 350 30 30 70 60 50 40 30 Sensor Cooling Temperature C Figure 17 EM gain vs sensor cooling temperature IXon3 SECTION 3 Page 30 lt ANDOR WU enn FEATURES amp FUNCTIONALITY 3 1 6 RealGain Real and Linear gain Through a detailed analysis of the complex EM voltage dependence Andor have successfully converted the relationship between EM gain and the EM clock voltage setting into a linear one Importantly the actual EM gain can be selected directly from a linear scale displayed in software No more guesswork with arbitrary gain units on a non linear scale the gain you ask for is the gain you get Select the best gain to overcome noise and maximize dynamic range Also although EM gain is temperature dependent Andor s linear and real gain calibration extends to any EMCCD cooling temperature Selecting x300 EM gain 9 50 C or at 100 C gives the same x300 actual gain This de
54. ct IXon3 SECTION 3 Page 29 p ANDOR WU eem FEATURES amp FUNCTIONALITY 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 16 below the dependence of EM gain on EM voltage is sharp note the logarithmic scaling This arises because the signal electrons acquire energy as they are accelerated through the EM electric field and once this field strength reaches the threshold needed to overcome the bandgap energy the impact ionization rate rises rapidly This sharp dependence has meant that the software control of EM gain in all EMCCD cameras to date has been via a non linear scale with most of the amplification occurring within a relatively small portion at the top of the overall scale Thus considerable fine tuning by the user to determine an optimal gain setting has been required and even then the actual gain is determined only through measurement of a stable light source with and without gain applied Real EMGain 350 370 390 410 430 450 EM Clock Voltage Volts Figure 16 EM gain vs EM clock voltage Figure 17 shows how the EM gain varies with temperature this dependence arising primarily from photon scattering of electrons when they are accelerating in the EM electric field The scattering causes a loss of energy which in
55. cycle series will complete before the exposure phase starts During the exposure there are no vertical clocks running however there will be horizontal clocks to ensure that the shift register continues to be kept clean Once the exposure time has elapsed the charge built up in the Image area is quickly transferred into the Storage area From the Storage area the charge is read out as normal At the completion of the readout the camera restarts the external keep clean cycle If the camera is in Fast External Trigger mode it will accept a trigger event immediately and start the next exposure If however the camera is in normal external trigger the camera will perform sufficient External keep clean cycles to ensure the Image area is fully cleaned before it will accept an external trigger Once this period has passed Normal and Fast External Trigger operate the same Fast External Trigger is useful in those cases where there is very little background light and the user is looking for the fastest frame rate With Fast External Trigger you may see variation in the background contribution to the signal from light that may have been allowed to fall on the sensor during the readout of the previous image Fast external trigger does not mean that when a trigger is accepted that the system will respond quicker than in normal external trigger mode Idle keep clean Storage area read cycle Waiting for Cycle Time out phase Start command Exposure period
56. de however the number of times the cycle is repeated is determined by the cycle time set by the user The keep clean is completed with a sufficient number of vertical shifts to ensure both the image and storage areas are charge free Number of times pattern repeated dependent on cycle time Number of vertical clocks will depend on the number of rows on the sensor Next acquisition starts p Image amp storage clocks Horizontal clocks Total time set by Read out phase Kinetic Cycle time defined by user Figure 26 Internal Keep Clean Cycle iXon3 SECTION 3 Page 49 p ANDOR nene FEATURES amp 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 When an external trigger is detected the current cycle will complete before the exposure phase starts It is worth noting that although the external keep clean cycle will complete the current cycle this will not result in the total loss of signal as only one vertical shift will have occurred For pulsed light of very short time duration microseconds i e of the order
57. e contact Andor for a replacement Depending on the Terms and Conditions of your Warranty you may be charged for this replacement 1 3 6 Fuse replacement The camera itself does not have a fuse However if a U K BS 1363 mains lead has been supplied it contains a fuse whose characteristics are as follow e Rated Current 5 A e Rated Voltage 240 Vac e Type BS 1362 e Size 0 25 x 1 inch 1 3 7 Overheating Care should be taken to ensure that the camera does not overheat as this can cause system failure Overheating may occur if either of the following situations arises e The air vents on the sides of the detector head are accidentally blocked or there is insufficient or no water flow e The ambient air temperature is higher than 30 C To protect the camera from overheating a thermal switch has been attached to the heat sink If the temperature of the heat sink rises above predefined limit the power supply to the cooler will cut off and a buzzer will sound The cut out will automatically reset once the head has cooled It is not recommended that you operate in conditions that would cause repeated cut outs as the thermal switch has a limited number of operations NOTE When using water cooling always use water that is above the dew point of the ambient environment otherwise condensation may occur please see page 14 IXon3 SECTION 1 Page 13 ANDOR ANDO INTRODUCTION 1 3 8 Working with electronics T
58. ead Noise of the system Read noise is produced during the readout process mostly by the output amplifier but also has contributions from the digitization electronics This sets the minimum signal level that can be detected by the camera as any signal level below the read noise level will be indistinguishable from the read noise itself Read noise has therefore been the major limiting factor for low light level detection in CCDs for many years until the introduction of EMCCD cameras by Andor Technology in 2000 By applying EM gain a weak signal that would otherwise be indistinguishable from the read noise can be amplified above the read noise level and thus be read out as a useful signal This amplification of the signal before being read out effectively reduces the read noise level of the camera and even at relatively modest EM gain settings the effective read noise can be reduced to less than 1 electron r m s One other point to note is that since read noise increases with increased readout rate the application of EM gain really comes into its own at higher readout rates as any increase in the read noise can be overcome simply by increasing the EM gain For example an iXon3 897 typically has a read noise of 50 electrons rms when reading out at 10MHz This can easily be reduced to lt 1 electron by applying gt x50 EM gain IXon3 SECTION 3 Page 25 lt ANDOR WOO enm FEATURES amp FUNCTIONALITY Figure 13 below shows Signal to Noise S
59. een the fixed voltage electrode and the clocked electrode is sufficiently high for the electrons to cause impact ionization as they transfer The impact ionization causes the generation of new electrons i e multiplication or gain 2 Secondly the EMCCD is designed with hundreds of cells or pixels in which impact ionization can occur and although the probability of amplification or multiplication in any one pixel is small only around x1 01 to x1 015 times over the entire length of the EM register the probability is very high and substantial gains of up to thousands can be achieved 93 41 ode 42 343 Ot EX EP E ee it Moe eec 93 41 ode 42 343 Ot E itr icd DEM ind LES ua URGE MM cl Sh Le o x transfer direction electron potential Figure 12 Gain register operation IXon3 SECTION 3 Page 24 lt ANDOR ees FEATURES amp FUNCTIONALITY 3 1 2 EM Gain amp Read Noise As explained on the previous pages 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 spectacular improvement in low light detection is that it negates the effect of any electronic noise that may be generated by the read out electronics All CCD cameras have an associated minimum electronic noise floor which is often termed the R
60. ensuring that this ground breaking ultra sensitive technology can deliver a prolonged quantitative service to the user and if these highly sensitive sensors are used with due care and attention ageing can be minimized and should not present any real problem to the user More details of this ageing effect and Andor s solutions can be found on page 32 but listed below are some guidelines to minimize the EM gain ageing process e Do not use EM gain values greater than necessary to overcome the read noise A rule of thumb is that a gain of x4 or 5 the rms read noise accessible from the spec sheet or performance sheet is more than sufficient to render this noise source negligible In practice this can always be achieved with EM Gain of less than x300 often much less Pushing gain beyond this value would give little or no extra Signal to Noise benefit and would only reduce dynamic range e Only select the extended EM gain scale of x1000 for single photon counting applications and always ensure that the signal falling onto the sensor is indeed within the regime of low numbers of photons per pixel e Turn down the gain when the camera is not acquiring e Try not to over saturate the EMCCD sensor IXon3 SECTION 1 Page 16 ANDOR ANDO INTRODUCTION 1 3 12 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 o
61. er 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 In this mode the camera will run the Idle Keep Clean Cycle until the Start command is issued by the PC which is identical to all the modes previously discussed On receipt of this command the camera will switch to running the normal Internal Keep Clean until a Software Trigger command is issued by the PC This event will start the exposure and readout sequence On completion of the readout the camera will return to the Internal Keep Clean until the next Software trigger is issued Idle keep clean Storage area read cycle Waiting for Cycle Time out phase Start command Exposure period Exposure period lt gt Image area clocks Storage area clocks Horizontal clocks Software trigger Fire output Start command Internal Keep Clean Image area shifted into storage area Horizontal clocks 9 running Figure 36 Software trigger in non frame transfer mode iXon3 SECTION 3 Page 60 p ANDOR e FEATURES amp 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
62. erature of the CCD simply to be dependent on or vary with the heat sink temperature Therefore a temperature sensor on the CCD combined with a feedback circuit that controls the operating current of the cooler allows stabilization of the CCD to any desired temperature within the cooler operating range 3 2 2 Fan settings The speed of the cooling fan can also be controlled useful if working in experimental configurations which are extremely sensitive to vibration The vast majority of applications including optical microscopy can be used with the default highest fan speed since the vibrations from the fan are minimal However some applications can be extremely sensitive to even the smallest of vibrations such as when combining an optical set up with patch clamp electrophysiology or atomic force microscopy and it can be useful to either select a slower fan speed or to temporarily turn off the fan altogether for the duration of the acquisition If the fan is being turned off altogether depending on the cooling temperature selected and on the ambient temperature the acquisition duration can be as long as 15 20 minutes before temperature begins to rise The fan must then be turned on again to give the head time to re stabilize dissipate built up excess heat from the peltier TE cooler before the next acquisition is begun NOTE If water cooling is being used the fan can be turned off and exceptional cooling performance maintained indef
63. etectors on the market The company is also playing a pivotal role in increasing our understanding of this ground breaking technology In September 2003 it hosted the 1 International EMCCD Symposium in Limavady Northern Ireland a dedicated conference which looked at the current usage and future development of EMCCDs This was followed in April 2005 by the 2 International EMCCD Symposium held in Connecticut USA Please go to www emccd com for further details iXon3 SECTION 4 Page 74 ANDOR ee 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 iXon3 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 Incoming photons are allowed to fall on the uncovered portion of the array and the accumulated charge is then rapidly shifted into the masked storage region for transfer to the serial output register While the signal is being integrated on the light sensitive portion of the sensor the stored charge is read out Frame transfer devices have typically faster frame rates than full frame devices and have the advantage of a high duty cycle i e the sensor is always collecting light A potential disadvantage of t
64. f shadowing particles directly in the focal path The iXon3 range comes equipped with an internal C mount shutter Whilst not being required for frame transfer operation which is a shutter free readout mode it is good practice to close the shutter when the camera is not in acquisition use for a reasonable period It is also advisable to use the software to close the shutter when exposing the camera to the open environment i e removed from a microscope C mount or focusing lens whilst power is still flowing to the camera When the camera power is turned off the C mount shutter closes automatically and the camera can be moved freely We recommend that the C mount opening is covered when the camera is not in use If there is evidence of particulate contamination on the front window it is possible to clean the window by blowing dry air gently over the window surface However the shutter has to be kept open for this procedure which means that the camera has to be powered up Therefore since light can access the EMCCD sensor during this time we recommend that EM Gain is turned off readily selectable through the software iXon3 SECTION 1 Page 17 ANDOR e TECHNOLOGY INSTALLATION 2 1 INSTALLING THE HARDWARE The system requires a PCI PCle compatible computer PCI 2 2 for CCI 22 amp CCI 23 cards or PCle for the CCI 23 controller cards shown on page 9 and the minimum recommended PC specifications are as fo
65. ge will terminate the exposure Global clear used to keep image area clean Exposure period 1 Exposure period 2 i H T Image area clocks i L Storage area clocks f m Horizontal clocks Extemal trigger Fire output Image area shifted Storage area read into storage area out phase Exposure period defined by extemal pulse Global clear used to Horizontal clocks keep image area continue running clean Exposure period 1 Exposure period 2 lt gt lt B Image area clocks O Storage area clocks Horizontal clocks Extemal trigger Fire output Note exposure period starts Note Falling edge before the readout MUST occur after Exposure period has completed read out completed defined by extemal pulse Figure 31 External Exposure Trigger in Frame Transfer mode 885 model only IXon3 SECTION 3 Page 55 ANDOR Ny TEonnoroay FEATURES amp FUNCTIONALITY 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 The camera is now ready to start the real exposure sequence The timing sequence is illustrated in the figure below During the exposure the FIR
66. he computer equipment that is to be used to operate the iXon3 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 All cables should be fastened securely into place in order to provide a reliable connection and to prevent accidental disconnection The power supply to the computer system should be switched off when changing connections between the computer and the camera The computer manufacturer s safety precautions should be followed when installing the PCI Controller Card into the computer The circuits used in the camera head and the PCI controller card are extremely sensitive to static electricity and radiated electromagnetic fields and therefore they should not be used or stored close to EMI RFI generators electrostatic field generators electromagnetic or radioactive devices or other similar sources of high energy fields Types of equipment that can cause problems include Arc welders Plasma sources Pulsed discharge optical sources Radio frequency generators and X ray instruments 1 3 9 Condensation You may see condensation on the outside of the camera body if the temperature of the cooling water is too low or if the water flow is too great The first signs of condensation will usually be visible
67. he protection provided by the equipment may be impaired 1 3 2 Environmental conditions Indoor use only Altitudes up to 2000 m Operating temperature 0 C to 40 C e Maximum relative humidity lt 70 non condensing Other voltage fluctuations as stated Over voltage category 1 This is designed to withstand the normal transient voltages expected at a mains socket Pollution degree 2 Only non conductive pollution occurs Occasionally temporary conductivity caused by condensation is to be expected Electromagnetic compatibility This is a Class A product In a domestic environment this product may cause electromagnetic interference in which case the user may be required to take adequate measures IXon3 SECTION 1 Page 12 ANDOR er INTRODUCTION 1 3 3 Regular checks The state of the product should be checked regularly especially the following e The integrity of the enclosure e Any water hoses used e The AC DC External Power Supply e The mains cable NOTE Do not use equipment that is damaged 1 3 4 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 PAT testing NOTE Do not use equipment that is damaged 1 3 5 Replacement parts A PS 20 see page 20 which is the only external power supply recommended for use with the iXon camera has been supplied to you If this unit fails or is damaged pleas
68. his architecture is the charge smearing during the transfer from the light sensitive to the masked regions of the CCD although they are significantly better than full frame devices The smearing being more prevalent when exposure times are closer to the time taken to shift the charge under the mask in the order of milliseconds The Andor iXon3 is the best camera on the market for minimizing such smear as the vertical clock speeds can be tuned via the software to deliver the fastest parallel shifts in the industry which has the further advantage of faster overall frame rates especially when using sub array and or pixel binning readout options Essentially the EMCCD sensor is capable of detecting single photon events without an image intensifier achievable by way of a unique electron multiplying structure built into the chip Traditional CCD cameras offered high sensitivity with readout noises in single figure lt 10e but at the expense of slow readout Hence they were often referred to as slow scan cameras The fundamental constraint came from the CCD charge amplifier To have high speed operation the bandwidth of the charge amplifier needs to be as wide as possible but it is a fundamental principle that the noise scales with the bandwidth of the amplifier hence higher speed amplifiers have higher noise Slow scan CCD s have relatively low bandwidth and hence can only be read out at modest speeds typically less than 1MHz EMCCD cameras av
69. ically reduce the true dynamic range of the camera Ideally for maximum dynamic range whilst maintaining improved Signal to Noise S N the EM gain setting should be set equal to the read noise at the readout speed selected value obtainable from the performance sheet that comes with the delivered system Pre amplifier gain selection in CCDs is traditionally used to trade off S N vs dynamic range A higher PreAmp setting means fewer electrons count resulting in a lower system noise floor therefore a higher S N However high PreAmp settings may not match well to the pixel well depth of the sensor therefore a lower setting can be selected to meet the full well depth potential e g a PreAmp setting yielding 1 5 e count may be selected to ensure that the 65536 digitization levels of a 16 bit A D is closely matched to a 100 000 e pixel well depth A PreAmp setting of 1 e count while giving a lower noise floor would not harness the full 100 000 e well depth The situation is not nearly as straightforward for EMCCDs because 1 EM gain overcomes readout noise and amplifies signals relative to the digitization noise which is fixed for a given PreAmp setting 2 Gain register pixels have a greater well depth than the imaging pixel well depth The latter point can be particularly confusing and indeed has led to confusion in the field What this has meant is that we have set some of the lower pre amp settings associated with the EM output to match the exte
70. ine Offset The baseline or bias level is an electronic offset added to the output signal from the EMCCD sensor to ensure that the displayed signal level is always a positive number of counts This baseline level often tends to increase with decreasing sensor cooling temperature For all iXon3 cameras it is factory calibrated to approximately 400 counts at a cooling temperature of 75 C NOTES e At warmer temperatures the baseline level will decrease and may move below zero resulting in a signal of zero counts being displayed This can be overcome either by moving to a lower cooling temperature or by using the baseline offset option which adds up to 1000 counts to the baseline level e Conversely at colder temperatures than the calibration temperature the baseline may increase slightly and this can be countered by using the baseline offset option to subtract up to 1000 counts from the baseline level 3 3 5 2 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 Any drift in the baseline level can be corrected by using the Baseline Clamp option Baseline Clamp corrects each individual image for any baseline drift by subtracting an average bias signal from each image pixel and then adding 100 counts to ensure that the displayed signal level is alway
71. initely IXon3 SECTION 3 Page 34 lt ANDOR emen FEATURES amp FUNCTIONALITY 3 3 SENSOR READOUT OPTIMIZATION To allow the camera to be optimized for the widest range of applications it is important to have flexibility in the readout options available some of these include e Cooling please see page 34 e Sensor preamp settings e Variable horizontal readout rate e Variable vertical shift soeed e Output amplifier selection e Baseline settings e Binning and sub image settings These options and an explanation of how to optimize them are explained on pages 36 42 IXon3 SECTION 3 Page 35 p ANDOR ce FEATURES amp FUNCTIONALITY 3 3 1 Sensor PreAmp 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 today To overcome this shortcoming and access the range of signals from the smallest to the largest and to optimize the camera performance it is necessary to allow different pre amplifier gain settings However it is only ever recommended selecting something other than the default highest PreAmp most sensitive setting for applications that are extremely challenged by dynamic range concerns It is very important however that for such high dynamic range applications the user applies even more care to the amount of EM gain applied high EM gain can drast
72. installation For detailed instructions on how to install the program software please refer to the software manual supplied with your camera IXon3 SECTION 2 Page 22 p ANDOR aae FEATURES amp 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 iXon3 camera is the latest EMCCD a revolutionary technology capable of single photon detection An EMCCD is a silicon based semiconductor chip bearing a two dimensional matrix of photo sensors or pixels This matrix is usually referred to as the image area The pixels are often described as being arranged in rows and columns the rows running horizontally and the columns vertically The EMCCD in the camera is identical in structure to a conventional Charged Coupled Device CCD but with the shift register extended to include an additional section the Multiplication or Gain Register as shown in figure 11 below o IMAGE SECTION STORE SECTION ON CHIP CHARGE TO VOLTAGE CONVERSION HHHH HHHH OUTPUT READOUT MULTIPLICATION REGISTER REGISTER Figure 11 EMCCD structure IXon3 SECTION 3 Page 23 p ANDOR kan FEATURES amp FUNCTIONALITY During an acquisition using a conventional Frame Transfer CCD FT CCD the image area is exposed to light and an
73. ise from the dark signal can be reduced A1 1 18 Signal To Noise Ratio The Signal to Noise Ratio commonly abbreviated as S N or SNR is the ratio between a given signal and the noise associated with that signal Noise has a fixed component and a variable component shot noise which is the square root of the signal Thus the S N usually increases improves as the signal increases The maximum S N is the ratio between the maximum signal i e the saturation level and the noise associated with that signal At near saturation levels the dominant source of noise is the shot noise of the signal iXon3 APPENDIX Page 86 ANDOR ee APPENDIX A1 2 MECHANICAL DIMENSIONS Mounting points 6 off 1 4 20 UNC Tapped x 15mm deep 137 8 5 42 147 5 78 0006809088860800 Focal Plane 17 5 mm from face plate 4 off M5 x 5mm deep 42 0 1 65 DIRECTION FOR CABLE 0 Figure 47 Dimensions of 860 885 amp 897 models Mounting points 6 off 1 4 20 UNC Tapped x 15mm deep 137 8 5 42 38 0 1 49 8 B f 25 3 B B Focal Plane 17 5 mm from face plate 46 5 1 83 Figure 48 Dimensions of 888 mode iXon3 APPENDIX Page 87 ANDOR ee APPENDIX A1 3 DECLARATION OF CONFORMITY Belfast Office Corporate Headquarters 7 Millennium Way Springvale Business Park Belfast BT12 7AL Northern Ireland Tel 44 28 9023 712
74. lable for other iXon3 models since this mode requires an 885 Global Clear function please see page 57 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 The ability to overlap the readout with the exposure period allows for very high frame rates In order to ensure that light falling on the Image area before the start of the exposure does not contribute to the measured signal the CCD is placed in a special keep clean mode This keep clean mode uses the feature Global Clear which is only available on a limited range of CCD sensors and hence not available on all iXon3 cameras Although the start of the exposure can overlap the read out phase of the previous image the end of the exposure cannot This is because the end of the exposure is marked by shifting the Image area into the Storage area It is not possible to use the same feature as is used to prevent light that fell before the exposure starts from contributing to the measured signal as this would cause the already accumulated charge to be cleared NOTE If the falling edge occurs during the read out phase it will be ignored and the next falling ed
75. letion of the exposure period the camera performs the number of vertical shifts defined by the sub area height set by the user and then again wait for the exposure period before the next set of vertical shifts This process is repeated until the number in the series has been captured at which point the readout starts External trigger keep clean running with Number of vertical clocks depends on sub area height global clear on 885 E v Image amp Storage area clocks Horizontal clocks External Trigger Fire output LL eur Number of repeats set Read phase Exposure time by series length Figure 39 External Start trigger in Fast Kinetics mode IXon3 SECTION 3 Page 63 lt ANDOR INEO emen FEATURES amp FUNCTIONALITY 3 6 SHUTTERING The iXon range of cameras can be supplied with a built in shutter The shutter is intended for taking background images and protecting the camera from excessive light and dust It is not designed to operate at the high frame rates the camera is capable off Under normal operation the shutter should be set to Permanently Open and the shutter open and close times to 0 seconds If you do need the shutter to open and close automatically during your experiment then set the opening and closing times to 50ms iXon3 SECTION 3 Page 64 lt ANDOR A moo FEATURES amp FUNCTIONALITY One of the distinctive features of the iXon3 is the capability to quantitatively capture
76. livers a new benchmark of simplicity and ease of operation to the user and sets a new precedent in what should be expected from EMCCD technology 1000 900 800 700 600 500 400 Measured EM Gain 0 100 200 300 400 500 600 700 800 900 1000 Software Gain Setting Figure 18 RealGain calibration in the iXon3 the same linear relationship holds across all cooling temperatures iXon3 SECTION 3 Page 31 p ANDOR NN FEATURES amp FUNCTIONALITY 3 1 7 EM Gain Ageing What causes it and how is it countered As already noted in the discussion on safe camera operation in Section 2 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 This ageing effect appears to be dependent on the amount of charge that is passed through the gain register combined with the actual EM electric field strength that it is transferred through It seems to be very strongly dependent on the EM electric field strength Therefore when operating at high EM gains the ageing rate can be disproportionately greater Fortunately it has been observed that this ageing effect itself decreases with time meaning that with proper use the device should remain useful for many years As part of Andor s EMCCD production process all sensors are exposed to conditions that results in much of the shorter term ageing having
77. ll refund all fees associated with the return of any product that has been reported as defective within 30 days of delivery 1 2 8 Failure to pay invoices when due may result in the interruption and or cancellation of the standard warranty 1 2 9 Andor warrants the replacement or repaired parts components to be free from defects in materials and workmanship for twelve months from the date of dispatch or for the reminder of the warranty period whichever is longer 1 2 10 For products returned under warranty Andor will extend the complete product warranty by 30 days iXon3 APPENDIX Page 92 ANDOR ea APPENDIX Hardware and Software WARRANTY SERVICE 1 3 Service Description 1 3 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 1 3 2 In order to be eligible for warranty repair or replacement the equipment must be suffering a defect which meets the criteria set out in the supply contract and must be within its specified warranty period Services such as upgrades to Hardware and Software are excluded from the scope of this service description and should be ordered separately 1 4 Access to
78. llows e 3 0 GHz single core or 2 6 GHz multi core processor e 2GB RAM e 100 MB free hard disc to install software at least 1GB recommended for data spooling e PCI 22 PCI X 1 0 or PCle slot e 10 000 rpm SATA hard drive preferred for extended kinetic series SATA RAID 0 recommended for iXon 885 e g Seagate Barracuda Western Digital Caviar RE or VelociRaptor etc e Windows XP Vista and 7 or Linux In all cases the operating system should be on a separate hard drive and the hardware controller should be on a separate PCI bus IXon3 SECTION 2 Page 18 ANDOR e INSTALLATION 1 Firmly press the connector into the chosen expansion slot e g 2 For maximum cooling when the supplied PCI card has an Auxiliary Power connector flylead this can be connected to a suitable point on the power supply of the PC e g aS NOTE Should any problems be experienced with this connection please contact your nearest technical representative 3 Making sure that the card s mounting bracket is flush with any other mounting brackets or filler brackets to either side of it secure the Controller Card in place Replace the cover of the computer and secure it with the mounting screws if applicable Reconnect any accessories you were using previously IXon3 SECTION 2 Page 19 AN DOR ee INSTALLATION 2 2 CONNECTORS MDR 36 interface connector water connectors 42x42x12 cabe is attached at 6
79. lso requires knowledge of the bias offset and the EM Gain The calculation path is shown in figure 40 below minus bias offset x pre amp counts _ lt signal counts X signal electrons EM Gain A s QE wavelength of interest E E Original signal c c DON SIBI in incident photons in electrons Figure 40 Count Convert calculation path Furthermore knowledge of the Quantum Efficiency QE at each wavelength and light throughput properties of the camera window enables this process to be taken a step further allowing the signal to be estimated in photons incident at each pixel For this step the user must input the signal wavelength In fluorescence microscopy for example this would correspond to the central wavelength defined by a narrow band emission filter matched to the fluorophore of interest If the spectral coverage of the signal on the detector is too broad such that the QE curve varies significantly throughout this range then the accuracy of the incident photon estimation would be compromised The Count Convert functionality of the iXon3 provides the flexibility to acquire data in either electrons or incident photons with negligible slow down in display rate Furthermore the option exists to record the original data in counts and perform this important conversion to either electrons or photons as a post conversion step while retaining the original data IXon3 SECTION 3 Page 65 lt ANDOR
80. measure of a camera s ability to capture valuable photons A high QE results in more photons being converted to photoelectrons within the CCD pixels Once converted the photoelectrons in a given pixel must overcome the detection limit or noise floor of the camera which is set by the system noise EMCCDs deliver superior sensitivity by maximizing QE and minimizing system noise through the unique gain control feature Single photon events are now well within the capabilities of super sensitive EMCCD technology IXon3 SECTION 4 Page 73 ANDOR 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 These levels of sensitivity are vital for low light life science and physical science imaging applications such as single molecule detection live cell microscopy weak luminescence detection or demanding astronomy applications to name only a few 4 1 5 What is Andor Technology s experience with EMCCDs Andor Technology was the first company to introduce an EMCCD based detector in 2000 Since then the company has led the way in the development of EMCCD detectors introducing the first back illuminated EMCCD in January 2003 Andor now offers the widest range of EMCCD based d
81. med delay before starting the readout phase The camera continues in this cycle until the number of images requested has been captured Because the Image area is not cleaned between trigger events the effective exposure time is the time between events The User Defined Delay is to allow for the capture of events which occur after the trigger pulse In the case of the first trigger the effective exposure time is given by the user defined delay since keep clean cycles have been running up until the first trigger This is in contrast to the subsequent exposure periods which are defined the time between the external trigger events Thus for experimental protocols that involve Continuous Wave CW light the first image will be dimmer some protocols may require that this image is discarded NOTE In the case of the 885 camera range the global clear feature will be ON until the first trigger is received External trigger cycle running while waiting Storage area read for first trigger with Exposure period 1 out phase global clear on 885 Exposure period 2 Exposure period 3 Image area clocks i Storage area clocks sne pm E S Horizontal clocks EL OO Fire output 11 LJ First external trigger Image area shifted Horizontal clocks continue to run after into storage area Second external trigger readout completes Global clear not active User settable delay Figure 29 External Trigger in Frame Transfer mode IXon3 SECTION 3
82. mode Step4 With the image now in the Storage area the captured image is read out The time taken to read out the image is again the same as in the Frame Transfer mode Step5 On completion of the read out the CCD is completely cleared ready to acquire the next image The CCD will remain in the Keep Clean Cycle until the end of the accumulation or kinetic cycle time depending on the acquisition mode i e back to Step 1 As at least one Keep Clean Cycle is performed between each exposure the minimum exposure time is no longer set by the time to read out the image IXon3 SECTION 3 Page 45 p ANDOR NUR FEATURES amp FUNCTIONALITY 3 4 2 1 Points to note about using an FT CCD as a standard CCD e The exposure time accumulation cycle time and the kinetic cycle time are independent e The minimum exposure time is not related to the time taken to readout the image e External trigger operates as if the CCD was an NFT CCD e 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 e For short exposure times the image may appear streaked as the time taken to shift the Image area into the Storage area and the exposure time may be of similar magnitude but much less than a ral non frame transfer e Light falling on the Image area while the Storage area is being read out may contaminate the image in the Storage area due to charge spilling verti
83. n read out either with EM Gain ON or alternatively through the conventional amplifier i e standard CCD operation Again this plot assumes a photon wavelength at which the QE of the sensor is 9096 Specifically this figure applies to 897 and 888 models where the user has the choice of either EMCCD or conventional amplifiers At these slower speed operations when one has the choice to read out as a conventional CCD it can often be advantageous to do so in order to achieve better signal to noise Indeed the plots show that the cross over point is at 42 photons pixel below which it is still advised to readout through the EM amplifier with Gain applied 100 SIN ideal SIN 1MHz Conventional S N EM ON 1MHz 42 photons 100 DO Photons pixel Assuming 90 QE 0 1 Figure 14 EM Gain ON vs Conventional Amplifier signal to noise plots for back illuminated iXon3 EMCCDs at 1MHz readout speed applies to 897 and 888 models iXon3 SECTION 3 Page 27 p ANDOR Wc ee FEATURES amp FUNCTIONALITY 3 1 4 Multiplicative Noise Factor amp Photon Counting It is impossible to know 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 At reasonably high gain levels g
84. nd Storage area e There are no Keep Cleans during the acquisition sequence e Due to the very short exposure times streaking may be evident IXon3 SECTION 3 Page 47 ANDOR WA onno FEATURES amp FUNCTIONALITY 3 4 4 Keep Clean Cycles iXon3 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 Finally we will look at the keep clean cycle running while the camera is waiting for an external trigger event to occur When the camera is idle i e not actively capturing images it is repeatedly running the Idle Keep Clean Cycle This cycle is composed of a vertical shift followed by a series of horizontal shifts The number of horizontal shifts is dependent on the actual CCD When the Start command is received from the PC the camera will complete the current keep clean cycle and then perform a sufficient number of vertical shifts to ensure both Image and Storage regions are completely charge free see the figure below On completion of this sequence the camera is ready to run the exposure sequence The exact exposure sequence will depend on several factors including the trigger and the readout
85. nded well capacity of the gain register pixels as reported by the sensor manufacturers E2V or Tl This means that these pre amp settings are designed to be used with EM Gain Otherwise the lower well capacity of the imaging pixels will saturate long before the A D This is why some users have been confused at not being able to reach the full 16k counts of the 14 bit A D channel when they hadn t applied EM Gain IXon3 SECTION 3 Page 36 ANDOR WU o reenocoes FEATURES amp FUNCTIONALITY Basically Andor recommend using the default highest value PreAmp setting e g x4 8 setting of the iXon3 897E giving 11 3 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 x300 EM gain except for single photon counting experiments At this highest PreAmp setting the 14 bit A D would saturate 16 380 x 11 3 e count 180 800 e In our opinion this is a resaonable range to cover the majority of low light measurements For example with an EM gain of x300 RealGain it would take 600 electrons in a pixel of the sensor to reach this A D saturation limit Say the QE is 80 at the wavelength of interest then this corresponds to maximum of 750 photons falling onto that pixel That is perfectly satisfactory dynamic range for the vast majority of low light imaging applications The core reason for us wishing
86. nitive or consequential damages or loss of use 1 2 2 The following hardware components have warranties greater than 12 months Vacuum Warranty Andor provides a 7 Year warranty on its UltraVac seal for iXon3 cameras The UltraVac seal provides a permanent hermetic vacuum head which protects the CCD sensor Should the vacuum fail during the warranty period Andor will repair the vacuum and the components protected by it including the CCD sensor If you suspect a vacuum failure typically shown by degradation in quantum efficiency or cooling performance then you should stop using the camera immediately and contact your seller support representative Continued use of the unit once vacuum failure is suspected will void the warranty on the sensor and the components held inside the vacuum Components protected by the vacuum but damaged or defective due to any cause other than vacuum failure are subject solely to the standard warranty terms ICCD Andor provides a 2 year warranty for its ICCD products Any damage caused by laser burn bleaching of the photocathode brought about by over illumination of the cathode or ion damage of the cathode brought about by excessive numbers of photoelectrons in the Multichannel plate will not be covered by the warranty IXon3 APPENDIX Page 91 ANDOR APPENDIX 1 2 3 The following products and parts have specific warranty limitations X RAY Cameras Andor s standard warranty terms apply t
87. o x ray cameras except for the sensor and other exposed parts which are not covered in those models a where the sensor is openly exposed typically DO DX models and or b where the sensor is used for the direct detection of x ray photons Sensor Andor does not warrant sensors to be completely free from defects Items considered as consumables are not covered under this warranty including but not limited to the following items cables fibre optics filters Third party products not manufactured by Andor are not covered under this warranty The customer will only be entitled to the benefit of any such warranty or guarantee as is given by the manufacturer to Andor unless specifically agreed in writing by both parties 1 2 4 Andor guaranties that the supplied Software substantially conforms to published specifications original license Andor does not warrant software to be error free or that Customers will be able to operate software without problems or interruptions The standard software warranty period is 12 months from dispatch 1 2 5 During Warranty customers have access to Andor support to report product defects only Warranty does not include training or consultancy services 1 2 6 The Warranty period is deemed to start at the date of dispatch from Andor s manufacturing facility 1 2 7 Customers must notify the Andor customer service centre within 30 days of taking delivery of a product or part they believe to be defective Andor wi
88. of one vertical shift the resultant image may appear to have shifted one row Actual read phase External trigger i Exposure time pattern depends Keep Clean cycles i on user selection Image amp Storage clocks Vertical FUUGA Register clocks Horizontal JL External trigger input Fire output Read out phase starts here by shifting image area into storage area An external trigger occurring anywhere inside this time Horizontal register window will be captured by clocks continue to this cycle Global clear on run during exposure 885 active until External period trigger pulse received Figure 27 External Trigger Keep Clean Cycle NOTE The 885 range of iXon3 cameras have a global clear feature which can be used to remove all the charge accumulated in the whole Image section of the sensor simultaneously This feature is enabled in all 885 models when external trigger is selected It is particularly useful in external trigger mode when the light level pre trigger is quite bright as it will reduce the effect of vertical streaking IXon3 SECTION 3 Page 50 p ANDOR WET NE FEATURES amp FUNCTIONALITY 3 5 TRIGGERING OPTIONS The iXon3 range of cameras have several different triggering modes These include Internal External and Fast External External Start External Exposure and Software Trigger It should be noted that not all the triggering options are available on all cameras Note also that m
89. of slower frame rates There are number of different horizontal readout rates available on all iXon3 models Please refer to the performance sheet for readout rates available on your particular model 3 3 3 Variable Vertical Shift Speed The vertical shift speed is the time taken to vertically shift all pixels one row down with the bottom row entering the shift register The ability to vary the vertical shift speed is important for several reasons It is possible using the different vertical speeds to better synchronize the frame rates to external events such as a confocal spinning disc Faster vertical shift speeds also have benefits such as lower Clock Induced Charge CIC A drawback with faster vertical shift speeds is that the charge transfer efficiency is reduced effectively reducing the pixel well depth This is particularly important for bright signals as a pixel with a large signal is likely to have some charge left behind if the vertical shift speed is too fast This will result in degraded spatial resolution Slower vertical clocks ensure better charge transfer efficiency giving maximum pixel well depth but result in a slower maximum frame rate To improve the transfer efficiency the clocking voltage can be increased using the vertical clock voltage amplitude setting However the higher the voltage the higher the clock induced charge Thus the user must make a measured judgement as to which setting works best for their situation for example
90. oid this constraint by amplifying the charge signal before the charge amplifier and hence maintain unprecedented sensitivity at high speeds By amplifying the signal the readout noise is effectively by passed and as such EMCCD readout noise is no longer a limit on sensitivity and can often be considered negligible Please see pages 23 amp 24 for further details on EMCCD technology and sensor architecture IXon3 SECTION 4 Page 75 ANDOR Pao HARDWARE 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 However it is important to understand that all such environments are not the same and the underlying technology used can seriously impact camera life and performance A permanent hermetic vacuum head is an essential component of high end imaging and spectroscopy EMCCD cameras A permanent vacuum requires not only a hermetic seal but also low outgassing These criteria are what Andor s UltraVac vacuum process uniquely ensures It is the low outgassing see page 78 that is the real challenge and in reality what sets the real limit on long term performance Andor has developed and utilized the UltraVac process over more than 10 years so it is proven with 1000 s of
91. or the Customer shall ship the PART to Andor at customer expense The customer is responsible for return shipping and insurance costs Any products returned without an RMA number may be refused and returned to the customer at their expense Andor shall provide a single point of return for all products 1 5 3 On receipt of the part at the Andor repair facility Andor shall carry out the necessary fault diagnosis and repair and return the part to the Customer iXon3 APPENDIX Page 93 ANDOR APPENDIX 1 5 4 The method of shipment and choice of courier for the return will be at Andor s discretion Delivery Duties Unpaid DDU Incoterms 2000 Andor does not guarantee the arrival time of the part 1 5 5 Customer must adhere to Andor packing instructions including anti static precautions when shipping the defective unit as any damage incurred during shipment to Andor will not be covered under warranty The packing instructions can be obtained from Andor as part of the part request procedure 1 5 6 If the part is not economically repairable then a replacement part new or refurbished will be supplied at Andor discretion and expense 1 5 7 In case of replacement the replacement unit becomes the property of the Customer on an exchange basis 1 5 8 In case of misuse the Customer will be contacted to decide the course of action These actions may include Scrapping the part Return of the defective unrepaired part to the
92. orbed When a UV or visible photon is absorbed by the detector itcan at best produce only one photoelectron Photons of different wavelengths have different probabilities of producing a photoelectron and this probability is usually expressed as Quantum Efficiency QE or Spectral Response QE is a percentage measure of the probability of a single photon producing a photoelectron while spectral response is the number of electrons that will be produced per unit photon energy Many factors contribute to the QE of a CCD but the most significant factor is the absorption coefficient of the silicon that serves as the bulk material of the device A1 1 14 Readout Readout is the process by which data are taken from the pixels of the CCD and stored in computer memory The pixels which are arranged in a single row are read out individually in sequence Readout involves amplifying the charge on each pixel into a voltage performing an analog to digital conversion then storing the data in computer memory The time taken to perform this operation is known as the read time A1 1 15 Saturation Saturation is the largest signal the CCD can measure A signal is measured in terms of the amount of charge that has built up in the individual pixels on the CCD chip A number of factors determine the maximum amount of charge that the CCD can handle A1 1 16 Scans Keep Clean amp Acquired The CCD is continually being scanned to prevent its becoming
93. ot noise from the signal is additionally dependent on the signal level itself If either the signal or the dark signal falls to zero their respective shot noise also falls to zero The total pixel noise is not however 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 readnoise darkshot sigshot where e total is the pixel noise e readnoise is the readout noise e darkshot is the shot noise of the dark signal e Sigshot is the shot noise of the signal A1 1 12 2 Fixed Pattern Noise Fixed Pattern Noise FPN consists of the differences in count values read out from individual pixels even if no light is falling on the detector These differences remain constant from read to read The differences are due in part to a variation in the dark signal produced by each pixel and in part to small irregularities that arise during the fabrication of the CCD Since fixed pattern noise is partly due to dark signal it will change if the temperature changes but because it is fixed it can be completely removed from a measurement by background subtraction iXon3 APPENDIX Page 84 ANDOR See APPENDIX A1 1 13 Quantum Efficiency Spectral Response The glossary refers to signals as a number of electrons More strictly speaking these are photoelectrons created when a photon is abs
94. pixel through gain register 200 000 pixels illuminated IXon3 SECTION 3 Page 33 lt ANDOR WU etm FEATURES amp 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 Therefore the minimum absolute operating temperature of the EMCCD depends on the temperature of the heat sink Andors vacuum design means that we can achieve minimum cooling temperatures unrivalled by other manufacturers The maximum temperature difference that a TE device can attain is dependent on the following factors e Heat load created by the CCD e Number of cooling stages of the TE cooler e Operating current 3 2 1 Cooling options The heat that builds up on the heat sink must be removed and this can be achieved in one of the two following ways 1 Air cooling a small built in fan forces air over the heat sink 2 Water cooling external water is circulated through the heat sink using the water connectors on the head and this can take one of the following forms e Recirculation e Chilling All Andor iXon3 systems support both cooling options Whichever method is being employed it is not desirable for the operating temp
95. r to other devices should it be required IXon3 SECTION 1 Page 10 ANDOR INTRODUCTION The iXon3 system is designed to be powered from a PS 20 external Power Supply Block PSB which is used to supply power to the Thermoelectric cooler within the camera The PSB requires an AC mains input between 90 264 V 47 63 Hz and a maximum supply current of either 1A 115V or 0 5A 9 230V The output of the PS 20 is 7 5V DC at 4 0A maximum The PS 20 is fitted with a 3 pin IEC connector for the electrical supply input and the wall socket must be connected to the building s protective earth system The connection to the iXon3 is made via a 2 1 mm jack connector Power requirements Voltage 7 5V 5 Current 4A maximum at peak cooling Ripple amp Noise 1 maximum Total Power 30 W maximum NOTE 1 Cooling is only available when the PSB is connected to the camera 2 In the UK or other countries using UK standard electrical systems the mains input into the PS 20 must be fitted with a 240V 5A fuse 1 2 5 Software Your iXon3 may have been supplied with Andor Solis or Andor iQ software or with the Andor SDK However it is also compatible with a range of 3 party software options offering optimized acquisition control and analysis functionality For further details of Andor software capabilities and software options please go to the following page on our website http www andor com products software IXon3 SECTION 1
96. range makes use of a four stage see NOTE below 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 The iXon3 is expertly designed to yield maximum heat dissipation via either forced air cooling in built fan or water cooling which in combination with Andor s UltraVac vacuum process results in market leading cooling performance A recirculator or a chiller can be purchased from Andor Technology to provide convenient and effective heat dissipation through water cooling The iXon3 camera also contains temperature control components which regulate the cooling of the camera and ensure that a stable temperature is maintained between and throughout measurements Permanent all metal seal emn Heat Removal e Vacuum Window anti reflection coated CCD TE Cooler Figure 44 Ultravac metal hermetic vacuum sealing NOTE DV885 models have a three stage peltier cooler DU885 models have a four stage peltier cooler IXon3 SECTION 4 Page 77 ANDOR er HARDWARE 4 4 OUTGASSING Outgassing is the release of a gas trapped in material It is a problem encountered in high vacuum applications Materials not normally considered absorbent can release enough
97. s to circumvent the Multiplicative Noise also known as Noise Factor Multiplicative noise is a by product of the Electron Multiplication process and affects both EMCCDs and ICCDs In fact it has been measured to be significantly higher in ICCDs The noise factor of EMCCDs is well theorized and measured to account for it you increase the shot noise of the signal by a factor of square root 2 x1 41 This gives the new effective shot noise that has been corrected for multiplicative noise The effect of this additional noise source on the overall Signal to Noise ratio can be readily viewed in the S N plots in the technical note entitled EMCCD signal to noise plots Photon Counting Mode does not measure the exact intensity of a single photon spike it merely registers its presence above a threshold value It does this for a succession of exposures and combines the individual binary images to create the final image As such this mode of operation is not affected by the multiplication noise which otherwise describes the distribution of multiplication values around the mean multiplication factor chosen The end result is that low light images acquired through this mode of acquisition are improved by a factor of x1 41 Signal to Noise compared to a single integrated image with the same overall exposure time IXon3 SECTION 3 Page 70 p ANDOR m N FEATURES amp FUNCTIONALITY To successfully photon count with EMCCDs there
98. s a higher frame rate than standard external trigger NOTE Once a sufficient number of keep cleans have been performed External and Fast External Trigger are identical External Start is a mixture of External and Internal Trigger In this mode the camera will perform a sequence of External Keep Clean Cycles while waiting for one external trigger event to occur and then start the acquisition process going Once this external trigger event has occurred the camera will switch to internal trigger and the acquisition will progress as if the camera was in internal trigger mode External Exposure Trigger is a mode of operation where the exposure time is fully controlled by the external trigger input While the trigger input is high the CCD is accumulating charge in the Image area When the external trigger goes low the accumulated charge is quickly shifted into the Storage area and then read out in the normal manner Software Trigger is a mode whereby the camera and software are in a high state of readiness and can react extremely quickly to a trigger event issued via software 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 These modes are explained and illustrated in more detail in the following sections IXon3 SECTION 3 Page 51 lt ANDOR eem FEATURES amp FUNCTIONALITY 3 5
99. s a positive number of counts NOTE Before activating Baseline Clamp please ensure that the baseline level is above zero counts for the cooling temperature selected IXon3 SECTION 3 Page 40 p ANDOR venen FEATURES amp FUNCTIONALITY 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 act of reading out contributes to noise There are two types of the binning as follows e Vertical Binning Where charge from two or more rows of the EMCCD chip are moved down into the shift register before the charge is read out The number of rows shifted depends on the binning pattern selected Thus for each column of the EMCCD chip charge from two or more vertical elements is summed into the corresponding element of the shift register The charge from each of the pixels in the shift register is then shifted horizontally to the output amplifier and read out e Horizontal Binning Where charge from two or more pixels in the serial register are transferred into the output amplifier and read out as one combined data value Thus the charge from two or more of the horizontal elements is effectively summed into the output amplifier before being readout Combining both the vertical and horizontal binning methods
100. s the flexibility to trial and error photon count 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 1000 images could be broken down into groups of 20 photon counted images yielding 50 time points If it transpires that better SNR is required the original dataset could be re treated using groups of 50 photon counted images yielding 20 time points Time Se 9 80000000 A L e aaa a 1 Lower SNR IR higher temporal 2 Higher SNR lower temporal Figure 43 Schematic illustration of how photon counting can be applied to a kinetic series as a post processing step affording increased flexibility in trail and error trading SNR vs temporal resolution IXon3 SECTION 3 Page 72 ANDOR TECHNOLOGY 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 EMCCD technology sometimes known as on chip multiplication is an innovation first introduced to the digital scientific imaging community
101. saturated with dark current see Dark Signal on page 80 e f the Scan is being used simply to clean the CCD i e it is a keep clean scan the charge from the CCD is discarded e n an acquired scan however the charge undergoes analog to digital conversion and is acquired into computer memory so that it can be used for subsequent processing and display it is read out see Readout above Unless the context specifically indicates otherwise scan in this User Guide generally refers to an acquired scan A1 1 17 Shift Register The Shift Register usually consists of a single row of elements or pixels running parallel to and below the bottom row of light gathering pixels the image area on the CCD chip The shift register is protected from light by an aluminium mask The elements in the shift register have a greater capacity to store charge i e a greater well depth than the other pixels on the CCD chip IXon3 APPENDIX Page 85 ANDOR See APPENDIX A1 1 17 Shot Noise Shot Noise is due to basic physical laws and cannot be removed Any signal whether it is a dark signal or a light signal will have shot noise associated with it Most simply defined If the signal or dark signal N electrons the shot noise is the square root of N You can do nothing about the shot noise of your signal but by choosing minimum exposures and operating the CCD at suitably low temperatures the dark signal and hence the no
102. se warmer water 20 C or even higher if it is very humid The minimum CCD temperature would then be limited to a higher value iXon3 SECTION 1 Page 15 ANDOR ee INTRODUCTION 1 3 11 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 It is important to note that this ageing effect applies to any EMCCD camera manufacturer that incorporates L3Vision sensors into their cameras In the Andor iXon3 range this refers to the 897 888 amp 860 models EMCCD cameras incorporating Impactron EMCCD sensors from Texas Instruments have shown rates of EMCCD saturation induced ageing that are orders of magnitude slower than those with E2V sensors exposed to comparable light intensity and gain NOTE 885 iXon3 models contain Impactron sensors from Texas Instruments which do not exhibit EM gain ageing or at most exhibits it at a negligible level A technical note entitled Longevity in EMCCD and ICCD which further explains this phenomenon can be downloaded from the following website http www andor com library publications 2appz543 If left unchecked this ageing phenomenon has the potential to significantly compromise the long term quantitative reliability of EMCCD cameras Andor have recognized this ageing issue and have implemented innovative measures to stabilize the EM gain on these sensors
103. situations where the TTL trigger occurs before the light event you are trying to capture This effectively moves the exposure window in time but the exposure time is still the period between trigger events e There is no need for a mechanical shutter The exposure time is long compared to the time required to shift the image into the Storage area and therefore image streaking will be insignificant iXon3 SECTION 3 Page 44 NDOR es FEATURES amp FUNCTIONALITY 3 4 2 Capture Sequence in Non Frame Transfer Mode with an FT CCD It is also possible to operate an FT CCD in a Non Frame Transfer NFT mode In this mode of operation an FT CCD acts much like a standard CCD The capture sequence for this mode is illustrated here Continuously Clean CCD Keep Clean Cycle Minn n lt n T cT m Step2 Step 3 Step 1 Keep Clean Cycle 1 Al m lt lt Step 4 lt Figure 23 Capture sequence NFT mode Step 1 Both Image and Storage areas of the CCD are fully cleared out Step 2 On receipt of a start acquisition command the CCD stops the Keep Clean Cycle and an acquisition begins The image builds up in the Image area of the CCD until the exposure time has elapsed at which point the read out process starts Step3 The first phase of this process is to quickly shift the charge built up in the Image area into the Storage area The time required to move the charge into the Storage area is the same as in Frame Transfer
104. t 30 this uncertainty introduces an additional noise component called Multiplicative Noise This noise source is only present in signal amplifying technologies and is a measure of the uncertainty inherent to the signal multiplying process For example during each transfer of electrons from element to element along the gain register of the EMCCD only a small probability exists that the process of impact ionization will produce an extra electron during that step This happens to be a small probability but when executed over gt 590 steps a very large overall EM gain results However the downside to this process results from the probabilities Due to this there is a statistical variation in the overall number of electrons generated by the gain register from an initial charge packet This uncertainty is quantified by a parameter called Noise Factor and detailed theoretical and measured analysis has placed this Noise Factor at a value of 2 or 1 41 1 for EMCCD technology Note This noise source is significantly greater for the Multi Channel Plate MCP of ICCDs than for the gain register of the EMCCD ICCDs have noise factors typically ranging from 1 5 to gt 2 So this is an additional form of noise that must be taken into account when calculating Signal Noise for these detectors However one way to better understand the effects of this noise source is in terms of an addition to the shot noise of the system Extra multiplicative noise has the same
105. t Kinetics FK is a special readout mode that uses the actual CCD as a temporary storage medium and allows an extremely fast sequence of images to be captured The capture sequence is illustrated here ZEAN Continuously clean CCD Keep Clean cycle lt lt h nn Step 2 Step 3 Step 1 SM EP WES p ADM n p 5 pr A LD p m lt n lt n Step 4 Step 5 Step 6 Figure 24 Capture sequence Fast Kinetics mode Step 1 Both the Image and Storage areas of the CCD are fully cleaned the Keep Clean Cycle Step 2 The CCD stops the Keep Clean Cycle and the acquisition begins The image builds up on the illuminated sub area of the CCD Step 3 The CCD remains in this state until the exposure time has elapsed at which point the complete CCD is clocked vertically by the number of rows specified by the user Step 4 amp 5 The process is continued until the number of images stored equals the series length set by the user Step 5 At this point the sequence moves into the readout phase by first vertically shifting the first image to the bottom row of the CCD The CCD is then read out in the standard method 3 4 3 1 Points to consider when using Fast Kinetics mode e Light must only be allowed to fall on the specified sub area Light falling anywhere else will contaminate the data e The maximum number of images in the sequence is set by the position of the sub area the height of the sub area and the number of rows in the CCD Image a
106. tandard Warranty policy and procedures as it relates to services obtained by a Customer under warranty It does not replace or supersede any Product or Customer specific Warranty terms and conditions 1 1 2 Warranty is a guarantee of quality of supplied goods Software amp Hardware It is an obligation to rectify or replace product defects during an agreed period of time 1 2 Standard Warranty Policy 1 2 1 Andor s Limited Standard Warranty Policy on Hardware warrants all new products to be free from defects in materials and workmanship for 12 months from the date of dispatch Exceptions to the standard hardware warranty offer exist and are shown in 1 2 2 1 2 3 below Within this period Andor will at its sole option repair or replace any components which fail in normal use Such repairs or replacements will be made at no charge to the Customer for parts or labour however the Customer shall be responsible for any transportation and insurance costs from the Customer premises to the Andor designated point of return Andor shall be responsible for transportation and insurance costs related to returning the repaired or replacement unit to the Customer The customer shall be responsible for any import duties taxes and customs clearance fees associated with the return of the unit This warranty does not cover failures due to abuse misuse accident or unauthorized alterations or repairs Andor assumes no responsibility for special incidental pu
107. tart 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 As there is no keep clean cycle running while waiting for the external trigger the real exposure time is the time between each trigger A consequence of this is that if your experiment has a constant background signal but your trigger period is not fixed you may see different background levels in your signal As with internal trigger the data is only read off the sensor when the capture sequence has completed Exposure time is time Number of vertical clocks between triggers External trigger depends on sub area height keep clean running with global clear on 885 i Image amp Storage area clocks Horizontal clocks External Trigger Fire output Number of repeats set Read phase by series length User settable delay Figure 38 External Trigger in Fast Kinetics mode iXon3 SECTION 3 Page 62 NDOR NCC mns FEATURES amp 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 of 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 On comp
108. test Frame Rate EM amplitier frame rates of the camera Especially effective when combined with sub array binning selections Configured to capture low light images with time intervals Time Lapse EM Amplifier between exposures Overlap frame transfer readout is deactivated Time Lapse amp Short Exposures Configured to minimize vertical smear when using exposure EM Amplifier lt 3ms Combines EMCCD low light detection with the absolute highest EMCCD Highest Dynamic Range dynamic range that the camera can deliver Since this requires EM amplifier E slower readout frame rate is sacrificed Optimized for slow scan CCD detection with highest available CCD Highest Dynamic Range dynamic range Recommended for brighter signals OR when it is Conventional Amplifier possible to apply long exposures to overcome noise floor Configuration recommended for photon counting with individual Photon Counting exposures 10sec Photon Counting with Long Exposures Configuration recommended for photon counting with individual 10 sec exposures 10sec iXon3 SECTION 3 Page 67 NDOR m FEATURES amp FUNCTIONALITY 3 9 PUSHING FRAME RATES WITH CROPPED SENSOR MODE The iXon3 offers Cropped Sensor Mode which carries the following advantages e Specialized readout mode for achieving very fast frame rates sub millisecond exposures from standard cameras e Continuous rapid spooling of images spectra to hard disk e
109. to run Horizontal clocks Image area shifted during exposure continue to run after into storage area readout completes Storage area read out phase Figure 28 Internal Trigger in Frame Transfer mode iXon3 SECTION 3 Page 52 lt ANDOR WU eem FEATURES amp FUNCTIONALITY 3 5 1 2 External FT When the camera is idle it is running 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 will repeat this cycle X times where X is the number of image rows on the sensor before it will accept any external trigger events Once this period is over the camera will continue running the External Keep Clean cycle until an External Trigger is received At that point the current external keep clean cycle is completed and the camera stops all vertical clocking and waits for the programmed user delay period before starting the read phase During the readout phase the Image area is transferred rapidly to the Storage area The Storage area is then read out in the normal way Once the readout is complete the camera continues to wait for the next external trigger event While the camera is waiting for the trigger event the shift register is continually clocked but the Image and Storage areas are not On the next trigger the camera again waits for the program
110. troller card to camera cable e Power supply block and correct power cable for the country where the camera is to be used The following items are also available as optional accessories e Mounting Posts see page 21 1 2 1 Camera we Figure 1 iXon3 camera IXon3 SECTION 1 Page 9 ANDOR ge INTRODUCTION 1 2 2 Controller Cards Figure 2 CCI 22 Figure 3 CCI 23 Figure 4 CCI 24 The Controller cards CCI 22 CCI 23 or CCI 24 buffer data from the camera before transfer to the computer memory via the PCI bus The CCI 22 amp CCI 23 require a PCI 2 2 slot the CCI 24 requires a PCle x1 slot All boards are well shielded against electrical interference Your iXon3 will be supplied with the controller card that is optimal for your camera model Controller cards have a 26 pin interface for connection via a cable to the PC and an auxiliary connector The pin outs for the cards are shown on page 79 1 2 3 Controller Card Cables The controller cards require the following connecting cables for correct operation Figure 6 Internal Molex connector cable Figure 5 PCI controller card to camera cable e The controller card connector cable is used to connect the camera to the PCI controller card e The power cable is connected within the computer between any available Molex connector and the PCI controller card NOTE The internal power cable is wired to leave a free connector for supplying powe
111. we can ignore its shot noise Furthermore if a suitably low operating temperature and short exposure time can be achieved the lowest detection limit will equal the readout noise A1 1 10 Exposure Time The Exposure Time is the period during which the CCD collects light prior to readout A1 1 11 Frame Transfer Frame transfer is a special acquisition mode that is only available if your system contains a Frame Transfer CCD FT CCD An FT CCD differs from a standard CCD in 2 ways Firstly it contains 2 areas of approximately equal size as follows 1 The first area is the Image Area which is located at the top and farthest from the read out register This is the light sensitive area of the CCD 2 The second section is the Storage Area and is located between the Image Area and the Readout Register This section is covered by an opaque mask usually a metal film and hence is not sensitive to light Image Area Storage Area Xr mI zr ELC H The second way in which a FT CCD differs from a standard CCD is that the Image and Storage areas can be shifted independently of each other These differences allow a FT CCD to be operated in a unique mode where one image can be read out will the next image is being acquired It also allows a FT CCD to be used in imaging mode without a shutter Note This is only applicable when the camera is running in Accumulate or Kinetic mode iXon3 APPENDIX Page 83 ANDOR 9 APPENDIX
112. ws No of rows in the Image area x vertical shift rate Once the Image area has been shifted into the Storage area the Image area stops vertically shifting and begins to accumulate charge again i e the next exposure starts While the Image area is accumulating charge the Storage area is being read out This readout phase can take tens of milliseconds to seconds depending on the image size readout pattern and readout speed On completion of the readout the system will wait until the exposure time has elapsed before starting the next read out i e returning to Step 3 IXon3 SECTION 3 Page 43 lt ANDOR WC emm FEATURES amp FUNCTIONALITY e n this mode there are no keep cleans between images during an accumulation or kinetics series as they are not necessary e 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 e The accumulation cycle time and the kinetic cycle time are fully dependent on the exposure time and hence cannot be set via software e n external trigger mode there are no keep cleans and the External trigger starts the read out phase The exposure time is the time between external triggers and hence the user cannot set the exposure or cycle times However the user can define the amount of time between the external trigger event occurring and the readout starting This can be useful in those

A USER'S GUIDE TO

Contents

Download Pdf Manuals

Related Search

Related Contents