OASIS-4i User Guide
Contents
1. 18 169 mm Tiles 0 0 0 MB Pattern Fields X 10 Y 11 Total 110 Fig 13 F 8 Ifthe Turboscan option is installed and enabled you may now see a dialog asking whether you wish to use Turboscan or Standard Scan You may choose either but it is probably best to start by using standard scanning to ensure that everything is working satisfactorily before trying Turboscan mode If the Turboscan mode is not installed then the scan will simply start without a prompt 7 Press the Start Scan button 9 Let the scan complete as indicated by the progress bar 10 When the scan is completed it should look like the example below Fig 14 Revision B Page 22 Objective Imaging Ltd i Surveyor File Edit View Control Image Scan Window Help x s mU Open Save Lenses Navig Setup Scan Help Scan Reduction Factor 1 zb RH gt gt ua Be 5 t5xugs c6 gt Joystick Configure Capture Desktop Now Capture Window Now et 73 074 17 972 mm Tiles 110 28 4MB Pattern Fields X 10 Y 11 Total 110 d Exit Fig 14 Using the Map Tools By now you should be starting to feel comfortable with the basic principles of defining and running scan patterns It s time to try a few new things Why not try out the following l a Turn the Pattern Borders off and on2. Select the objective lens and mag changer lens that are currently in use on the microscope bu Primary Objective Mag Changer u Lens Lens Samba 1X 1 0 XY Cal 0 23318 0 23330 pm pixel OK Cancel Help Revision B Page 36 Objective Imaging Ltd Define Lens Automation Settings This group of dialogs allows the user to define the values appropriate for each discrete objective defined on the system Although it is not possible to stipulate the correct settings for every possible objective it is generally the case that high powered objectives will require slower axis speeds and smaller travel ranges than lower powered objectives It is important to set reasonable values to avoid motor stalling and to achieve consistent and reliable operation Stage Define Lens Automation Settings Objectives Stage Focus Autofocus Advanced Sex Led Gef d Eat Kol 1 DOS os baal Ce pel ke Kaal Gei ee 031 T EM Axis Cruise Speed L ER 29 7 463 mm sec d 63x B3 10x Y xis Cruise Speed DI willy W Lense 29 7 463 mm sec Axs Ramp Normal Y Aus Ramp Normal Y Use same values for X and Y DK Cancel OK Settin Description g P X Axis Cruise Speed Use the scroll control to adjust the cruise speed from 1 100 of the setting previously defined in the System Properties Stage dialog The actual travel in mm sec is displayed Y Axis Cruise Speed Use the scroll control
3. Encoders Enabled Encoder Auto Correct Encoder Accuracy Enables control of the axis via joystick inputs Reverses the direction of movement for joystick deflections Indicates whether the coordinate system of the axis has been defined Indicates whether a motor has been detected on the axis Indicates the current microstepping resolution for the axis Indicates whether X and Y axis encoders are fitted to the stage Checkboxes allow encoder to be enabled or disabled Allows enabling of closed loop operation for encoders Defines precision of closed loop movement in microsteps Remember that the Apply button must be pressed for settings changes to take effect Revision B Page 32 Objective Imaging Ltd Focus System Properties System Stage Focus Controller I Enabled DASIS 4i Initialize Cruise Speed Acceleration o Slow D Step Size um 0 00250000 Backlash Correction Joystick Joystick Drive Sense Initialized Motor Detected Microstepping Encaders Fitted Encoder Enabled Iv Enabled Reversed Yes Yes 40000 Yes Jv Enabled Mouse Wheel Control Enabled Speed 20 DK Cancel Apply Help Setting Description Enabled The axis is present and available for use Cruising speed Sets the target cruise speed for the axis Possible values are 1 255 Acceleration The currently selected acceleration ramp table Four tables are av
4. 12 The Turboscan pen niekai aE E ENEAS ea EE YEN E E EEE 14 Getting Started DDR 16 Checks to make before starting niine inei Eed ete tete eee dta ie aia dad dn 16 Calibration and Setup osten ent EES 18 Definino and Running a Scan iet ettet te er eit dete ttt rea ta d te indita 20 Using the Map Tools ee eee et tette ib em d a tein eH Ra det edad 23 Alienmentand Calibration zt tete GEES EES 25 Setting an approximate calibration value essent tiennent tentent ttes 26 Correcting camera f tatiON ssis iud idi edite te NEE 26 AutosCalibtate ascen EES 28 The Update Map Furictioti timete ede que eb i dee a eR 28 Sutveyot Daloe Desctiptions tne mere se resonet eee ia deii 29 Cotnhipuratoti abd SED e tes ottiene n a en Ped les dete Ie sd ted nase 29 Define ens etuer teet a ler asciende E 35 Objectives 7 Mas Changer canonnier Qu RO DUO 35 KT GE 36 Detitie hens Automation Settings ine riii ette tte ere eet ei dide e e a Ra 37 MC Eege eegend 37 i E eher ees 38 JAUEOLOGUSu a t thereon ete n dp RO pe tu eee e E ua dent d e t eene a 38 Advanced t in EO Hardt eebe 41 KT WEE 42 IRI naan 42 Sean Pattern PtODettiesz accen eqq e D a EIE IRE Uv ID a De D ERR ERA 46 attente e eee edet EE EE 46 Focusing ea PRONE O Soa nad ee aia E tive seed sateen N eins 47 Revision B Page 3 Objective Imaging Ltd Field Of ME 48 Calibratiorand leegent eegene 50 Calibrate Lens Camera Set UP eu
5. Motor Detected Microstepping Encoders Fitted Encoder Encoder Encoder accuracy A Axis Yes 150 E Normal D 2 000 Iw Enabled Iw Enabled Reversed Yes Yes 40000 Yes Iw Enabled Auto Correct microsteps Y Axis 150 1 Normal D 2 000 Iw Enabled Iw Enabled Iw Reversed Yes Yes 40000 Yes v Enabled Auto Correct microsteps Yes i Initialize Cancel Apply Help Setting Description Enabled The axis is present and available for use Cruising speed Sets the target cruise speed for the axis Possible values are 1 255 Acceleration The currently selected acceleration ramp table Four tables are available Slow Normal Fast and User Lead screw pitch The displacement per revolution of the axis in mm Backlash correction Revision B Enables backlash correction ensuring the end point of each movement is approached from the same direction This is achieved by slightly overshooting the desired position when moving in one direction then returning to the position from the opposite direction Movements from the opposite direction are unaffected The amount of overshoot is specified in the flash memory and can be set using the OASIS Flash Memory Setup application Page 31 Objective Imaging Ltd Setting Description Joystick Joystick drive sense Initialized Motor detected Microsteps per rev Encoders Fitted
6. System Properties Stage Note also that the best results especially in correcting camera rotation are achieved by starting with calibration of the highest powered objective and working downwards Finally it is worth remembering that physical conditions can alter over time and systems are susceptible to dirt heat vibration etc For this reason it is worth periodically checking the calibration to ensure that it remains accurate Setting an approximate calibration value 1 Maximise the live image window and select Calibrate Lens from the Control Menu A menu similar to that shown above will be displayed 2 Move around the sample using Joystick Smart Move Controller or Soft Joystick until you find a small but distinctive particle Ensure it is really part of the specimen not dust and focus it Then position it in the top left green ring 3 Press the top left SET button in the Calibration section of the dialog This will change from a question mark to a tick 4 Now move the particle to the bottom right green ring and press the bottom right SET button The calibration value in microns per pixel will be calculated and shown 5 You now have an approximate calibration value Use the top left directional arrow button to return the particle to the top left green ring If it is slightly mis positioned use the Soft Joystick nudge buttons to place it in the centre of the green ring Correcting camera rotation 1
7. score is detected 5 Fine Followed By Peak This method performs a fine autofocus and follows it with a local peak search as described above 6 Peak Search This method only performs a search for a peak using the technique described earlier Note that the autofocus dialog has an Autofocus button which allows the user to try the values set and assess the result before confirming the settings The graphical representation of the focus scores and the selected peak position is also useful in confirming that suitable values have been entered If the autofocus operation results in a Max Min value less than the Focus Score Range Limit it will be shown as Failed In this case try altering some of the parameters elsewhere in Define Lens Automation Settings such as Z speed increase the range or try an alternative method Revision B Page 39 Objective Imaging Ltd Define Lens Automation Settings Objectives Stage Focus Autofocus Advanced 5X 10 Autofocus Method Coarse Autofocus Sweep v 50x DIL 20x Range pm EY 000 63 100x Focus Score Range Limit 2500 Focus Profile willy Max Min 4516191 Lens Status OK Focusscoe 4229941 OK Cancel Apply Help Setting Description Autofocus Method Select one of the 6 supported methods described above Range Set the required range in microns over which the Z axis will be driven An entered value of 100 microns for example will drive 5
8. shows that the item is hardware Revision B Page 6 Objective Imaging Ltd Items shown in bold are essential Items shown in alics are strongly recommended but not mandatory 0000 O O OO Suitable laboratory or research grade microscope OASIS 4i 4 Axis PCI Automation Controller Stepper motor driven XY scanning stage Motorised Focus adaptor or suitable motorised Z in microscope High specification PC Cables dependent on stage focus and camera type Surveyor Software Image acquisition module for Surveyor OI JOY3 joystick module or Leica Smart Move controller RS422 linear encoders for X and Y axis Navigator Software Module for Multiple Scan Control SURVEYOR FIREWIRE DIGITAL CAMERA VIDEO CAMERA OASIS DC1 Digital o NTSC or PAL Video camera interface module Camera Trigger cable o Supported Turboscan Software Framegrabber o OASTS AF video and AF module FIREWIRE DIGITAL CAMERA VIDEO CAMERA TURBOSCAN Supported firewire PP Note Video camera must be aga 2 E capable of shutter speed of at igital autofocus requires least 1 4000 d OASIS DC1 SE E Turboscan Software o OASIS AF video and AF module Revision B Page 7 Objective Imaging Ltd Chapter INSTALLATION Before attempting to install the Surveyor application the OASIS 4i automation controller hardware and drivers should already have been installed and verified Similarly the camera manufacturer s softwar
9. to adjust the cruise speed from 1 100 of the setting previously defined in the System Properties Stage dialog The actual travel in mm sec is displayed X Axis Ramp Set the required ramp acceleration profile for the axis There are 4 possible values Slow Normal Fast or User Revision B Page 37 Objective Imaging Ltd Setting Description Y Axis Ramp Set the required ramp acceleration profile for the axis There are 4 possible values Slow Normal Fast or User Same values for X and Y Check this box to make any value entered by applied to both axes This is normally desirable Focus Define Lens Automation Settings Objectives Stage Focus Autofocus Advanced tow ve ee RP Krea 3 H eth KK Z Axis Cruise Speed 29 0 373 mm sec Z Axis Ramp Normal Y Setting Description Z Axis Cruise Speed Use the scroll control to adjust the cruise speed from 1 100 of the setting previously defined in the System Properties Focus dialog The actual travel in mm sec is displayed Z Axis Ramp Set the required ramp acceleration profile for the axis There are 4 possible values Slow Normal Fast or User Autofocus The system offers a number of different methods of performing an autofocus operation but these have basic similarities For each image received from the camera a Focus Score is Revision B Page 38 Objective Imaging Ltd automatically calculated based on the sharpness of edges gradien
10. using the H button Revision B Page 20 Objective Imaging Ltd 3 Using the joystick Leica SMC or Soft Joystick manoeuvre the XY stage to a position where a portion of the specimen is beneath the objective and thus visible in the live image window Ensure it is reasonably in focus 4 On the Stage View you will see that the small green crosshair graphic moves as you move the stage in X and Y always indicating the current position Ii 5 Select the scan define tool L and use it to draw a small area around the current position as shown in Fig 12 below i Surveyor File Edit View Control Image Scan Window Help MIR XE gt Open Save Lenses Navig Setup Scan e P Scan Reduction Factor 1 Oislr2tM Live Image m XP Gl e awe pzHpsg Dees xs a v6 About Configure Capture Desktop Now Capture Window Now XY 107009 74117 mm Ties 0 0 0 MB Pattern Fields X 10 Y 11 Total 110 6 Now switch to the Map View by clicking on the button Your screen will look something like Fig 13 below Revision B Page 21 Objective Imaging Ltd gt Surveyor File Edit View Control Image Scan Window Help SG NM ERE o Halt Open Save Lenses Navig Setup Scan Help P Scan Reduction Factor 1 SET Live Image 1X F B gt mm MEELEL EE BiG Fi eke a 96
11. warning before the initialisation starts Please ensure that the microscope objectives and condensor are well clear of the stage and that nothing will obstruct the stage over the full range of its travel 3 Once the initialisation is completed the stage will be positioned at the centre point of its travel Press the Stage View button 4 Your display should now look something like Fig 10 below Ds Note that the Scan Window now represents the entire area of travel of the stage The small i n P ie is green crosshair graphic in the centre of the stage area indicates current position The Revision B Page 18 Objective Imaging Ltd hatched area around the periphery of the stage travel area indicates the setting of soft limit switches 6 Using a joystick trackball or the Soft Joystick move the stage until the specimen is beneath the objective Set appropriate microscope illumination and focus until you have a good image in the image window on the display top right Joystick Fig 10 T When the software is first installed a default set of objective lenses is loaded From the Control drop down menu select the Define Lens option With this you can either modify the default lenses or create new ones to suit your actual microscope configuration See the detailed documentation of this process in section XXX 8 It is necessary for each objective to be separately calibrated Calibrati
12. 0 microns above and 50 microns below the origin position Focus Score Range Limit This value is intended to avoid false autofocus results such as might be caused by noise or blank fields It is recommended to find a blank field perform an autofocus operation and then enter a value in this variable that is twice the Max Min value shown Revision B Page 40 Objective Imaging Ltd Advanced This dialog is primarily for use by experienced users especially where there is an automated microscope Define Lens Automation Settings Objectives Stage Focus Autofocus Advanced Lamp ze Fe JOS Aperture s50 T Top lens in place Pafocalty 0 000 Not Set Clear Apply Settin Description g P Lamp Adjust the slider to set the default intensity of illumination for the chosen objective Aperture Set the required level of aperture opening using the slider bar Parfocality Adjust the Z position until the chosen lens is in focus and press the Set button The amount of Z offset is automatically calculated and will be applied each time the lens is selected Revision B Page 41 Objective Imaging Ltd Scan These dialogs define the detailed conditions that apply to the execution of a scan Scan Setup These dialogs define the detailed conditions that apply to the execution of a scan Actions This dialog defines the primary conditions applying to a scan Actions Scanning View Select t
13. A primary cause of poor calibration and resulting poor image stitching is rotation of the camera relative to the stage Even a rotation of 0 1 degrees will have a significant adverse affect on image stitching 2 The alignment section of the calibration dialog is designed to allow rotation to be visually identified and corrected 3 Starting with the particle in focus and positioned in the top left green ring check the Horizontal box and press the ALIGN button This will cause the system to repeatedly drive the particle from the top left green ring to the top right green ring and back again As Revision B Page 26 Objective Imaging Ltd each move is made the top 2 small images will be updated to show exactly where the particle goes relative to the crosshair 4 Whilst the align process is active very gradually rotate the C Mount adaptor until the 2 images are identically aligned relative to the green cross hair on each image 5 Once you are satisfied that the horizontal alignment is as near perfect as possible gently tighten the C mount grub screw to lock the camera in position taking care not to cause any movement 6 Now confirm that the rotation is correct by performing the same test on the Vertical axis and finally by checking both the Vertical and Horizontal axes check that all 4 images are identically aligned An example of a reasonably well calibrated objective prior to auto calibration is shown below Calibra
14. B Page 54 Objective Imaging Ltd Process Hl am Setup Dialog Best The contents of the Process dialog display advanced features specific to your make and model of camera Please refer to your camera s documentation regarding the use of the settings available for your camera Revision B Page 55 Objective Imaging Ltd Shading QiCam Setup Dialog Exposure Color Balance Process Shading Info To implement shading correction select a blank white field Then press the Setup Shading Correction button Setup Shading Correction Shading Correction can be turned on and off using the check box below Iw Shading On Note shading correction should be setup each time the optical path is changed in any way Le Change of Objective Lamp Intensity or Condenser setting 10 490 Frames Sec OK Cancel Setting Description Setup Shading Correction This operation must be performed on a blank field to be effective It will automatically calculate the amount of shading in the image and adjust each incoming image to compensate for this Shading on This checkbox allows the shading correction to be enabled or disabled Revision B Page 56 Objective Imaging Ltd Appendix TROUBLESHOOTING GUIDE Problem Possible Causes Solution OASIS 4i card not detected by Windows Plug and Play does not find OASIS 4i card e Card not fully seated into PCI slot e Conflict with another catd on PCI bus Ensure cat
15. Description Width of field of view This will normally be automatically set from the camera definition Height of field of view This will normally be automatically set from the camera definition Pixel Width X This is the calibrated value of the X axis expressed in microns per pixel Pixel Width Y This is the calibrated value of the Y axis expressed in microns Revision B Page 48 Objective Imaging Ltd Settin Description g P per pixel Revision B Page 49 Objective Imaging Ltd Calibration and Alignment See also the section on Calibration eatlier in this manual Calibrate Lens Calibrate Lenses Set calibration for this objective and mag changer A E lens combination H 20 1 0 Select Alignment Rotate Camera to achieve best alignment jw Horizontal Align Iw Vertical Ain Calibrate using Stage Drive an object into each circle and select the corresponding Set button E Sl d Set zl gt e e Rotation Drive an object into the top left circle and press Calibration Auto Calibrate Adjust the camera to minimize else 10 233177 rotation angle The images above should Microns per Pixel X Update show the same image when the calibration is M Microns per Pixel Y 10 233298 En correct Set Cancel Apply Heb Setting Description Select Select required combination of objective and mag changer for calibration Alignment Select either Horizontal or Vertical or both and t
16. ND io oc AIIN 3 3V 4 eo GND Revision B Page 64 Objective Imaging Ltd Appendix OASIS 4 SPECIFICATIONS Stepper Performance 4 Independently controlled Micro step resolution 1 64 Full step 0 028 degrees with 200 step rev motor Maximum speed 512 KHz micro steps sec 8 KHz half steps sec Minimum speed 32 Hz micro steps sec 1 Hz half steps sec Maximum motor current 0 5A to 1 25A phase in 5mA steps Maximum motor supply voltage 30V typically 12V Minimum motor supply voltage 10V Command overhead Move XYZ lt 10 us Controller Response time Move XYZ 20 us Acceleration deceleration profiles Preset slow normal fast or user definable Position counter accuracy 32 bits General Processor DSP ADSP 2181 Processor clock frequency 32 MHz Non volatile memory 1 Mbit Flash for program and user configuration storage Reset method Hardware watchdog software PC reset selectable as required Switch on time 1 s fully functional Bus Interface Type PCI 2 2 Compliant Bus master No Operating Frequency to 33 MHz System Safety Watchdog timer function Resets board on processor fail Watchdog timeout 1 6s Drive current limit 4 A max per motor Drive current limit response time 4 ms typical Thermal shutdown Yes Temperature monitor Yes Drive voltage monitor Yes Hardware limit switch inputs Definable N O or N C Software limits User defined Software Stop individual or all axes com
17. Objective Imaging Ltd PL2 25 way D type female F axis connector Fourth axis connector designed to be connected to filter wheels motorized zoom and general purpose motor drive Connected to PL2 via ribbon cable F axis Sine Out F axis Sine Return F axis Cosine Out Duc fes 0 1 2 3 4 5 Pin Pin 597 2 nc 8 PL1 9 way D type male Trackball Mouse port on front panel RS232 port designed to connect to a serial mouse or trackball H 5 Signal N C data receive data transmit DTR GND DSR RTS CTS o Oo OC1 RR o rm N C Revision B Page 63 Objective Imaging Ltd PL7 26 way header male Analogue J oystick po rt Pin Signal Pin Signal 1 VRef 14 GND 2 GND 15 DSP Serial Port Data transmit 3 Joystick X Input 16 GND 4 GND 17 DSP Serial Port gated SCLK 5 Joystick Y Input 18 GND 6 GND 19 DSP Serial Port Receive Frame Sync RFS 7 GND 20 N C 8 N C 21 DSP Serial Port Data Receive 9 45V 22 N C 10 N C 23 DSP IRQE Focus Digi knob A signal 11 DSP Serial Port gated SCLK 24 N C 12 GND 25 TTL Input Focus Digi knob B signal 13 DSP Serial Port Transmit 26 N C Frame Sync TFS PL4 10 way header male TTL input port TTL 3 3V compatible input port 5 Signal Input 0 GND Input 1 GND Input 2 GND Input 3 G
18. RELATED TECHNICAL SUPPORT INCLUDING WITHOUT LIMITATION DAMAGES OR COSTS RELATING TO THE LOSS OF PROFITS BUSINESS GOODWILL EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGES IN NO EVENT WILL OBJECTIVE IMAGING LTD OR ITS SUPPLIERS BY LIABLE FOR ANY CLAIM BY ANY OTHER THIRD PARTY ARISING OUT OF YOUR USE OF THE PRODUCT IN NO EVENT WILL OBJECTIVE IMAGING LTD AND ITS SUPPLIERS LIABILITY EXCEED THE AMOUNT PAID BY YOU FOR THE PRODUCT SOME JURISDICTIONS DO NOT ALLOW THE LIMITATION OR EXCLUSION OF LIABILITY FOR INCIDENTAL OR CONSEQUENTIAL DAMAGES SO THE ABOVE LIMITATION OR EXCLUSION MAY NOT APPLY TO YOU DISCLAIMER OBJECTIVE IMAGING LTD RESERVES THE RIGHT TO MAKE CHANGES IN SPECIFICATIONS AT ANY TIME AND WITHOUT NOTICE THE INFORMATION PROVIDED BY THIS DOCUMENT IS BELIEVED TO BE ACCURATE AND RELIABLE HOWEVER NEITHER OBJECTIVE IMAGING LTD NOR ITS SUPPLIERS ASSUME ANY RESPONSIBILITY FOR ITS USE OR FOR ANY INFRINGEMENT OF PATENTS OR OTHER RIGHTS OF THIRD PARTIES RESULTING FROM ITS USE NO LICENSE IS GRANTED UN ANY PATENTS OR PATENT RIGHT OF OBJECTIVE IMAGING LTD All trademarks in this document are trademarks of their respective companies Revision B Page 2 Objective Imaging Ltd Table of Contents KEE 6 CoDfIgUfAtiOfs x cicer pens re bed ette deter e ende ee oe bo deo tud t oben b nics 6 erer Deet 8 Installing Surveyor and Associated Components essent teens 8 Nerd dd rdc ace onsbesuicevesbes Anaea E aa TEENA A EAN Ee A EEEE AOE E Ea
19. S 4i controller was provided as part of an integrated solution your first contact should by to your system vendor They will be most familiar with your overall system and any specialized configuration details To contact Objective Imaging directly please visit www oljectiveimaging com for contact details for your area Revision B Page 59 Objective Imaging Ltd Revision B Page 60 Objective Imaging Ltd Appendix CONNECTOR INFORMATION Refer to the following schematic for connector placement on the OASIS 4i card PLA TIL PL5 Motor input port power PL2 Fourth axis output SK1 XYZ output video I O general logic output Pii Trackball serial port PL7 Analogue port for Joystick or OI SNP PCI Connector Revision B Page 61 Objective Imaging Ltd SK1 44 way HD type female XYZ video and digital outputs on front panel The main connector for XY stage Z focus video I O XYZ encoder input and digital output signalling rin Sa Ile Video nV 5 Zis Cosine Reim 28 xenos s vessmon Omm s axis Sino Rew s voun is xesSmReun s zume BCEE RE Key No connect 37 Open Collector Output 1 100R current limit resistor Key No connect 5V Fused 1A Toe Ground Video in C Le vum U 19 UO Control 1 Open Collector Output 2 No current limit resistor 20 Z Encoder B 42 412 V Fused 1A Revision B Page 62
20. addition to the potential error messages shown above there is also a group of possible error messages relating to camera status The actual error message displayed will vary depending on the exact type of camera for which the system is configured If no camera has been selected the user will be prompted to select the correct model of camera from the dropdown menu Image Some special conditions exist which apply to configuring of video cameras These are covered in a special section Appendix B at the end of this manual Calibration and Set up Note that the two main windows of the Surveyor can be resized The contents will be automatically rescaled to fit the size set All dialogs including the Soft Joystick can also be moved to a position on the screen of the user s choosing When the application is closed down the size and position of each window and dialog will be remembered and these settings will be applied the next time the application is launched It is now time to set up the system in preparation for your first scan following the steps shown below L Set up the camera 2 Initialise the stage Before the software is used for the first time the system does not know where the stage is positioned For this reason the Stage View window is shown in grey Initialisation is done by going to the Control Menu at the top of the Surveyor window and selecting the Stage and Init options The system will issue a
21. ailable Slow Normal Fast and User Step Size The distance travelled in microns for a single microstep Backlash correction Revision B Enables backlash correction ensuring the end point of each movement is approached from the same direction This is achieved by slightly overshooting the desired position when moving in one direction then returning to the position from the opposite direction Movements from the opposite direction are unaffected The amount of overshoot is specified in the flash memory and can be set using the OASIS Flash Memory Setup application Page 33 Objective Imaging Ltd Setting Description Joystick Joystick drive sense Initialized Motor detected Microstepping Encoders Fitted Encoders Enabled Revision B Enables control of the axis via joystick inputs Reverses the direction of movement for joystick deflections Indicates whether the coordinate system of the axis has been defined Indicates whether a motor has been detected on the axis Indicates the current microstepping resolution for the axis Indicates whether an encoder is fitted Checkboxes allow encoder to be enabled or disabled Page 34 Objective Imaging Ltd Lenses Define Lens This dialog allows the user to define the objectives and magnification changers to be used on the system In order for an objective to be used it must firstly be defined and then calibrated Note that lenses may be added or removed and th
22. already installed on the system If it is not then it will be installed and the system restarted After system restart press Install the Surveyor Application again ES Install Digital Camera Drivers Matrox Meteor II Driver This option presents the dialog shown below Fig 2 allowing the user to specify which drivers should be installed dependent on the hardware to be used Revision B Page 9 Objective Imaging Ltd Opal Camera Support pal camera Sus C hjective Install QImaging QICAM Digital Support E Install JVC KY F1030 OHCI FireWire Support E Install Matrox Meteor Il Support Install Leica DFC Support 2002 3 Objective Imaging Ltd All rights reserved In all cases the software drivers that came with the camera or framegrabber should already have been installed following the manufacturer s instructions This is checked before the Objective Imaging driver is installed If it is detected that the manufacturer s driver software has not been installed an appropriate warning message will be issued An example is Fig 3 is shown below Failed to Install e J The Matrox Meteor Drivers and Software Library are not installed Please install your Matrox Software and then rerun this application to install the correct OI Server OK If the manufacturer s software has been properly installed the following informational message Fig 4 will be displayed before installation of the Objective Imaging driver Revisi
23. and is particularly well suited to use with a multi slide stage Surveyor s ability to generate high resolution mosaic images provides a powerful and novel method of visualising a specimen The specimen overview is an aid to understanding the relationships between microscopic features and overall structure Once you have created a scanned mosaic you can save your specimen s details as a workspace or export the full resolution mosaic for use with image publishing and analysis packages Our software has been carefully designed to offer a comprehensive range of facilities with a strong emphasis on versatility and ease of use With minimal experience it should be possible to produce excellent mosaic images Good results depend however on the system being well configured and set up and on the user becoming reasonably familiar with the available facilities and functionality The principal purpose of this manual is to provide practical guidance on configuration set up and use of Surveyor and Navigator Although manuals such as this are typically referenced occasionally for advice on a specific question it is strongly recommended that new users read sections 1 3 completely Configurations A number of different configurations of hardware and software are possible and these are closely interrelated The diagram and notes below illustrate the options Table 1 Surveyor and Turboscan Configurations W indicates that the item is software O
24. ass Imaging SURVEYOR WITH TURBOSCAN USER GUIDE Revision C Objective Imaging Ltd Warning This board contains static sensitive components Please take the necessary precautions when handling and installing the board to prevent damage or malfunction Federal Communications Commission Compliance Statement NOTE This equipment has been tested and found to comply with the limits for a class A digital device pursuant to part 15 of the FCC Rules These limits are designed to provide reasonable protection against harmful interference when the equipment is operated in a commercial environment This equipment generates uses and can radiate radio frequency energy and if not installed and used in accordance with the instruction manual may cause harmful interference to radio communications Operation of this equipment in a residential area is likely to cause harmful interference in which case the user will be required to correct the interference at his own expense Changes or modifications to this product not expressly approved by the party responsible for compliance could void the user s authority to operate the equipment Copyright 2005 Objective Imaging Ltd All rights reserved LIMITATION OF LIABILITIES IN NO EVENT WILL OBJECTIVE IMAGING LTD OR ITS SUPPLIERS BE LIABLE FOR ANY INDIRECTION SPECIAL INCIDENTAL ECONOMIC COVER OR CONSEQUENTIAL DAMAGES ARSING OUT OF THE USE OF OR INABILITY TO USE THE PRODUCT USER DOCUMENTATION OR
25. assessing the impact on the stitching until no further improvement is possible 5 When you are satisfied with the result on the tile stitching press the Apply button for the new values to take effect Revision B Page 28 Objective Imaging Ltd Chapter SURVEYOR DIALOG DESCRIPTIONS Configuration and Set up System Properties This dialog allows general settings to be changed for stage and focus Note that these are default settings and may be overridden by lens specific values set in the Define Lens Automation dialog Revision B Page 29 Objective Imaging Ltd System System Properties System Stage Focus Hardware PCB Version Y2 61 Driver Version 2 07 43 Motor Volts OK Temperature OK ADC Y Input OK ADC X Input OK Autofocus Module Fitted NOT FITTED Autofocus Type 0 Autofocus Typel 0 Video Encoder FAIL Camera Input NOT FITTED Camera Channel 0 Camera Frequency 60 Hz Camera Type Monochrome Serial Device Detected NOT FITTED Mouse Detected NOT FITTED Trackball Fitted NOT FITTED Ieustiel Fittad MOT FITTED OK Cancel Apply Help The System tab is informational and details the current configuration of the OASIS controller Revision B Page 30 Objective Imaging Ltd Stage System Properties System Stage Focus Lead Screw Pitch mm Enabled Cruise Speed Acceleration Backlash Correction Joystick Joystick Drive Sense Initialized
26. ayed Selection frame border width Revision B Select width for field borders Page 45 Objective Imaging Ltd Scan Pattern Properties The dialogs are accessed from the Scan Setup menu Pattern Scan Pattern Properties Pattem Focusing Field of View Pattern Type Rectangle X Define Pattem Number of fields mz Number of fields in Y x step size 31 6 19 Auto Step Size Y step size 234 23 Iv Overlap field edges Scanning E al by 32 E pixels Total fields Total area sq mm 100 Width mm 7 8225 Height rm DK Cancel Apply Help Setting Description Pattern Type Select required format of scan from list Note that for Turboscan mode only a rectangle is permitted Number of Fields in X Optionally enter number of X fields This will be overridden if Number of Fields in Y X step size Revision B the scan area is drawn directly using the scan area draw tool Optionally enter number of X fields This will be overridden if the scan area is drawn directly using the scan area draw tool Normally the step size in microns is automatically calculated from the calibration value when a scan area is defined or the auto step size button is used It can be manually defined here if needed Page 46 Objective Imaging Ltd Setting Description Y step size See X step size above Overlap field edges The combination of checkbox and pixel value
27. ction box in the dialog and re run the scan still zoomed to see the impact of the change Continue to make small changes until no further improvement is possible Settings Dialog Backlash Correction XY Correction fo nms Z Correction Optimise Memory Usage Revision B zl Ams Page 43 Objective Imaging Ltd Scanning Actions Scanning View Current Pattem Info Scan type Rectangle Total Fields 100 Load Pattern Width 3 169 mm Pattern Height 2 350 mm Save Fields 10 Y Fields 10 X Step Size 316 19 um Y Step Size 234 23 um Auto set origin to current position on Run Iw Auto set step sizes when defining pattern Iw Auto set No of Fields when defining pattern Apply Setting Description Aiuto set origin to current Checkbox which controls whether scan origin is set to current position on run position Aluto set step sizes when Ensures that fields in scan are contiguous defining pattern Auto set No of fields when Specifies that number of required field to fully scan an area is defining pattern determined automatically Revision B Page 44 Objective Imaging Ltd View This dialog defines some conditions applying to the appearance of the scan map Setting Desctiption Map View Choose required Map View from list Show movement trace Optional display of scan trace Show field borders Optional display of field borders Border Style Specifies style of borders displ
28. d is fully seated into PCI slot along entire length Move OASIS 4i card to another free PCI slot OASIS 4i card is listed as an unknown PCI device in Windows Device Manager e OASIS 4i driver not installed Perform driver installation procedure My 3 party application software cannot recognize OASIS 4i card e OASIS i driver not installed e Application s support library for OASIS 4i card not installed Perform driver installation procedure Run application s motorized controller installation procedure refer to the application documentation for further details My 3 party application recognizes the OASIS 4i card but the motots are not wotking Revision B e Motor power not connected e Motor cable connectors disengaged or faulty Page 57 Ensure OASIS 4i motor power connector PL5 is fitted with a power supply plug Ensure motors are connected fully fitted at OASIS 4i connector SK1 and at motor end of cables Objective Imaging Ltd Problem Possible Causes Solution e OASIS i is not properly configured for the type of automation hardware fitted Run OASIS configuration wizatd to setup the card for your system e Axis positions are outside the limits of travel Run OASIS configuration wizard or 3 party application options to initialize the axis coordinate system The system is stalling when making movements e Insufficient power to motor
29. d on the OASIS Installation CD to configure and confirm the functionality of system components Revision B Page 16 Objective Imaging Ltd When starting Surveyor for the first time it is possible that an error message will be displayed if the configuration and settings are detected to be incorrect Possible messages and their cause are shown below OASIS Controller Not Found Please check hardware installation 9 Failed to open OASIS automation controller Vi Do you wish to continue in simulated mode Yes No Fig 8 This message Fig 8 indicates that the software cannot establish communication with the OASIS controller This means either that the OASIS card is not present or that it is incorrectly inserted into the PCI slot of the PC If present ensure that the card is fully inserted into the PCI slot The software cannot function other than in simulation mode without an OASIS card Another possible message is shown below Fig 9 Please contact your vendor For licensing information OK eo You are not licensed ko use this appliation Fig 9 This message indicates that the software has not detected the code in the OASIS flash memory that authorises use of the software If you see this message it is necessary to contact your vendor for the licence code Installing a licence code is a quick and simple process and details will be provided with the code Revision B Page 17 Objective Imaging Ltd In
30. drives e Insufficient power to motor drives e Insufficient power to motor drives e The drive lead screw is damaged Adjust maximum motor current using the OASIS Flash Memory Configuration utility Use parallel motor windings to increase current in motor phases Increase motor drive voltage using external 24V power supply Contact automation mechanics manufacturer for setvice details The XY stage does not halt when a physical limit is reached An axis is not moving the correct distance when attempting to step a known amount e Limit switch direction is incofrect for stage type e Axis calibration incorrect e The axis is stalling e Encoder if fitted is configured incorrectly Run OASIS configuration wizard to auto detect limit switch direction and polarity Set axis pitch or step size using OASIS or 34 party application software See troubleshooting section for stalling during movement Run OASIS configuration wizatd for encoders or define encoder settings using OASIS Flash Memory Configuration utility The Joystick is not working Revision B e Internal cable connection Page 58 Verify internal connection from joystick cable connector Objective Imaging Ltd Problem Possible Causes Solution error plate to PL7 on back end of OASIS 4i card ensure red stripe on ribbon cable is aligned to Pin 1 on connector PL7 If You Need Help If your OASI
31. e and drivers should have been installed To do this follow the separate OASIS 4i installation notes provided with the controller These notes explain the procedure that should be followed to install your Surveyor software and associated components Please read them completely before starting Installing Surveyor and Associated Components When the supplied CD is inserted it will automatically load the Installation Menu Fig 1 below The sequence of the menu items should be followed to complete the initial installation Although Surveyor will run under all modern versions of Windows Win98 ME 2000 and XP it is recommended that Windows XP Professional is used Revision B Page 8 Objective Imaging Ltd Surveyor Installation Surveyor Installation O amp Install Surveyor and Supporting Components Install Digital Camera Drivers Matrox Meteor Il Driver Installation Notes Fig 1 Install the Surveyor Application and Supporting Components This option will run an installation procedure automatically transferring all necessary files and software elements to a designated folder on your computer s hard drive For the default installation simply press Next at each displayed dialog during the installation For first time installation it is strongly advised that the user accepts the defaults Special Condition Windows 98 If Windows 98 operating system is installed Surveyor requires that Microsoft DirectX8 1 is
32. eir sequence in the list can be altered to suit user preferences Note also that this dialog allows the user to specify whether changing objectives is to be performed manually or by a supported automated turret changer Objectives Mag Changer Define Lenses DI Objectives ie Mag Changer 5x Objective Lens Settings 10 Lens Name 50 DIL B 8 20x Magnification B d B3X m 100 Position Numerical Aperture Em Add Remove Manual m Setting Description Lens Name Any desired name can be given to an objective Magnification Enter the magnification of the lens currently this value is not used in system calculations Position The relative position of the objective in the turret currently this value is not used in system calculations Numerical Aperture If a value is entered it can be used to automatically calculate Revision B Page 35 Objective Imaging Ltd Setting Description appropriate Z movements in some operations such as autofocus Select Lens This dialog allows the user to select the objectives and magnification changers to be used on the system In order for an objective to be used it must firstly be defined and then calibrated Simply choose the combination of Objective and Mag Changer that matches the physical conditions on the microscope If the objective has not been calibrated a warning message is displayed The lens must be calibrated before use Select Lens
33. eme era ttt be tav dde D Tete tte Rhe E e OR P i e ARR ED t RT ee dta eege EES 53 Color Balai Ces s secet pi eeu evite cid e EE ett va A ett e I Its 54 lucere ee 55 SNERIDIPEPR T 56 Troubleshooting Guilde pero vtro te epe des qa pe ied debe ro tetra 57 TE You Need Beleeg T 59 Connector nfotmatiofi ies niece titu etes Dee 61 SK1 44 way HD type female XYZ video and digital outputs on front panel 62 PL2 25 way D type female F axis Connector ENEE 63 PL1 9 way D type male Trackball Mouse port on front Dance 63 PL7 26 way header male Analogue Joystick pott EE 64 PL4 10 way header male TTL input pott EEN 64 OASISA tege 65 Revision B Page 4 Objective Imaging Ltd Revision B Page 5 Objective Imaging Ltd Chapter WELCOME TO SURVEYOR Objective Imaging s Surveyor software integrates high performance scanning tools in an easy to use application for creating viewing and saving ultra high resolution mosaic images With Surveyor you can scan a selected area or an entire slide quickly and accurately and then effortlessly relocate to areas of interest with a simple click Additionally with the optional Navigator module it is possible to define multiple workspaces and scan areas each of which retains a unique identity and distinct operational parameters The combination of Surveyor and Navigator offers complete versatility and control of multi specimen scanning
34. ent Views of the scan may be chosen The first of these as shown above Fig 5 is called the Map View In this view the entire selected scan area is shown scaled to fit within the display part of the window The alternative View available is called the Stage View and this is shown below Fig 6 4 Surveyor File Edit View Control Image Scan Window Help EIS NL D NIA RA Hak Help Open Save Lenses Navig Setup Scan 3 Scan Reduction Factor 1 te xX PEEL gt LHCE Map or Stage View Select 2 Joystick X Fig 6 In the Stage View the display portion of the Scan Window contains a representation of the entire stage The total possible stage travel area is surrounded by a hatched border to indicate the soft and hard limits of travel The actual current position is indicated by the small green crosshair symbol and above and to the left of this is a representation of the selected scan area scaled relative to the entire stage area This view can be very useful when selecting scan areas and locating the specimen especially when Revision B Page 13 Objective Imaging Ltd large or multi slide stages are used The Stage View is used extensively with the Navigator software module Switching between the Stage View and the Map View is simply a click on the appropriate toolbar icon as shown above The second primary window is the Image Window This di
35. entered causes the fields in the scan to be overlapped This is recommended for most cases especially where encoders are used Scanning format Select either snake scan or raster scan Better stitching results will often be obtained when raster scan is selected as this eliminates backlash Focusing Scan Pattern Properties Pattem Focusing Field of View m Automatic Focus Enable Auto Focus Perform Auto Focus every E EX fields m Predictive Focus Enable predictive focus correction Setting Description Enable Auto Focus Checkbox to select whether autofocus will be performed Note that autofocus only applies to standard scanning and not to Turboscan The settings used will be those defined in the Define Lens Automation dialogs Perform Auto Focus everynn Specify the frequency at which the autofocus is to be Revision B Page 47 Objective Imaging Ltd Setting Description fields performed Enable predictive focus Checkbox to enable or disable predictive focus Note that correction predictive focus can be used with any mode of scanning and may also be used in combination with autofocus Field of View Scan Pattern Properties Pattern Focusing m Field Dimensions Field of View Width of field of view pixels Height of field of view pixels Calibration Pixel Width D microns Pixel Height Y microns Cancel Apply Help Setting
36. examined the accuracy of stitching by zooming and examining image tile borders you may need to make further fine adjustments to calibration to achieve the best possible results 4 Atthe end of this manual is a section which suggests likely reasons for commonly occurring problems Revision B Page 24 Objective Imaging Ltd Chapter ALIGNMENT AND CALIBRATION Precise calibration of each lens is a key pre requisite to achieving good mosaic tile stitching The dialog below has been designed to offer a comprehensive and easy to use set of functions Calibrate Lenses Set calibration for this objective and mag changer lens combination Select 20 1 0 Rotate Camera to achieve best alignment Alignment Iw Horizontal ES Iw Vertical Calibrate using Stage Drive an object into each circle and select the corresponding Set button a D I DR I a Set 2 Calibration Microns per Pixel x 0 233177 Update M Microns per Pixel Y 10 233298 m Cancel Apply Help Revision B Page 25 Auto Calibrate EE 1 Drive an object into the top left circle and press Auto Calibrate Adjust the camera to minimize rotation angle The images above should show the same image when the calibration is correct ont eee Rotation Objective Imaging Ltd The proposed way to perform lens calibration is described below Note that if you have linear encoders these should be turned ON Control Menu
37. he Actions to Perform at each field in the scan Iw Acquire field of view thumbnail image Thumbnail reduction factor Ze TurboScan Turboscan Settings C Standard Scan Iw Show Select Scan Mode Dialog on Run Pause for a specified length of time Length of pause seconds 0 500 E Display a message prompt Prompt Click OK to move to the next field Cancel Apply Help Revision B Page 42 Objective Imaging Ltd Setting Description Acquire Field of View Thumbnail Reduction Factor Turboscan Standard Show select scan mode dialog on run Pause for a specified length of time Display message prompt Turboscan Settings Checkbox which controls whether thumbnail images are acquired to display in map view Specifies the level of compression applied to thumbnails Specifies the basic type of scan to be performed Determines whether selection of scan mode will be shown before scan commences Option to pause during standard scan mode for specified length of time Specifies message text to be displayed during pause This dialog is presented when the Turboscan Settings button is pressed in the Setup Actions dialog above This is provided to allow users to make very fine adjustments to a Turboscan in order to improve image tile alignment and focus With a small scan area run Turboscan then zoom at the junction of 4 tiles Make a small adjustment using the XY corre
38. hen press the align button to start automated movement to aid camera alignment Calibrate using stage This section is used to move from ring to ring and set position for calculation of calibration value See separate section on Revision B Page 50 Objective Imaging Ltd Setting Description calibration earlier in the manual Microns per Pixel X Optionally enter required value and press update map to see effect on real scan See separate section on calibration earlier in this manual Microns per Pixel Y See above Auto Calibrate See section on calibration earlier in this manual Revision B Page 51 Objective Imaging Ltd Camera Set up Note that exact dialog functionality is automatically tailored to suit the characteristics and facilities of different camera types The following dialogs are illustrative of typical settings Select Input Select Input GlCam Firewire Use Hardware Acceleration Auto Refresh Image m Trimming Frame Borders Top o 4 Let o a Right o a Bottom H OK Cancel Setting Description Select Select required camera from those installed by highlighting it in the list Use Hardware Acceleration This should not normally be enabled It is intended for advanced users with special requirements only Auto Refresh Images This should not normally be enabled It is intended for advanced users with special requirements only Trimming Frame Borders This allows the user to
39. ility Revision B Page 15 Objective Imaging Ltd Chapter GETTING STARTED In later sections this manual provides detailed explanation and examples of all the functions and settings that exist within the Surveyor software For new users howevet it is often useful to start by following a simplified set of guidelines that will enable a scan to be successfully defined and executed That is the purpose of this section The following steps are recommended 1 Checks to make before starting 2 Calibration and set up 3 Defining and Running the scan 4 Using the map tools Checks to make before starting The Surveyor software provides sophisticated and fast control of stage automation focus and image acquisition In order to achieve good results it is essential that all the necessary components both hardware and software are present and correctly installed Instructions for installing OASIS hardware are contained in the printed Installation Guide provided with each OASIS 4i controller This is also supplied as a PDF file on the Installation CD Instructions for installing the Surveyor software and also the necessary framegrabber or digital camera support are provided at the start of this manual It is essential that these are followed precisely to ensure that the software components are correctly installed Check that all cables and connections are correctly fitted and use the OI Configuration Wizard and OASIS application supplie
40. mand UO Encoder inputs Phase quadrature 5V each axis Maximum count rate 512 KHz O C output current limited 1 100 Ohm in series O C output unprotected 1 100 mA max Home input filter wheel 1 10k pull up to 5V General Purpose UO 4 3 3V 12V Via 44 way connector resettable fuse protected 1 1A 45V Via 44 way connector resettable fuse protected 1 1A S232 ports 2 1 used for Trackball mouse control of XYZ axes Analogue port 1 joystick interface Phase quadrature UP 1 for Z axis control SVHS video I P 1 75R terminated for use with optional Autofocus module SVHS video O P 1 buffered video in 75R drive Revision B Page 65 Objective Imaging Ltd Power Reqm t Max Connectors 5 V 1 596 12 V X596 12 V 45 10 28V motor supply PC Power Supply Drive Encoder Limit UO connector Trackball Mouse connector 4 axis RS232 Motor power 1 75A 100 mA 50 mA 1 4 x motor phase current x number of axes driven simultaneously PC power of 250W or higher is required in some models the fitting of an additional cooling fan is recommended 44 way female high density d type with screw fixings 9 way male d type standard serial port 25 way female d type with screw fixings optional 9 way male d type standard serial port optional 4 way male disk drive power connector normally connected to PC power supply Physical Dimensions Environment Revision B Length Height excl
41. on B Page 10 Objective Imaging Ltd j The QImaging QCapture Suite is present The Appropriate OI Server will be Installed OK Fig 4 Revision B Page 11 Objective Imaging Ltd Chapter SURVEYOR OVERVIEW Surveyor was designed to provide fast and flexible automated scanning for microscopy You can easily design and execute various types of scan patterns and quickly create mosaic images of all or part of your specimen Let s start by identifying the key elements of the user interface Fig 5 Surveyor Efe Fie Edt View Control Image Scan Window Help Drop Down Menus Image Toolbar S HIC E 2 gt Open lige nd E M Scan Reduction Factor 1 d XE SH ee ea Bie EF t s a8 O6 BEER Scan Window Toolbars CH X Se e cbe E m ae E e s e e em eng SE CA SES e i EE R S a 7e j X Live Image 2 e Soft Joystick gt ON GAS x D e S e ial Joystick UD ET 2 3 Scan Window Map View Fig 5 Revision B Page 12 Objective Imaging Ltd The Surveyor user interface has two primary windows The first of these is the Scan Window contains everything connected with the scan and the resulting mosaic image This includes at the top of the Scan Window a double row of tool icons with which to control scan settings and execution Within the Scan Window two differ
42. on is the process whereby a spatial value in microns is determined for a camera pixel The accuracy of this microns pixel conversion factor is critical to achieve good quality stitching in the mosaic image See the detailed documentation of this process in section XXX 9 Finally it is necessary to set up a few default values before your first scan Go to the large E Setup icon near the top of the display Setup and select the tab labelled Actions This will present a dialog like the one below Fig 11 Revision B Page 19 Objective Imaging Ltd Actions Scanning View Select Scanning Mode TurboScan Turboscan Settings Standard Scan Iw Show Select Scan Mode Dialog on Run Select the Actions to Perform at each field in the scan Iw Acquire Image Use 2Stack Method Image Format BMP Pause for a specified length of time Length of pause seconds 000 4 Display a message prompt Prompt Click OK to move to the nest field DK Cancel Apply Help Fig 11 10 Enter settings as shown above and press Apply button 11 Youare now ready to start Scanning Defining and Running a Scan There are many different ways in which users can determine where to scan but the following notes describe a simple and effective way to get started 1 Select your LOWEST powered objective previously calibrated above 2 Set the Map window to the Stage View by
43. ring and repeat the process by moving this time to the bottom left ring During this process the system is automatically measuring and making fine adjustment to the calibration value On completion of these two operations the system will drive to each or the 4 rings in turn and will then present the 4 images acquired together with the calculated degree of rotation detected If all 4 images are near identical and the rotation factor is very small certainly less than 0 05 then the lens is well calibrated and the stitching results should be good The Update Map Function This is a new facility that allows the user to empirically fine tune the calibration value by visually assessing the effect of a change on the stitching in a real mosaic 1 Firstly define a small scan area on the specimen a 4 x 4 pattern is adequate and perform a standard scan Now zoom on the mosaic until you have the boundary where 4 fields meet in the centre of the map window 2 Make a note of the exact X and Y calibration values shown in the calibration dialog 3 Now manually change one of the values by a small amount and press the Update Map button You will see the map redrawn to reflect the changes calibration value If no movement of the field boundaries is evident when a small change is made it is because the change in value is too small to have an effect In this case make a slightly larger change and retry 4 Continue changing values and
44. s under some circumstances enabled scanning and mosaic image building to be performed at significantly higher speed than is possible with conventional scanning technology There are some restrictions on the physical system configuration that is appropriate and these are detailed in separate technical notes This ultra fast scanning capability is an optional extension to Surveyor and gives an approximately fourfold increase in scanning speed If the option is enabled the operator may Revision B Page 14 Objective Imaging Ltd select whether a particular scan is to be performed as a Turboscan or a standard scan This mode selection can be set as a default and may easily be changed Although the resulting mosaic images will be virtually indistinguishable there are some significant operational differences that should be considered For technical reasons when running in Turboscan mode only a rectangular scan pattern may be used and it is not possible to apply autofocus or pause duting a scan execution Whilst it is not possible to apply conventional autofocus or pause during Turboscan execution a facility exists within Surveyor to apply Predictive Focus correction as the scan progresses This facility automatically adjusts focus during the scanning process based on the calculated plane of the specimen For more details of setting up and using this facility see the appropriate section of these notes or the Surveyor Help fac
45. splays the live image as received from the camera fitted to the microscope This Image Window allows you to see live on screen exactly what would be visible through the eyepieces on the microscope Surveyor combines automated scanning with digital image acquisition to allow you to capture images during the scan and create a mosaic image of the specimen Each field of view as shown in the Image Window becomes a tile in the mosaic allowing you to see a survey overview of your specimen in the Scan Window s map display Using the Scan Window s tools you can easily use the mosaic image as a map for relocating the stage to interesting regions or more accurately defining an area to be scanned at another magnification In addition to the core functions associated with defining and executing scan patterns and generating mosaic images Surveyor also provides a range of facilities to save restore and print images and other system elements The final element in the user interface and one which provides easy and intuitive control of the main aspects of microscope automation is the Soft Joystick Fig 7 This is discussed in more detail later in this manual A 54473 800 Y 415848 800 Z 82 895 THE TURBOSCAN OPTION Surveyor was designed to produce high quality mosaic images easily and quickly The emphasis in developing Surveyor was placed on simplicity of use and quality of results A recent technical innovation ha
46. t detected in the image The point of best focus is determined to be that where the focus score is highest In each method the speed at which Z is driven is automatically calculated based on the numerical aperture of the lens if this was entered when the lens was defined If the numerical aperture was not entered default values are used There are 6 possible methods described below Note that in all cases the best results will be obtained where Z backlash has been enabled 1 Coarse Autofocus Sweep This method drives through the defined range using a speed that ensures that a focus score is acquired at intervals 4 times greater than the calculated focal depth of the objective This is a fast method that gives an approximation of the best focus position 2 Fine Autofocus Sweep This method sets the speed such that focus score intervals are half of the focal depth of the objective This is slower but 8 times more precise than the coatse method 3 Coarse Followed By Fine This method performs a coarse autofocus followed by a fine autofocus The range of the fine autofocus is set by the distance represented by 5 coarse focus scotes the centre of which is the coarse peak 4 Coarse Plus Peak Search This method performs a coarse autofocus operation followed by a local search for a peak The local seatch moves in one direction and monitors the focus scores received until it they worsen At this point the direction is reversed until a peak focus
47. te Lenses Set calibration for this objective and mag changer Eet lens combination ES 20X 1 0X Select Alignment Rotate Camera to achieve best alignment r V Horizontal Align Iw Vertical n Calibrate using Stage Drive an object into each circle and select the corresponding Set button Sl d EH al si ai Set z Rotation 0 0931 74 0 089002 Drive an object into the top left circle and press Calibration Auto Calibrate Adjust the camera to minimize i rotation angle The images above should Microns per Piel 0 233333 Ge show the same image when the calibration is Microns per Pixel Y fo 232905 5d xe OK Cancel Apply Help Auto Calibrate The entire process of aligning the camera is not easy but it is well worth taking the necessary time and effort to get it near perfect as this will have a major impact on the quality of stitching that can be achieved Revision B Page 27 Objective Imaging Ltd Auto Calibrate Once the first 2 steps have been satisfactorily completed you are ready for final fine adjustment This is an automated function 1 Again position a small and distinct particle in the top left hand green ring 2 Press the auto calibrate button The system will drive the particle most of the way towards the top right green ring in a single step and then complete the move in a series of much smaller steps It will then return to the top left
48. trim the image coming from the camera by removing pixels from edges It is normally only used with video cameras where undesirable effects e g ringing can occur at image edges Revision B Page 52 Objective Imaging Ltd Exposure QiCam Setup Dialog Exposure Color Balance Process Shading Info Exposure d emm 12 ps 150 us 17 896 mins Gain 0 600 Offset 2048 10 459 Frames Sec Setting Description Exposure Select a blank field and use the slider bar to set the green channel intensity to the position shown Gain If necessary set the gain to the required value using the slider bar Excessive gain is normally undesirable and will adversely effect image quality Offset This control in combination with Gain can be used to increase or decrease contrast in the image if needed Revision B Page 53 Objective Imaging Ltd Color Balance QiCam Setup Dialog Exposure Color Balance Process Shading Info White Balance Set Defaults 2 5 a 1 00 a 2 20 a 71 00 Frames Sec or Cancel Settin Description g P White Balance Pressing this button will automatically adjust the color balance of the camera shown graphically by the histograms coinciding This operation must be performed on a blank field to be effective Individual channels If desired the individual color components can be manually set using the slider controls Revision
49. uding connectors Operating temperature Storage temperature Page 66 248 mm x 102 mm 9 3 4 x 4 0 to 35 C ambient 0 to 70 C Objective Imaging Ltd ing Ltd Objective Imag The Bury Newmarket Road Cambr idge CB5 9AQ Great Britain b iveimaging com ject o WWW
50. using the button Ges En b With the borders set off select the MoveTo XY Position tool Le click on the scanned area You will see that the microscope stage is immediately moved to the indicated position and the live image display shows the area selected Revision B Page 23 Objective Imaging Ltd c Now tty the Zoom tool Clicking on the scanned area with the left mouse button will increase the zoon factor whilst using the right mouse button will decrease it If you have a mouse with a centre wheel or button a double click on this will return to the original unzoomed state d Now with the map zoomed try the Pan tool ze e Try out the other tools to see what they do If you need information read the appropriate section of this manual below This section has been designed to help a nem user get started It does not cover every aspect of the software or all the functions available Hopefully if it is followed the user will have gained some confidence and understanding of how to set up and use the basic facilities There are a few points of general guidance that can usefully be mentioned at this point 1 All the tools including the Define Scan Area tool can be used equally on either the Stage View or the Pattern View 2 It is worth taking your time to explore and understand the many facilities available and to read the remainder of this manual as needed 3 Once you have done a few scans and
Download Pdf Manuals
Related Search