UltraScan User’s Guide Reference Series Gatan, Inc. 5933 Coronado Lane Pleasanton, CA 94588 Tel (925) 463-0200 FAX (925) 463-0204 May 2004 895.MANUAL Revision 2.
Preface About this Guide This UltraScan Reference Series User’s Guide is written to provide a brief description of the camera’s operating principles, instructions on how to install the camera, and an introduction to imaging in DigitalMicrograph. For additional discussion of image processing, refer to the DigitalMicrograph User’s Guide.
Disclaimer Gatan, Inc., makes no express or implied representations or warranties with respect to the contents or use of this manual, and specifically disclaims any implied warranties of merchantability or fitness for a particular purpose. Gatan, Inc., further reserves the right to revise this manual and to make changes to its contents at any time, without obligation to notify any person or entity of such revisions or changes. Copyright and Trademarks © 2002. All rights reserved.
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Table of Contents ULTRASCAN USER’S GUIDE REFERENCE SERIES ................................................................................................... 1 PREFACE................................................................................................................................................................................I ABOUT THIS GUIDE .....................................................................................................................................................
5 CARE AND MAINTENANCE................................................................................................................................. 5-1 5.1 GENERAL PRECAUTIONS ..................................................................................................................................... 5-1 5.1.1 Peltier cooler maintenance............................................................................................................................ 5-1 5.1.
List of Figures FIGURE 2-1 FIGURE 2-2 FIGURE 2-3 FIGURE 2-4 FIGURE 2-5 FIGURE 2-6 FIGURE 2-7 FIGURE 2-8 FIGURE 2-9 FIGURE 2-10 FIGURE 2-11 FIGURE 2-12 FIGURE 2-13 FIGURE 2-14 FIGURE 2-15 FIGURE 3-1 FIGURE 3-2 FIGURE 3-3 FIGURE 3-4 FIGURE 3-5 FIGURE 3-6 FIGURE 3-7 FIGURE 3-8 FIGURE 3-9 FIGURE 3-10 FIGURE A 1 FIGURE A 2 FIGURE A 3 FIGURE A 4 FIGURE A 5 FIGURE A 6 FIGURE A 7 FIGURE A 8 FIGURE A 9 FIGURE A 10 FIGURE A 11 CAMERA CONTROLLER .......................................................................
1 Introduction The Gatan UltraScan™ family of cameras is designed to deliver the ultimate quality in transmission electron microscope images. It is the first digital camera system with the potential to replace film as a recording medium in the TEM. New technology has been introduced at every stage of the imaging process to improve resolution, sensitivity, dynamic range, linearity and speed of operation.
2 Getting Started The following steps will enable the first-time user to switch on the digital camera, launch DigitalMicrograph and prepare for the acquisition of an image. • Make sure that the viewing chamber is at the proper vacuum. • Make sure the water and the three color-coded pressure lines are correctly connected to the camera and proper water pressure is maintained. • Switch on the CCD camera controller (Fig. 2-1), the LED will turn green. • Flip the Shutter switch to AUTO.
The Workplace Figure 2-1 Camera controller Power switch Shutter switch Peltier switch 2.1 The Workplace When DigitalMicrograph is launched, you will see the commonly used tools (left side), the Image Acquisition and Saving tools (right side), and the Result window as shown in Figure 2-1. These tools are composed by “floating” windows fully stackable to allow customization. UltraScan User’s Guide Reference Series Rev 1.
Camera Configuration Figure 2-2 DigitalMicrograph Workplace Commonly used tools Image display Image acquisition and saving tools Results window 2.2 Camera Configuration If the camera is already configured by a Gatan service engineer, this section can be ignored. Before starting acquiring images, it is necessary to configure the camera. This process is shown in Figure 2-3. UltraScan User’s Guide Reference Series Rev 1.
Camera Configuration Figure 2-3 (a) Camera Menu (b) Camera configuration • Select Configure Camera in the Camera menu (Figure (2-3a). • In the Camera configuration dialog box (Figure 2-3b), you can change the name of the camera by typing in the Name field. • Image rotation can be specified in the Rotation pull-down menu. • The coordinates for column defect correction are entered in the Defects field.
Set Bias Levels 2.3 Set Bias Levels In 4-channel CCD readout, the entire CCD sensor is divided into 4 sectors (called quadrants). It is common that each quadrant has a different bias level. This can result in CCD images with visible quadrant (like a chess board pattern). Under the Camera menu (Figure 2-3), Set Bias Levels routine automatically measures and sets the bias for each quadrant. The bias setting is written to the First Light Controller.
Quadrant Correction Reference Figure 2-4 Set the target intensity 2.4 Quadrant Correction Reference The above Set Bias Levels routine removes gross contrast variation from quadrant to quadrant. The remaining variation can be removed by the Prepare Quadrant Correction Reference routine. Before running the Prepare Quadrant Correction Reference routine, make sure the CCD has reached its stable temperature (reading from the front panel of the First Light controller).
Gain Normalization minutes for US1000 (2k x 2k) and US4000 (4k x 4k) respectively. Once the procedure completes, a reference image is stored in DigitalMicrograph “Reference Images” folder for later use. Typically it is not required to run this routine frequently. It is important to run Gain normalization routine (next section) after Prepare Quadrant Correction Reference in order to activate the linearization correction routine, so that it is applied to all the future acquired images. 2.
Magnification Calibration • Use “graphite” or any crystalline samples having known lattice spacing • Use the FFT method. It is very important to make sure DigitalMicrograph software correctly reads the TEM magnification. If the communication between the computer and the TEM is established, the magnification is read automatically. Otherwise, please make sure DigitalMicrograph is set to prompt the user to enter a value for TEM magnification every time an image is to be acquired.
Magnification Calibration In the “Magnification” section in the “Global Microscope Info” window (Figure 2-4) choose: • Source from: User • Ask User: Always • Click OK 2.6.1 Low magnification • Figure 2-7 Record an image of a cross grating sample (Figure 2-7) Cross grating sample • Choose “Calibrate image…” under the “Microscope” menu (Figure 26). Follow the on screen instructions (Figure 2-8) Figure 2-8 Instructions window A red line will appear on the image.
Magnification Calibration Figure 2-9 Figure 2-10 • Position it on a feature of known size. • Press OK on the “Calibrate image” window. • Enter the correct distance for the selected feature (for example 10 line pairs of cross grating sample where the distance = 10 x 0.463µm) in the “Calibration” window and select the units (see Figure 2-9). Calibration window • Press OK. • Choose YES in the next window (see Figure 2-9) to complete the magnification calibration.
Magnification Calibration Figure 2-11 Magnification table The first column represents the nominal TEM magnification and the second column is the actual magnification at the CCD. 2.6.2 “High” magnification • Figure 2-12 Record a lattice image of the crystalline sample (Figure 2-12). High-resolution image of a crystalline sample • Choose “Calibrate image from “Microscope” menu (Figure 2-6). UltraScan User’s Guide Reference Series Rev 1.
Magnification Calibration A diffractogram will be calculated (Figure 2-13). Figure 2-13 Diffractogram • Follow the on screen instructions (Figure 2-14) A red line will appear on the diffractogram. Figure 2-14 • Position the endpoints of the red line on two symmetrical diffraction peaks (Figure 2-13). • Press OK to specify the reciprocal unit and the d-spacing (in the corresponding real units) in the next window (Figure 2-15).
Magnification Calibration Figure 2-15 Calibration window UltraScan User’s Guide Reference Series Rev 1.
3 Image Acquisition This chapter contains some instructions on how to acquire an image and a description of the most frequently used floating windows. Now you are ready to: • Insert the sample, • Find a region of interest • Start using the CCD camera to view your specimen. 3.1 View The view mode (shown in Figure 3-1) allows user to observe Live (continuous) images on the monitor.
View off this feature. When the box is not selected the user is in control of the exposure time that can be changed by either typing in the exposure time box and then pressing the Enter key, or by hitting the up and down arrow keys to respectively double or halves the exposure time. To view a continuous image of the sample: • Select the Camera inserted box or make sure it is selected.
Image Notes Figure 3-2 Focus Loupe The acquisition can be stopped by: • Pressing Stop View, or • Pressing the Spacebar. 3.2 Image Notes The user can type in notes in the Image Info window shown in Figure 3-3. Saving an image will automatically save the image notes with the image file. The Up/down arrows allow user to browse through the images saved in a session when using the AutoSave function (Section 3.5 below). UltraScan User’s Guide Reference Series Rev 1.
TEM Session Information (Global Info) Figure 3-3 Image Info 3.3 TEM Session Information (Global Info) Before acquiring any images, it is recommended to enter the correct information about the sample, operator, TEM name, etc. Click on the Global Info button (Figure 3-3) to type in all these information. This function can also be accessed under the Microscope menu. The global information is saved automatically with every image that is acquired. 3.
Image Saving and Printing 3.5 Image Saving and Printing The recorded images are displayed on the monitor. Pressing on the floppy disk icon or on the printer icon in the Saving palette (Figure 3-5) the image can be saved or printed respectively. Images can be easily saved in any user specified directory with a common root name. Figure 3-5 Saving window Report view Saving Set-up button Print image Save image 3.5.
Image Saving and Printing 3.5.3 Report Options Click on the Report Options button to view the dialog box shown in Figure 37. You can choose to have any parameters listed to be included in your report. You can also add a logo file and image notes to the report. Figure 3-7 Saving Data Bar Custom item allows user to add text information to every report page. This feature is useful to add the name of your institution, or the name of your TEM lab.
Image Saving and Printing Figure 3-8 Custom Items Type the text in the Single line item (for example the name of your TEM lab) and then click the Add button. Now the text is entered in the window of the Single line item. Click OK. The style of the Custom item can be easily changed in the Report page (next section). 3.5.4 Report The report button (the one with a page and a magnifier on the Save palette in Figure 3-5) will toggle between report view (Figure 3-8 a) and image view (Figure 3-8 b).
Image Saving and Printing Figure 3-9 (a) Report view (b) Image view Users can customize the layout and selection of parameters on the page (for example, using pointer to move the text around) and then save the setting as a report template. This is done by clicking the Save As Default Layout button in the Save setup dialog. The Custom item on the page can be changed to different text style to make it more visible. First position it on the Report page and then choose the font and size of your liking.
Image Saving and Printing Figure 3-10 Control palette UltraScan User’s Guide Reference Series Rev 1.
4 Quick Reference The steps necessary for operating Gatan CCD camera are summarized here. • Make sure that the viewing chamber is at the proper vacuum. • Make sure the water and the three color-coded pressure lines are correctly connected to the camera and proper water pressure is maintained. • Switch on the CCD camera controller. • Flip the Peltier Cooler switch to the COOL position. For best results it is recommended waiting (2 hours or more) for the system to stabilize.
Image Saving and Printing • Click on “Start View” on the View palette in Search mode (Figure 31) to position sample area of interest. (disable Auto Exposure). • Click on Focus Loupe on the View palette (Figure 3-1) to check the final focus. Make sure Auto Survey is checked. • Click on Start Acquire button in the Image Acquire palette (Figure 34). (disable Auto Exposure). • Click on Report View button on the Saving window (Figure 3-5) to view image in print preview mode.
5 Care and Maintenance This chapter contains some general tips on the care and maintenance of your UltraScan camera. It also contains a list of questions that are often asked by users. 5.1 General Precautions The following are some general precautions users should adhere to in the care and maintenance of their camera. 5.1.1 Peltier cooler maintenance • In standard operation conditions the temperature display is set to a temperature of -25ºC. The temperature should never exceed 50ºC.
General Precautions If the flow rate of the cooling water deviates significantly from the value originally set, make sure the lines are not obstructed and adjust the pressure regulator to bring the flow back to the original level. Remember, if the water flow stops while the Peltier cooler is on, an over-temperature condition will be detected and the automatic protection will shut down the cooler. • The Peltier cooler should not be left on when the TEM cooling water is turned off or fails.
General Precautions There is no defined cutoff where the scintillator will be damaged. Rather, damage can result from prolonged exposure of the scintillator to a very high beam intensity (above 30,000 counts in binned by 1 mode and 60,000 counts in binned by 2 and higher modes). If you have no saturation with a short exposure, then there is no danger.
Most Often Asked Questions by which time the beam might already have hardened the film. That fact can be used to diagnose the presence of oil if the user takes an image at a low kV periodically to check for the presence of oil. Examine the surface of the scintillator. If the surface of the scintillator becomes dirty or scratched, ship the camera to Gatan for service. Do not attempt to clean the scintillator yourself as damage can result. 5.1.
Most Often Asked Questions Check if the shutter cables are properly connected. Run the Set Bias routine. Check the “Camera View” floating window to see if the “Camera Inserted” box is checked (camera inserted). Check if the Shutter switch on the UltraScan controller is set to AUTO. Check if the beam has drifted. Check if the TEM viewing screen is lifted. Check if you have a film plate stuck above the camera in the TEM. You may have an image and not being able to see it.
Most Often Asked Questions Check that the shutter switch on the controller is set to AUTO. It could be a bad reference image. Retake another one. Check that the shutter is functioning correctly. If it is, the shutter indicator light on the controller would go on and off as you take an image. 9. When viewing, the image sometimes gets suddenly bright/dark, what is happening? Sudden changes in the contrast may be due to stray x-ray photons that saturate some of the pixels. 10.
Most Often Asked Questions about 10,000 counts/sec ( in 2 times binned mode) and switch the shutter switch on the controller to Open. Expose the scintillator for 2-3 min, switch back to Auto, and take another image. UltraScan User’s Guide Reference Series Rev 1.
Appendix 1 Hardware description A1 System Requirements To use the UltraScan Reference series CCD cameras, the following hardware and software systems are required: Windows 2000 Professional or Windows XP Professional Minimum 512 MB RAM (1GB RAM preferred) 40GB, 1GHz Hard-drive or better Pentium III or later Available microscope’s bottom port Water connections Air connections Gatan Microscopy Suite (GMS) software 1.1 or later UltraScan User’s Guide Reference Series Rev 1.
A2 Description FireWire capability A2 Description An UltraScanTM Reference Series camera acquires an electron microscope image into a computer in four stages. First a scintillator converts the electron image into a high-resolution light image. Then a fused fiber-optic plate captures the light from each point in the image and channels it to the CCD. The CCD then converts the transferred light image into a second electron image.
A2 Description TM Figure A 1 UltraScan Reference Series camera mounted on a TEM column. Water line Air lines Figure A 2 Controller’s front panel UltraScan User’s Guide Reference Series Rev 1.
A2 Description A2.1 Front panel controls • Figure A 3 Power switch: A green LED indicates when the power is ON. Controller’s front panel: shutter control • Shutter Control (Figure A3): LEDs 1 and 2 indicate the state of shutters 1 and 2 respectively. An illuminated LED corresponds to a shutter Open state. • AUTO/OPEN Switch (Figure A3): When set to AUTO, the state of shutters 1 and 2 is controlled by the computer.
A2 Figure A 4 Description Controller’s front panel: Temperature • Temperature display (Figure A4): Displays the CCD operating temperature in degrees Celsius when the First Light Controller is connected to an UltraScan Camera. • Heatsink Switch (Figure A4): Momentary switch. When depressed, the temperature display monitors the temperature of the thermo-electric cooler heat sink. Used to check water cooling efficiency of the UltraScan camera.
A2 Description A2.2 Controller’s back panel Figure A 5 • Supply Voltage: 100-240 V AC • Insulating rating of external circuits: 1500 V • Operating Conditions: 15 – 25 C • Power Entry Module: AC line voltage is connected through a universal power cord. The power entry module is compatible with either single or dual fusing.
A2 Description • Figure A 6 Camera Connector (Figure A5): Connections to the UltraScan camera are via a 62 pin connector located on the rear of the controller. Controller’s back panel: air connections • Air Connections (Figure A6): The microscope air line at 60 PSI is connected to the AIR “IN” connection located on the rear panel. The camera insertion air line is connected to the AIR IN port. If an “inserted camera” state is requested by the user, an electronic air valve connects AIR IN to AIR OUT.
A2 Figure A 7 Description Controller’s back panel UltraScan User’s Guide Reference Series Rev 1.
A3 Installation Figure A 8 US 4000 SP block diagram. text UltraScan System 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 11. 12. 13. 14. 15. 16. 17. 18. 19. 20. 21. 22.
A3 Installation • Place the black camera cable between the controller and the knee well of the microscope. Place with the male end towards the camera. • Connect the female end of the camera cable to the controller. • Connect the controller line cord to the power strip. • Make sure that the controller is set to OFF. • Connect the male end of the camera cable to the camera. Warning: Do not connect or disconnect the camera cable with the controller power on. Damage may occur. A3.
A3 Installation The two inline fittings of the T must be of a compatible size to the air line. As the lines of different microscopes may have different diameters, it is a good idea for the installer to have his own Ts at hand in case the supplied Ts do not fit. The perpendicular fittings of the supplied Ts fit tubes 4 through 6. If the installer’s Ts are used, their perpendicular fittings must also fit tubes 4 through 6. • Connect tube 6 to the perpendicular fitting of the T along the compressed-air line.
A3 Installation • Connect tubes 4 and 5 to the remaining two fittings on the Ts along the open line. • Connect tubes 2 and 3 to tube 5 and 6 respectively through their quickdisconnect fittings. • Connect the male quick-disconnect fitting of tube 1 to the outlet on the backside of the controller labeled Air Out (Figure A6). • Snap the male quick-disconnect fitting of tube 4 into the inlet on the backside of the controller labeled Air In (Figure A6).
A3 Installation • When the pump-down cycle is complete, restore the configuration of the pressure lines to the normal configuration as shown in figure A9. Plug tube 1 into Air Out on the backside of the controller and tube 3 into tube 6. A3.3 Water lines Figure A10 shows how the camera is connected to the microscope’s watercooling system.
A3 Installation Note that temperatures lower than 20 °C may result in condensation accumulating in the CCD camera head electronics. This may interfere with normal functioning of the camera. • Connect line 1 to the pressure regulator end of line 2. • Connect line 2 (flow meter end) to line 3 and the other end of line 3 to the water inlet on the camera head. • Connect one end of line 4 to the water outlet on the camera head and the other end to line 5 to complete the loop.
A3 Installation A3.4 Electrical connections The diagram in Figure A11 shows the electrical connections in the system. Figure A 11 Electrical diagram. Red LED goes out whenever cable #1 is connected correctly Power cord 1 CAMERA IN FIBER OPTIC OUT Connect green ground wire to microscope ground 2 SHUTTER OVERRIDE 1 2 1 2 AUX Power cord Shutter override interface Shutter interface • Connect the controller to the multiple outlet strip. The computer should not be plugged into the outlet strip.
A3 Installation A3.5 • Connect the green ground wire on the outlet strip to the microscope ground. • Run the Fiber Optic cables between the controller and the computer. Shutter-control output The Shutter-Control output (shown in figure A11) is on a BNC connector on the back panel of the controller (Figure A7). A3.6 • Connect one end of the Shutter-Interface cable to the Shutter-Control output on the controller.
Appendix 2 CE certification UltraScan User’s Guide Reference Series Rev 1.
DECLARATION OF CONFORMITY DECLARATION OF CONFORMITY (According to ISO/IEC GUIDE 22 and EN 45014) Manufacturer’s name: Gatan Inc. Manufacturer’s Address: 5933 Coronado Lane Pleasanton, CA 94588 U.S.
DECLARATION OF CONFORMITY Position: President and CEO Index A arrows, 3-3 Auto Exposure, 3-1, 3-4, 4-2 Auto Survey, 3-1, 4-2 B F FFT, 2-7 fiber-optic plate, II film, 1-1, 2-7, 5-2, 5-4, 5-5, 5-6, II Focus Loupe, 3-1, 3-2, 3-3, 4-2 Focus mode, 3-1 binning, 5-4, 5-5 G C Calibrate image, 2-8, 2-9, 2-11 calibration, 2-7, 2-9, 2-10, 2-12 Camera menu, 2-4, 2-6, 4-1, 5-6 CCD, i, 1-1, 2-1, 2-4, 2-6, 2-7, 2-10, 3-1, 3-4, 3-8, 4-1, 5-2, 5-3, 5-4, 5-5, 5-6, I, II CE certification, XVII, XIX Configure Camera,
DECLARATION OF CONFORMITY N Name field, 2-4 noise, 1-1, II P Peltier, 2-1, 4-1, 5-1, 5-2, 5-3 print, 3-7, 3-8, 4-2 R Reference, i, 1-1, 2-6, 4-1 region of interest, 3-1 Report Options, 3-5, 3-7 resolution, 1-1, 2-11, 3-1, 3-4, 5-4, II retraction, 1-1, 5-5, II S scintillator, 5-2, 5-3, 5-6, II Search mode, 3-1, 3-2, 4-2 sensitivity, 1-1 Set up, 3-5 shutter, 2-4, 5-3, 5-5, 5-6 speed of operation, 1-1 Standard, 1, 1-1, I, II, III Start Acquire, 3-4, 4-2 Start View, 3-2, 4-2 T TEM, 1-1, 2-7, 2-10, 3-4, 3-
