USER’S GUIDE iKon-L Andor Technology plc 2009 www.andor.com Version 1.
TABLE OF CONTENTS PAGE SECTION 1 - ABOUT THE ANDOR IKON-L 14 1.1 - WORKING WITH THE USERS GUIDE 14 1.2 - HELP 14 1.3 - TECHNICAL SUPPORT Europe USA Asia-Pacific China 15 15 15 15 15 1.4 - SYSTEM 16 1.5 - OPTIONAL EXTRAS 16 1.6 - MAIN COMPONENTS 1.6.1 - Camera 1.6.2 - Power Supply Units (PSU) 1.6.2.1 - PS40 1.6.2.2 - PS29 1.6.3 - Attaching a Lens 1.6.4 - Mounting Posts 17 17 18 18 19 20 21 1.7 - SAFETY PRECAUTIONS & SAFE CAMERA OPERATION 1.7.1 - Care of the camera 1.7.
TABLE OF CONTENTS PAGE SECTION 2 - INSTALLATION 28 2.1 - COMPUTER REQUIREMENTS 28 2.2 - INSTALLING THE SOFTWARE & USB DRIVER 28 2.3 - INSTALLING THE HARDWARE 2.3.1 - Connectors 2.3.
TABLE OF CONTENTS PAGE SECTION 3 - USING THE IKON-L 33 3.1 - STARTING THE APPLICATION 33 3.2 - MAIN WINDOW BUTTONS 34 3.
TABLE OF CONTENTS PAGE SECTION 4 - PRE-ACQUISITION 38 4.1 - SETTING TEMPERATURE 38 4.2 - SETUP ACQUISITION 4.2.1 - Run Time Control 4.2.2 - Remote Control 39 40 41 4.3 - SPOOLING 4.3.1 - Virtual Memory 43 44 4.
TABLE OF CONTENTS PAGE SECTION 5 - ACQUIRING DATA 46 5.1 - INITIAL ACQUISITION 5.1.1 - Real time 46 47 5.2 - DATA TYPE SELECTION 5.2.1- Definition of Data Types 48 48 5.3 - ACQUISITION TYPES 5.3.1 - Autoscale Acquisition 5.3.2 - Take Background 5.3.3 - Take Reference 5.3.4 - Acquisition Errors 52 52 53 53 53 5.4 - ACQUISITION MODES & TIMINGS 5.4.1 - Single 5.4.2 - Accumulate 5.4.3 - Kinetic 5.4.3.1 - Frame Rates 5.4.4 - Fast Kinetics 5.4.4.1 - Readout Mode & Fast Kinetics 5.4.
TABLE OF CONTENTS PAGE Section 5 (continued) 5.10 - IMAGE 5.10.1 - Sub Image 5.10.1.1 - Draw 5.10.1.2 - Superpixels 5.10.1.3 - Image Orientation 69 70 71 71 71 5.11 - VIDEO MODE 72 5.12 - PHOTON COUNTING 73 5.13 - VERTICAL PIXEL SHIFT 5.13.1 - Shift Speed 5.13.2 - Vertical Clock Amplitude Voltage 75 75 75 5.14 - HORIZONTAL PIXEL SHIFT 5.14.1 - Horizontal Pixel Shift Readout Rate 5.14.2 - Pre-Amplifier Gain 76 76 76 5.15 - TIMING PARAMETERS 5.15.1 - Baseline Clamp 77 77 5.16 - SHUTTER 5.16.
TABLE OF CONTENTS PAGE SECTION 6 - DISPLAYING DATA 84 6.1 - DISPLAY MODES 84 6.2 - DISPLAY PREFERENCES 85 6.3 - AXIS DEFINITIONS 86 6.4 - AXIS SETUP 87 6.5 - ZOOM BOX 88 6.6 - ZOOMING & SCROLLING 6.6.1 - Zoom In & Zoom Out 6.6.2 - Scrolling 6.6.3 - Reset 89 89 89 89 6.7 - 2D DISPLAY MODE 6.7.1 - 2D display mode preferences 6.7.2 - Peak Search 6.7.2.1 - Peak Search Sensitivity 6.7.3 - Peak Labeling 6.7.3.1 - Labels on Peaks or Troughs 6.7.3.2 - Maximum Number of Labeled Peaks 6.7.3.
TABLE OF CONTENTS PAGE Section 6 (continued) 6.9 - IMAGE DISPLAY MODE 6.9.1 - Image display mode preferences 6.9.1.1 - Always maintain aspect ratio 6.9.1.2 - Show 2D cross sections 6.9.1.3 - Show palette bar 6.9.1.4 - Large Cursor 6.9.2 - Palette Bar 6.9.2.1 - Selecting Color / Grayscale 6.9.3 - Rescale 6.9.4 - High & Low Contrast Overview 6.9.4.1 - Increasing & Decreasing Contrast 6.9.5 - Brightness Overview 6.9.5.1 - Adjusting the Brightness 103 104 104 105 105 105 106 107 108 110 111 112 113 6.
TABLE OF CONTENTS PAGE SECTION 7 - HANDLING FILES 122 7.1 - MENU OPTIONS 7.1.1 - Close 7.1.2 - Save 7.1.3 - Save As 122 124 124 124 7.2 - EXPORT AS 7.2.1 - ASCII 7.2.2 - AVI 7.2.3 - Bitmap 7.2.4 - GRAMS 7.2.5 - JPEG 7.2.6 - MPEG 7.2.7 - Raw Data 7.2.8 - TIFF 125 126 127 127 127 128 128 129 131 7.3 - CONFIGURATION FILES 132 7.
TABLE OF CONTENTS PAGE SECTION 8 - CALIBRATION 134 8.1 - CALIBRATION OPTIONS 134 8.2 - MANUAL X-CALIBRATION 8.2.1 - Supplying calibration details 8.2.2 - Applying Calibration 8.2.2.1 - Calibrate 8.2.2.2 - Data are Non-Monotonic 8.2.2.3 - Too Few Points 8.2.2.4 - Undo 8.2.2.5 - Close 135 136 138 138 139 140 140 140 8.3 - X-CALIBRATION BY SPECTROGRAPH 8.3.1 - Setup Spectrograph 8.3.1.1 - Calibrate As Red-Blue 8.3.1.2 - Communications 8.3.1.3 - Other Spectographs 8.3.1.4 - Reverse Spectrum 8.3.1.
TABLE OF CONTENTS PAGE SECTION 9 - WORKING WITH PROGRAMS 150 9.1 - WORKING WITH ANDOR BASIC 9.1.1 - Command Line 9.1.2 - Program Editor Window 9.1.3 - Accessing the Edit Functions 9.1.4 - Cut, Copy, Paste, Undo 9.1.5 - Search 9.1.6 - Replace 9.1.7 - Run Program 9.1.8 - Run Program by Filename 9.1.
TABLE OF CONTENTS PAGE APPENDIX 154 A1.1 - GLOSSARY A1.1.1 - CCD A1.1.1.1 - Readout Sequence of a CCD A1.1.2- Accumulation A1.1.3 - Acquisition A1.1.4 - A/D Conversion A1.1.5 - Background A1.1.6 - Binning A1.1.6.1 - Vertical Binning A1.1.6.2 - Horizontal Binning (Creating Superpixels) A1.1.7 - Counts A1.1.8 - Dark Signal A1.1.9 - Detection Limit A1.1.10- Exposure Time A1.1.11 - Noise A1.1.11.1 - Pixel Noise A1.1.11.2 - Fixed Pattern Noise A1.1.11.3- Readout Noise A1.1.
ABOUT THE ANDOR iKon-L SECTION 1 - ABOUT THE ANDOR iKon-L Thank you for choosing the Andor iKon-L. You are now in possession of revolutionary new CCD camera, designed for the most challenging low-light imaging applications. Its unique features and design are discussed in more detail within this User Guide. This guide is designed as a road map for the iKon-L camera, and contains information and advice to ensure you get the optimum performance from your new system.
ABOUT THE ANDOR iKon-L 1.
ABOUT THE ANDOR iKon-L 1.4 - SYSTEM Andor’s iKon-L exploits the processing power of today’s desktop computers. The system’s hardware components and their comprehensive software provide speed and versatility for a range of spectroscopic or imaging applications and set-ups. The main components of Andor iKon-L systems are as follows: • USB Quick Launch Guide • Detector Head (hereinafter referred to as a camera) • USB 2.
ABOUT THE ANDOR iKon-L 1.6 - MAIN COMPONENTS The main components are described on the next few pages. 1.6.
ABOUT THE ANDOR iKon-L 1.6.2 - Power Supply Units (PSU) 1.6.2.1 - PS40 The PS40 is the main power supply for the camera. There is 1x input and it is rated at 24V dc, which can be supplied from either the PS-29 (see next page) or the users own supply. The output is via a dedicated 16-pin cable which connects into the camera as shown in figure 4 below.
ABOUT THE ANDOR iKon-L 1.6.2.2 - PS29 The PS29 can be used to supply 24Vdc @ 150 Watts to the PS40.
ABOUT THE ANDOR iKon-L 1.6.3 - Attaching a Lens F-mount Lenses can be easily attached to the cameras as shown below: Firstly locate the lens catch as shown above Press the catch down, screw the lens in carefully counter-clockwise and it will then lock into position To remove the lens, simply follow the procedure in reverse.
ABOUT THE ANDOR iKon-L 1.6.4 - Mounting Posts Mounting posts can be fitted on one side of the camera that can be used to mount the camera if standalone operation is required. There are 3 holes for the ¼ -20unc mounting posts, with 1.0” spacing between each.
ABOUT THE ANDOR iKon-L 1.7 - SAFETY PRECAUTIONS & SAFE CAMERA OPERATION 1.7.1 - Care of the camera THERE ARE NO USER-SERVICEABLE PARTS INSIDE THE CAMERA. YOUR CAMERA IS A PRECISION SCIENTIFIC INSTRUMENT CONTAINING FRAGILE COMPONENTS. ALWAYS HANDLE THE DETECTOR WITH CARE. DAMAGE CAUSED BY INCORRECT MAINTENANCE OR PROCEDURES WILL INVALIDATE THE WARRANTY. 1.7.
ABOUT THE ANDOR iKon-L 1.7.4 - Working with Electronics The computer equipment that is to be used to operate the camera 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.
ABOUT THE ANDOR iKon-L 1.7.6 - Cooling The CCD 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 CCD-chip) to its ‘hot side’ (the built-in heat sink). Therefore the minimum absolute operating temperature of the CCD depends on the temperature of the heat sink.
ABOUT THE ANDOR iKon-L 1.7.6.1 - Air cooling Air cooling is the most convenient method of cooling, but it will not achieve as low an operating temperature as water cooling (see below). Even with a fan (see NOTE immediately below), a heat sink typically needs to be 10ºC hotter than the air (room) temperature to transfer heat efficiently to the surrounding air. Therefore the minimum CCD temperature that can be achieved will be dependent on the room temperature.
ABOUT THE ANDOR iKon-L 1.7.6.2 - Water cooling A flow of water through the heat sink removes heat very efficiently, since the heat sink is never more than 1ºC hotter than the water. With this type of cooling, the minimum temperature of the CCD will be dependent only on the water temperature, not on the room temperature. For detailed performance figures please refer to table 2 below. Water cooling, either chilled though a refrigeration process or re-circulated (i.e.
ABOUT THE ANDOR iKon-L 1.7.6.4 - Dew Point graph The Dew Point graph 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. Figure 9: Dew point graph For example, using a DZ model you will need 10ºC cooling water to guarantee performance down to -100ºC. In the relatively dry atmosphere of an air-conditioned lab, cooling water at 10º should not present any problems.
INSTALLATION SECTION 2 - INSTALLATION 2.1 - COMPUTER REQUIREMENTS The minimum computer requirement for correct iKon-L operation is as follows: • 2.4GHz Pentium Processor with 1GB RAM • Windows 2000, XP or Vista • USB 2.0 compatibility • 32MB of free hard disc space 2.2 - INSTALLING THE SOFTWARE & USB DRIVER 1. Terminate & exit any programmes which are running on the PC. 2. Insert the Andor CD and the InstallShield Wizard should start. If it does not start automatically, run the file setup.
INSTALLATION The following dialog box appears: 6. Click Next > and the following dialog box appears: 7. Click Next > and the progress bar will start to update, e.g.
INSTALLATION 8. When the progress bar stops updating, a message similar to the following will appear: PLEASE READ THE MESSAGE AND OBSERVE ANY IMPORTANT INFORMATION RELEVANT TO YOUR SYSTEM, THEN RESTART THE PC, AS PER THE FOLLOWING PROMPT: 9. Select the Yes, I want to restart my computer now option, then click Finish. Your computer should then reboot automatically. After the PC has been restarted, the icon should now be installed on your desktop. You are now ready to start the application.
INSTALLATION 2.3 - INSTALLING THE HARDWARE 2.3.1 - Connectors Figure 10: iKon-L rear connectors There are 6 connection points on the rear of the iKon-L as shown above. Three of the connectors are industry-standard SMB (SubMiniature B) connectors which are labelled from left to right as follows: • Shutter • Fire • Ext Trig These are used to send or receive Triggering and Firing signals, which are described later in this manual.
INSTALLATION 2.3.2 - Water cooling pipes Two connectors are fitted to the camera in order to allow water cooling pipes to be connected, e.g.: These can be connected to a water cooler or recirculator to improve cooling.
USING THE iKon-L SECTION 3 - USING THE iKon-L 3.1 - STARTING THE APPLICATION On the desktop, click on the icon and the Solis Splash Screen appears briefly: The Main Window then appears, e.g.
USING THE iKon-L 3.2 - MAIN WINDOW BUTTONS The Main Window is your ‘entry point’ to the system. The menu options that you select from either execute functions directly, or launch further windows/dialog boxes that let you select the functionality you require. Some menu options on the Main Window are also represented as easy-to-use radio buttons, as shown in Table 3 below.
USING THE iKon-L • The Display menu and its associated buttons will not appear until you open a Data Window, e.g.: • The Edit & Search menus and their associated buttons appear only when a Program Editor Window is active, e.g.
USING THE iKon-L 3.3 - HOT KEYS Hot keys (or shortcuts) as shown in Tables 4, 5 & 6 enable you to work with the system directly from the keyboard, rather than via the mouse. Table 3: Data Acquisition Hot Keys KEY STROKE DESCRIPTION F3 Start Real Time Signal Acquisition F5 Take signal F6 Toggle Autoscale Acquisition On/Off F9 Autoscale Ctrl + B Take background Ctrl + R Take reference Esc Abort Acquisition Table 4: Data Window Hot Keys (N.B.
USING THE iKon-L Table 5: Data Window Hot Keys (continued) DISPLAY MODE KEY STROKE DESCRIPTION 2D 3D IMAGE F7 Toggle Palette F8 Reset F9 Rescale Alt + F9 Toggle Rescale Mode Ctrl + F9 Scale to Active (See Displaying Data section) F10 File information Table 6: Hot Keys for Andor Basic Programming Language KEY STROKE DESCRIPTION Ctrl + P New program Ctrl + E Run program Esc Abort acquisition / program Ctrl + L Command line Context sen
PRE-ACQUISITION SECTION 4 - PRE-ACQUISITION 4.1 - SETTING TEMPERATURE For accurate readings, the CCD should first be cooled, as this will help reduce dark signal and associated shot noise. To do this, either select the Temperature option from the Hardware drop-down menu on the Main Window: or click the button in the bottom-left of the screen. This will open up the Temperature control dialog box : Select On in the Cooler check box.
PRE-ACQUISITION 4.2 - SETUP ACQUISITION To select the mode of acquisition prior to data capture, you can choose one of the following options: • Click the • Type in Ctrl+A from the keyboard • Select Setup Acquisition from the Acquisition drop-down menu: button, The Setup Acquisition Dialog box appears, e.g.: As you select an Acquisition Mode you will notice that you are able to enter additional exposure-related parameters in a column of text boxes.
PRE-ACQUISITION 4.2.1 - Run Time Control The Run Time Control provides the user with the ability to control the following parameters using slider controls: • EM Gain (if applicable) • Exposure time of the CCD The controls are activated by clicking on the button on the Main Window. When selected, the dialog box appears, e.g.
PRE-ACQUISITION 4.2.2 - Remote Control The Remote Control (figure 12 on page 42) allows various commands of the Solis software to be modified using an infra-red signal sent to a Receiver (figure 13 on page 42). The range of operation of the remote control is up to a distance of 12m from the receiver along the line of sight. Connect the lead from the Remote Control Receiver to a serial RS232 Com Port at the back of your computer.
PRE-ACQUISITION The remote control has two modes of operation.
PRE-ACQUISITION 4.3 - SPOOLING The Andor Solis software allows you to spool acquisition data direct to the hard disk of your PC. This is particularly useful when acquiring a series of many images. The amount of data generated by a Kinetic Series of, for example 1000 acquisitions, is huge and more than most PC RAM can handle. To select click on the Spooling tab and the Spooling dialog box appears e.g.
PRE-ACQUISITION 4.3.1 - Virtual Memory In addition to the Spooling function, it can also be useful to have the Virtual Memory (VM) function enabled. This will speed up the retrieval of large data sets and allow larger data sets to be acquired. This works by buffering data in the Hard Drive of the PC. To switch on, select the Virtual Memory… option from the File menu, e.g.: This will open the Virtual Memory dialog box: Tick the Enable box and select the required Threshold.
PRE-ACQUISITION 4.4 - AUTO-SAVE Auto-Save allows you to set parameters and controls for the auto saving of acquisition files thus removing the worry of lost data and files. To select, click on the Auto-Save tab on the Setup Acquisition dialog box The Autosave dialog box appears, e.g.: Tick the Enable Auto-Save box. If selected, acquisitions will be saved automatically when each one is completed. Each subsequent auto-saved file will over-write the previously auto-saved one.
ACQUIRING DATA SECTION 5 - ACQUIRING DATA 5.1 - INITIAL ACQUISITION To start an initial data acquisition you can either: • Click the • Press F5 on the keyboard • Select the Take Signal option from the Acquisition drop-down menu as shown: button on the Main Window, The Data Window opens (labeled #0 Acquisition) and displays the acquired data, according to the parameters selected on the Setup Acquisition Dialog box. e.g.
ACQUIRING DATA When you acquire data, by reading out a scan or a series of scans of the CCD-chip at the heart of the detector, the data are stored together in a Data Set, which exists in your computer’s Random Access Memory (RAM) or on its Hard Disk. You can also create a data set via the Andor Basic programming language. #n uniquely identifies the data set while the data set is being displayed and is temporary.
ACQUIRING DATA 5.2 - DATA TYPE SELECTION You can select the type of information that you want the system to compute and display whenever you perform the Take Signal function. When the Setup Data Type option of the Acquisition drop-down menu is selected, the Data Type dialog box opens: The descriptions of the data types are shown in Table 7 which follows on the next 2 pages. The acquired data are presented under the Sig tab of an Acquired Data Window.
ACQUIRING DATA Table 7 - Data types OPTION FUNCTION Counts represents raw, digitized data (i.e. no calculations have been performed on the data) from the CCD detector’s analog to digital (A/D) converter. Counts Please refer to the detailed performance sheet accompanying your particular CCD detector for the number of electrons that correspond to 1 count.
ACQUIRING DATA Table 7 - Data types (continued) OPTION FUNCTION A measure of light absorbed by an object (i.e. they represent the object’s Optical Density - OD). If Reference is the background corrected incident intensity, and Signal - Background the transmitted intensity (i.e. the intensity of light which has passed through the material being examined), then Absorbance units Transmission = (Signal - Background) / Reference.
ACQUIRING DATA As an example, the system will compute % Absorptance as: 100 x (1 - (Signal - Background) / Reference). The illustration below shows a typical use of Background, Reference and Signal for computations such as %Absorptance or %Transmittance: The default data type (used when you capture data and have not explicitly made a selection from the Data Type dialog box) is Counts.
ACQUIRING DATA 5.3 - ACQUISITION TYPES From the Acquisition drop-down menu on the Main Window, you can make the following data acquisition selections: • Take Signal (see pages 44 - 45) • Take Background • Take Reference Provided you do not change the acquisition parameters, the scans you take for background and reference are automatically used for subsequent data acquisitions whenever you perform Take Signal. 5.3.
ACQUIRING DATA 5.3.2 - Take Background The Take Background option of the Acquisition drop-down menu instructs the system to acquire raw background data. These are as counts of the Acquisition Window. No calculations are performed on these data. The data type you select via Setup Data Type on the Acquisition Menu may require you to perform Take Background before you perform Take Signal. NOTE: You do not necessarily have to take Background data prior to each Acquisition of SIGNAL data.
ACQUIRING DATA 5.4 - ACQUISITION MODES & TIMINGS An acquisition is taken to be the complete data capture process that is executed whenever you select Take Signal, Take Background, or Take Reference from the Acquisition Menu or whenever you click the Take Signal button. By contrast, a scan (i.e. an ‘Acquired Scan’ in the definitions that follow) is 1x readout of data from the CCDchip. Several scans may be involved in a complete data acquisition.
ACQUIRING DATA 5.4.2 - Accumulate Accumulate mode allows you to add together in computer memory the data from a number of scans to create an ‘Accumulated Scan’ e.g.: You can select the following parameters in the Setup Acquisition dialog box: • Exposure Time • No. of Accumulations: i.e. the number of scans you want to add together • Accumulated Cycle Time: i.e. the period in seconds between each scan.
ACQUIRING DATA 5.4.3 - Kinetic Kinetics mode allows you to record the temporal evolution of an event, by capturing a series of scans or accumulations at a specified rate or time interval. In the Setup Acquisition dialog box you can key in the following parameters: • Exposure Time (secs): the time during which charge is to be collected on the CCD. NOTE: Should you attempt to enter too low a value, the system will default to a minimum Exposure Time. • No.
ACQUIRING DATA 5.4.4 - Fast Kinetics Fast Kinetics allows exposure times on a microsecond timescale. Use Fast Kinetics when you need an exposure time that is smaller than the minimum Kinetic Cycle Time in a standard Kinetic Series. In Fast Kinetics the image to be recorded is imaged across a certain section of the CCD. The non-illuminated part of the CCD is used for storage of image before readout.
ACQUIRING DATA 5.4.4.1 - Readout Mode & Fast Kinetics The data from each of the spectra in the Fast Kinetics series is stored as an image. Select Image from the Readout Mode drop down list on the Setup Acquisition Window. Fast kinetics is not available in multi-track mode. With Fast Kinetics you may use the following Trigger Modes: Internal, External, Fast External and External Start.
ACQUIRING DATA 5.4.5 - Cosmic Ray Removal Cosmic rays are very high energy particles, originating in outer space, that enter the Earth’s atmosphere and produce a shower of further high energy particles. When one of these particles passes through the CCD it will produce between 0 and thousands of photoelectrons in a very small area (usually 1 to 4 pixels) and due to the low read noise of the CCD this will appear as a spike of up to several hundred counts.
ACQUIRING DATA 5.5 - TRIGGERING MODES The Triggering modes are selected from a drop-down list on the Setup Acquisition dialog box: Depending on which Acquisition Mode is selected, the options available are: • Internal • External • Fast External • External Start 5.5.1 - Internal In Internal mode, once you issue a data acquisition command, the system determines when data acquisition begins.
ACQUIRING DATA IMPORTANT NOTE FOR ALL EXTERNAL TRIGGERING FUNCTIONS: If you have a shutter connected and are using External triggering, you must ensure that the shutter is OPEN before the optical signal you want to measure occurs. 5.5.2 - External In External mode once you issue a data acquisition command, data will not be acquired until your system has received an External Trigger signal generated by an external device (e.g. a laser).
ACQUIRING DATA 5.5.
ACQUIRING DATA 5.6 - READOUT MODES The Readout Modes available from the Setup Acquisition dialog box let you use the CCD chip at the heart of the camera to collect/readout data. The options available are as follows: • Image • Multi-track • Full Vertical Binning (FVB) The Binning patterns used in each readout mode are as follows: Binning is a process that allows charge from two or more pixels to be combined on the CCD-chip prior to readout.
ACQUIRING DATA 5.7 - BINNING The horizontal and vertical Binning parameters determine the dimensions of any superpixels (see below for description) you may choose to create. The software presents a selection of five of the most common binning patterns: • 1 x 1 pixels • 2 x 2 pixels • 4 x 4 pixels • 8 x 8 pixels • 16 x 16 pixels. For example, if you enter 4 x 4 binning the CCD-chip is notionally divided into a matrix of superpixels which each measure 4 x 4 pixels and provide a signal for readout.
ACQUIRING DATA 5.7.2 - Full Vertical Binning FVB allows you to use the CCD-chip as a Linear Image Sensor (or LIS - a photodiode array). The charge from each column of pixels (each column being the chip height) is combined, or binned, on the chip to give a single value per column. To define the binning in FVB mode, click on the FVB tab in the Setup Acquisition dialog box: For some spectrographs, it may be necessary to change the direction in which the data is displayed on screen.
ACQUIRING DATA In some instances spectral rate can be more important than spatial/spectral resolution. For such applications horizontal binning can be applied by setting the number in the Horizontal binning section to a value greater than one. For example, using a DU934N-BV camera in FVB with horizontal binning = 1 will produce a spectrum 1600 pixels wide, with each pixel containing the summation of the charge in one column.
ACQUIRING DATA 5.8 - CROP MODE To obtain the highest possible spectral rates the system can be configured to operate in Crop Mode. This mode can be selected by clicking on the Crop Mode tab in the Setup Acquisition dialog box, the following dialog box appears: This mode is activated by clicking the tick box beside Enable Crop Mode. You can now enter a value in the box labeled ‘Top’ within the Crop Settings dialog box.
ACQUIRING DATA 5.9 - MULTI-TRACK Multi-Track mode allows you to create one or more tracks. You can define (in rows) the height of each track and the offset, which in effect ‘raises’ or ‘lowers’ on the CCD-chip the pattern of tracks from which you will readout charge. In this way you can adjust the position of the tracks to match a light pattern produced on the CCD-chip by a fiber bundle, for example.
ACQUIRING DATA 5.10 - IMAGE When the Image option from the drop-down menu is selected, the dialog box changes, e.g.: The user can then to set and control various Binning Patterns and define Sub Images of the iKon-L CCD. By default, taking an Acquisition supplies you with a count from each pixel on the CCD, in effect allowing you to take a picture of the light pattern falling on the pixel matrix of the CCD. This default is referred to as a Full Resolution Image.
ACQUIRING DATA 5.10.1 - Sub Image For the purpose of initial focusing and alignment of the camera, or to increase the readout speed, you may use the software to readout data from a selected area (or Sub Image) of the CCD. When the iKon-L is running in Sub Image mode, only data from the selected pixels will be readout. Data from the remaining pixels will be discarded.
ACQUIRING DATA 5.10.1.1 - Draw In addition to the previous methods of defining a Sub Image on the CCD, you can also use the Draw Option to select the size and location of your Sub Image. In order to use the Draw Option, you must first acquire a full resolution image. This will be the template on which you will draw your Sub Image. Click on the button then use the Draw tool to select the size and position of your Sub Image by dragging rulers form the X and Y-axis.
ACQUIRING DATA 5.11 - VIDEO MODE When the Video Mode tab on the Setup Acquisition dialog box is clicked, the Video Mode dialog box opens, e.g.: The following parameters can then be changed: • Exposure Time • Delay: The interval required between scans. NOTE: If you attempt to enter too low a value, the system will default to a minimum delay.
ACQUIRING DATA 5.12 - PHOTON COUNTING Photon Counting is a technique used to record very low-level signals that might otherwise be lost in background noise. When the photon flux is low, Photon Counting can be utilized. By ‘low’ we mean that there is little chance that two photons will arrive at the same pixel (or binned set of pixels) in the same readout period. In photon counting mode the CCD is continuously readout without any gaps between scans (so that no signal is lost).
ACQUIRING DATA Figure 14: Normal accumulation of 100 scans Figure 15: Photon counting with accumulation of 100 scans iKon-L SECTION 5 Page 74
ACQUIRING DATA 5.13 - VERTICAL PIXEL SHIFT 5.13.1 - Shift Speed Shift Speed (usecs) specifies the time taken to shift charge from one row on the CCD sensor to the next. Speeds which appear un-bracketed in the drop-down list are guaranteed to meet all the system specifications and as a general rule we would recommend using the fastest un-bracketed speed for all measurements.
ACQUIRING DATA 5.14 - HORIZONTAL PIXEL SHIFT 5.14.1 - Horizontal Pixel Shift Readout Rate The Horizontal Pixel Shift 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. Slower readout rates will generate less noise in the data as it is read out.
ACQUIRING DATA 5.15 - TIMING PARAMETERS Depending on which combination of Acquisition, Readout & Triggering modes is selected, various timing parameters become available as follow: • Exposure Time (secs) • No. of Accumulations • Accumulation Cycle Time (secs) • Kinetic Series Length • Kinetic Cycle Time (secs) 5.15.
ACQUIRING DATA 5.16 - SHUTTER The built-in shutter can be used to take a reference or background if Full Vertical Binning is selected. For either Multi-Track or Image mode, the shutter is required to avoid unnecessary signals/light falling on the CCD during the readout process, otherwise the image will be smeared. When the Shutter Control option is selected from the Hardware drop-down-menu, or the button is clicked, the Shutter Control dialog box opens e.g.
ACQUIRING DATA • Fully Auto is the simplest shutter mode, as it leaves all shuttering decisions to the system. When you perform Take Signal the shutter opens for the duration of the Exposure Time you have entered in the Setup Acquisition dialog box. NOTE: This option will automatically provide suitable shuttering for the majority of data acquisitions. The shutter will be closed for background data acquisitions and will be opened for all other data acquisitions.
ACQUIRING DATA NOTE: The shutter pulse is fed from the Shutter SMB on the back of the camera.
ACQUIRING DATA 5.16.1 - Time to Open or Close Shutters take a finite time to open or close and this is sometimes called the Shutter Transfer Time (STT). The documentation supplied by the shutter manufacturer should indicate the STT you can expect from your particular shutter. In the case of a CCD detector, the STT gives enough time for the shutter to open before acquisition starts and enough time to close after acquisition finishes and before readout commences.
ACQUIRING DATA 5.16.2 - Accumulate Cycle Time & No. of Accumulations If you have selected Accumulate or Kinetic as the acquisition mode, with Internal triggering, you can also select the Accumulation Cycle Time and No. of Accumulations. • The Accumulation Cycle Time is the period in seconds between each of a number of scans, whose data are to be added together in computer memory to form an Accumulated Scan. • The Number of Accumulations indicates the number of scans you want to add together 5.16.
ACQUIRING DATA 5.17 - FILE INFORMATION Details of the Acquisition selection can be viewed by clicking the button on the Main Window which opens the Information dialog box (you can enter your own notes in the Comments box): The table below details the type of information contained in the dialog box. Filename The filename associated with the active Data Window ( If the data has not yet been saved this will default to Acquisition) Date and time The date & time at which the acquisition was made.
DISPLAYING DATA SECTION 6 - DISPLAYING DATA 6.1 - DISPLAY MODES Once the parameters for the data acquisition have been set and data has been successfully acquired, there are 3 main options available to display the data, which are as follows: • 2D • 3D • Image The Display drop-down menu also offers various options to change the various formats of the display as shown here : Some of the options are also available via icons on the Main Window and these are shown later in this section.
DISPLAYING DATA 6.2 - DISPLAY PREFERENCES The way data is displayed in the various modes can also be changed. From the Display menu drop-down options, select the Preferences option as shown: The Display Preferences dialog box appears, e.g.: By clicking on the appropriate tab, you can select or deselect certain features associated with the data window for the mode of your choice.
DISPLAYING DATA 6.3 - AXIS DEFINITIONS In descriptions of the data window and in on-screen captions the terms x-axis, y-axis and data-axis are used as follows:• The x- and y-axes define a pixel’s position on the two-dimensional CCD-chip, e.g.: • The x-axis (or horizontal display axis) is parallel to the readout register and may be calibrated in pixels or in a unit of your choice.
DISPLAYING DATA 6.4 - AXIS SETUP When you are in 2D or 3D display mode and the Axis Setup option on the Display menu is selected, the Axis Setup dialog box opens as shown: The minimum & maximum values you wish to appear on the x- and data-axes (the horizontal and vertical display axes respectively) of your data window can be entered in the text boxes.
DISPLAYING DATA 6.5 - ZOOM BOX In 2D & Image modes, you can also zoom into an area by drawing a Zoom Box. In both instances, hold down the primary mouse button and pull the cursor in a diagonal across the screen around the area that you are interested in. In 2D mode, the top and bottom edges of the zoom box demarcate the range of values that will be shown over the full height of the data-axis. Having drawn the zoom box, release the mouse button to perform the zoom operation.
DISPLAYING DATA 6.6 - ZOOMING & SCROLLING The following functions are available in data windows whilst in 2D & 3D Display modes: • Zoom in • Zoom out • Scroll 6.6.1 - Zoom In & Zoom Out On a data window in 2D or 3D display mode, pairs of Zoom In & Zoom Out buttons are provided on both the x- and data-axes of the trace.
DISPLAYING DATA 6.7 - 2D DISPLAY MODE To view data in 2D, either select 2D from the drop-down menu or click on the button. Data is then displayed as an unlabelled trace, e.g.
DISPLAYING DATA 6.7.
DISPLAYING DATA 6.7.2 - Peak Search 6.7.2.1 - Peak Search Sensitivity The Peak Search Sensitivity option Determines the manner in which the cursor moves between peaks/troughs when you key in Ctrl + Right Arrow or Ctrl + Left Arrow. • A low sensitivity (e.g. 1) means the system will find the most prominent peaks or troughs • A high sensitivity (e.g. 5) means less obvious peaks or troughs will be found NOTE: This parameter relates only to Peak Search, not to Peak Labeling. 6.7.3 - Peak Labeling 6.7.3.
DISPLAYING DATA 6.7.4 - 2D with Peak Labeling To label peaks automatically, either select 2D from the drop-down menu or click the button. The data window display will change e.g. : When labeling is selected, you can label a peak manually by double clicking it. To remove a peak label, double click it again. If you switch off peak labeling, (by clicking the button), your manual labeling will be lost. NOTE: To manually label peaks accurately, it is best to zoom in on the trace as described on page 89.
DISPLAYING DATA 6.7.5 - Overlay The ability to Overlay data traces is useful if you wish to compare several traces on the same axes. You can display up to nine 2D traces simultaneously in the same data window. The data window in which you intend to display the overlaid traces must be in 2D display mode. Only the data which were originally in that data window can be saved or modified when the data window is active.
DISPLAYING DATA • When you have taken all the reference acquisitions required, keep the last live acquisition window active and open the previously saved SIF files. • Click the button on the live #0 Acquisition data window and the Add Another Trace To Display dialog box appears: The selection list displays the names of data sets that are already being displayed in a data window.
DISPLAYING DATA • Once you have selected the required file(s) and clicked OK, the display will change, e.g.: NOTE: You can add up to a maximum of 8 overlays to your original data trace. The original data trace is always displayed in blue. Each new overlay appears in a unique identifying color and the Active Trace button is displayed on the left in the same color. • To manipulate the trace you want, click on the Active Trace button corresponding to the color of the trace you wish to work with.
DISPLAYING DATA 6.7.5.1 - Overlay and Keep The Overlay and Keep feature is used only with ‘live’ data acquired into the #0 Acquisition Window. If you have just acquired data that you think you might want to compare with subsequent data, click the button. In the #0 Acquisition window, the live trace will appear in blue but overlaid with a copy in red and the new data window containing the selected data will be shown minimized at the bottom of the screen, e.g.
DISPLAYING DATA 6.7.5.2 - Scale to Active If you have overlaid a number of traces, the Scale to Active option becomes available on the Display Menu, e,g,: When Scale to Active is selected, all the data traces in your data window will be plotted against the scales of the active trace, e.g. for the red trace: Vertical axes will be rescaled even if the units do not match those of the active trace. 6.7.5.
DISPLAYING DATA 6.7.6 - 2D with Chemical Labels If an Andor Shamrock spectrograph is connected to the iKon-L, the following buttons become active: • Chemical Labels • Periodic Table When the Periodic Table button is pressed, the Periodic Table of Elements dialog box opens, e.g: When the required labels have been selected and the Chemical Labels button is button is then clicked, the 2D display will show the labels, e.g.: NOTE: Selecting the Toggle All option will show all elements.
DISPLAYING DATA 6.7.7 - Baseline Correction With Baseline Correction, a series of points on a signal are selected through which a smooth, continuous reference is obtained. This reference is subsequently subtracted from the original signal and the resultant spectrum saved to a new data set. To select the function, click the button and the Baseline correcting dialog box appears, e.g.: The user can now enter and define customized baselines.
DISPLAYING DATA 6.8 - 3D DISPLAY MODE If you have acquired data in Imaging mode or as a Kinetic series you can view the traces taken from all the rows or tracks on one set of axes in a data window. Select the 3D option from the Change Display Mode option on the Display menu or click the button and a data window will appear e.g.
DISPLAYING DATA 6.8.
DISPLAYING DATA 6.9 - IMAGE DISPLAY MODE Data acquired in Imaging mode can be viewed as an image in a data window. You can then adjust the color or brightness using the controls associated with the Palette Bar (see next page). Select the Image option from the Display drop-down menu or click the button and an image will appear, e.g.: The cross-hair (see also Large Cursor and Show 2D Cross Sections under Preferences later in this section) moves to any point on the image that you click.
DISPLAYING DATA 6.9.1 - Image display mode preferences When the Image tab on the Display Preferences dialog box is selected, the following options are made available: 6.9.1.1 - Always maintain aspect ratio • When the Always maintain aspect ratio option is ticked, 2 special buttons appear on the data window, i.
DISPLAYING DATA 6.9.1.2 - Show 2D cross sections When Show 2D cross sections is selected on the Display Preference dialog box, 2D Side Traces are displayed parallel to the vertical and horizontal edges of the display area, e.g.: The long edge of each Side Trace is calibrated in the same units as the corresponding edge of the display.
DISPLAYING DATA 6.9.2 - Palette Bar The Palette bar: runs across the top of the data window. This shows the full palette of grays or colors available in each color mode. The palette is graded so that lower data values correspond to the darker tones to the left of the palette, and higher data values correspond to the brighter tones to the right of the palette. • The arrows to the left of the Palette bar on the data window allow you to adjust the minimum distinguishable data value (i.e.
DISPLAYING DATA 6.9.2.1 - Selecting Color / Grayscale The display appears initially in grayscale, e.g. : Clicking on the button causes the data window to cycle through the following modes: • Color, e.g. • Iterated Grayscale (a small sequence of grays is repeated at intervals to cover the same range of data as grayscale), e.g.
DISPLAYING DATA 6.9.3 - Rescale When a data window is open and you click on the button on the button bar of the Main Window, the system displays against an appropriate data scale all data that falls within the range selected on the x-axis. In Image display Mode, it will also be displayed in appropriate colors or grayscale tones.
DISPLAYING DATA Autoscale Acquisition performs a similar function for the display of data as they are being acquired. It can be selected from the Acquisition drop-down menu, or by clicking the following buttons: = ON = OFF Alternatively, you can press F6 on the keyboard. Rescale is available for all the Display Modes. The following comments take rescaling in Image display mode as a specific example.
DISPLAYING DATA 6.9.4 - High & Low Contrast Overview Assume your original data are rescaled. Data-Axis To achieve high contrast, the computer scales a smaller range of data with the same number of colors as it used for rescaling. Max Min Original Data Range Any data value greater than the maximum in the displayed data range is represented by the brightest color (white). Any data value lower than the minimum in the displayed data range is represented by the darkest color (black).
DISPLAYING DATA 6.9.4.1 - Increasing & Decreasing Contrast You can use the pairs of left-right arrows at either end of the Palette Bar to increase or decrease the displayed data range (i.e. ‘shrink’ or ‘stretch’ the scale on the palette) and thereby alter the contrast of the data shown in Image display mode. You can also use the + and – keys to do the same function. Increase Displayed Data Range Increasing the displayed data range (‘shrinking’ the scale).
DISPLAYING DATA 6.9.5 - Brightness Overview Data-Axis To make the data shown in Image display mode brighter, the computer uses the same Max Original Data Range number of colors as it used for rescaling to scale lower data values. Thus any data originally represented by darker colors are now represented by brighter colors. Min Brighter Data-Axis Max To make the data shown in Image Display Mode darker, the computer uses the same number of colors as it used for rescaling to scale higher data values.
DISPLAYING DATA 6.9.5.1 - Adjusting the Brightness You can alter the brightness of the data shown in Image display mode by moving the displayed data range so that it covers higher or lower data values. To move the displayed data range, place the cursor on or just below the Palette Bar (the cursor changes to a finger) and, holding down the primary mouse button, ‘slide’ the scale on the palette to the left or right.
DISPLAYING DATA 6.10 - DATA HISTOGRAM The Data Histogram dialog Box is launched either by clicking on the icon on the Main Window, or selecting Data Histogram from the Display drop-down menu. This tool allows you to plot a histogram, or graph, between the maximum and minimum data points in the displayed range. It also contains a filter drop down menu, which allows for more accurate analysis and presentation of data values, e.g.
DISPLAYING DATA Values can be modified either by typing in the new values in the Low and High text boxes or by dragging the red arrows and bars below the histogram, e.g.
DISPLAYING DATA 6.11 - REGION OF INTEREST Region of Interest (ROI) is an important post-acquisition tool, used for quantitative analysis and it can be selected either by clicking the button or selecting Region of Interest from the Display drop-down menu. When ROI is selected, the following dialog box opens: An ROI can be drawn on the image by positioning your cursor on the red ROI, and dragging out the using the corner handles.
DISPLAYING DATA There are 3x buttons in the bottom-left of the ROI dialog box: Clicking the View button will present and group your ROI data, according to each individual ROI region selected on the image. It will also display the pixel co-ordinates of the ROI(s) for that scan, e.g.: Clicking the Scan button will present and group your ROI data, according to individual data scans. It will also display the pixel co-ordinates for the ROI(s) for that scan, e.g.
DISPLAYING DATA The ROI can be switched on and off by clicking the (Show ROI) button. When Show ROI is selected on, the selected ROI will be displayed and outlined by red boxes, e.g. for Full Vertical Binning.: When Show ROI is selected OFF, the red ROI boxes are hidden. NOTE: When Show ROI is selected ON, it is not possible to position the cross hair cursor on the image to perform zoom in or zoom out functions. The Edit ROI function is only available when Show ROI is selected On.
DISPLAYING DATA 6.11.1 - ROI Counter The ROI Counter identifies the current active ROI. It can also be used to select and isolate a particular ROI, which can be a useful tool, e.g. if two ROIs are overlapping or are layered on top of each other. By clicking the down arrow, you can also see how many ROIs are currently defined. 6.11.2 - Hot Spot Approximation Hot Spot Approximation can be used to take a selected percentage of the highest data values within a given ROI.
DISPLAYING DATA 6.12 - TIME STAMP When the Time Stamp button is clicked, the Display Preferences dialog box opens, e.g.: The Time Stamp feature allows you to add to the display the time at which the acquisition, or each scan in a kinetic series, occurred, e.g.: Time & date information, or time relative to the start of the acquisition can be displayed by selecting Enabled, then selecting the appropriate option in the Style drop down list.
DISPLAYING DATA 6.13 - PLAYBACK After a Kinetic series acquisition has been has been taken, it can be played back again for analysis. • To replay, click the button and the acquisition will display again as taken. • To pause, click the button. • To stop click the button. Playback autoscale performs a similar function to Autoscale acquisition and is selected from the button on the top of the main window. =ON = OFF The sequence can also be viewed with different parameters set.
HANDLING FILES SECTION 7 - HANDLING FILES 7.1 - MENU OPTIONS The File drop-down menu on the Main Window has the following options: Some of the options available are typical ‘Windows facilities’ to Open, Save, Print files, etc. but some are specific to Andor Solis software to let you create or run programs.
HANDLING FILES Selecting Open... from the drop-down menu or clicking on the button opens a standard dialog box, e.g.: If you select a Data file (.sif), the system launches a data window with the appropriate file displayed, e.g.: If you open a Program file (.pgm), the system launches a Program Editor window and makes available a selection of editing tools on the Main Window (please refer to Editing Programs in Section 9), e.g.
HANDLING FILES 7.1.1 - Close Close removes the active Data Window or Program Editor Window from the Main Window. You will be prompted to save any unsaved data to an appropriate filename. 7.1.2 - Save Selecting Save or stores the contents of an active and previously saved Data Window or Program Editor Window under the current filename. 7.1.3 - Save As Save as...
HANDLING FILES 7.2 - EXPORT AS Export As… opens the Export As dialog box, e.g.: Depending on the Display & Readout modes selected, the file can be saved in one or more of the following formats: 1. Ascii XY (.asc) 2. Bitmap (.bmp) 3. Jpeg (.jpg) 4. TIFF (.tif) 5. Raw data (.dat) 6. AVI (.avi) 7. Mpeg (.m1v) 8. GRAMS (.spc) Table 9 below shows a matrix of the actual combinations available.
HANDLING FILES 7.2.1 - ASCII File extension = .asc ASCII (American Standard Code for Information Interchange) is the most common format for text files in computers and on the Internet. In an ASCII file, each alphabetic, numeric, or special character is represented with a 7-bit binary number. 128 possible characters are defined. Exporting Data as ASCII text means you can subsequently import your data into other applications (such as spreadsheets) that use the ASCII format.
HANDLING FILES 7.2.2 - AVI File extension = .avi An AVI (Audio Video Interleaved) file is a sound and motion picture file that requires a special player. After you have selected AVI files (.avi) from the Save as type drop-down menu, allocated a filename and clicked Save, the AVI Export dialog box appears, e.g.: You can then select which series of data to export to the file. 7.2.3 - Bitmap File extension = .
HANDLING FILES 7.2.5 - JPEG File extension = .jpg JPEG (Joint Photographic Experts Group) is a group of experts that develops and maintains standards for a suite of compression algorithms for computer image files. JPEG is a term used for any graphic image file produced by using a JPEG standard. When you create a JPEG or convert an image from another format to a JPEG, you are asked to specify the quality of image you want.
HANDLING FILES 7.2.7 - Raw Data File extension = .dat The .dat file comprises data only and has no header information of any kind. The original data set remains unchanged. After you have selected Raw data (*.dat) from the Save as type drop-down menu, allocated a filename and clicked Save, the Export # dialog box appears, e.g. This allows the user to save a data set (currently in memory) to a file located on disk.
HANDLING FILES Table 10: Types of .dat files Data type No. of Bytes Range (1) 16 bit integer 2 -32,768 to 32,767 (2) 32 bit integer 4 -2,147,483,648 to 2,147,483,647 (3) 32 bit float 4 -38 3.4 x 10 +38 to 3.4 x 10 (1) Saves a data set to a 16 bit integer .dat file. NOTE: If a data value exceeds the limits of a 16-Bit integer (<-32,768 or > 32,767), that data value is truncated to the corresponding limit (e.g. if a data value is 36,000 units then the value is truncated to 32,767 units).
HANDLING FILES 7.2.8 - TIFF File extension = .tif TIFF (Tagged or Tag Image File Format) is used for storing bitmapped images and is widely supported by commercial publishing packages. After you have selected from the Save as type drop-down menu and allocated a filename, the TIFF export dialog box appears, e.g.: You can then choose the parameters you require to be displayed.
HANDLING FILES 7.3 - CONFIGURATION FILES File extension = .cfg A configuration file contains the values that appear on the system’s dialog boxes whenever the application is launched, or whenever a configuration file is newly loaded. Using configuration files is an easy way to tailor the overall application set-up to suit particular experiments. Configuration files reside in the same directory as the executable (.exe) of the application itself. The factory-supplied configuration file (.
HANDLING FILES 7.4 - PROGRAM SELECTION The menus for working with Programs are selected from the File drop-down menu of the Main Window as shown: Working with programs is explained in more detail in Section 9.
CALIBRATION SECTION 8 - CALIBRATION 8.
CALIBRATION 8.2 - MANUAL X-CALIBRATION Using newly acquired or previously stored data, select Manual X-Calibration from the Calibrate menu. The Manual X-Calibration dialog box appears, e.g.: The number (#n) of the data window (or #0 in the case of an Acquisition Window) appears on the title bar of the dialog box.
CALIBRATION 8.2.1 - Supplying calibration details To manually calibrate a data window, first use the drop-down lists on the Manual X-Calibration dialog box to choose the label and the units you wish to use for the x-axis. The available labels and units are shown in table 11 below. Your chosen unit will appear on the top of the right-hand column of the two columns to the left of the Manual XCalibration dialog box.
CALIBRATION Rather than position the cross-hair by clicking a point, you may choose to move the cross-hair left or right using the horizontal scroll bar on the Manual X-Calibration dialog box. • Click the Single Scroll Arrows at either end of the scroll bar to move the cross-hair by one pixel at a time. • Click the Double Scroll Arrows to move the cursor from peak to peak (i.e. conduct a Peak Search) in accordance with the sensitivity level you have set using the Display Preferences dialog box.
CALIBRATION 8.2.2 - Applying Calibration 8.2.2.1 - Calibrate Depending on the selections made using the check boxes on the Manual X-Calibration dialog box, clicking the Calibrate button will apply calibration to the active data window and/or to future data acquisitions.
CALIBRATION 8.2.2.2 - Data are Non-Monotonic Your data may be Non-Monotonic if you have entered an incorrect value for one or more points on your data trace. An instance of grossly inaccurate manual calibration is shown here: From Pixel 706 to Pixel 953 the user has indicated a fall in wavelength, despite the preceding rise in pixel 690. In such a case, an illegal non-monotonic calibration (as shown on the graph below) results.
CALIBRATION However, a non-monotonic calibration may come about even in cases where your data are not as grossly inaccurate as those shown in the example above. A non-monotonic calibration sometimes results if you attempt to calibrate points that are very close together on your trace, even if, for example, you are entering rising wavelength values against rising pixel values. In its background processing, the system models the calibration data (the user-supplied reference points) as a cubic polynomial.
CALIBRATION 8.3 - X-CALIBRATION BY SPECTROGRAPH To calibrate data using the spectrograph, select the X-Calibration by Spectrograph option from the Calibration Menu. The Spectrograph X-Calibration dialog box will appear e.g.: NOTE: The dialog box can also be opened by selecting the Setup Spectrograph option from the Hardware menu on the main window.
CALIBRATION 8.3.1 - Setup Spectrograph Before you can perform a calibration using the spectrograph, you must ensure that the system knows which spectrograph you are using. To select the type of spectrograph to be used, click the Setup Spectrograph button on the Spectrograph X-Calibration dialog box and the Setup Spectograph dialog box appears, e.g.
CALIBRATION 8.3.1.2 - Communications The radio buttons in the Communications section of the Spectrograph Setup Dialog box can be used to establish an interface between your computer and the spectrograph. 2 If you are using an Andor Shamrock, you can also choose between USB or I C control links. Select Shamrock Control from the Hardware drop-down menu and the Shamrock Control dialog box appears e.g.: 2 Select USB for USB control or for I C select CCD, then click OK.
CALIBRATION 8.3.1.5 - X-Axis Label & Units The Spectrograph X-Calibration Dialog box allows you to select, from scrollable drop-down list boxes, an XAxis Label for your data window and an appropriate Unit of measurement.
CALIBRATION To change the x-axis units of an active data window which you have previously calibrated, select the Change Units option on the Calibrate Menu. The Change X-Calibration of Acquisition dialog box will appear on your screen, e.g.: • From the X-Axis Label drop-down list choose whether you want the x-axis to represent Wavelength, Pixel Number or Raman Shift. • From the Units drop-down list, choose the units that you want to use for your recalibration.
CALIBRATION 8.3.1.6 - Center Wavelength / Center of Raman Shift The system allows you to adjust your spectrograph so that light of a chosen Wavelength or a chosen Raman Shift falls on the center of the CCD-chip. These are referred to as the Center Wavelength and the Center of Raman Shift respectively. If you have chosen Wavelength as your X-Axis Label, enter the Center Wavelength in the text box provided on the Spectrograph X-Calibration dialog box.
CALIBRATION 8.3.1.7 - Offset By entering a value in the Offset text box of the Spectrograph X-Calibration dialog box you can compensate for small misalignments of the detector or the wavelength drive in your spectrograph. A positive value will cause the x-axis of the data window to move to the right (relative to the trace) by the corresponding number of pixels. A negative value will cause the x-axis to move to the left.
CALIBRATION 8.3.1.9 - Micrometer Setting For certain non-motorized spectrographs, the system will calculate a Micrometer Setting that corresponds to the Grating and the Center Wavelength / Center of Raman Shift you have chosen. The Micrometer Setting allows you to manually adjust the angle of the diffraction grating (by means of the micrometer on the spectrograph housing), so that light of the wavelength / Raman shift of your choice falls on the centre of the CCD-chip.
CALIBRATION 8.3.2 - Processing Data via the Command Line 8.3.2.1 - Command Line The Command Line allows you to enter one-line commands that are written in the Andor Basic programming language. These commands are used to manipulate acquired data. Several command lines can be entered and they are separated by ‘:’. The open the Command Line dialog box, either click the button or select the Command Line option from the Command drop-down menu.
WORKING WITH PROGRAMS SECTION 9 - WORKING WITH PROGRAMS 9.1 - WORKING WITH ANDOR BASIC The Andor Basic programming language allows you to create programs for customized control of data acquisition and customized manipulation of data. For more detailed information, please refer to the Programmer’s Guide to Andor Basic. The system provides facilities to let you Edit, Save and Run your programs. 9.1.
WORKING WITH PROGRAMS 9.1.4 - Cut, Copy, Paste, Undo • Cut • Paste or Copy text that you have highlighted then paste the text into a new position inserts cut or copied text into the position following the cursor, or replaces text that you have highlighted • Undo causes the text to revert to its state before the last change was made 9.1.
WORKING WITH PROGRAMS 9.1.6 - Replace To Replace items, select Replace… from the Search drop-down menu: In the Find what text box, type in the search string and in the Replace with text box, type the word or phrase that you want to use instead, e.g.: • Click the Replace button to change the next occurrence of the search string (or the highlighted search string if you have just used Find Next). • Click Replace all to replace the search string wherever it occurs after the current cursor position.
WORKING WITH PROGRAMS 9.1.8 - Run Program by Filename You may also run a program by means of the Run Program by Filename option on the File Menu. Select Run Program by Filename from the File drop-down menu: A standard Open dialog box appears, from which you may select the file whose contents you want to run. The file containing the program appears on screen as an iconized Program Editor Window and the program begins to execute immediately. 9.1.
APPENDIX APPENDIX A1.1 - GLOSSARY If this is the first time you have used an Andor CCD, the glossary that follows will help familiarize you with its design philosophy and some of its key terminology. A1.1.1 - CCD A Charge Coupled Device (or CCD) 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.
APPENDIX A1.1.1.1 - Readout Sequence of a CCD In the course of readout, charge is moved vertically into the shift register, and then horizontally from the shift register into the output node of the amplifier. The 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 CCD-chip.
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 analog signal, ranging from zero to the saturation value.
APPENDIX A1.1.6.1 - Vertical Binning In Vertical Binning, charge from two or more rows of the CCD-chip is moved down into the shift register before the charge is read out. The number of rows shifted depends on the binning pattern you have selected. Thus, for each column of the CCD-chip, charge from two or more vertical elements is summed into the corresponding element of the shift register.
APPENDIX A1.1.6.2 - Horizontal Binning (Creating Superpixels) Shifting the charge horizontally from several pixels at a time into the output node is known as Horizontal Binning. Horizontal binning in combination with Vertical binning allows you to define so-called superpixels that in Image Display Mode represent as a single picture element charge that has been binned from a group of pixels.
APPENDIX 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 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.
APPENDIX A1.1.11 - Noise Noise is a complex topic, the full exploration of which is beyond the scope of this glossary. Noise may, however, be broken down into two broad categories: 1. Pixel Noise 2. Fixed Pattern Noise A1.1.11.1 - 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.
APPENDIX A1.1.12 - 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 absorbed. When a UV or visible photon is absorbed by the detector it can 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.
APPENDIX A1.1.14 - 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. A1.1.15 - Scan Types: Keep Clean & Acquired The CCD is continually being ‘scanned’ to prevent its becoming saturated with dark current (see dark signal). If the Scan is being used simply to ‘clean’ the CCD (i.e.
APPENDIX A1.
APPENDIX A1.3 - TERMS & CONDITIONS 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.
APPENDIX A1.4 - WARRANTIES & LIABILITY 1. Subject to these Conditions set out below, the Seller warrants that the Goods will correspond with their specification at the time of delivery and will be free from defects in material and workmanship for a period of 12 months from the date of delivery. 2. The above warranty is given by the Seller subject to the following conditions: 2.
APPENDIX 5. Where any valid claim in respect of the Goods which is based on any defect in the quality or condition of the Goods or their failure to meet specification is notified to the Seller in accordance with these Conditions, the Seller shall be entitled to replace the Goods (or the part in question) free of charge or, at the Seller’s sole discretion, refund to the Buyer the price of the Goods (or a proportionate part of the price), but the Seller shall have no further liability to the Buyer. 6.
