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EN_OPUS 6.0 Video.book

1. 51 6 4 6 Predefining Measurement Positions assa 53 6 4 7 Editing Measurement Positions a a 57 6 4 8 Measuring Marked Positions a z 58 6 4 9 Displaying the Spectrum of certain Measurement Position 58 6 4 10 Exporting Images and Measurement Positions 59 6 4 11 Deleting Images or Measurement Positions 59 OAD limage Processing ed OL oire erta eer Oe eas wien ten eure Ste 60 6 4 13 Illumination Correction 452 05 dg Gai ZEATE bien 60 6 4 14 Saving Data and Closing the Video Window 61 6 5 Video assisted Measurement without 3D A 62 6 5 1 General Information ci cin Garaio bin Me oda pate le Gete 62 63 2 MIGASURCINENL eti mirare teia oan eTa dda EEE TZ 62 6 5 3 Saving Video Images iss ZG eget aga EO gag dari 63 Special OPUS Windows ccc cece ccc c cess cescceces 65 7 1 Opening a special AN EAMAN 65 7 2 SARRA AEA 65 7 3 SID WIN AAE 66 7 4 Map Spec Window a cot ack de eevee bae Rae ae Beane 67 7 5 Map Video Spec Window gae exten ai Eb ge et aia 68 7 6 Overview Window Ek EA EEE E Ra aa RGR A 68 7 7 VideoPostrun AAA 69 Motorized Knife Edge Aperture 0 cece cere cece ees 71 8 1 Changing the Aperture Settings c 0e Gi dae wads i alee ae Faw 71 8 2 Measuring at pre defined Positions u u 75 Append esae E e Ea E ea E ale Ee dle 77 A l Rotation of the Camera atz garapenek gn ETERS ebenen EE a 77 A 2 Image as received by the AAE 78 A 3
2. A 3 IRscope Il and Hyperion without Optical Camera Adapter The detector area is a square with a side length of 0 25mm These side lengths are magnified by Mp x My times by the optics and projected onto the CCD chip of the camera With Mp 10 and My 1 5 a square with a side length of 3 75mm is projected on the CCD chip i e the detector receives only that part of the sample which appears in the center of the 3 75 x 3 75mm area of the CCD chip The CCD chip area is 6 3 x 4 72mm of which the detector receives 3 75 6 3 x 100 60 of the image in x direction and 3 75 4 72 x 100 80 of the image in y direction measured from the center point Operating in PAL video mode the CCD chip generates an image of 768 pixel in x direction and 576 pixel in y direction Thus the detector size corresponds to 3 75 6 3 x 768 457 image pixels in x direction and 3 75 4 72 x 576 457 pixels in y direction Note that the percentage of the image received by the detector does not depend on Mo and thus remains the same when the objective is changed The size of the green square in the live video image does not directly correspond to a certain length in the object plane but to the detector size in the detector plane A 4 IRscope Il and Hyperion with Optical Camera Adapter The above description section A 3 applies to this configuration as well with the only exception that My is reduced by a factor 0 45 Therefore the detector image projected on the CCD chi
3. d 3 Can read Frontpanel Cancel 3 4 Move to Saved Stage Z Position if available Check Which Devices Exist Figure 10 Selecting electronic Options for the Imaging Device Some microscopes e g IRscope II Hyperion 1000 2000 3000 are equipped optional electronic accessories Motorized Aperture For information about the motorized knife edge aperture refer to section 5 3 Autofocus Can read frontpanel i e the option to read and set up the settings of the microscope control panel using the computer Move to saved stage z position if available Select this option only if you work with a motorized x y stage This option causes the stage to move automatically to a predefined background measurement posi tion as soon as you start a background measurement To check whether the stepper motors really exist for these options click on the Check which Devices exist button figure 10 The options for which the stepper motors have been found are shown in blue color If Note Do not select the options for which no stepper motors have been found Otherwise instructions will be send permanently to the stepper motors during the measurement As no stepper motor exists an error message appears your microscope is not equipped with at least one of these electronic options the message Existing options are shown in blue color is not displayed Bruker Optik GmbH OPUS VIDEO 17 Configuring the Video Hardware Sele
4. a Video setup dialog hardware control panel b Live video image window c Red frame indicating the used CCD area d Green frame indicating area detected by the IR detector e Cross hairs f Spectrum window displaying already acquired spectra g Ruler h Overview video image window i Button to exit the video mode j Online help button k Image selection drop down list 1 Spectrum window displaying the spectrum in real time m Current stage position n Current cursor position 0 Overview image processing status 36 OPUS VIDEO Bruker Optik GmbH Window for video assisted Measurement The live video image window b displays the video image in real time as recorded by the camera The upper spectrum window f displays the spectra which have previously been acquired and already been stored in the 3D file The lower spectrum window 1 displays the live spectrum in real time i e the spectrum that is used to monitor the intensity before the actual measurement is started but not stored in the 3D file The video image window on the right h is intended for the overview video image Initially the overview video image win dow is black All subwindows can be resized by dragging the splitter bars between the subwindows to another position In the live video image window there is a red frame c indicating that part of the live video image which will be used to assemble the overview video image This frame can
5. OPUS Spectroscopy Software User Manual VIDEO gt lt BRUKER de 2006 BRUKER OPTIK GmbH Rudolf Plank Str 27 D 76275 Ettlingen www brukeroptics com All rights reserved No part of this publication may be reproduced or transmitted in any form or by any means including printing photocopying microfilm electronic systems etc without our prior written permission Brand names registered trade marks etc used in this manual even if not explicitly marked as such are not to be considered unprotected by trademarks law They are the property of their respec tive owner The following publication has been worked out with utmost care However Bruker Optik GmbH does not accept any liability for the correctness of the information Bruker Optik GmbH reserves the right to make changes to the products described in this manual without notice This manual is the original documentation for the OPUS spectroscopic software Table of Contents 1 Introduction eg dio E oa Seda eak eae dE EKEK 1 2 Hardware Requirements AAA 3 2 1 Spectrometer a diak GEN A Ee dda 3 22 Az aa GA 3 2 3 Video Camefa eretz edad als Cee onani eia b Mee hak ohare Sens 3 2 4 MA Heda RAE 4 3 Software TG UAG AZ AGATE 5 4 Installing the Video Hardware cc cece cece ree eeeees 7 4 1 Display Settings a tc wade eni Re ees to ae E a E Belew EERS 7 4 2 Firmware Check IRscope II amp Hyperion A z 7 4 3 Removing the Optical Camera Adapter IRs
6. 6 5 2 Measurement Another difference between the two video modes are the missing spectrum win dows in the video window of the mode without 3D Compare figure 67 with figure 35 Moreover in the video mode without 3D you can select the Advanced Measurement function of the OPUS Measure menu to define differ ent parameter values and to check the signal during a video session In the video mode with 3D it is impossible to start a measurement using the standard Mea surement dialog box In case you perform a video assisted measurement without 3D the acquired spectra are combined with the video images you have already taken during the video session The resulting files contain one spectrum each and possibly sev eral video images 62 OPUS VIDEO Bruker Optik GmbH Video assisted Measurement without 3D E image g 0 Sa ZEIA Cursor X 64566 Ready Figure 67 Video Window of the Video Mode without 3D 6 5 3 Saving Video Images During a video session without 3D the images and the measurement position markers are collected for the time being in the Graph and Annotation data blocks of a file having the extension OIF OPUS Image File Name and path of this file is automatically identical to the file name and the path you have entered in the Video assisted measurement dialog window on the Advanced page When you start a video assisted measurement without 3D mode all images and measurement position marks which have been
7. Then the software tries to align the selected sample feature with the center of the camera with the result that this sample feature is now in the center of the image displayed in the live video image window If this is not the case the current scaling factors need to be improved This is done automatically by clicking again on the same image feature The software calculates the offset in pixel and adjusts the scaling factor accordingly In order to improve the scaling accuracy maximize the live video image win dow Select an image point which is far off center preferably close to a corner of the image or move the stage using the joystick to position the image point close to a corner This method however is not suitable for microscopes with image inversion e g IRscope I as it will result in negative scaling factors Negative scaling factors can also occur if the stage cables are not connected cor rectly Furthermore inappropriate spindle factors of the stage and insufficient stepper motor accuracy may lead to unsatisfactory results Therefore the objec tives can also be scaled without using an x y stage provided a micron ruler is available Reflectance Transmittance Mode In order to switch between reflectance and transmittance mode you can either use the microscope control panel buttons or click on the respective buttons in the Video Setup dialog box figure 38 Note that you have to activate the Can read Frontpanel check box in
8. 45900 45800 45700 X Micr Rotation 70 ri Inclination 30 5 j l AN bui LD bua KM A EA X d J Ju J A zd X 45948 63 gt x 45750 43 Z 24663 60 Ze z lanzan H ze E 3800 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 Figure 73 Map Videot Spec Window 7 6 Overview Window The Overview window displays snapshots and overview video images without spectral information See figure 74 It is mainly used to create plot scripts which contain an video image Open an Overview window as described in section 7 1 and load the 3D file in that window by dragging and dropping the GRAPH data block from the OPUS file manager window to the Overview window Depending on the number of video images you have taken you can have the desired image been displayed by selecting the corresponding image number in the drop down list in the lower part of the overview window To print an image use the Quickprint function in the OPUS Print menu 68 OPUS VIDEO Bruker Optik GmbH VideoPostrun Window E pe ga 2 E Figure 74 Overview Window 7 7 VideoPostrun Window Open an VideoPostrun window as described in section 7 1 and load the 3D file in that window by dragging and dropping the GRAPH data block from the OPUS file manager window to the VideoPostrun window Alternatively you can open a VideoPostrun window by double clicking on the GR
9. IRscope II and Hyperion without Optical Camera Adapter 79 AA IRscope II and Hyperion with Optical Camera Adapter 79 AO IRscope T gei E E EAR Ek e daaa Eee e TE E baie 79 A 6 IRAMANSCODE 240 53 6405 ata a ee otek C546 SAR ee eee BE ees 80 1 Introduction OPUS VIDEO allows to display a live image of a sample as viewed through the ocular of a microscope on a video screen In combination with a computer con trolled x y sample stage and the OPUS MAP software a surface can be mapped and an overview image generated from multiple video frames Spectral infor mation can be collected from the sample surface in correlation to these images In order use to the video functions a frame grabber board and a video camera has to be installed Bruker Optik GmbH OPUS VIDEO 1 Introduction 2 OPUS VIDEO Bruker Optik GmbH Spectrometer 2 Hardware Requirements To ensure an optimum functioning of the OPUS VIDEO software certain hard ware requirements must be met The computer requirements depend on the fol lowing used components e Spectrometer e x y sample stage of the microscope e Video equipment video camera and frame grabber 2 1 Spectrometer Spectrometers connected to the PC using an Ethernet cable Tensor Vertex IFS125 Senterra require an Ethernet interface In case they are to be integrated also into a LAN another Ethernet interface Ethernet card may be necessary Acquisition processor c
10. This effect can partly be corrected by the software using only the sufficiently illuminated center part of the image for the assembly of the overview image In addition a flat field correction option is available to equalize the illumination See section 6 4 13 4 4 Orientation of the Video Camera Although the software is capable of inverting the video images in both direc tions x and y direction we recommend not using this software based image inversion function because it increases the CPU time drastically If the image is either not inverted or inverted in both axes as in the case of the IRscope II and the Raman Scope it is recommended to turn the camera by 180 degrees instead of using the software to invert the image If the IRscope II is used without the optical camera adapter as recommended above the camera must be turned until the BNC plug faces the binocular and the power connector points in the opposite direction The camera orientation must be checked carefully to ensure that the edge of the video image runs parallel to the edge of the stage Other wise there will be a visual gap when overview images are assembled as explained in the appendix 8 OPUS VIDEO Bruker Optik GmbH Orientation of the Video Camera If the camera is mounted in combination with the optical camera adapter the camera must be rotated by 180 degrees compared to the camera mounted with out the optical camera adapter If only one image direction
11. a background spectrum either at the current position or at a pre defined background position using the same aperture settings as later for the sample measurement To predefine a background position right click on the live or overview video image and select Defining Posi tions gt Background Position Move the stage back to the sample measurement position Start the measurement by right clicking on the live or overview video image and selecting Starting Measurement gt Measure Current Position or Measure Marked Positions Note Before starting an interactive video assisted measurement first ensure that the cursor position correctly tracks the movement of the sample stage 6 4 2 Snapshot and Overview Image To be able to identify the measured sample later you need to take an image of the sample which is stored together with the spectrum You can either take a snapshot showing the current area enclosed by the red frame in the live video image or generate an overview image of the sample surface To take a snapshot right click on the live video image and select Video Image gt Snapshot figure 36 To generate an overview image right click on the live video image and select Video Image gt Set Scan Overview Image Area The follow ing window opens Bruker Optik GmbH OPUS VIDEO 47 Video assisted Measurement Define Area of Overview Image al xi Define the area of the overview image by movi
12. and IR VIS mode Moreover the software can read theses settings from the microscope and is capable of auto focussing provided these options have been purchased For reading out the microscope settings firmware version 1 5 or higher is required 4 OPUS VIDEO Bruker Optik GmbH Microscopes 3 Software Requirements The OPUS VIDEO package is required to display the live video image of the sample on the PC screen and to save retrieve and plot the images The OPUS MAP software controls the x y sample stage if installed and the OPUS VIDEO software creates an overview image from individual images Using the overview image or the live video image measurement positions can be defined interactively Then the x y sample stage moves to the measurement positions selected on the screen The advanced mode of the video software writes all data spectra images mea surement positions annotations into one 3D file To access these data files you need the OPUS 3D package In particular the OPUS 3D software is required if a sample surface has been measured in a grid pattern and you want to display the results in the form of a 3D plot or contour plot showing the intensity ver sus the measurement position It is possible to use the OPUS VIDEO software without having the optional OPUS 3D software installed on the PC In video assisted measurement mode without 3D a single spectrum file is generated for each acquisition point of the sample
13. assisted measurement mode without 3D Each single video image plus the corresponding spectrum is stored in a separate file i e this mode yields several files The number of files is identical to the number of the measurement repetitions For viewing the measurement results of these files afterwards use a VideoPostrun window as well 7 Image jee ID r Figure 51 Lower Part of a VideoPostrun Window Detail View 52 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode Note In latter case Start video stream before first acquisition a continuous recording of video images video film is started asynchronously and the video film is stored in an avi file At the moment the use of this option is still restricted for the following reasons The resulting avi file is not compressed so that the file will increase to an enormous size within a very short time The file can increase to sev eral gigabytes per minute e OPUS does not yet allow of replaying the video film To do that another appropriate commercial program e g Windows Media Player is required The video file is not stored in a data block of the corresponding OPUS file but as an independent avi file So a logical assignment of the spectra to the video images of the film or vice versa is not possible e Specify the criterion either measurement time or number of repeti tions for the automatic termination of the me
14. be resized interactively The green frame d indicates that part of the sample which is detected by the IR detector The cross hairs e in the center of the live video image help you to size and position your sample The green frame as well as the cross hairs can be deactivated by right clicking on the live video image selecting Video Image and deselecting Overlay Detector Size or Overlay Crosshair See figure 36 Mouse Mode gt Hardware Control Snapshot Video Image Measurement Spots Grid A Set Scan Overview Image Area Scan Overview Image Defining Positions gt E Za Illumination Correction gt Moving To Defined Positions gt p e Overlay Detector Size Starting Measurement A a v Overlay Crosshair v Overlay Annotation texts v Overlay All Apertures Figure 36 Video Image Menu In area at the bottom of the main window there is a help button j providing information about the OPUS VIDEO software The Jmage drop down list k contains all video images acquired so far and shows which of the images is cur rently displayed Next to the drop down list the current stage position m and the current cursor position n is displayed Both positions are given in microns in relation to the zero position of the stage In addition these positions are also displayed in the live video image window During data acquisition the ampli tude and position of the
15. for the stage control Note Check whether you have selected the correct objective before starting the distance measurement Figure 44 Measuring a Distance in the Overview Image 46 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode 6 4 6 4 1 Performing a Video assisted Measurement with 3D Mode General Procedure To perform a video assisted measurement proceed as follows 1 2 3 4 5 6 7 8 9 Adjust focus and illumination and set the measurement mode reflec tance transmittance using the Video Setup dialog See section 6 2 1 figure 35 Locate a sample region of interest by moving the stage using either the mouse mode functions Move to Click Mode or Pan Mode the Video Setup controls Stage Position Control or the joystick Generate an overview image or take a snapshot of the sample video image by right clicking on the live video image and selecting Video Image Snapshot The snapshot or the overview image will be displayed in the overview window Move the object to be measured to the center of the image Set the aperture in such a way that only the relevant part of the sample is shown You can predefine several sample measurement positions in the run up to the measurement by right clicking on the live or overview video image and selecting Measurement Spots Grid For detailed informa tion refer to section 6 4 6 Acquire
16. gt Hardware Parameters Video Setup Objective IE IE Micron pixel x Y Illumination 2 25 E Fluorescence ON Scale 0 2311 0 231 Focus jo ZER E dia Bright contr color m E Start activity Zero Auto i E Calibrate E zZz zZz E SE SG Oo Nn Figure 38 Video Setup Dialog Box in case of an IR Microscope 38 OPUS VIDEO Bruker Optik GmbH Window for video assisted Measurement Objective Drop Down List Illumination Control Fluorescence ON Button IR VIS IR VIS Mode Buttons Brightness Contrast Color Sliders Contrast Button Histogram Button ZIOEI EI EGO E gt Setting the parameters of the driver for the camera in question bei Video Image Snapshot Set Scan Overview Image Area Scaling Function for Objective and Stage Current Scaling Factor Reflectance Mode Button Transmittance Mode Button Manual Focus Control Automatic Focus Control Focus Zero Point Selection Stage Position Control Calibrating the Stage Mark Measurement Positions Measure Marked Positions GER ARA GA A A E E a Alo Collect Background at Current Position Objective Drop Down List This list contains all objectives you have selected in the Select Available Objec tives dialog box figure 9 Always ensure that the objective selected in the drop down list corresponds to the actu
17. i e you can import a list of measurement positions cre ated with OPUS MAP into OPUS VIDEO and vice versa Another way of reus ing a list of measurement positions is to simply drag the annotations ANNO block of a file which has previously been created using the OPUS VIDEO soft ware into the live video image window 6 4 11 Deleting Images or Measurement Positions The Delete menu figure 63 allows you to delete the current overview image and all measurement positions which have not yet been measured Measurement positions which have already been processed cannot be deleted To open the Delete menu right click on the overview image Bruker Optik GmbH OPUS VIDEO 59 Video assisted Measurement Mouse Mode Video Image Measurement Spots Grid Defining Positions Moving To Defined Positions Starting Measurement Export Import f e Se ees Delete Image Delete Measurement Positions Delete Image processing Figure 63 Delete Menu 6 4 12 Image Processing The Image Processing functions are only available and visible if the OPUS OBJECT software package has been purchased and registered These functions are used to automatically detect areas of interest in the video image and to measure them automatically by moving the x y sample stage to the appropriate measurement positions These functions are described in detail in the OPUS OBJECT manual 6 4 13 Illumination Corr
18. interferogram are also displayed in the area at the bot tom of the main window The overview image processing status shows current rendering activities e g resizing or zooming Depending on whether you right click on the live video image or the overview video image the appearing pop up menus are slightly different See the follow ing figure Bruker Optik GmbH OPUS VIDEO 37 Video assisted Measurement Mouse Mode Hardware Control Video Image Measurement Spots Grid gt Defining Positions gt Moving To Defined Positions gt Starting Measurement gt Mouse Mode Video Image Measurement Spots Grid Defining Positions JA Moving To Defined Positions gt Starting Measurement b Export b Import b Delete JA Image processing gt Figure 37 Pop up Menu of a Live Video Image and b Overview Video Image These functions are described in detail in the following sections 6 2 1 Video Setup Dialog for FT IR Microscopes When the video window opens figure 35 the Video Setup dialog appears auto matically in the upper corner on the left Use this dialog to define measurement mode illumination sample position etc To close this dialog click on the zio button in the upper right corner of the dialog box If you want to open the Video Setup dialog later once again right click on the live video image and select Hardware Control
19. is inverted as in case of the IRscope I software image inversion cannot be avoided to assemble over view images To invert the x or y axis of the IRscope I select the option Flip image in x or Flip image in y during the setup of the imaging device See figure 24 in section 5 2 Whether the x or the y axis needs to be flipped depends on the orientation of the camera Bruker Optik GmbH OPUS VIDEO 9 Installing the Video Hardware 10 OPUS VIDEO Bruker Optik GmbH Setting up the Mapping Device 5 Configuring the Video Hardware 5 1 Setting up the Mapping Device If you use a computer controlled x y stage you have to register the stage con troller Select the Optic Setup and Service function in the Measure menu The Optic Setup and Service window opens Click on the Devices Options tab Acti vate the Mapping Device check box figure 1 and click on the Setup button e Optical Bench Devices Options Interferometer AGP Export Options Service Optic Communication V Source Setup MV Use login operator name I Beamsplitter EIO I Automatic Accessory Recognition I Optical filter Setup b Gain Switch Gain IV Aperture Setup I Multiplexed data T tris aperture IV Wait for devices ready Setup J Polarizer setup P PLL Laser Multiply V Channel Setup I User signals Sample changer Setup I AQP with Digital Filters IV Detector Setup I Ext synchronisation Sonde Setup b Preamplifier gain Setup IV Mapping device Setup IV Velocity
20. it using the Del key on the keyboard You can also select all measurement Bruker Optik GmbH OPUS VIDEO 57 Video assisted Measurement positions belonging to a grid by pressing the Shift key while left clicking on any measurement position marker In this way the whole grid can be relocated or deleted You can edit the measurement positions either in the live video image window or the overview video image window Both windows will be updated accordingly Figure 61 Editing Measurement Positions 6 4 8 Measuring Marked Positions When all measurement positions have been defined you can start the data acquisition by selecting Starting Measurement gt Measure Marked Posi tions figure 47 As a result the stage automatically moves to the first measure ment position Then a spectrum is acquired stored in the 3D file and displayed in the upper spectrum window This procedure is repeated for all defined mea surement positions As soon as a measurement position has been processed its label changes from M to the corresponding number of the spectrum in the 3D file In addition the color of the label corresponds now to the color of the spec trum in the display window 6 4 9 Displaying the Spectrum of certain Measurement Position During the measurement only the last acquired spectrum is displayed in the upper spectrum window After the measurement you can display every spec trum by clicking on the corresponding measu
21. nor mal spectrum window See figure 72 The upper subwindow 3D window displays only one of the possible plots xyz xy zy or xz at a time by default the xyz plot The lower subwindow displays the spectrum at the current position of the z axis marker line For detailed information about this window type refer to the OPUS 3D Manual Rotation 70 Inclination 30 X 45948 63 x 45750 43 Z 24663 60 Z 24873 46 Sample 1 1 RW cron 3750 3500 3250 3000 2750 2500 2250 2000 1750 1500 1250 1000 750 Figure 72 Map Spec Window Bruker Optik GmbH OPUS VIDEO 67 Special OPUS Windows 7 5 Map Video Spec Window The Map Vid Spec window consists of three subwindows two 3D windows and a normal spectrum window See figure 73 In the two upper 3D subwin dows displays one of the possible plots xyz xy zy or xz For the display of the video image select in the pop up menu the xz plot Then select in the pop up menu the Properties function and activate on the 3D properties page the Video image option button The lower subwindow displays the spectrum at the given intersection point of the x and z axis marker lines For more information about the functionality of this special window refer to the OPUS 3D Manual 25000 24900 524800 4 ZU 24700 24600 T ZZ T 46000
22. sample stage MCL will appear grayed in the Device drop down list In case of a communica tion error between controller and computer the message Error in writing to com port will be displayed See figure 30 A communication error can occur for example if the controller has been connected to the wrong serial port or if the joystick switch on the front panel of the LANG controller is set to H instead of A To test the communication with the stage activate and then deactivate Activate Joystick check box If this command works correctly the message Wait will pop up If this message is not displayed and the communication with the stage fails an error message will be displayed Video assisted measurement i x H Basic Advanced Optic H Acquisition FT Display Background Gi Stage Check Signal Device MEL I Activate joystick Calibrate Stage Error in writing to COM port Figure 30 Error Message Communication Error Possible failure causes are e the stage controller is connected to the wrong COM port of the PC e the cable is defective e the joystick switch on the front panel of the LANG controller is set to H manual mode instead of A automatic mode 30 OPUS VIDEO Bruker Optik GmbH XIY Stage Calibrate Stage Clicking on this button moves the stage to its zero position and resets the counters to zero If the stage works correctly this command should move the stage backwards and
23. selecting Starting Measurement gt Measure Current Position or Measure Marked Positions See also section 6 4 6 The measurement spot is marked in both the live video image and the overview image The resulting sample spectrum appears in the upper spectrum window f in figure 35 e To interrupt a sample measurement click on the green status bar and select Stop task e You can save a sample measurement stage position to find it later again To do this right click on the live or overview video image and select Defining Positions gt Load Positionl 2 or Special Position 1 2 After you have changed the stage position you can move the stage back to the stored position s using the Moving To Defined Positions command of the pop up menu 50 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode Mouse Mode Hardware Control gt j Video Image gt i Measurement Spots Grid gt i Background Position Load Position 1 Load Position 2 Sp cial Position 1 Special Position 2 Defining Positions Moving To Defined Positions gt Starting Measurement Figure 48 Storing the x y Stage Position e Ifyou want to repeat a measurement with a different number of scans or with a different scan time for the sample and background measure ment right click on the live or overview image and select Starting Measurement gt Change Measurem
24. the Knife Edge Aperture Parameters 72 OPUS VIDEO Bruker Optik GmbH Changing the Aperture Settings As soon as you have selected one aperture a small dialog box labeled Knife Edge Aperture appears at the button of the video image window Note Do always select only one aperture This dialog box allows you to change the size and the rotation angle of the aper ture manually by entering the corresponding values Furthermore the dialog box has three buttons Position Open and Calibrate Clicking on the Position button moves the x y stage to the measurement position and sets the aperture to the desired size and angle If you click on the Open button the aperture opens to such an extent that it disappears from the field of view whereas if you click on the Calibrate button the aperture closes again by moving all motors to their front end switches Note Opening and calibrating the aperture may take quite a long time If the fol lowing error message appears Bruker FTIR x ea AQP Read timeout Wiederholen Abbrechen the timeout value in the registry should be set to a higher value To do this go to the entry HKEY LOCAL MACHINE SYSTEM ControlSet001 Service Bruk erIR Parameters and set parameter AQP Timeout from its default value 6000 mil liseconds to 2000 milliseconds If the aperture is used for the first time in conjunction with a new computer the aperture zero position equals the position after calibrating the knife
25. try it again until the stage tracks the mouse correctly Bruker Optik GmbH OPUS VIDEO 45 Video assisted Measurement Add Text Annotation This function allows you to add an annotation in the video image by moving the cursor to the desired position in the video image pressing the left mouse button and entering the desired text Edit Measurement Positions amp Annotations If the Edit Measurement Positions amp Annotations function in the mouse mode menu figure 42 is activated left clicking on a measurement point invokes a rectangle figure 43 which can be moved by dragging and dropping deleted using the Del key on the keyboard or resized Resizing only enlarges the marker for a better visualization but does not change the measurement position Note that a defined measurement position can only be edited i e deleted or moved to another position in the run up to a measurement After the measure ment editing a measurement position is no longer possible Figure 43 Editing a Measurement Position Measure Distances This function allows you to measure distances Place the cursor at a starting point press the left mouse button and move the cursor to the desired end point while keeping the mouse button pressed As a result a distance vector is shown in the live image window and in the overview image window as a white and a red line respectively At the line end point the distance value is displayed using the same unit as
26. 000 T 6 Hyperion3000 Figure 8 Selecting the Microscope Device Bruker Optik GmbH OPUS VIDEO 15 Configuring the Video Hardware This dialog box contains the available imaging devices that allow you to take pictures of the sample Note that not all listed imaging devices are IR microscopes but also special optical systems e g IMAC external sample chamber for measurements using a FPA detector EOS FT Raman micro scope and HELIOS infrared microscope for ATR measurements Select the imaging device you want to work with and click on the OK button Available Objectives If you click on the Available Objectives button figure 7 the following dialog box opens Select Available Objectives for Hyp3000Mit FPA A x v 1 15xIR GO WEIS Cancel 7 36 x ATR 9 Grazing angle 10 20 x ATR 16 20 x Refl C 17 20 x ATRISi Figure 9 Selecting the Objectives You have to select the objectives that can be used in conjunction with the microscope you have selected on the previous dialog box figure 8 Note The selected objectives are offered as options in the Objective drop down list of the Video assisted measurement dialog box figure 4 Electronic Options If you click on the Electronic Options button figure 7 the following dialog box opens 16 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device Select possible Options for Hyp3000Mit FPA x
27. 27 39 40 71 Offset 40 73 74 Offset correction 34 Optical camera adapter 8 9 18 19 27 79 Optical options 18 Overview video image 1 5 25 37 38 41 43 44 45 46 47 48 50 51 53 59 68 71 Overview video image window 36 37 45 54 55 56 58 62 Overview window 68 P PAL standard 40 79 Pan mode 45 47 PCI slot 3 4 Pinhole 34 Predefining measurement positions 53 R Raman laser 44 80 Raman mode 44 Ramp 32 Rectangular grid of measurement positions 56 74 Red frame 36 37 Reflectance mode 4 39 40 47 Reflection 18 Registration key 12 Repeated video measurements 51 Resolution 32 RS 232 interface 3 S Sample measurement 50 Sample measurement position 47 49 50 76 Scaling factor 19 24 27 39 40 45 77 Serial port 32 Signal intensity 49 50 Snapshot 39 43 47 68 Source 26 Spatial resolved measurement 66 Spectrum file 5 35 63 Spectrum window 35 36 37 50 54 58 62 69 Speed 32 Spindle factor 40 45 Stage acceleration 32 Stage controller 11 Stage position 31 36 37 41 47 50 53 75 Stage position control 41 Stage setup 31 Stepper motor 3 17 28 32 33 S video signal 22 T Timeout 32 Transmittance mode 4 34 39 40 47 U USB interface 3 4 23 Vv Video film 53 Video image 52 62 63 Video image window 35 Video input channel 21 Video option 20 Video setup 36 40 Video signal 22 23 video standard 24 Video stream 52 53 VideoPos
28. 4100 24200 1239x799 T T a a e 7 T 7 T e 3600 3400 3200 3000 2800 2600 2400 2200 2000 1800 1600 1400 1200 1000 800 600 EEE E Cursor X67548 Feady H repa Y 24042 Figure 54 Live Spectrum Mode Arbitrary Measurement Positions To define arbitrarily measurement positions select in the pop up menu Mea surement Spots Grid gt Mark Measurement Positions figure 55 and click either in the live video image window or in the overview image window on the positions you want to mark for the sample measurement These measure ment positions will be saved and labeled with the letter M in both the live video image window and the overview image window 54 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode Hardware Control gt Mouse Mode gt video Image gt Measurement Spots Grid Mark Measurement Positions Defining Positions JA Define Linear Measurement Grid Define Rectangular Grid Define Elliptical Grid Moving To Defined Positions gt Starting Measurement JA Edit Measurement Positions Figure 55 Defining Measurement Positions Linear Grid of Measurement Positions If all measurement positions are to be located on a straight line use the Define Linear Measurement Grid function in the Measurement Spots Grid menu Then place the cursor on the desired first measurement position press the left mo
29. APH data block of the 3D file in question Depending on the image size the loading process may take several seconds The VideoPostrun window consists of two subwindows a video window and a spectrum window See figure 75 The left subwindow displays both video snapshots and assembled overview images Depending on the number of video images you have taken you can have the desired image been displayed by selecting the corresponding image number in the drop down list in the lower part of the overview window To print an image use the Quickprint function in the OPUS Print menu As shown in figure 75 all labels and measurement position markers are dis played together with the video image When you click on one of these measure ment position markers the corresponding spectrum will be displayed in the right spectrum window To display several spectra at the same time press the Ctrl key while clicking on the desired measurement position markers The spectrum window is similar to the standard OPUS spectrum window To modify the dis play properties right click on the spectrum window and use the pop up menu functions For detailed information refer to the OPUS Reference Manual Bruker Optik GmbH OPUS VIDEO 69 Special OPUS Windows 24800 24900 25000 25100 24700 24500 24600 Image gt 2 E 2 Figure 75 VideoPostrun Window 70 OPUS VIDEO Bruker Optik GmbH Changing the Aperture Settings Mot
30. Setup I Transient recorder Setup I High Pass Filter Setup T Imaging device Setup M Low Pass Filter Setup Correlation mode Setup Setup Result Spectrum Save Settings Cancel Help Figure 1 Optic Setup and Service Dialog Box Selecting the Mapping Device The Devices Options dialog box opens Enter the type of x y sample stage installed on your microscope As shown in figure 2 two types of x y stage con trollers LANG and CANBUS are available for video mapping When using an external LANG controller the first line must contain the entry MCL see figure 2 Otherwise the software automatically assumes the use of a CANBUS controller For the internal LANG controller there are two entries Lstep and Lstep atr These entries should not be modified as they belong to two pre defined ini files having the same name Lstep ini and Lstep atr ini The option Lstep enables the manual movement of the stage in x and y direc tion and the manual focus setting 1 e moving the stage manually in z direc tion The option Lstep atr is only intended for mapping measurements using Bruker Optik GmbH OPUS VIDEO 11 Configuring the Video Hardware the ATR objective In this case the stage movement in z direction is automati cally controlled by the computer The intention of the exclusively computer controlled stage movement is z direction is the prevention of an inadvertent damage of the ATR crystal as a manual stage movement in z dir
31. Time Resolved Measurement ed FPA Step Scan EA Continuous Scan FPA Measurement Figure 3 Measure Menu The Video assisted measurement dialog box opens ideo assisted measurement 5 x H Basic Advanced Optic i Acquisition FT Display Background XY Stage Check Signal Experiment Load fpa XPM Operator Name Defaut Sample Name Instrument Test Sample Form Eneray Test and S N Test Path D MEAS Filename ENERGY O Imaging Device HypaMitFPA 7 Objective fis XIR x Background Single Channel Start Video Assisted Measurement Start Measurement without 3D Exit Cancel Help Figure 4 Video assisted Measurement Dialog Box Before starting a video assisted measurement or a measurement using the FPA detector you have to select the installed imaging device from the corresponding drop down list The drop down list in turn contains only those imaging devices that have been set up before To do this select in the OPUS Measure menu the function Optic Setup and Service and click on the Devices Options tab Bruker Optik GmbH OPUS VIDEO 13 Configuring the Video Hardware Optic Setup and Service j xj Optical Bench Devices Options InterferometerzaaP Export Options Service Optic Communication MV Source Beamsplitter I Optical filter IV Aperture I tris aperture Polarizer V Channel I Sample changer IM Detector b Preamplifier gain Vv Velocity I High Pass Filter b L
32. VIDEO VID2 Check 2 Composite DDD 3 Composite 2 VID1 Cancel OO Figure 16 Selecting the Video Input Channel Bruker Optik GmbH OPUS VIDEO 21 Configuring the Video Hardware The frame grabber cards have three analog inputs one input for the S video sig nal and two inputs for the composite signal To check whether there is a video signal at the selected video signal input chan nel click on the Check button Thereupon the video image of the selected input channel is displayed under the list box See the following figure Select ideo Input Channel for Hyp3000MitFPA 1 5 VIDEO VID2 OK 2 Composite 1 VIDO 3 Composite 20 101 Cancel Figure 17 Input Channel with Video Signal If there is no video signal at the selected input channel either the following error message figure 18 or a noisy video image with blue flight strips figure 19 is displayed Opus x OLC_STS_NO_VIDEO_SIGNAL There is no video signal detected at the Front end Figure 18 Error Message in case of an analog Video Camera 22 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device Select ideo Input Channel for Hyp3MitFPA x 1 S VIDEO VID2 2 Composite 1 COAX or VIDO 3 Composite 2 ID1 Figure 19 Video Image with no Video Signal detected If there is no video signal detected check whether the camera is switched on and whether the video cable is c
33. age In case of PCs with the display implemented on the motherboard the latter requirement can cause problems and possibly can make an additional display plug in board necessary Bruker Optik GmbH OPUS VIDEO 3 Hardware Requirements An instrument configuration consisting of a Tensor or Vertex spectrometer a Hyperion microscope a x y sample stage and the digital video camera Infinity1 require for example the following hardware components e Short PCI slot for LAN integration if desired e Long PCI slot for LSTEP card for controlling the x y stage e USB 2 0 interface e High capacity PC power supply unit or alternatively an external power supply unit for the LSTEP card e DirectShow compatible display that is capable of showing overlays possibly a separate display card that requires a AGP or PCI slot If an analog video camera is used instead of the digital camera Infinity1 the USB 2 0 interface and normally an external power supply unit are not needed Instead another PCI slot for the frame grabber card is required 2 4 Microscopes The following types of microscopes are supported e IRscope I II e Hyperion 1000 2000 3000 e RamanScope LILI e Senterra dispersive Raman microscope e EOS FT Raman accessory e Helios MIR ATR unit e IMAC macrochamber for measurements using the FPA detector IRScope II and Hyperion enable a computer controlled switching between reflectance mode transmittance mode VIS IR
34. ally used objective Otherwise the scal ing factor of the microscope will be incorrect and neither the interactive nor the automatic motion mode of the x y sample stage will work correctly Scaling Function Each objective must be assigned to a proper scaling factor in order to position the x y stage exactly with regard to the cursor position on the video image Although you can use the default scaling factors provided for each objective it may be desirable to fine tune these values depending on the requirements of your experiment Bruker Optik GmbH OPUS VIDEO 39 Video assisted Measurement The scaling factor for the current objective in microns per image pixel is dis played below the objective drop down list A video image generated by a PAL standard video camera consists of 768 pixels in the x direction and 576 pixels in the y direction Consequently the default value of 1 104 microns pixel covers a sample area of 768 x 1 104 848 microns in the x direction and 576 x 1 104 636 microns in the y direction The scaling factors differ by a factor of 768 640 when using NTSC type cameras because this video standard produces images of 640 x 480 pixels Clicking on the Scale button opens a window which prompts the user to select a prominent image feature by clicking on it in the live video image window Based on the current scaling factors the software determines the distance between this feature and the center axis of the camera
35. asurement by clicking on the corresponding option button and entering either the desired measuring time in seconds or the desired number of repetitions e Click on the Start Repeated Video Measurements button to start the measurement cycle After you have started the measurement cycle a Stop button appears in the lower part of the video window See figure 52 Clicking on this button aborts the measurement cycle if required Stage X 44653 3 Y 36896 1 Cursor 44680 9 Ready Image 1 vi ral Stop Y 36834 8 Figure 52 Lower Part of the Video Window 6 4 6 Predefining Measurement Positions Apart from performing a measurement at the current stage position you can also predefine a number of measurement positions at which the sample is auto matically measured in one run You can specify either arbitrary measurement positions or use a default pattern of measurement positions e g a rectangular grid The measurement positions can be specified either in the live video win dow or the overview window However if an overview image has been assembled from a large number of regions its scale may be too coarse to accurately select the measurement posi tions Therefore the overview image can be zoomed to full image resolution To do this right click on the overview image select Mouse Mode gt Zoom Mode and draw a rectangle around that part of the overview image that is to be enlarged Alternatively use the and keys of y
36. be adjusted in different ways using the Video Setup dialog box using the corresponding slider E in figure 38 provided the camera has a DirectDraw interface using the Contrast button F in figure 38 and e using the dialog box of the corresponding camera driver which is invoked by clicking on the button H in figure 38 Note that this contrast setting is not manage by OPUS 42 OPUS VIDEO Bruker Optik GmbH Window for video assisted Measurement Eigenschaften von Opus Frame Grabber EA Contrast Contrast Level Default Abbrechen Figure 40 Contrast Setting Window Setting the Parameters of the Camera Driver Clicking on this button opens a dialog box which allows the setting of the parameters of the camera driver provided the camera has a DirectDraw inter face The appearing dialog box depends on the installed digital camera The definable parameters vary from camera to camera except the following parame ters brightness contrast and color They can be defined for all cameras in this dialog box Note As the driver software for the installed camera is delivered by the manufac ture of the camera in question OPUS is not able to identify and to store the set tings you have made in this dialog box Start Activity These buttons are shortcuts for existing pop up menu functions Hei Snapshot Button Clicking on this button takes a snapshot of the live video image The effect of this bu
37. camera 3 21 22 42 Annotation 5 46 48 59 61 Aperture angle 74 Aperture position 72 Aperture rotation angle 72 73 Aperture setting 47 49 50 71 74 75 76 Aperture size 72 73 74 Arbitrary measurement positions 54 ATR objective 12 19 33 Autofocus 17 Automatic focus control 39 41 B Background measurement 17 49 50 Background measurement position 17 75 76 Background spectrum 44 47 49 50 51 75 76 Beamsplitter 26 Bitmap 25 BMP 59 BNC plug 8 Brightness 39 42 43 C Calibrate stage 31 41 Camera driver 39 42 CANBUS controller 3 11 19 33 Capture device 20 42 CCD area 60 CCD chip 19 24 27 77 79 80 Channel 26 Color 39 42 43 COM port 32 Composite signal 22 Computer controlled x y stage 11 Contrast 39 42 Cross hairs 36 Cursor position 36 37 39 47 D Deleting images 59 Deleting measurement positions 59 Detector 26 27 78 79 Detector offset 34 Dichroic beamsplitter 41 Digital camera 3 23 42 DirectDraw interface 42 DirectShow filter 23 DirectShow compatible digital camera 21 42 DirectShow compatible display 3 4 Display resolution 7 Display settings 7 Driver software 43 DT31313 DT3153 3 E Editing annotations 46 Editing measurement positions 46 57 Electronic options 16 Elliptical grid of measurement positions 57 Ethernet cable 3 Ethernet interface 3 Exporting images 59 Exporting measurement positions 59 F Firmware version 4 7 Fla
38. ce driven by the stage Options are 70000 and 20000 The correct value depends on the stage model The Resolution value can be smaller than one step of the stepper motor since the motor can also perform fractional steps Enter the desired value in the corre sponding field Note that the unit is microns The values for the X Range and the Y Range depend on the stage model Note that these values must be defined in the unit specified in the Units field If you change the unit in the Units field you also have to change the X Range and Y Range values accordingly Save your settings by clicking on the Save settings button After having selected the correct COM port and switched the LANG controller to the automatic mode A communication should be established Check the correct cable connection by calibrating the stage Switch to the XY Stage dialog window of the Video assisted measurement dialog box figure 29 and click on the Calibrate Stage button Now the stage should move backwards and to the right side of the microscope If this is not the case either the connections of the X and Y cable have to be changed or the stage is not mounted correctly LStep Stage Controller internal LANG Controller To specify the parameters for an LStep stage select in the Devices Options dia log window figure 2 the corresponding LStep option and click on the Setup button next to the entry field The following dialog window opens 32 OPUS VIDEO Br
39. collected in the OIF file till then are attached to the resulting spectrum file If you have forgotten to take a video image before the measurement the result ing spectrum file does not contain an image But you can take an image later and add it to the spectrum file using the Copy Data Block function in the File menu if required If you want the resulting spectrum file to contain a video image it is recommended to take it before the measurement Bruker Optik GmbH OPUS VIDEO 63 Video assisted Measurement Mouse Mode Hardware Control Video Image Measurement Spots Grid Defining Positions Moving To Defined Positions 5 0 t Collect Background at Current Position Collect Background at Background Position Live Spectrum Live Igram Check Signal Measure Current Position Measure Marked Positions Pause Scanning Gontinue Scanning Stop Scanning Change Measurement Parameters Figure 68 Select the Measurement Parameters 64 OPUS VIDEO Bruker Optik GmbH Opening a special OPUS Window Special OPUS Windows 7 1 Opening a special OPUS Window To ensure an adequate display of the acquired data resulting from a video assisted measurement in 3D mode the OPUS software provides a number of special window types To open a window of a special type select the New Regis tered Window function in the Window menu The dialog box figure 69 opens The drop down list contains al
40. cope II and Hyperion only 8 4 4 Orientation of the Video Camera ya lt 5 esat tis agata e eizera 8 5 Configuring the Video SEAU 11 5 1 Setting up the Mapping Device egiazki eda dire eian iez eo 11 5 2 Setting up the Imaging Device cece cece eee eens 12 5 2 1 Imaging Device AAE 15 5 2227 Vide OPNONS a a E EE ee ie a 20 5 2 3 Define beee Sd TA ZT Zia Vee E 26 5 3 Selecting the Motorized Aperture Option u u 28 5 4 KIN SASS aatik PA aes Dee Gigi perak AM hE Ae me ed 29 5 4 1 Checking the operational Reliability of the Stage 29 SE Stade SCUD AEEKO 31 5 5 Selecting Measurement Parameters assa 34 5 6 Offset Corretto A baia eae EE Sabena ed sawn mo Eto a 34 6 Video assisted Measurement 0 cece cece eee eee eee 35 6 1 General Information Sarrik ie eae a erein Ee Oitia 35 6 2 Window for video assisted Measurement usus 35 6 2 1 Video Setup Dialog for FT IR Microscopes 4 38 6 2 2 Video Setup Dialog for Raman Microscopes 44 6 3 Functions of the Pop up Menu Item Mouse Mode 45 6 4 Performing a Video assisted Measurement with 3D Mode 47 64 1 General Procedure es digita waning Ped az dutea 47 6 4 2 Snapshot and Overview Image 00 00 eee eee eee 47 6 4 3 Performing a Background Measurement 49 6 4 4 Performing a Sample Measurement assa 50 6 4 5 Performing Repeated Video Measurements
41. cquisition gt Automatic Termination Criterion Total time 10 Repetitions Total repetitions b Start Repeated Video Measurements Abbrechen igure 50 Repeated Video Measurements Dialog Window Define the time interval in seconds between the measurements by entering the desired value in the field Repeat measurement every x seconds The value 0 means that the next measurement starts imme diately after the previous one Decide whether either one video image is to be taken before each measurement or a video stream is to be started before the first mea surement by activating the corresponding option button Note In the first case Take a single video image before each measurement the type of file in which the spectra and the video images are stored depends on the video assisted measurement mode i e with or without 3D e Video assisted measurement mode with 3D All acquired spectra and all recorded video images are stored together in one single 3D file i e the resulting 3D file contains n spectra and n video images To view the mea surement result afterwards open a VideoPostrun window This OPUS window type allows you to switch between the individual images See figure 51 The spectrum which belongs to the currently selected image is displayed in the right subwindow of the VideoPostrun window In this way a logical assignment of the spectra to the video images or vice versa is possible e Video
42. ct possible Optionms for Hyp3000MitFPA L x 1 Motorized Aperture OK V7 2 Autofocus B ideian read Frontpanel Cancel 4 Move to Saved Stage Z Position if available Existing Options are shown in blue color Figure 11 Microscope without optional electronic Accessories Optical Options If you click on the Optical Options button figure 7 the following dialog box opens S elect Available Optical Options for Hyp3000Mit FPA KE x v 1 Reflection 3 0ptical Camera Adapter 4598 0 Cancel 4 Fluorescence Figure 12 Selecting optical Options for the Imaging Device Some microscopes are equipped with the following optical options Reflection IR VIS Optical camera adapter Fluorescence 18 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device The availability of these options can not be checked electronically If you have installed or removed the optical camera adapter the image on the CCD chip changes Therefore always click on the Set Scaling Factors to Default button figure 7 after the installation or removal of the optical camera adapter in order to enter new scaling factors in the imaging device file Motorized X Y Stage If you click on the Motorized X Y Stage button figure 7 the following dialog box opens x O1 MCL 2 Canbus 100 LStepStage Cancel 101 L5tep TR Stage Figure 13 Selecting the motorized x y stage T
43. e Raman fibre at which you achieve maximum IF intensity then click Save Save Zero Figure 34 Correcting the Detector Offset 34 OPUS VIDEO Bruker Optik GmbH General Information Video assisted Measurement 6 1 General Information The OPUS VIDEO software package allows both video assisted measurements with and without 3D mode When you perform a video assisted measurements in the 3D mode all spectra acquired during a mapping measurement are stored automatically in one single 3D file Afterwards you can have these spectra displayed in a 3D plot 3D plots i e intensity of a trace over the measured area are only possible if the mea surement positions have been specified in a regular grid pattern form To open a 3D file and to process the data of such a file the optional OPUS 3D software package is required For displaying the measurement results a number of spe cial OPUS window types is available When you perform a video assisted measurements not in the 3D mode each measured spectrum is stored in a single spectrum file i e the number of gener ated files is identical to the number of acquired spectra during the video assisted measurement The spectra acquired in this way can not be displayed in a 3D plot afterwards So this kind of video assisted measurement does not require the OPUS 3D software package If your microscope is not equipped with a motor ized x y sample stage all spectra are acquired at the sam
44. e X button in the upper right corner of the window Bruker Optik GmbH OPUS VIDEO 61 Video assisted Measurement 6 5 Video assisted Measurement without 3D 6 5 1 General Information The video assisted measurement mode without 3D does not require the optional OPUS 3D software package to view the video images and spectra after the mea surement as all spectra are stored in separate files like during a normal measure ment Images which have been taken before the measurement and which are displayed in the overview video image window are stored automatically together with the single spectra All images which have been taken during a video session i e as long as the live video image window is open are stored in a separate file having the extension OIF OPUS Image File To start a video assisted measurement in the non 3D mode select in the OPUS Measure menu the Video assisted measurement function and click on Start Measurement without 3D button figure 66 Start Video Assisted Measurement Start Measurement without 3D Figure 66 Starting a video assisted Measurement without 3D Apart from the above mentioned difference between the two modes nearly all the other functions including x y stage control taking overview images and microscope front panel control are available in the video mode without 3D as well Therefore only the differences between video mode with 3D and without 3D are described in the following sections
45. e bar will act as return or enter key and generate a new text line The color of the annotations can be changed by right clicking on the annotation This will bring up the pop up menu Select the Annotation function and click on Change Color Assign another color to the text by clicking on the desired color To delete annotations click on the Remove function 48 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode 6 4 3 Performing a Background Measurement Before starting a sample measurement you have to acquire a background spec trum The background spectrum has to be acquired using the same aperture set ting as for the sample measurement s later on Therefore optimize the aperture setting for the sample before starting the background measurement To do this proceed as follows e Move the stage to the desired sample measurement position by click ing on the respective spot in the overview image Ensure that the function Move to Click Mode in the Mouse Mode menu figure 42 is activated Position the stage in such a way that the sample area of interest is in the center of the overview image e Close the aperture manually until only that part of the sample is visi ble that is to be measured Before starting the background measurement check the signal intensity To do this proceed as follows e Right click on the live or overview video image and select Starting Measurement gt L
46. e measurement posi tion In this case select the video assisted measurement mode without 3D 6 2 Window for video assisted Measurement To perform a video assisted measurement select the Video assisted measure ment function in Measure menu The Video assisted measurement dialog box figure 4 opens If you click on the Start Video Assisted Measurement button the OPUS software opens automatically the window for video assisted mea surements in 3D mode shown in figure 35 This window consists of four sub windows two video image windows and two spectrum windows If you click in the Video assisted measurement dialog box figure 4 on the Start Measurement without 3D button the OPUS software opens automatically the window for video assisted measurements without 3D mode shown in figure 67 The only difference between these two windows are the two missing spectrum subwindows in case of the window without 3D mode Bruker Optik GmbH OPUS VIDEO 35 Video assisted Measurement a b c d ID g h i Video Setup x trator Video Measurementdefa ilt ows 2 Objective 8x 15x1R X Scale Micron pixel X Y 0 2311 0 2311 Porto ma ZE Fluorescence ON p Focus z vs eei E MIS Zero Auto Bright contr color E PUES ee gt Start ei s ERRE aT E Display default owsi S E video Measurembnt efault ows 2 NM bx a erez G k I m 0 Figure 35 Video Window
47. e measurement positions and assign the specified aperture setting to it Then right click on this or another measurement position and select Aperture Set All Apertures to Selected Aperture from the pop up menu See the following figure Remove Remove All EI Change Color Aperture gt v Show Aperture v Show All Apertures Change Aperture Set This Aperture to Last Selected Aperture Set All Apertures to Selected Aperture Figure 81 Aperture Menu If only a subset of measurement positions is to be measured using the same aperture setting set the aperture for one of these measurement positions and leave it selected Then right click on another measurement position of this sub set and select Aperture Set This Aperture to Last Selected Aperture from the pop up menu figure 81 If you want to analyze a linear or rectangular grid of measurement positions the software computes automatically an aperture size that covers the available space exactly See the figures 82 and 83 Figure 82 Linear Grid of Measurement Positions 74 OPUS VIDEO Bruker Optik GmbH Measuring at pre defined Positions Figure 83 Rectangular Grid of Measurement Positions Although the individual measurement positions of these grids can be assigned to different aperture settings in practice this is rarely the case 8 2 Measuring at pre defined Positions In order to obtain usable spectra you have t
48. ection If the video image is not evenly illuminated e g it gets darker towards the edges there are two ways of correcting the illumination e Using only the evenly illuminated part in the center of the image Select Video Image gt Illumination Correction gt Set useful CCD area in the pop up menu See figure 64 e Performing a Flatfield Correction First place a white unstructured sample e g a piece of paper on the stage and select Measure Flat field Image in the Illumination Correction menu Each sample image is divided by the flatfield image The result should be an evenly illu minated video image Hardware Control Mouse Mode 29600 Gi rr TE video Image Snapshot Measurement Spots Grid gt Set Scan Overview Image ASA Zea E Scan Overview Image Defining Positions A Illumination Correction Set Useful CCD Area Moving To Defined Positions E EEE 7 v Overlay Detector Size Measure Flatfield Image d ZE v Overlay Crosshair Load Flatfield Image v Overlay Annotation texts Automatic Flatfield Correction v Overlay All Apertures hm sa Figure 64 Illumination Correction 60 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode After the flatfield image has been measured it is smoothed to enhance the qual ity and the evenness of the image If the smoothing has been carried out
49. ection holds a potential risks for damaging the ATR crystal Devices Options a x M100 L5tepStage M101 L5tep TRStage ltem UP Item DOWN Add New ltem Delete Item Restore Factory Defaults Figure 2 Devices Options Dialog Box Registering the Mapping Device If your microscope is not equipped with a motorized x y stage make sure the Mapping Device check box is not activated 5 2 Setting up the Imaging Device Select the Video assisted measurement function in the OPUS Measure menu If this function is disabled i e grayed and not black you may not have the appro priate access rights to run the software Make sure the option Show all functions is checked in the Customize menus dialog box OPUS Setup menu If the prob lem persists a new registration key is required which enables the Video soft ware A registration key can only be generated by Bruker For more detailed information see the OPUS Reference Manual 12 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device Measure Manipulate Evaluate Display Prin sh Advanced Measurement Setup Measurement Parameters ae Routine Measurement Hj Repeated Measurements Z Rapid Scan Time Resolved Measurement eA Direct Command Entry g Optic Setup and Service Optics Diagnostics EK Temperature Control Motorized Stage Control ie Video Assisted Measurement IE Time Resolved Step Scan S Chromatography Step Scan Modulation Interleaved
50. edge aper ture See the Knife Edge Aperture dialog window in figure 79 As shown in the following figure the aperture zero position can be a slightly tilted aperture Knife Edge Aperture x Se Angle p ap 4p 4 C Aperture Offsets Figure 80 Performing an Offset Bruker Optik GmbH OPUS VIDEO 73 Motorized Knife Edge Aperture In order to obtain a zero tilt at an aperture angle of zero degrees the aperture angle has to be offset To do this click in the Knife Edge Aperture dialog box on the Offsets option button and change the Angle value using the arrow buttons until the aperture and the red rectangle representing the aperture are parallel to each other Then click on the Aperture option button Thereafter any position command using an angle of 0 90 180 270 or 360 degrees should lead to a proper vertical horizontal alignment of the aperture The X and Y value for the offset should remain unchanged i e X and Y 0 If you have to define several measurement positions proceed as described above By default every new measurement position gets assigned the default or last used aperture size If the objects to be analyzed are of different size the aperture size can be adjusted individually to the object size However if all positions are to be measured using the same aperture setting there is no need to specify the aperture setting for each measurement position individually In this case select one of th
51. ent Parameters The following dialog box opens Sample Scan Time 5 Scans Background Scan Time 5 Scans V Measure BG position every N sample positions 1 Cancel Figure 49 Changing Measurement Parameters You can specify the Sample Background Scan Time either as number of scans or in seconds For automated measurements you can also define that a background spectrum is acquired every Nt sample posi tion 6 4 5 Performing Repeated Video Measurements The OPUS VIDEO software allows the repetition of a video measurement in defined time intervals at a fixed defined measurement position With this kind of video measurement you can document sample changes both in form of video images and in form of IR spectra This kind of measurement however is only possible with a microscope that allows of a simultaneous sample viewing and IR data acquisition e g HELIOS or HYPERION with VIS IR option To perform repeated video measurements proceed as follows e Right click on the live video image and select Starting Measure ment gt Start Repeated Video Measurement See figure 47 Bruker Optik GmbH OPUS VIDEO 51 Video assisted Measurement Thereupon the dialog window shown in figure 50 opens Repeated ideo Measurements xj m Repetition Repeat measurement every 0 Seconds 0 No delay m Mio mode F Take a single video image before each measurement Start video stream before first a
52. er the number of grid positions and the other parameters No of Grid Positions in Xx No of Grid Positions in Y Lower left position microns Lower left position Y microns fi 7246 7 DeltaX microns 846334 Delta microns 20 4928 Cancel Figure 58 Defining a Rectangular Grid of Measurement Positions Enter the desired parameters in the corresponding fields and click on the OK button As a result a rectangular grid of measurement positions is displayed both in the live video image window and in the overview video image window The measurement positions are labeled with the letter M as shown in the follow ing figure 56 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode OIUU 92ZUU Figure 59 Resulting Rectangular Grid of Measurement Positions Elliptical Grid of Measurement Positions In case of circular or elliptical objects you can arrange the measurement posi tions in form of an elliptical grid To do this select in the pop up menu Mea surement Spots Grid gt Define Elliptical Grid 7120 7140 7160 7180 7200 7220 7240 7260 Figure 60 Elliptical Grid of Measurement Positions 6 4 7 Editing Measurement Positions You can relocate or delete measurement positions using the Edit Measurement Positions function in the Measurement Spots Grid menu Select a measure ment position marker by left clicking on it Then drag it to another position or delete
53. erial Port COM COM2 BAUD 9600 PARITY n DATA 8 STOP 2 to off xon off odsr off octs on dtr off rts off idsr off Timeout sec fo Units 0 2m 1 mm Omicron 8 Ramp fi0 9 Speed BIE 13 Spindle x 1000000 14 Spindle Y foo 15 Resolution C x Range ME BSR units Y Range IE be units GO Save settings Restore defaults Cancel Figure 31 Setup of a LANG Controller Bruker Optik GmbH OPUS VIDEO 31 Configuring the Video Hardware By default the Serial Port field is set to COM2 In case you have connected the LANG controller to COM1 you have to change this value The Timeout value defines duration before an error message will be displayed in case of a communication error with the controller The default value is 30 and should not be changed Specify the unit for the lateral stage movement in the Units field Valid units are centimeters value 2 millimeters value 7 and microns value 0 The X and Y range is set in these units Define in the Ramp field the stage acceleration The default setting is 50 We recommend a lower value e g 0 if you operate the stage at a higher speed 70 Define in the Speed field the stage speed The default value is 50 This value means a rather low speed and should be used when the stage is heavily loaded Otherwise you can set the speed to 70 Adjust the X Spindle and Y Spindle value until the reading of the LANG control ler is identical to the actual distan
54. ervice function The dialog window shown in figure 5 opens Click on the Devices Options tab activate the Imaging Device check box and click on the Setup button Select the connected imaging device from the list field figure 6 or if empty create a new entry by clicking on the Add New Item button Select this entry and click on the Setup button next to the entry field The Setup for Image Device dialog box figure 7 appears Click on the Elec tronic Options button The following dialog window opens Select possible Options for Hpy3000Mit FPA E x deian read Frontpanel 4 Move to Saved Stage 2 Position if available Check Which Devices Exist Figure 27 Selecting the Motorized Aperture Option Activate the Motorized Aperture check box Working with the motorized knife edge aperture requires that the stepper motors MOT32 MOT33 and MOT34 are known to the spectrometer electronics i e are listed in the spectrometer motor table To check whether the stepper motors are already known to the system or whether the motors are electrically connected the motorized aperture has to be installed into the microscope click on the Check which Devices Exist button The options for which the stepper motors have been found are shown in blue color 28 OPUS VIDEO Bruker Optik GmbH XIY Stage Select possible Options for Hyperion with Knifeeda er re E E x GUE EEE 2 Autofocus ld deian read Frontpanel Cancel M4 Mo
55. focus the optics on the region of interest The specified value indicates the stage position in rela tion to an arbitrarily defined z position Note that there is no feedback between the microscope focus adjustment knob and the Manual Focus Control of the Video Setup dialog Automatic Focus Control Clicking on the Auto button focuses the microscope on the sample The effect of this button is identical to the Autofocus function of Hardware control menu figure 37 The autofocus function is not available if you work with the ATR objective Focus Zero Point Selection Clicking on the Zero button assigns the value zero to the current z position of the stage See also the above section Manual Focus Control Stage Position Control Using this control panel you can move the stage in x and or y direction The speed of the stage movement depends on the cursor position when clicking on this control panel Clicking close to the center results in a slow stage movement while clicking in the peripheral region leads to a faster stage movement Alternatively you can move the stage position by clicking on the live or over view video image and selecting the corresponding Mouse Mode function See chapter 6 3 Calibrate Button After a computer reboot clicking on this button calibrates the motorized stage i e the stage moves to its predefined home position Bruker Optik GmbH OPUS VIDEO 41 Video assisted Measurement Bri
56. ghtness Contrast Color Control In case of an analog video camera these sliders allow you to manually control these parameter settings of the frame grabber card Note In case of a digital video camera these parameters can only be set using these sliders if the camera has a DirectDraw interface Otherwise these sliders are deactivated MA Histogram Button This button is only available if you have selected a DirectShow compatible video camera e g Infinityl USB 2800 Video when setting up the video cap ture device See figure 15 Clicking on this button opens the Histogram window See figure 39 The his togram allows you to assess the image contrast The contrast is set optimally when the histogram extends over the complete x axis range In the example shown in figure 39 there are only medium brightness values high and low brightness values are missing In this case an extension of the histogram over the complete x axis range is achieved by increasing the brightness and reducing the contrast Figure 39 Histogram Window Contrast Button This button is only available if you have selected a DirectShow compatible video camera e g Infinityl USB 2800 Video when setting up the video cap ture device See figure 15 Clicking on this button opens the window shown in figure 40 Using the con trast level slider you can adjust the contrast setting as desired Note In case of a digital video camera the contrast can
57. his dialog box contains all motorized x y stages that are supported by OPUS The option MCL stands for the large x y stage controlled by an external LANG controller For a motorized stage controlled by a LSTEP card the following options are available LStepStage and LStepATRStage The option LStepStage allows a manual stage movement in x y and z direction In case you want to perform a mapping measurement using the ATR objective you have to select the option LStepATRStage This option allows only a computer controlled stage move ment in z direction in order to prevent an ATR crystal damage Note The stage movement in z direction requires an optional third stepper motor The CANBUS controllers are used normally in conjunction with the RamanScope Bruker Optik GmbH OPUS VIDEO 19 Configuring the Video Hardware FPA Device If you have selected a microscope e g IRscope II and Hyperion 3000 that can be equipped with a FPA detector focal plane array detector you can select a FPA device by clicking on the corresponding button in the Setup for Imaging Device dialog box figure 7 The following dialog box opens x Cancel Figure 14 Selecting a FPA Device To select a FPA device you have to set up a transient recorder beforehand Measure menu gt Optic Setup and Service zz Devices Options tab gt Transient Recorder check box Enter for example the following string 7 FPA pcdig dll Do not forget to ente
58. ive Spectrum figure 47 Now the instru ment starts to acquire single channel spectra The signal intensity is displayed in the status bar b Mouse Mode Hardware Control Video Image Measurement Spots Grid a 2 Collect Background at Current Position Collect Background at Background Position Live Spectrurr ctrum Live Igram Check Signal Measure Current Position Measure Marked Positions Pause Scanning ce en EEE OLD 3 Da Gontinue Scanning Stop Scanning Change Measurement Parameters Start Repeated Video Measurement heme pr pe e e EZ EEE EE ss d o Q 4000 3600 3000 2500 2000 1500 Image TZI o dan B Cursor X 64691 Ready Figure 47 Activating the Live Spectrum Mode Bruker Optik GmbH OPUS VIDEO 49 Video assisted Measurement Note To obtain accurate data the A D converter should not be oversaturated Oversaturation occurs when the signal intensity reaches 32767 counts In general the signal intensity should not be higher than 25000 counts because in case of a background measurement there is no sample to absorb light and therefore the signal intensity will be higher compared with a sample measurement If the signal intensity is too high close the microscope apertures to reduce it e To stop the data acquisition right click on the green status bar and select Stop task Alternatively you can right click on the live or overview image and select Starting Measu
59. l available OPUS window types ChromPostrun Cluster Analysis CorrelChart Displa Figure 69 Drop Down List containing the available OPUS Window Types To 3D files resulting from a video assisted measurement the following window types are relevant e 3D e 3D e Map Spec e Map Video Spec e Overview e VideoPostrun Note When you load a 3D file the data are displayed by default in a 3D win dow 7 2 3D Window This window type displays only one of the possible plots xyz xy zy or xz ata time by default the xyz plot See figure 70 You can switch between these plots by selecting the desired plot type in the pop up menu For detailed infor mation about the functionality and the pop up menu of the 3D window refer to the OPUS 3D Manual In the following figure the 3D properties have been selected in such a way that the video image is displayed below the 3D plot for example Other presentation variants are also possible See OPUS 3D Manual Bruker Optik GmbH OPUS VIDEO 65 Special OPUS Windows Rotation 70 Inclination 30 a X 45948 63 b 45750 43 a Z 24663 60 Z 24873 46 a Sample 1 1 Index 0 X Micron Z Micran Figure 70 3D Window The 3D plot visualizes the spectral changes against space In this case one is talking about spatial resolved measurements or mapping measurements The three dimensional data presentation is achieved by assembling the spect
60. ng the stage to the outermost edges of the overview area of interest using the joystick or the mouse Then click on the Add region button To delete the last added area click on the Delete Region button After you have defined all desired areas click on the Overview Area now defined button Add Region Delete Region Overview Area now defined Cancel Figure 45 Scan and Assemble Overview Image Area Dialog Box Define the sample regions that are be included in the overview image by mov ing the stage to the desired positions and clicking on the Add Region button After you have defined all sample regions of interest click on Overview Area now defined to start the overview image assembling The overview image con tains all previously defined sample regions and is displayed in a separate video image window See figure 35 Sample Regions defined by clicking Add Region Resulting Overview Image Figure 46 Example for Defining an Overview Image After you have generated an overview image you can navigate the stage by clicking in the overview image window on any spot you like Text annotations can be added to the overview image by selecting the Add Text Annotation function from the Mouse Mode menu figure 42 Left click on the image position where the text should appear A dialog opens in which you can enter the annotation text Note that the spac
61. nts If you click for example on the Detectors button the following dialog box opens Select possible Detectors for Hyp3000MitFPA q x j0 Test Ramp 1 Ge Diode CJ4 NIR Diode Cancel M1 InGa s TE M Zee Diode 4990 0 9 Figure 25 Selecting Detectors The list box contains all options you have set up beforehand by activating the corresponding check box on the Optic Setup and Service dialog box figure 5 and clicking on the Setup button next to the respective check box 26 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device You can restrict the available detectors in the list box figure 25 in such a way that only reasonable detector options are available when you perform measure ments with the imaging device If you select for example only the InGaAs Te detector in the list box measurements can be performed using only this detec tor If you select another detector in the Detector Settings drop down list in the Video assisted measurement or Continuous Scan FPA Measurement dialog box the drop down list will have a red background as shown is figure 26 ideo assisted measurement H Basic Advanced A Optic H Acquisition FT Display Background XY Stage Check Signal Source Setting Beamsplitter Optical Filter Setting Measurement Channel Background Meas Channel Detector Setting Scanner Velocity Sample Signal Gain Background Signal Gain Tungs
62. o measure background and sample with the same aperture setting Thus the software attempts to measure also a new background spectrum if a sample measurement position with a new aper ture setting is encountered Therefore it is absolutely necessary to define a stage position at which the background spectrum is to be acquired To define a background measurement position move the sample stage to a suited position right click on the live video image and select Defining Positions Background Position in the pop up menu Mouse Mode Hardware Control Video Image Measurement Spots Grid Defining Positions Background Position Load Position 1 Load Position 2 Starting Measurement JA Special Position 1 Tae ies Special Position 2 Figure 84 Defining Positions Menu Moving To Defined Positions gt Once the background measurement position is defined you can start the mea surement by selecting Starting Measurement gt Measure Marked Posi tions Bruker Optik GmbH OPUS VIDEO 75 Motorized Knife Edge Aperture Mouse Mode Hardware Control Video Image Measurement Spots Grid Defining Positions red Moving To Defined Positions OA gt gt gt T Starting Measurement Collect Background at Current Position Collect Background at Background Pasition Live Spectrum Liye Igram Check Signal Measure Current Positi
63. of the overview image is stored in full resolution Only if the overview image size exceeds 4 000 x 4 000 pixel it is compressed to this maximum size By default this option is deactivated If you activate the option Play Sound during Image Capture there will be a clicking sound during the image capture provided that your PC is equipped with an audio card and a loudspeaker system In case of the IRscope I microscope figure 24 two further option may occur Flip image in x Flip image in y These options flip the image in x or y direction As in case of the IRscope I the camera image is optically inverted in the x direction it is necessary to compen sate for the optical inversion by the software Depending on the camera orienta tion the image must be flipped either in x or in y direction before overview images can be correctly assembled However as flipping the image requires CPU power this option should only be activated if overview images are to be generated Bruker Optik GmbH OPUS VIDEO 25 Configuring the Video Hardware Select possible Image options for IRScopel e x 3 Flip image in y dele Sound during Image Capture Figure 24 Image Options for IRscope 5 2 3 Define Useful Settings for The Define Useful Settings for group field figure 7 contains a number of but tons labeled Sources Channels Detectors and Beamsplitters Use these buttons to define useful settings for these optical compone
64. on rked Positions Pau Gontinue Scanning Stop Scanning Change Measurement Parameters Figure 85 Starting Measurement Menu As soon as you have actuated this command the following message box appears TM ei All Apertures and Background Position defined Figure 86 OPUS Message The OPUS VIDEO software asks you whether you have defined all apertures and a background measurement position At this stage you have a last chance to specify the aperture settings as desired and to define a background measurement position before the measurement actually starts During the measurement the x y stage may move forward and backward quite a lot because each time a measurement position is encountered of which the aper ture setting does not correspond to the one of the current background spectrum the x y stage moves to the background measurement position and a background spectrum is acquired using the new aperture setting Thereafter the x y stage moves to the sample measurement position and a sample spectrum is acquired 76 OPUS VIDEO Bruker Optik GmbH Rotation of the Camera Appendix The appendix covers details about the optics of the various instruments avail able A 1 Rotation of the Camera As already explained in section 4 4 setting the correct scaling factors is not suf ficient to generate overview images In addition the CCD chip edges of the video camera must be aligned parallel to the x and y direction of the
65. onnected to the right inputs A completely black or white video image indicates that there is a video signal detected at the input channel but the illumination setting is too dark or too light In case of a digital video camera the following error message figure 20 appears if either the camera is not connected to the USB interface or one of DirectShow filters is not installed on the PC or the filters can not be connected with each other for whatever reason No Infinity1 USB 2 0 Camera Framegrabber found not initialized Figure 20 Error Message in case of a digital Video Camera Video Camera If you click on the Video Camera button figure 7 the following dialog box opens Bruker Optik GmbH OPUS VIDEO 23 Configuring the Video Hardware Select a ideo Camera for Hyp3000Mit FPA xj GUI eten SSC PAL 7 lnfinity1 USB 2 0 Camera 1280 1024 8 DFK 31 FO3 1024 768 Cancel Figure 21 Selecting a Video Camera Select the installed video camera The selection of the correct video camera is of crucial importance as each video camera has a slightly different CCD chip size and a different number of pixels and consequently individual scaling factors Furthermore the selection of the correct video standard PAL and NTSC is important as you have to set the video standard in the frame grabber driver cor respondingly Most of the video cameras have the PAL standard A wrong video standard manifests i
66. ontrolled spectrometers e g Vector22 IFS28 IFS55 IFS66 IFS88 IFS120 need to be equipped with an ISA slot 2 2 x y Sample Stage The x y sample stage can be controlled either by an internal controller LSTEP card of the manufacturer LANG or an external controller of the manufacturer LANG or a CANBUS controller The internal controller requires a long PCI slot and a high capacity PC power supply unit because the stage stepper motors are supply with power by the PC Alternatively the power supply of the LSTEP card can be realized by means of an external power supply unit This variant is especially recommendable if the PC has to supply also the digital camera with power via an USB interface In case of the external LANG controller the PC must be equipped with a RS 232 COM interface The CANBUS controller does not require any additional PC resources 2 3 Video Camera Video images can be acquired by either an analog video camera plus frame grabber or a digital video camera which is connected to the USB interface The frame grabber is a plug in card DT3131 or the older version DT3153 manufac tured by Data Translation that occupies a short PCI slot When using a digital video camera an USB 2 0 interface must be available USB 1 x is not suffi cient Moreover a high image resolution requires a fast CPU gt 1GHz In addition the PC display needs to be DirectShow compatible and has to be able to show overlays over the live video im
67. orized Knife Edge Aperture When you start a video session the motorized knife edge aperture is always open 8 1 Changing the Aperture Settings To change the aperture settings you have to define a measurement spot by right clicking on the live video image or the overview video image provided an overview video image has already been created and selecting Measurement Spots Grid Mark Measurement Positions from the pop up menu Mouse Mode gt Hardware Control b Video Image Measurement Spots Grid Mark Measurement Positions Define Linear Measurement Grid Define Rectangular Grid Define Elliptical Grid Defining Positions Moving To Defined Positions gt 7 T gt Lee ee Edit Measurement Positions Figure 76 Measurement Spots Grid Menu In addition to the red cross labeled with M marking the center of the measure ment position a red rectangle appears indicating the aperture size used for this measurement position In case of the 15 x objective the default aperture size is 50 x 50 microns in the object plane Red Rectangle Red Cross gex 461 247 30212 Figure 77 Knife Edge Aperture indicated in the Video Image Bruker Optik GmbH OPUS VIDEO 71 Motorized Knife Edge Aperture To change the size position or rotation angle of the aperture you first have to select the aperture either by clicking with the left mouse button on it or b
68. our keyboard to scale up or down the defined detail of the image You can move the overview image using the arrow keys up down left right of the keyboard Pressing the Pos 1 key resets the image to the original scaling Bruker Optik GmbH OPUS VIDEO 53 Video assisted Measurement Mouse Mode No action Video I i Move to Click Mode GEO Pan Mode i LA Measurement Spots Grid had Test Ek Defining Positions gt Edit Measurement Positions amp Annotations Moving To Defined Positions Measure Distances Starting Measurement Zoom Mode Export A Import A Delete gt Image processing A b e zz rn Figure 53 Mouse Mode Zoom Function Note If your microscope can operate in the VIS IR mode it can be helpful to acquire single channel spectra while scanning the sample surface for potentially interesting measurement positions To do this select in the pop up menu Starting Measurement s gt Live Spectrum Using this function single channel spectra will be continuously measured using the same parameter set as for the actual measurement later The resulting live spectrum is displayed in the lower spec trum window 1 in figure 35 At the same time the intensity of the corresponding interferogram as well as its peak position is shown below the spectrum window 3500 3250 3000 2750 2500 2250 2000 1750 41500 1250 1000 750 e 23700 23800 23900 24000 2
69. ow Pass Filter Setup Setup Setup Setup Setup Setup Setup Setup Setup IO ELLE Setup ZO Setup Ed IV Use login operator name I Automatic Accessory Recognition IV Gain Switch Gain J Multiplexed data IV Wait for devices ready Setup I PLL Laser Multiply I User signals I AQP with Digital Filters Setup I Ext synchronisation Sonde IV Mapping device Setup Setup Setup Setup Setup Result Spectrum IV Transient recorder IV Imaging device Correlation mode Save Settings Cancel Help Figure 5 Optic Setup and Service Dialog Box Setting up the Imaging Device Activate the Imaging Device check box as shown in figure 5 and click on the Setup button The Devices Options dialog box figure 6 opens This dialog box contains only those imaging devices that have already been set up If you want to set up a new imaging device click on the Add New Item button and enter a string with the following syntax number lt equal sign lt description of the imag ing device e g 1 Hyp3000MitFPA Note You can enter any number however take into consideration that each imaging device is assigned to an unambiguous number Choose a description of the imaging device that can be used as file name Imaging Device M 1 Hyp3000MitF PA M2 Raman Scope Format Deyices Options 4 x Cancel Item UP ltem DOWN Edit Item Add New Item Delete Item Resto
70. p surface is a square with a side length of about 1 7mm This is only 27 of the image in x direction and 36 in y direction and corresponds to 205 pixels in x and y direction A 5 IRscope The above description section A 3 applies to the IRscope I as well with the only exception that Mp is 15 Therefore the detector image projected on the CCD chip surface is a square with a side length of 5 6mm This is 90 of the image in x direction and 120 in y direction corresponding to 685 pixels in both directions i e the detector image in y direction is larger than the CCD chip To avoid the rectangle being larger than the video image the detector area the live video image is smaller than it actually is Bruker Optik GmbH OPUS VIDEO 79 A 6 Ramanscope The Raman detector collects scattered radiation from that part of the sample which is illuminated by the Raman laser The CCD chip of the video camera is also sensitive to Raman laser light Thus the illuminated circular area of the laser spot on the sample is visible in the video image at sufficient laser power Therefore no frame is used to mark the sample area in the live video image In case of Raman measurements the option Show Detector Size should be deacti vated 80 OPUS VIDEO Bruker Optik GmbH Index Numerics 3D file 5 37 58 61 65 66 68 69 3D mode 35 47 62 63 3D plot 5 35 66 3D window 65 3D window 65 66 A Add text annotation 46 Analog
71. r the supplement pcdig dll as it invokes the function library DII which is necessary for the FPA detector oper ation 5 2 2 Video Options The Video Options group field on the right side of the Setup for Imaging Device dialog box figure 7 contains a number of buttons Use these buttons to set up the options that are concerned with capturing video images Capture Device If you click on the Capture Device button the following dialog box opens 20 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device Select a Yideo Capture Device for Hyp3000Mit FPA x 01 073153 2 DT3131 Cancel _ 3 USB 2800 Video 4 Video to 1394 Converter 5 Infinity USB 2 0 Camera 6 DFK 31F03 Check Which Devices Exist Figure 15 Selecting a Video Capture Device This dialog box contains all available video capture devices The options DT3153 and DT3131 are frame grabber cards for analog cameras that OPUS supports The options for DirectShow compatible digital cameras are Infinity1 and US 2800 Video The options Video to 1394 Converter and DFK 31F03 can not yet used Click on the Check which Devices Exist button to check whether which of these cards is installed in your computer and works Existing cards are displayed in blue Video Input Channel If you click on the Video Input Channel button figure 7 the following dialog box opens Select ideo Input Channel for Hyp3000MitFPA x 1 S
72. ra that have been acquired at each measurement position and stored in the 3D file to a 3D plot In case the 3D file results from a spatial resolved measurement the physical units of the of the x axis and the z axis are length units e g micron or millimeter And the y axis shows the absorption intensity versus the space 7 3 3D Window The 3D window consists of four subwindows Each subwindow displays one plot type the xyz plot in the left upper subwindow the xz plot in the right upper window xy plot in the left lower subwindow and the zy plot in the right lower subwindow See figure 71 The size of the subwindow can be changed by moving the border lines with the pressed left mouse button Moreover you can define the 3D properties for each subwindow separately For detailed informa tion refer to the OPUS 3D Manual 66 OPUS VIDEO Bruker Optik GmbH Map Spec Window Rotation 70 Inclination 30 X 45948 63 K 45750 43 Z 24663 60 Z 24873 46 ZZ Sample 1 1 Index 0 Y No Y unit defined N w EEE EET 46000 45900 45800 45700 X Micron d 24600 24700 24800 Z Micron a 46000 45900 45800 45700 Micron Figure 71 3D Window 7 4 Map Spec Window 24900 25000 The Map Spec window consists of two subwindows a 3D window and a
73. rdware 5 5 Selecting Measurement Parameters Before starting a measurement you need to specify suitable measurement parameters in the Video assisted measurement dialog box figure 4 For more information on how to specify a parameter set refer to the OPUS Reference Manual To load an experiment parameter set click on the Basic tab Then click on the Load button and browse the directory to locate an appropriate parameter set 5 6 Offset Correction Ideally the focus of the IR beam should be identical to the center of the live video image If this is not the case you have to correct the offset To do this put a pinhole on the stage in sample position switch to the transmittance mode and align the pinhole with the center of the video image indicated by the cross hairs Focus on the pinhole Now move the pinhole slightly off center while monitoring the IR signal Make sure that the whole area in the vicinity of the pinhole center is covered Ideally the maximum IR signal should be observed when the pinhole is centered in the video image If the maximum IR signal is found at a pinhole position slightly off center this offset can be corrected auto matically Right click on the live video image window and select Setup Hard ware gt Define Detector Offset in the pop up menu Click on the Save button when the stage is positioned to yield the maximum IR signal Define dector offsef from center E Click to the position of the pinhol
74. re Factory Defaults Setup Figure 6 Device Options Dialog Box Selecting the Mapping Device 14 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device To set up an imaging device first click on the entry in question and then on the Setup button next to entry field The Setup for Imaging Device dialog box appears setup for Imaging Device Hypaooomierra x r Hyp3000Mit FRA Options m Video options Microscope Device A Available Objectives A Electronic Options A Optical Options A Motorized X Y Stage A Capture Device A Video Input Channel A Video Camera A Image Format A Image Options A FPA Device M Define useful settings fo Sources A Channels A Detectors A Beamsplitters A Cancel Help Set Scaling Factors to Defaults A Figure 7 Setup for Imaging Device Dialog Box All options and settings that have not yet been set up are indicated by a warning sign A next to the corresponding button A warning sign disappears after hav ing set up the corresponding option Before starting a measurement you have to set up all options and settings with a warning sign 5 2 1 Imaging Device Options Microscope Device If you click on the Microscope Device button figure 7 the following dialog box opens Select Available Microscope Device x 0 None _ 1 IRiscopel 2 Riscopell 3 RamanS cope 4 Hyperion1 000 5 Hyperion2
75. rement gt Stop Scan ning figure 47 Clicking again on Live Spectrum continues the acquisition To acquire a background spectrum proceed as follows e Move the stage to a sample free area and start the background mea surement by right clicking on the live or overview video image and selecting Starting Measurement gt Collect Background at Cur rent Position i e a background spectrum will be acquired at the cur rent stage position You can save that stage position for further background measurements by right clicking on the live or overview video image and selecting Defining Positions gt Background Position Note Make sure that the same aperture setting is used for both the sample mea surement and the background measurement e Ifyou have saved a stage position for the background measurement and you intend to acquire sample spectra at several measurement positions you can specify that a background spectrum is acquired at regular intervals To do this right click on the live or overview video image select Starting Measurement gt Change Measurement Parameters and define the number of sample measurements after which a background measurement is to be performed 6 4 4 Performing a Sample Measurement To acquire a sample spectrum proceed as follows e Move the stage back to the selected sample measurement position and start the data acquisition by right clicking on the live or overview video image and
76. rement position marker provided the Mouse Mode is set to No Action figure 53 You can also display several spectra at the same time by pressing the CTRL key while clicking on the corre sponding measurement position markers Apart from the spectra which have already been displayed you can see the ones you have just selected 58 OPUS VIDEO Bruker Optik GmbH Performing a Video assisted Measurement with 3D Mode 6 4 10 Exporting Images and Measurement Positions You can export the overview image to a file or to the clipboard To do this right click on the overview image select Export from the pop up menu figure 62 and specify where the overview image is to be exported to If you export the overview image to a file it will be saved in either JPEG format or BMP format depending on which check box you have activated in the Select an Image Format dialog box figure 22 You can also export the current measure ment positions They are saved in a XY file and can later be imported to repro duce a measurement Mouse Mode gt video Image gt Measurement Spots Grid Defining Positions Moving To Defined Positions gt Starting Measurement A Export Export Image to Clipboard Import gt Export Image to File Export Measurement Positions Delete Image processing Figure 62 Export Menu The list of measurement positions in the XY file is compatible with the OPUS MAP software
77. s installed STA00 ANS MSRhgfedcha e g STA00 ANS MSRO1001000 will be returned Each letter a to h represents one bit of the 8 bit response and has either the value 1 or 0 Digit Bit Value a 0 not in use b 1 not in use 2 1 IR d 3 1 VIS Bruker Optik GmbH OPUS VIDEO 7 Installing the Video Hardware Digit Bit Value e 4 1 VIS IR 1 MEAS button active 1 REFLECTANCE 1 TRANSMITTANCE NLD MN f g h 3 Enter MSR56 5 and press return The status of the illumination will be checked If the value MOT 120 is returned switch the spectrometer off and on again If the return value is still MOT 120 this indicates that the firmware has to be updated Note Always switch on the IRscope II and the Hyperion before you switch on the spectrometer Otherwise the automatic reading of the microscope settings will result in errors 4 3 Removing the Optical Camera Adapter IRscope Il and Hyperion only IRscope II and Hyperion systems are mainly used with an optical camera adapter between the microscope and the video camera to provide the same field of view for the camera and the binocular We recommend removing of this opti cal camera adapter if you intend to generate overview images because the illu mination of the video image decreases drastically towards the edges making it impossible to assemble an overview image with homogeneous illumination
78. scope e g Senterra the Video Setup dialog has in part different buttons See figure 41 In the following only those buttons are described that are exclusively relevant to a Raman microscope Video Setup Objective bia 7 Micron pixel LITZ 0 1133 w s E A Zero Auto X B dete e pa D es Calibrate Start activity ca Figure 41 Video Setup Dialog Box in case of a Raman Microscope Activates the Raman Mode Measurement Mode Activates the VIS Mode Switches off the Raman Laser berb 2 Switches on the Raman Laser 44 OPUS VIDEO Bruker Optik GmbH Functions of the Pop up Menu Item Mouse Mode 6 3 Functions of the Pop up Menu Item Mouse Mode Click with the left mouse button on either the live or the overview video image and select the Mouse Mode menu This menu contains the following func tions Mouse Mode AS No action Move to Click Mode Hardware Control Pan Mode ideo I GO b S Add Text Annotation Measurement Spots Grid Edit Measurement Positions amp Annotations Defining Positions A Measure Distances Moving To Defined Positions gt Starting Measurement Figure 42 Mouse Mode Control No action If you select this function no special mouse function is activated Move to Click Mode If you select this function the stage moves to any position that has been selected by positioning
79. stage movement Otherwise the resulting overview image assembled from snap shots will show discontinuities at the borders of adjacent image frames Assuming the x y sample stage is slightly tilted in relation to the camera the resulting overview image would look like the overview image in figure 78 Snapshot 3 Snapshot 2 Snapshot 1 Object of Interest Resulting Overview Image Figure 78 Overview Image resulting from a tilted Camera Orientation In this example the camera is tilted clockwise in relation to the stage Correct this misalignment by turning the camera counterclockwise Bruker Optik GmbH OPUS VIDEO 77 A 2 Image as received by the Detector The software allows to display a green rectangle in the live video image to visu alize that part of the image that is received by the detector Show detector size command from the pop up menu This size is determined by the geometry of the beampath CCD camera chip Object Image Ts Detector Image Magnifying element in the upper part of the scope maps intermediate image onto CCD chip magnification My Intermediate images 0f object and detector IR Detector 45 Mirror Magnifying element maps detector into intermediate EEE Objective Magnification Mg Magnification Mp Figure 79 Beampath of the Optics OPUS VIDEO Bruker Optik GmbH IRscope Il and Hyperion without Optical Camera Adapter
80. suc cessfully the following message appears Flatfield correctly initialized and saved Figure 65 Flatfield Correction Message The flatfield image is stored as a Bitmap file FLATFIELD BMP in the OPUS directory If you want to perform the flatfield correction later you have to load the flatfield image using the Load Flatfield Image function before starting the flatfield correction by selecting the Automatic Flatfield Correction function figure 64 Note If you look at the flatfield image using a graphics program you will see that the y axis is inverted This has no effect on the flatfield correction 6 4 14 Saving Data and Closing the Video Window When you close the video window all image data measurement position mark ers and annotations are stored automatically in the same 3D file i e the file used for this experiment which will be closed and is no longer accessible for saving additional data The 3D file automatically appears in the OPUS browser window and consists of up to three data blocks a 3D block containing all acquired spectra an image block GRAPH containing several images and an annotation block ANNO Both the image block and the annotation block are OPUS reports which can be displayed in a report window However it is more useful to view the images and the spectra in special OPUS windows See also section 7 After you have finished the video assisted measurement close the video win dow by clicking on th
81. surface similar to a regular measurement Bruker Optik GmbH OPUS VIDEO 5 Software Requirements 6 OPUS VIDEO Bruker Optik GmbH Display Settings 4 Installing the Video Hardware 4 1 Display Settings We recommend a display resolution of 800 x 600 SVGA or 1024 x 768 XGA pixels Set the color palette to the True color mode Other modes will only display a grey background instead of an image Problems may arise if the PC display controller does not support a color depth of 32 bit per pixel but for example only 24 bit per pixel as it sometimes occurs with controllers that are integrated into the motherboard In this case the framegrabbing will not work unless the PC is equipped with a separate display supporting a color depth of 32 bit per pixel Note It is not recommended to use screen savers during image acquisition as they may interfere with the video software 4 2 Firmware Check IRscope II amp Hyperion The OPUS VIDEO software tries to read the settings of the microscope front panel buttons and the illumination But this is only possible if the microscope operates with firmware version 1 5 or higher Otherwise the chip containing the firmware has to be updated Test the installed firmware version using the OPUS Direct Command Entry function 1 Select Direct Command Entry from the Measure menu 2 Enter MSR 4 and press return The status of the front panel buttons will be read If the proper firmware i
82. ten NIR Quartz z OPEN b E Front bd Eun KHz m Automatic ba Automatic b E Window in Points 200 Switch Gain Delay after Device Change Delay Before Measurement Figure 26 Video assisted measurement dialog box Optic page Set Scaling Factors to Default Do not forget to click on the Set Scaling Factors to Default button figure 7 if you have not yet specified the scaling factors for a new imaging device or if you have changed settings that have an influence on the projection of the video image on the CCD chip This is the case if you e select a new microscope e add new objectives e install remove the optical camera adapter or e select a new video camera Save Setup Only if you have clicked on the Save Setup button figure 7 the options you have set are stored permanently and are available for video assisted measure ments or measurements using an FPA detector Bruker Optik GmbH OPUS VIDEO 27 Configuring the Video Hardware 5 3 Selecting the Motorized Aperture Option The optional motorized knife edge aperture can be used in conjunction with the following microscopes IRscope II Hyperionl1000 Hyperion2000 and Hyperion3000 This kind of aperture is completely controlled by the OPUS VIDEO software package Before starting a measurement with the motorized knife edge aperture you need to activate this option before To do this select in the OPUS Measure menu the Optic Setup and S
83. tfield correction 8 60 61 Flatfield image 60 61 Flip image in x 25 Flip image in y 25 Fluorescence 18 39 41 Focus zero point 39 41 FPA detector 13 16 20 Frame grabber 3 Frame grabber board 1 Frame grabber card 4 21 22 42 Frame grabber driver 24 Frontpanel 17 40 G Green frame 36 37 H Histogram 39 42 I Illumination 8 38 39 40 47 60 Illumination correction 60 Image format 24 Image inversion 8 9 Image option 25 Image processing 60 Imaging device 9 12 13 14 15 16 27 28 4 Input channel 22 Interferogram 54 IR mode 4 41 IR VIS mode 4 18 41 ISA slot 3 J Joystick 30 40 JPEG 25 59 L LANG controller 3 11 19 30 31 32 Linear grid of measurement positions 55 74 Live image 1 Live spectrum 37 49 50 54 Live video image 3 37 38 41 43 44 45 47 50 51 71 78 Live video image window 36 37 40 45 54 55 56 58 59 LSTEP card 3 4 19 31 M Manual focus control 39 41 Map Spec window 67 Map Vid Spec window 68 Mapping device 11 Marking measurement positions 39 44 MCL 11 19 30 31 Measurement position 5 46 50 54 55 56 57 58 59 71 73 74 75 76 Measurement position marker 58 61 63 69 Measuring distances 46 Measuring marked positions 39 43 58 Motorized knife edge aperture 17 28 29 71 Motorized x y stage 17 19 Mouse mode 45 46 47 48 49 53 Move to Click mode 45 47 49 N NTSC standard 40 O Objective 16
84. the Select possible Options dialog box figure 10 in order to read the status of the front panel The left reflectance mode button figure 38 is only visible if you have activated the Reflection check box in the Select Available Optical Options dia log box figure 12 Illumination Control This feature is only available for the microscopes IRscope II and Hyperion The setting controls the brightness of the microscope light source and will regularly be updated according to the settings of the potentiometer wheel located on the microscope control panel 40 OPUS VIDEO Bruker Optik GmbH Window for video assisted Measurement Fluorescence ON Button This button is only available if you have selected this optical option when set ting up the imaging device See figure 12 Clicking on it moves the dichroic beamsplitter into the fluorescence position and switches the microscope into the VIS and the reflectance mode IR VIS Mode This feature is only available for the microscopes IRscope II and Hyperion pro vided that you have activated the JR VIS check box in the Select Available Opti cal Options dialog box figure 12 Switch between the IR VIS or IR VIS mode using these buttons Manual Focus Control Providing the microscope is equipped with a motor to control the focus and the Autofocus check box has been activated see figure 10 you can use the Manual Focus Control to change the z position of the sample in order to
85. the cursor on the video image and pressing the left mouse button The stage moves in such a way that afterwards the selected point of the video image is in the center of the live video image This applies to both the live video image window and the overview video image window Pan Mode If you select the Pan Mode function you can drag an image point in the video image window to a new position using the mouse Select an object you want to move press the left mouse button and move the mouse to the desired position Release the mouse button Now the stage moves to the position that corresponds to the position selected using the software in other words the stage moves to that position at which you have released the mouse button This applies to both the live video image window and the overview video image window Both modes can be deactivated by selecting No action or any other mouse mode If the stage does not move to the desired position the scaling factors for the selected objective may be inappropriate In this case you have to fine tune the scaling factors See section 6 2 1 If this measure does not solve the problem make sure that the optical configuration microscope type optical adapter objective default scaling factors etc is set correctly If these settings are OK the spindle factors of the x y sample stage may be set incorrect See section 5 4 In this case exit the video mode change the spindle factors by a factor of two and
86. to the right side of the microscope The X Position and Y Position counters indicate the current stage position You can manoeuvre the stage by entering a desired x and y position in the Move to fields and clicking on Move to Position button As soon as the stage has reached its new position the X Position and Y Position counters will be updated to show the new stage position In case the x y sample stage is controlled by a LSTEP card bear in mind that after each computer reboot the software forgets the current stage position because OPUS does not store it Therefore after each computer reboot do not forget to recalibrate the stage To do this click either in the Video assisted mea surement dialog window gt page XY Stage on the Calibrate Stage button figure 30 or in the Video Setup dialog box on the Calibrate button figure 38 5 4 2 Stage Setup To set up the x y sample stage select in the OPUS Measure menu the Optic Setup and Service function Click on the Devices Options tab activate the Map ping Device check box and click on the Setup button See also section 5 1 Select the corresponding mapping unit by clicking with the left mouse button on it As a result a Setup button appears next to the entry field When you click on this button a dialog box opens The definable parameters of the appearing dialog box depend on the selected mapping unit MCL Stage external LANG Controller Setup of MCL Stage E Stage mel S
87. trun window 52 69 VIS mode 4 41 44 X X spindle 32 x y sample stage 1 3 4 5 11 29 30 31 35 39 45 77 Y Y spindle 32 Z Z lowering 33 Z lowering delta 33
88. tself in a test image that is instable in vertical direc tion i e the image is running permanently Click on the Check button to change the video standard in the driver To do this however you need to have the access rights as administrator Image Format If you click on the Image Format button figure 7 the following dialog box opens Select an Image Format for Hyp3000MitFPA x 1 Bitmap Cancel Figure 22 Selecting the Image Format 24 OPUS VIDEO Bruker Optik GmbH Setting up the Imaging Device You can choose between two image formats Bitmap and JPEG 75 A bitmap picture is a decompressed image The bitmap format allows you to store images without quality loss The disadvantage of this format is however the fairly large size of the resulting file which requires a large storage space In contrast to the bitmap format the JPEG format uses a compression algorithm to minimize the resulting file size The default compression ratio of 75 represents an acceptable compromise between file compression and information loss Image Options If you click on the Image Options button figure 7 the following dialog box opens Select possible Image options for Hyp3000MitFPA x 1 5ave all frames M4 Play Sound during Image Capture Cancel Figure 23 Selecting Image Options If you activate the option Save all frames the overview images are stored decompressed i e each individual image
89. tton is equivalent to Video Image Snapshot function of the live video image pop up menu g Set Scan Overview Image Area Button Clicking on this button allows the assembly of an overview image consisting of several snapshots of adjacent regions The effect of this button is equivalent to Video Image ee Set Scan Overview Image Area function of the pop up menu Ms Measure Marked Position Button Clicking on this button starts the measurement at all measurement positions defined so far The effect of this button is equivalent to Starting Measurement gt Measure Marked Positions function of the pop up menu Bruker Optik GmbH OPUS VIDEO 43 Video assisted Measurement BG Collect Background at Current Position Button Clicking on this button acquires a background spectrum at the current measure ment position The effect of this button is equivalent to Starting Measurement Collect Background at current Position function of the pop up menu Mark Measurement Positions Button Clicking on this button changes the mouse mode in such a way that clicking on a certain position in either the live video image or the overview image marks this position as to be measured The effect of this button is equivalent to Mea surement Spots Grid gt Mark Measurement Positions function of the live video image pop up menu 6 2 2 Video Setup Dialog for Raman Microscopes In case of a Raman micro
90. uker Optik GmbH XIY Stage Setup of Parameters LSTEP Stage x Stage LStepStage Units 0 degin 1 mm O micron x Range fo 200000 Units Y Range jo 200000 Units Parameters for Z movement in case of ATR mapping Z Lowering 2500 Z Lowering Delta 250 Save settings Restore defaults Cancel Save Settings Cancel Help Figure 32 Setup of a LStep Stage The parameters Units X Range and Y Range are already described in detail in the above section The parameters Z Lowering and Z Lowering Delta are only relevant to mapping measurements with ATR objective In case of this kind of measurement the stage movement in z direction is exclusively controlled by the OPUS software in order to prevent an ATR crystal damage A manual stage movement in z direction is not possible in this case It is recommended to use the displayed default parameter values CANBUS Controller In Parameter setup for CAN stepper motors dialog window figure 33 you specify the type of stage xy or xyz the numbers of the internal motors the microns per step and the maximum number of steps the motor is to perform Parameter setup for CAN stepper motors al x Motor number Microns per step Mas limit in steps 40 ig 25 3600 n fe 25 2400 xY Stage C xY Z Stage C X Stage R Phi Stage Cancel Figure 33 Setup of a CANBUS Controller Dialog Box Bruker Optik GmbH OPUS VIDEO 33 Configuring the Video Ha
91. use button and drag the cursor to the desired last measurement position As soon as you release the left mouse button a straight line appears the actual dis tance between starting and end point in micron is displayed in the video image and a dialog box opens prompting you to enter the total number of measurement positions including the coordinates x and y of the first measurement position Number of Measurement Positions E Start position X microns 48001 9 Start position microns fi 7324 1 Delta microns fi 53 298 Cancel Figure 56 Defining a Linear Grid Setting the Number of Measurement Positions After you have clicked on the OK button the line will be divided equally by the number of measurement positions you have entered in the corresponding field The measurement positions are marked both in the live video image window and in the overview video image window as shown in figure 57 Bruker Optik GmbH OPUS VIDEO 55 Video assisted Measurement 9900 10000 10100 10200 10300 DA Ld H 8 8 VEER 8 WE g E 3 Peer te eea Imagef4 ei d Stage X 10000 Y 10000 Cursor X 9565 Y 10025 Ready Figure 57 Resulting Linear Grid Rectangular Grid of Measurement Positions To define a rectangular grid of measurement positions select in the pop up menu Measurement Spots Grid gt Define Rectangular Grid and draw a frame using the cursor Then a dialog box figure 58 opens prompting you to ent
92. ve to Saved Stage 2 Position if available Existing Options are shown in blue color Figure 28 Imaging Device with Motorized Aperture Option If the motorized aperture is not found the reasons may be the fact that either the motor table in the spectrometer electronics needs to be updated or that the motorized knife edge aperture is not properly installed In case of doubt switching off the spectrometer for a short time with the microscope switched on may solve the problem Once the Motorized Aperture option is activated and found by the spectrometer electronics you can use this aperture in conjunction with the OPUS VIDEO software 5 4 X Y Stage 5 4 1 Checking the operational Reliability of the Stage This dialog window allows you to control the x y sample stage If you set up the instrument for the first time it is advisable to check whether the x y stage oper ates correctly Bruker Optik GmbH OPUS VIDEO 29 Configuring the Video Hardware ideo assisted measurement J xj H Basic E Advanced Optic Acquisition FT Display Background XY Stage Check Signal STEPStage Activate joystick Pd Zt b Stage status OK X Position 0 Move to 4 Micron Y Position 0 Move to Micron Z Position 0 Move to 4 Micron Move to Position Exit Cancel Help Figure 29 Video Assisted Measurement Dialog Box XY Stage Page If you have an external LANG controller connected to your x y
93. y click ing with the right mouse button on it and selecting Aperture Change Aperture from the pop up menu figure 78 Remove Remove All Change Color a Show Aperture l v Show All Apertures Change Aperture Set This Aperture to Last Selected Aperture Set All Apertures to Selected Aperture Figure 78 Aperture Menu After selecting the aperture there are small white squares on the red rectangle indicating that the aperture size position and rotation angle can now be changed interactively Positioning the mouse cursor on the corners of the aperture rectan gle the cursor shape switches to a curved arrow see figure 79 indicating that the rotation angle can be changed by dragging the corner to a new position If you position the mouse cursor on a white square that is located on median of the red rectangle the cursor changes to a double arrow indicating that the aperture size can be changed rator Manipulate Evaluate Display Print Macro Validation Setup Help 8 gt EEE BOR ZZ EANTA E EIET ET EEEE d HOE X Scale Micron pixel XY 0 2311 0 2311 Illumination u a Fluorescence ON Focus E E KK geX 461 2477 30212 x Position x GSE b Gb p 4 pen Aperture C Offsets Calibrate e000 zego erro 4500 e a Image p A Stage X 46124 Y 30212 Cursor X 45968 Y 30244 Figure 79 Changing

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