Andor Technology iXon Ultra 897 Operation & User’s Manual

Text of Andor Technology iXon Ultra 897 User Guide:

• Andor Technology iXon Ultra 897, WINDOWS GLOSSARY Page 165 Section 8 . 2 The window which you are currently working with is known as the Active Window. It is always positioned in the foreground of your screen. By the bolder color of its title bar, the active window is distinguished from other windows you may have open. Active Window A Check Box is included on a dialog box to let you select optional functional ity. When you click the box, a  appears in it, indicating that the particular option has been chosen. Several check boxes may appear together on a dialog box. You may select whatever combination of options you believe to be appropriate for your particular application

• Andor Technology iXon Ultra 897, ELECTRON MULTIPLYING CCDS Page 43 Section 3 . 1 In the following example, where each superpixel is of dimensions 2x2 pixels, charge from two rows is first binned vertically into the shift register; then charge from two pixels of the shift register is binned horizontally into the output node of the amplifier. The effect of the combined binning processes is a summed charge equating to a 2x2 ‘superpixel’. Since this example initially involves binning charge from two rows, the process begins in the same way as the previous example (see Steps 1 - 4 of Vertical Binning of Two Rows). Then horizontal binning begins.

• Andor Technology iXon Ultra 897, DISPLAYING DATA Page 115 Section 4 . 7 You may add up to eight overlays to your original data trace. The original data trace is always displayed in blue. Each overlay appears in a unique identifying color. ‘Add Another Trace To Display’ Dialog Box Use the color-coded Active Trace buttons to choose the trace you want to be able to manipulate in the Data Window. The values on the horizontal and vertical axes will change to correspond to the active trace (and will be presented in the same color as

• Andor Technology iXon Ultra 897, INDEX Page 176 Section 9 M Maintain Aspect Ratio, 106 N Noise, 46 O Overheating Causes, 130 Overlay, 114 Overlay and Keep, 115 P Palette Bar, 99 Show Palette Bar, 107 Paste Clipboard, 133 Program Editor Window, 139 Percentage Absorptance, 90 Percentage Reflectance, 90 Percentage Transmittance, 91 Power Supply Block, 15 Program Editor Window, 140 Programming Andor Basic, 139 Q Quantum Efficiency, 171 R Readout, 40 Real Time Acquisition, 82 Reference Take Reference, 65 Reflectance, 90 Region of Interest, 11

• Andor Technology iXon Ultra 897, TUTORIAL 1 Page 147 Section 7. 1 … Measuring Gain Factor at a Given Temperature Setting Using a Weak LED Light Source Additional Requirements Stable LED light source, Compatible camera lens, Darkened ambient conditions, Optional - Neutral density filters The object of this experiment is to make an approximate measurement of the true gain factor applied at a series of working empirical gain settings. Aim Attach the camera to the lens, either through C or F-mount adaptor as appropriate. Spacers can be inserted in order to optimise the working focal distances. Ideally the camera should be mounted on a retort stand, pointing downwards. The experiment can however be

• Andor Technology iXon Ultra 897, DISPLAYING DATA Page 97 Section 4 . 7 The system can display data in a number of ways. The display modes may be accessed from the Change Display Mode option on the Display Menu or from the corresponding buttons on the Main Window, once data have been acquired or retrieved. Change Display Mode The following Display Modes are available: Image, 2D, 3D Data acquired in an imaging mode (see SECTION 4.5 SETTING THE ACQUISITION) may be viewed as an image in a Data Window. Select the Image option on the Display Menu or click the Image button. For best results you should set your computer displ

• ELECTRON MULTIPLYING CCDS Page 36 Section 3 . 1 One of the electrodes (phases) in the Gain Register is replaced with two electrodes, the first is held at a fixed potential and the second is clocked as normal, except that much higher voltages (between 40V and 60V amplitude) are used than are necessary for charge transfer alone. The large electric field generated bet

• Andor Technology iXon Ultra 897, TUTORIAL 2 Page 151 Section 7. 3 Extending Dynamic Range in ‘Slow Scan’ Measurements By Accumulating Signal Although the iXon camera, due to it’s high-speed operation and ultimate EMCCD sensitivity performance, is very well suited to dynamic low light measurements, it can just as readily be applied to ‘slow scan’ non-dynamic quantitative measurements such as microtitre plate, gel or biochip reading. Operation under conditions of applied gain can enable very weak signals to be amplified above the camera read noise (this can be particularly pertinent in chemiluminescence / bioluminescence measurements), using lower exposure times than wou

• REGION OF INTEREST Page 118 Section 4 . 8 Region Of Interest Region of Interest is an important post-acquisition tool, used for quantitative analysis of data. Region of Interest, abbreviated to ROI, can be selected from the Display menu on the Main Window, or by clicking the ROI icon the task bar in the Main Window. Remember, the Display menu only becomes active after you hav

• Andor Technology iXon Ultra 897, INTRODUCTION Page 8 Section 1 . 1 In the software, all the controls you need for an operation are grouped and sequenced appropriately in on-screen windows. As far as possible, the descriptions in this User’s Guide are laid out in sections that mirror the Windows Interface. The following type-styles are used in the right-hand margin of the User’s Guide to pick out key features of the menus:- Using The Manual • Menu • Menu Option These styles are reflected in the format of the main texts. In addition, windows and dialog boxes are identified as: • Active Window / Dialog Box • Dialog Box - functional area • Dialog Box - option, par

• Andor Technology iXon Ultra 897, RUNNING PROGRAMS Page 142 Section 5 . 3 To run a program, make sure you have opened the appropriate .pgm file and ensure that the file name appears in the drop-down list box next the Run Program button; then click the Run Program button. Run Program To change the name of the file you want to run: either open the drop-down list and click the name of the file; or select an open Program Editor Window; or open the .pgm file from the File menu. You may also run a program by means of t

• Andor Technology iXon Ultra 897, USING THE COMMAND LINE Page 121 Section 4 . 9 Processing Data via the Command Line The Command Line Dialog Box is launched from the Command Line option on the Command Menu or from the Command Line Button on the Main Window. 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. To run a command, click Execute. See the accompanying User’s Guide to Andor Basic for details of how to use the Andor Basic programming language.

• Andor Technology iXon Ultra 897, HOT KEYS Page 29 Section 2 . 6 Hot keys (or shortcuts) let you work with the system directly from the keyboard, rather than via the mouse. F1 provides Help. The following hot keys relate to data acquisition: Key Strokes Description F5 Take signal scan F6 Autoscale Acquisition Ctrl + B Take background Ctrl + R Take reference Esc Abort Acquisition

• Andor Technology iXon Ultra 897, INSTALLING THE SYSTEM Page 22 Section 2 . 3 Connecting the System Connect the elements of your system as follows: • Plug your PC into the mains outlet to ensure grounding, but keep the power switched off. • Connect the Detector Head to the Controller Card using the Cable provided. The 36-way connectors on the cable are polarized so that there is only one way of installing the cable. It is important that this cable is securely fastened to provide a good grounding between the detector head and Controller Card. Your system has been supplied with a Power Supply Block (PSB) for cooling . The PSB connects to the detector he

• CHOOSING THE DATA TYPE Page 96 Section 4 . 6 bottom of the Data Window you will see up to three tabs, labeled Sig (Signal), Bg (Background), and Ref (Reference) which (where appropriate) identify data acquired via the functions Take Signal, Take Background, and Take Reference respectively. Click on the appropriate tab to display the trace you require. In description

• Andor Technology iXon Ultra 897, TUTORIAL 3 Page 158 Section 7. 3 increased (this may be more easily visualised by clicking the cursor in a background region of the image, then selecting the 2D icon), it is likely that background light is being leaked into the system. This can markedly reduce the effectiveness of this technology, since leaked background or unwanted background fluorescence is primarily contributing to the detection limit at higher gain settings, rather than the camera readout noise. This principle applies to all low-light microscopy techniques and efforts should be made to eliminate as far as possible any sources of background light. N.B. At higher gain settings, another sour

• Andor Technology iXon Ultra 897, SHUTTER CONTROL Page 123 Section 4 . 11 The Shutter Control Dialog Box provides you with a selection of options that determine when and how a hardware shutter should be used. Launch it by selecting the Shutter Control option on the Hardware Menu. Shutter Control Certain settings (e.g. Permanently Open and Permanently Closed) take effect as soon as you close the Shutter Control Dialog Box by clicking the OK button. Other settings will be applied whenever you acquire data (see: SECTION 4.4 DATA ACQUISITION - Making an Acquisition). Shutter Control D

• EMCCD GAIN Page 47 Section 3 . 2 Darksignal or dark current is just the same as in conventional CCDs. When judging the required operating temperatures to eliminate the darksignal contribution, usually a temperature where the darksignal shot noise is comfortably below the readout noise is selected. In this case, further cooling provides no benefit. For the EMCCD, how

• IMAGING GLOSSARY Page 170 Section 8 . 3 signal; and 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. Readout noise (which in our detectors is, in any case, low) is due to the amplifier and electronics: it is ind

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