Optical Diffractometer User Manual
Contents
1. reliably grounded 240V rms single phase 50Hz or 110V rms single phase 60Hz supply without the need to change any settings The following colour coding should used for power leads when connecting to the power supplies B brown line or hot BEN blue neutral fa yellow green earth or ground or black line or hot white neutral green earth or ground Note The Optical Diffractometer is fitted for a 5A T fuse in the live and a 5A T fuse in the neutral at the power input socket The 5A current rating is suitable for the full range of supply voltages GD00282 03 Page 8 Optical Diffractometer User Manual 3 2 Operating conditions The Optical Diffractometer has been designed for use in normal laboratory office conditions No special lighting arrangements are required The Optical Diffractometer is not intrinsically safe nor explosion proof It must not be operated in the presence of flammable gases fumes or chemical hazard 3 3 Electrical safety It is not necessary to gain access to the inside of the Optical Diffractometer during normal operation other than through the freely opening side and front access panels in the base unit Equipment repair must be performed only by qualified service engineers Components must not be replaced whilst the power cord mains lead is connected 3 4 Laser safety When operated normally the Optical Diffractometer is a class 1M laser system There is no requirement for a designated las2. 14 6 4 1 Summaty 5 5s v Tb RA DO HERI EORR TA aA fe ERR a 14 6 4 2 Using the sample Staga darsimda iiie nia i esee einn nannte a a a i nannte nana 15 6 4 3 Adjusting the stops ec bed tte A E a aR a ea nes 15 6 4 4 Laser diode intensity eese siiis sessi i nennen sinn nnns aiia aaa 15 6 4 5 Heal space image adjustment assesses eene nnne nnne nnns 16 6 4 6 Diffraction image adjustment seen eene nnne rnnt 16 6 4 7 Using the laser cross hair sisse se siiee seen nannte nani tnter inneren nnn nana 17 6 4 8 Using the Optical Diffractometer ssssssssssssss siint einn 17 6 4 9 Image calibration aiaiai e Lee eb on Sev a RAE havent a ERR chev eee 18 Ho Manera e ees adea ves Sada aci aV SM Ede e e 19 8 General SpeclrcallOT sii eo ette Rog SE ARM t rude Bett i adem eee 20 Appendix A International design Standards ssssssssm 21 Appendix B i i rr S 22 Appendix C Useful addresses z i oria ere eo ive S erat erede teras 23 GD00282 03 Page 4 Optical Diffractometer User Manual 1 INTRODUCTION This instrument was developed by Dr W B Amos for the MRC Laboratory of Molecular Biology Cambridge where Klug and De Rosier first introduced the diffraction analysis of electron micrographs in the 1960s Sira Technology Ltd have joined forces with MRC Laboratory of Molecular Biology to bring the instrument to the molecular biology research comm
3. be correctly installed in the PC for the application to run Each board should be connected by a 75Q video cable to the appropriate monochrome video camera image size 768 x 576 pixels 6 3 3 Initial display When the application is started it should immediately begin to show live video images from both cameras and the status window at top right will show Running The diffraction image will initially be displayed in the left main area the real space image in the right reduced area 6 3 4 Troubleshooting If the application does not start and you get is an error message box then it is likely that either the hardware two Picolo boards or the software MultiCam for Picolo driver is not correctly installed In this case refer to Euresys documentation You can also try running the Euresys application EasyGrab exe as a test of operation If the application starts but the status window shows Error on 1 or Error on 2 it indicates that there is no video signal detected by one of the boards It is likely that either power to the Optical Diffractometer is not turned on or else the video cables are disconnected After rectifying the situation click Run on the menu bar to start live video display If the real space image is labeled as being the diffraction image and vice versa then exchange the video cable connections at the back of the PC GD00282 03 Page 13 Optical Diffractometer User Manual 6 3 5 Controls Toggle
4. on the PC and click on the DIFFRACT shortcut on the desktop to start the image capture software 6 2 Shut down To shutdown close the image capture software Click on the Start button followed by Turn off Computer Select Turn Off The Optical Diffractometer should be powered down by first turning off the laser diode at the front panel and then depressing the off switch at the rear of the unit If the system is left powered up but unused for a significant length of time turn off the laser diode using the switch on the front panel to save laser diode lifetime 6 3 Optical Diffractometer image capture software nhau Real Space Image Display GD00282 03 Page 12 Optical Diffractometer User Manual 6 3 1 Summary The Optical Diffractometer software displays two live monochrome video images simultaneously on a PC screen One is the original real space image of the micrograph the other is the reciprocal space diffraction pattern At any time one of these images is shown full size i e at full pixel resolution the other reduced to half size the user selects which is displayed as the main image Snapshots of the main image may be saved to disk in Tagged Image File Format TIFF 6 3 2 Environment The program diffract exe is a Visual Basic application It runs on a PC under Windows 98SE and above A high resolution screen is required with the display set to 1280 x 1024 pixels Two EureCard Picolo boards must
5. used until its safe operation has been verified by a qualified engineer Until this verification has been performed the equipment should be labelled Unsafe Do Not Use to inform potential users of its status If for any reason the unit needs to be returned to the supplier the original packaging must be used GD00282 03 Page 7 Optical Diffractometer User Manual 3 BEFORE APPLYING POWER Please read all the following safety notices carefully before using the equipment Failure to comply with precautions highlighted in the safety notices violates the safety standards of design manufacture and intended use of the equipment If you are unclear about any of the points please contact your supplier before applying power to the unit Make sure the mains voltage selection on the back of the PC is set to the correct value see manufacturers quick setup guide The factory default setting is 230 3 1 General safety notice The equipment described in this manual has been supplied in a safe condition refer to Appendix A International Design Standards The equipment has been designed for indoor use No modification to the equipment should be attempted without the prior consent of the manufacturer 3 1 1 Power arrangement for the Optical Diffractometer The Optical Diffractometer mains input power socket is an IEC 320 type connector The power supply inside the Optical Diffractometer is universal and it can be connected to a
6. Optical Diffractometer User Manual GD00282 03 Manufactured by Sira Optical Diffractometer User Manual Laser warning Location Side access panel on base unit Laser warning for non interlocked protective housing Location Top cover of upper unit Laser warning Location within upper unit revealed when disassembled for servicing Laser warning logotype Location within upper unit revealed when disassembled for servicing FDA certification and identification Location Back of base unit THIS LASER PRODUCT COMPLIES WITH THE STANDARDS PRESCRIBED IN FDA REGULATIONS 21 CFR 1040 10 AND 1040 11 EXCEPT FOR DEVIATIONS PURSUANT TO LASER NOTICE No 50 DATED JULY 26 2001 MANUFACTURED SEPTEMBER 2003 Sira Technology Ltd South Hill CHISLEHURST Kent BR7 5EH England Figure 1 Facsimiles of Optical Diffractometer Safety Labels GD00282 03 Page 2 Optical Diffractometer User Manual Laser warning logotype label Class 3B Laser warning label Laser switch label Class 1M Laser warning label on side access panel Front access panel Figure 2 Optical Diffractometer front view showing label positions Laser warning for non interlocked protective housing label Rating label FDA certification and identification label Serial number label Video connector label Figure 3 Optical Diffractometer rear view showing label positions GD00282 03 Page 3 Opti
7. air line as this will typically contain oil WARNING Ensure that the unit is switched off and mains power removed before undertaking maintenance WARNING Operational maintenance does not necessitate gaining access to the inside of the instrument other than through the front and side access panels in the base unit If any fixed covers are removed the warranty is void WARNING If the cross hair generator is removed from its mount and the projection head is subsequently detached from the laser module there will be human access to Class 2 laser radiation A manufactures warning label is affixed to the laser module WARNING If any fixed covers in the upper unit are removed there will be human access to Class 3B laser radiation A warning notice is affixed on top of the instrument GD00282 03 Page 19 Optical Diffractometer User Manual 8 GENERAL SPECIFICATION Laser safety class 670nm and 635nm Class 1M Dimensions 610 x 400 x 510mm 24 x 15 7 x 20 1in LxWxH Weight 25 kg 11 4lb Power requirements 110V 240 VAC 50 60 Hz single phase Light sources Microlens laser diode 670nm of 8 10 mW for diffraction image Light emitting diode source for real space image with peak intensity at 520nm Low power laser cross hair generator 635nm to assist marking areas of interest Quoted lifetime of all sources exceed 5000 hours continuous operation Dynamic range Laser intensity variable over a 30dB range allowing the
8. cal Diffractometer User Manual Contents 1 Introduction erreme aa e a a a PU 5 2 Unpacking the Optical Diffractometer ccccccceeeeeeeeeeneceeeeeeeeeeeeeaaeeeeeeeeeeeeneeaaaees 7 3 Before applying DOWGI e520 cone seed d 8 3 1 General safety NOTCS ins acco teeta die eae eed aan eek 8 3 1 1 Power arrangement for the Optical Diffractometer sese 8 3 2 Operating Conditions errn ert ERE alates P e ER ca RERE 9 3 3 PIGCIIGASA Cty D E EUR PR gl eee cach ek Seca 9 3 4 PASS safely cete eb ceca nts ae teste c eee ats eu Cope DU 9 4 Before using the Optical Diffractometer for the first time sssesseseessssss 10 5 Optical Diffractometer main features sessssssssseeeeseeeenenen nme nnn 11 6 Operating Instructions ru iet proton Ert o eoe t een ma Met eaten oceeracmie etd d nee re pne ioe 12 6 1 SLANT UU aeter ep rend mua ede re te p ede nud terr tate tubc determina Dis 12 6 2 ST MENLO WE sisse utate mote bui I MU e MU 12 6 3 Optical Diffractometer image capture software sseseessese 12 6 3 1 SUMMAN e itai n m pe E e e E t t e i Rd bb Lr EE E eeu 13 6 3 2 Envirofmoelt i e bt teet RU hU ta ORE enn 13 6 3 3 Initial OISPIAY ii c ri ei i i a le p s e Pe ege 13 6 3 4 Troubleslooling 2 pa tp e S ep dde p ae ete 13 6 3 5 Blogo MP E 14 6 4 Optical Diffractomete zuo iro mat onsite coa Debes deo e ato te rtr Le base Pe eR etae adno dd
9. er safety area with restricted access However during servicing the following may occur e When covers from the upper unit are removed access to Class 3B laser radiation is possible e When the cross hair generator laser module is being replaced access to Class 2 laser radiation is possible Do not attempt to stare directly into the beam Do not attempt to insert a mirror or other reflecting device into the beam Do not unscrew any fixed covers The Optical Diffractometer carries certification and warning labels as shown in Figure 1 Note that the green light used for the real space image is from an LED source and is eye safe GD00282 03 Page 9 Optical Diffractometer User Manual 4 BEFORE USING THE OPTICAL DIFFRACTOMETER FOR THE FIRST TIME e Remove the a screws for the front and side access ES mum Side access panel gt transit screw Front access panel transit screw If for any reason the unit needs to be returned to the supplier the transit screws must be re fitted e With the shading tube in its upper position place the protective window assembly in the bearing mount recess and then place the sample stage on the bearing mount lt Shading tube in its upper position Sample stage Removable protective Eu uo Sree A Bearing mount i GD00282 03 Page 10 Optical Diffractometer User Manual 5 OPTICAL DIFFRACTOMETER MAIN FEATURES IB e Fast easy evaluation of electron micrograph
10. eter User Manual Use the diffraction image to view and assess the diffraction pattern If necessary adjust the laser intensity using the intensity knob or the fine focus by adjusting the camera carriage Change the magnification up or down by following the instructions above If a good image is obtained you can save it to disk See section 6 3 5 Use the laser cross hair generator to mark on your micrograph the region where the image was captured 6 4 9 Image calibration If you wish to calibrate your images you will need to view a micrograph with a test grating of precisely known dimensions It is good practice to capture reciprocal space images every time you change the magnification GD00282 03 Page 18 Optical Diffractometer User Manual 7 MAINTENANCE The only operational maintenance required of the user is to clean dust from the protective window that sits in the bearing mount recess see section 4 To remove the protective window for cleaning first remove the sample stage Light contamination of optical surfaces by dust is unavoidable in a normal laboratory and office environments and will not significantly affect the performance of the Optical Diffractometer Dust contamination may be reduced to an insignificant level by gently blowing with a proprietary dry gas jet duster Resist the temptation to remove dust from an optical surface using human breath as there is a high risk of surface contamination Also do not use a laboratory
11. examination of micrographs of almost any optical density Max micrograph viewing area 20mm square Adjustable masks allow rotation and reduction of target area as desired Constant basic setting 0 1mm 104 pixels in diffraction image 767 x 575 pixels total size Variable within the range 0 1mm 49 pixels to 0 1mm 316 pixels Easily calibrated using reference target Image capture device 2 GHz PC or better equipped with 1280 x 1024 display and dual input frame grabber 768 x 576 pixel Image capture software supplied installed Notes E amp OE All dimensions and weights are nominal Sira reserves the right the change this specification without prior notice GD00282 03 Page 20 Optical Diffractometer User Manual Appendix A International Design Standards Electromagnetic Conformity The equipment has been designed and manufactured to comply with the following specifications BS EN 61326 1998 Emissions BS EN 61326 1998 Immunity Electrical Safety The equipment has been designed and manufactured to comply with the following specification BS EN 61010 1 Laser Safety The equipment conforms to the standards prescribed in regulations FDA 21 CFR 1040 10 FDA 21 CFR 1040 11 except for deviations pursuant to Laser Notice 50 dated July 26 2001 and IEC 60825 1 GD00282 03 Page 21 Optical Diffractometer User Manual Appendix B Warranty Sira warrants and guarantees that all new equipment and parts supplied a
12. images e High contrast images from enclosed precision laser optics e Compact ergonomic hi tech design with small footprint suitable for desk top operation e Allows high resolution simultaneous display and capture of both diffraction and real space video images e Simple to set up use and maintain e Diffraction image magnification variable over a 6 fold range e Does not require a darkened room for use or restricted access for laser safety reasons e Laser cross hair for marking location of selected regions on the micrograph e Service contract available providing worry free year round operation with annual check up and replacement of limited life components e Complete with computer frame grabber and image capture software GD00282 03 Page 11 Optical Diffractometer User Manual 6 OPERATING INSTRUCTIONS 6 1 Start up There are three power cables for the Optical Diffractometer computer and monitor All three should be connected before power up There is an on off switch located at the rear of the Optical Diffractometer next to the power inlet In addition there is a green on off switch on the front of the unit which switches on and off the laser diode only Make sure that the coaxial cables are connected between the Optical Diffractometer and the frame grabber cards in the PC The Optical Diffractometer video connectors are labelled Real Space and Diffraction as are the corresponding frame grabber cards Switch
13. images Clicking the button swaps the camera images between the main and reduced image display areas Real space display Selecting the check box marked Enhance Real Space Image Display alters camera parameters according to the setting of the adjacent slider numeric entry box This can make it easier to discern darker features on the micrograph File Save Suspends acquisition and brings up a standard file save dialogue to allow the main image to be saved as a TIFF file tif with any required name and location The default save directory initialized when the application is started is c ltemp When the dialogue is closed acquisition resumes File Exit Terminates the application equivalent to using the X button at the top right corner of the window Run Restarts acquisition after using Stop or after error Status window goes to Running Stop Stops acquisition freezing displays Status window goes to Stopped About Brings up a box giving software version information and company contact details 6 4 Optical Diffractometer 6 4 1 Summary You can adjust the following e Region of sample being tested by moving the stage and by adjusting rectangular stops e Laser diode intensity to cope with different micrograph exposures e Real space image magnification focus and aperture e Diffraction image magnification and focus in 3 ranges 6 fold range GD00282 03 Page 14 Optical Diffractometer User Manual 6 4 2 Usi
14. ng the sample stage There are two rectangular sample holders designed to PR d accept standard form at NE position micrographs Before inserting AN the sample holder under the Pe shading tube move the tube to its upper position by depressing Soup enol the toggle and sliding it up see section 4 The holders can be freely moved around under the beam The stage rotates so that the eye can pick out faint features in the diffraction space image 00 in ncn n ntl Eo Sample stage Beam stop EXT 6 4 8 Adjusting the stops There are four independently adjustable beam stops on the shading tube that can be used to reduce the field of view of the instrument The real space view can be used to see exactly what the current field of view is 6 4 4 Laser diode intensity js The knob on the left of the upper P unit adjusts laser diode intensity sira as seen in the diffraction image Optical Diffractometer The internal mechanism allows Laser diode intensity fine control requiring 20 turns to go from minimum to maximum Note that the control has no end stop and wraps from maximum back to minimum adjustment Note also that adjusting this control has NO EFFECT on the real space image GD00282 03 Page 15 Optical Diffractometer User Manual 6 4 5 Real space image adjustment Pull open the front access panel to access the real space lens You can adjust the focus left ring magnification or zoom middle
15. re free from defects of material and construction and that all precautions which are usual and reasonable have been taken to secure excellence of materials and workmanship Accordingly Sira s liability shall be limited to replacing or repairing without charge any material or constructional defects which become apparent within 12 months after delivery to the original purchaser This warranty shall not apply to any equipment which on inspection by Sira is found to have defects resulting from accident transportation neglect misuse wear and tear or any other cause outside its control The supplier of the Optical Diffractometer cannot be held responsible for any equipment which is modified or used in a dangerous manner The manufacturer is unable to guarantee that the equipment is suitable for the purchaser s applications The way in which the equipment is used and the test results applied is entirely a matter for the purchaser Sira accepts no liability for damages consequential to the use of or defects in its products GD00282 03 Page 22 Optical Diffractometer User Manual Appendix C Useful Addresses Optical Diffractometer Manufacturer Sira Technology Ltd South Hill Chislehurst Kent BR7 5EH England Tel 44 0 20 8467 2636 Fax 44 0 20 8467 1902 Website http www sira co uk E mail biomed sira co uk GD00282 03 Page 23
16. ring and aperture right ring It is recommended that the aperture is left wide open for 0 Focus Aperture ring maximum real space image es brightness Close the front access panel after adjustment to minimise stray light entering the diffraction camera 6 4 6 Diffraction image adjustment G Do not touch the beam steering ee Mirror controls Diffraction camera carriage Accessory EE Pull open the side access panel to access the diffraction image adjustments Each of the two carriages can be moved along the bench to change the magnification and focus The left carriage carries the camera The right carriage carries an accessory lens holder with 3 different magnification powers DO NOT TOUCH the beam steering mirror controls View the diffraction image on the computer screen Adjust the location of the left carriage to obtain a sharp diffraction pattern GD00282 03 Page 16 Optical Diffractometer User Manual Close the side access panel after adjustment to reduce the stray light reaching the camera and maximise contrast To change the magnification change the lens being used on the accessory carriage by firmly pushing or pulling the lens holder in or out of the instrument The central setting is empty no magnification or reduction which is the normal setting In this setting the location of the accessory carriage along the bench has no effect To increase the magnification push the acce
17. ssory lens holder in until it clicks Then adjust the left carriage to re focus The highest magnification is achieved with the camera carriage at the far left and accessory carriage to the right To reduce the magnification pull the accessory lens holder out until it clicks Then adjust the right carriage to re focus The greatest reduction is achieved with the camera Carriage almost touching the accessory carriage After changing the magnification consider re calibrating the Optical Diffractometer by capturing an image from a test pattern see section 6 4 9 below 6 4 7 Using the laser cross hair A laser cross hair generator is available to enable you to Laser cross hair manually mark the edges of genera the micrograph to show the location of an area of interest Push the cross hair generator to the right until it clicks y Ihe cross hair comes on automatically Use a pen to mark the edges of the micrograph in line with the Shading tube 1 beam stop cross hair This shows where the Optical Diffractometer field of view is centred 6 4 8 Using the Optical Diffractometer Use the real space image to find areas of interest on your micrograph Adjust the real space display setting in the software see section 6 3 5 if your micrograph is heavily exposed and the image very dark If necessary use the beam stops on the shading tube to restrict the field of view to a small region GD00282 03 Page 17 Optical Diffractom
18. tometer is simple to operate and requires no special skills or technical background except for the biological interpretation of the images themselves GD00282 03 Page 5 Optical Diffractometer User Manual It is the responsibility of the user to ensure safe operation of the unit by reading this manual in full following the instructions within and taking all reasonable precautions in its operation This manual is subject to change without notice GD00282 03 Page 6 Optical Diffractometer User Manual 2 UNPACKING THE OPTICAL DIFFRACTOMETER Your system has been carefully tested for performance and safety It should reach you in perfect condition Inspect the packaging on delivery and if there is any damage immediately notify your supplier and the carrier In the event of damage all packing must be saved for later inspection Remove all external packaging The packaging will contain e Optical Diffractometer including o Main unit Large and small sample holders Sample stage Protective window assembly Two 750 video cables Mains Lead OQ O 59 Q e System PC including o Frame grabber cards documentation and software Manufacturers documentation and software Optical Diffractometer image capture software PDF version of user manual Keyboard Mouse Mains lead 00000 0 e Flat screen monitor o Manufacturers documentation and software o Mains lead and cables In the event of damage to the unit the equipment should not be
19. unity The prototype design proven in the MRC laboratory with thousands of hours of use by MRC scientists has been updated by Sira for manufacture and export Extensively tested by MRC scientists this diffractometer eliminates the difficulty of use and eye strain of earlier diffractometers Risk of direct user exposure to the laser light is eliminated The novel optical design allows the use of two high resolution video cameras to capture the diffraction pattern and the real space image simultaneously It is possible to scan over a micrograph rapidly using the real time video image and view at the same time the corresponding diffraction pattern and then capture both digital images to disk The magnification of both the real space and the diffraction images can be varied independently Real space and diffraction images of a biological sample Courtesy MRC Laboratory of Molecular Biology To facilitate the surveying of large numbers of micrographs particular attention has been paid to the stage of the Optical Diffractometer which allows translation and rotation of the image around a fixed centre The holder makes contact only with the edges of the micrograph and adjustable masking baffles do not make contact with it The instrument is straightforward to calibrate by scanning a reference target Instruments will be installed at the user s premises by trained technicians and instruction provided in its operation The Optical Diffrac
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