EN_OPUS 6.0 FPA.book
Contents
1. Bad Pixels For a detailed description of this pop up menu item refer to chapter 4 section 4 2 2 Detector Regions For a detailed description of this pop up menu item refer to chapter 4 section 4 2 2 5 3 Non video assisted Step Scan Measurement using FPA Detector This measurement is not a video assisted measurement i e the video mode interface window does not appear For information about step scan measure ments refer to the OPUS STEP Manual Bruker Optik GmbH OPUS FPA 33 Step Scan Measurement using FPA Detector 5 4 Displaying the Measurement Results For displaying the results of a measurement using the FPA detector the soft ware package OPUS 3D is required Immediately after the measurement you can display the results in an 3D window At that time however the spectra are displayed versus the pixel number and not as intensity over the detector surface because during the measurement no trace has been generated that assigns an intensity value to each pixel Therefore the measurement result does not yet contain a trace block After the measurement you have to generate such a trace block using one of the OPUS Evaluate functions e g integration quantitative analysis identity test factorization To display the intensity over detector sur face drag and drop the trace block and not the AB or TR block into the 3D window For more information refer to the OPUS 3D Manual 34 OPUS FPA Bruker Optik GmbH I2. OPUS Spectroscopy Software User Manual FPA 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 JOU LATE 1 Hardware Requirements cece ccc reece cece cee eeee 3 3 Configuring the Hardware cece ccc e cece cece eeeees 5 3 1 Setting up the Transient Recorder 2 0 cece c eee ene 5 3 2 Setting up the Imaging Device ar EAEE ceed ed EK ZEREA GEO Zbk 6 3 3 Setting up th Velocity dea aaa EE E E Paai 9 4 Continuous Scan Measurements using FPA Detector 11 4 1 Measurement Parameters a Ee e gaik e a ER ei de cape eed s 11 4 2 Video assisted
3. Setting up the FPA Detector When you select in the pop up menu the function Setup FPA Detector gt Show Control Panel two dialog boxes appear the Spectrometer dialog box and the FPA Detector Setup dialog box figure 33 The FPA Detector Setup dialog box is already described in detail in chapter 4 section 4 1 Measurement MEE Setup FPA Detector Show Control Panel Move Scanner to Maximum IR Intensity Find Settings automatically Setup FPA Image A Bad Pixels Detector regions x Optimize Frame rate Hz 3773 584961 Y Integration msec Guz ie Enable Offset Gain ae ae Syne None b Start Acquisition Superframe J Y r Direct command 3 bedi Line delay fed HOB A D delay e A Barg Send GA Detector bias _ er a AK Pixel number 4096 Reset Date of Evacuation Figure 33 Dialog Boxes Spectrometer and FPA Detector Setup The Spectrometer dialog box allows you to change the mirror position interac tively When you click on the Max button the mirror moves automatically to the position at which the interferogram has maximum signal intensity The same effect is achieved by selecting in the pop up menu the function Setup FPA Detector gt Move Scanner to Maximum IR Intensity With this mirror position you can now set up the FPA detector signal in the best possible way using the FPA Detector Setup dialog box 32
4. ment An advantage of this detector type is the extremely short measurement time when analyzing sample surfaces Normally a measurement using the FPA detector takes only a few seconds With the software package OPUS FPA you can perform both continuous scan measurements as well step scan measurements using the FPA detector In case you want to create and save video images as well the software package OPUS VIDEO is required For the control of the computer controlled x y stage you need the software package OPUS MAP To display and evaluate the mea surement data the software package OPUS 3D is necessary Bruker Optik GmbH OPUS FPA Introduction 2 OPUS FPA Bruker Optik GmbH Hardware Requirements Computer System For measurements using the FPA detector at least one free PCI slot for the FPA frame grabber card and a RS232 port are necessary In addition video assisted measurements require either a PCI video frame grabber card or a digital camera that is connected to a firewire IEEE 1394 or USB interface In case you work with a computer controlled x y stage you need also an external LANG control ler that is connected to a RS232 interface or the internal LSTEP board that requires a long PCI slot For measurements with a continuous scanner movement continuous scan mea surements there has to be an electrical connection between the optics and the FPA detector to synchronize the digitalization of the IR images with the scan
5. OPUS FPA Bruker Optik GmbH Non video assisted Step Scan Measurement using FPA Detector Clicking on the buttons lt or gt the mirror moves to the beginning or end of the interferogram To change the mirror position gradually click on the buttons lt and or gt The current mirror position is displayed in the field between these two buttons To start the measurement click on the Start Acquisition button The Direct command field is intended for entering and sending commands e g MOT commands for controlling certain mirrors to the optics For this kind of measurement the Optimize button in the FPA Detector Setup dialog box is available This button allows you to optimize the FPA detector parameter settings automatically in such a way that the dynamic range of the A D converter is used in the best possible way without cutting off the upper or lower signal intensity values This function works properly only with the slower detectors SBFJ108 The purpose of a manual or automatic optimization is to set the parameters Frame Rate Integration Offset and Gain in such a way that in the IR mode the signal intensity values are not above 15 of the maximum value 16383 in the oscilloscope window and in the VIS mode the signal intensity values do not fall below 10 of the maximum value 16383 in the oscilloscope window Setting up the FPA Image For a detailed description of this pop up menu item refer to chapter 4 section 4 2 2
6. continuous Scan Measurement using FPA Detector 15 4 2 1 Video Mode a ue EA 15 4 2 2 Pop up Menu of the Live FPA Image 04 17 4 3 Background Measurement using FPA Detector u z 26 4 4 Continuous Scan Measurement using FPA Detector 26 4 5 Kinetic Measurement using FPA Detector u z 26 4 6 Displaying the Measurement Results a z 27 5 Step Scan Measurement using FPA Detector 29 5 1 Measurement Parameters 0 gera E dare es Ek iE dran pe 29 5 2 Video assisted step scan Measurement using FPA Detector 31 5 2 1 Video Mode Interface e EE dagai sagt cain gee ee E dE 31 5 2 2 Pop up Menu of the Live FPA Image u z 31 5 3 Non video assisted Step Scan Measurement using FPA Detector 33 5 4 Displaying the Measurement Results a a 34 iii iv 1 Introduction The software package OPUS FPA allows data acquisition using the microscope HYPERION 3000 or the external sample chamber IMAC in conjunction with an optional FPA detector Focal Plane Array Detector The FPA detector is a multi element detector i e the detector consists of a matrix with 64 x 64 or 128 x 128 detector elements Similar to the CCD chip of a video camera the detector elements lie equidistant in a plane In contrast to a single element detector e g MCT detector the FPA detector can acquire data simultaneously at as many points as the detector has elements pixel with one single measure
7. continuous scan measure ment 15 VIS mode 14 33
8. refer to the OPUS Reference Manual For a detailed description of the XY Stage page see OPUS VIDEO Manual Basic Select in the Imaging device drop down list the option you have set up before as described in chapter 3 A field with a yellow background indicates that the FPA detector has to be evacuated as soon as possible For information about evacuating the FPA detector refer to the HYPERION User Manual Bruker Optik GmbH OPUS FPA 11 Continuous Scan Measurements using FPA Detector FT Select in the Phase Correction mode drop down list either the option Power No Peak Search or Mertz No Peak Search to prevent that the interferogram maxi mum peak is searched for every interferogram separately Otherwise in case of weak signal the peak position of several interferograms may be found too far away from the desired position As a consequence of this the spectra will be incompatible and the spectra calculation will be canceled Optic For devices which communicate with the PC using an acquisition processor AQP you have to define a variable velocity To do this you have to set up a variable velocity beforehand See chapter 3 section 3 3 Select in the Velocity drop down list the option Variable Hz and enter the desired velocity in Hz in the field that appears on the right of the drop down list See figure 10 This value is the effective scanner velocity at a bandwidth of 7900cm Scanner velocity Variable Hz
9. 3773 584961 v Integration msec foose7s0 ei Enable Offset Gan JEE Sync None gt pees Supertrame la gt Line delay _ rss EZ A D del Zita ZE Detector bias _ hres ok Cancel Pixel number 4036 Reset Date of Evacuation Figure 12 FPA Detector Setup Frame Rate The frame rate Hz is the velocity with which the images are read out from the detector For the FPA detector SBFJ108 applies the following The smaller the frame rate value is the more signal is detected by each detector element However do not enter a too small frame rate value as this leads to a detector overload See figure 14 For transmission measurements enter a frame rate value of 252 or 315Hz and for reflection measurements use a frame rate of 180 or 210Hz For the FPA detector SBF161 applies the following Select the maximum possi ble frame rate value 3773Hz and change the integration value correspond ingly Integration In case of FPA detector SBFJ108 of which the integration time is a fixed per centage of the frame rate you can only change the frame rate value in order to optimize the signal intensity In this case the ntegration drop down list is grayed FPA detectors SBF161 for which the frame rate and the integration time can be changed independently from each other select the highest possible frame rate value 3773Hz and change only the integration value in such a way that the signal inten
10. Detector Regions All pixels with intensity values that are within the limits specified by you are displayed in the maximum color in our example in white see figure 29 When you click on the OK button the program assumes your limit values calcu lates the number of contiguous regions of which the intensity values are within the specified limits in our example 2 contiguous regions and determines to which region a pixel belongs The result is stored in a text file with the name lt Detector gt rgn with lt Detector gt being the transient recorder you have set up as described in chapter 3 The text file contains a table with four columns Region Row no of the pixel Column no of the continuous no of the pixel interferogram spectrum l 29 16 1053 1 30 16 1054 2 30 27 1758 The first column indicates the region to which a pixel belongs The second and the third column contain the row number and the column number of the pixel detector element in the detector matrix The numbering begins with 0 0 in the lower left corner of the matrix and ends with 63 63 in the upper right cor ner This table can be used for example by a script or macro to calculate an average spectrum on the basis of all spectra belonging to a certain region Bruker Optik GmbH OPUS FPA 25 Continuous Scan Measurements using FPA Detector 4 3 Background Measurement using FPA Detector To start the background measurement directly click on the St
11. is described in detail in section 4 1 Measurement Parameters Setting up the FPA Image To change the color display of the live FPA image select in the pop up menu the function Setup FPA Image Show FPA Image as Bruker Optik GmbH OPUS FPA 21 Continuous Scan Measurements using FPA Detector Setup FPA Image A Show EEA Image as gt Scale to data Min Max Bad Pixels Detector regions A Measurement A 120C Setup FPA Detector gt Grayscale Inverted Grayscale False Color RGB v False Color Palette Oscilloscope Figure 24 Pop up Menu Item Setup FPA Image By default the live FPA image is shown as false color palette i e minimum signal intensity values black maximum signal intensity values white interme diate signal intensity values colored The other display options are shown in the following figures 25a and b as well as 26a and b Figure 25 a Grayscale b inverted Grayscale FPA Scale x 16000 14000 12000 10000 8000 6000 4000 2000 0 Figure 26 a False Color RGB b Oscilloscope 465x348 e Grayscale The signal intensity values are assigned to gray tones between black minimum intensity value and white maximum intensity value Inverted Grayscale The signal intensity values are assigned to gray tones between black maximum intensity value and white minimum intensity value e False Color R
12. number of the measurement that is to be displayed and scrolling through the individual mea surements For more information refer to the OPUS 3D Manual Bruker Optik GmbH OPUS FPA 27 Continuous Scan Measurements using FPA Detector 28 OPUS FPA Bruker Optik GmbH Measurement Parameters Step Scan Measurement using FPA Detector Step scan measurements using a FPA detector can only be performed with a step scan capable optical bench that communicates with the PC via an acquisi tion processor AQP Otherwise the following message appears This function is not supported for this optical bench Select in the Measure menu the FPA Step Scan function As a result the fol lowing dialog window opens FPA Step Scan Measurement xj H Basic Recorder Setup Advanced Optic H Acquisition ZU XY Stage Experiment Load HYPERION FPA GLOBAR XPM Operator name Administrator Sample name HYPERION FPA Sample form GLOBARTRANSMISSION Path C MANWESDEMO BIOMED HYPERION FPA File name HYPERIONFPA Imaging device Hyperion3000 ba Objective fis SIE X Start FPA Step Scan Measurement Exit Cancel Help Figure 30 FPA Step Scan Measurement Basic 5 1 Measurement Parameters Most pages of this dialog window Basic Advanced Optic Acquisition and FT are identical to a great extend to the corresponding pages of Advanced Measure ment dialog window For information about these measurement para
13. option Power should only be selected in case of a double sided acquisition mode XY Stage For information about the XY Stage page refer to the OPUS VIDEO Manual 5 2 Video assisted step scan Measurement using FPA Detector 5 2 1 Video Mode Interface When you click in the FPA Step Scan Measurement dialog window page Basic on the Start Video Assisted Step Scan FPA Measurement button figure 30 the video mode interface appears The video mode interface consists of three subwindows live video image window overview video image window and FPA image window and the Video Set dialog box See figure 15 Layout and operation of this video mode interface are identical to the video mode inter face of video assisted continuous scan measurements For more information refer to chapter 4 section 4 2 1 5 2 2 Pop up Menu of the Live FPA Image Right clicking on the FPA image opens a pop up menu that differs only slightly from corresponding pop up menu for video assisted continuous scan measure ments Therefore this section restricts only to the description of the differences For detailed information about the identical pop up menu functions refer to chapter 4 section 4 2 2 Bruker Optik GmbH OPUS FPA 31 Step Scan Measurement using FPA Detector Starting the Measurement To start a measurement select in the pop up menu the function Measurement gt Start FPA Measurement As a result the measurement starts immedi ately
14. the live video image and select in the pop up menu the function Hardware control Hardware Parameters For detailed information about the Video Setup dialog box refer to the OPUS VIDEO Manual 16 OPUS FPA Bruker Optik GmbH Video assisted continuous Scan Measurement using FPA Detector The live video image window b displays the video image in real time as recorded by the camera Normally the live video image is used to specify mea surement positions and to define sample areas for generating an overview video image consisting of several individual images For more information about generating an overview image refer to the OPUS VIDEO Manual The video image window f is intended for the overview video image Initially the over view video image window is black In the live video image window there is a red frame e indicating that part of the live video image which will be used to assemble the overview video image This frame can be resized interactively The green frame d indicates that part of the sample which is detected by the detector The cross hairs c 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 in the pop up menu the function Video Image and deselecting the option Overlay Detector Size or Overlay Crosshair Depending on whether you right click on the live vi
15. the option None In this mode the images are generated in an asynchronous manner 1 e not synchronous with the interferogram scanning During the measurement the synchronization mode is changed automatically by program so that the images are generated synchronously with the data acquisition The default settings of the parameters Line delay A D delay and Detector bias need not to be changed because the detector manufacturer has already set mean ingful values for these parameters The Reset Date of Evacuation button is used to mark the date of the last detector evacuation Click on this button after you have evacuated the FPA detector For information about evacuating the detector refer to the HYPERION User Manual As a result of this the yellow background of the drop down list Imag ing Device on the Basic page disappears Note A yellow background of the drop down list Imaging Device indicates that the default maximum hold time of the detector vacuum 48 days has been exceeded and the FPA detector needs to been evacuated as soon as possible 4 2 Video assisted continuous Scan Mea surement using FPA Detector 4 2 1 Video Mode Interface When you click in the Continuous Scan FPA Measurement dialog window page Basic on the Start Video Assisted Continuous Scan FPA Measurement button the following video mode interface appears The video mode interface consists of three subwindows See the following figure Bruker Optik GmbH OPUS F
16. A Motorized Y Stage A Image Options A EEA Device m Define Useful Settings fo Sources A Channels A Detect Set Scaling Factors to Defaults A bee d Beamsplitters A ms w Figure 5 Dialog Box Setup for Imaging Device 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 the setup of an option has been completed Before starting a measurement you have to set up all options and settings with a warning sign For more informa tion about setting up the imaging device refer to the OPUS VIDEO Manual As you want to perform a measurement using a FPA detector you have to select this detector To do this click on the FPA Device button See figure 5 The following dialog box opens Select FPA Device x e 7 FPA pedig dll Cancel Figure 6 Selecting the FPA Detector Select the FPA detector in question and click on the OK button 8 OPUS FPA Bruker Optik GmbH Setting up the Velocity 3 3 Setting up the Velocity For devices which communicate with the PC using an acquisition processor AQP you have to set up a variable velocity i e that also other than the pre defined velocities can be specified before the measurement is started provided your device is capable of step scan measurements To do this select in the Measure menu the Optic Setup and Service function a
17. GB The signal intensity values are displayed as fol lows minimum intensity value blue intermediate intensity values green maximum intensity value red 22 OPUS FPA Bruker Optik GmbH Video assisted continuous Scan Measurement using FPA Detector e Oscilloscope This option displays the minimum signal intensity value of a column in the detector element matrix in blue and the maximum signal intensity in red It allows you to find out extreme intensity values very quickly As an alternative to the pop up menu you can switch between the individual display options by double clicking on the FPA Scale Selecting the function Scale to data min max figure 24 adapts the color scale to the existing dynamic range in the FPA image with the result that maximum intensity values are displayed in the maximum color e g red in case of the display option False Color RGB and minimum intensity values in the mini mum color e g blue in case of the display option False Color RGB Alterna tively you can adapt the color scale to the signal intensity in the FPA image by double clicking on the live FPA image And you can change the assignment of the color scale to an intensity region interactively by moving the triangular slid ers in FPA Scale box using the mouse Bad Pixels Every FPA detector has some bad detector elements pixels of which the sig nal deviates from the other pixels regarding offset noise and gain E
18. PA 15 Continuous Scan Measurements using FPA Detector a b c JU e f Print Macro Validation Setup Hdp hh hb ZE Q A SESZ b GSR d 0 EJ M eaa Manipulate Evaluate Dispi sce IEE ark Micron pixel X Y 0 2311 0 2311 f rator Illumination rr s4 S Fluorescence ce ON For cus r us E Jo z MIS Zero Auto Bright contr color Fry FS activity Calibrate Start activity ce ES ZZ KE KE 0 2 h i JA k Figure 15 Video Mode Interface a Video Setup dialog box hardware control panel b Live video image window c Cross hairs d Green frame indicating the area detected by the detector e Red frame indicating the used CCD area f Overview video image window g Online help button h Image selection drop down list for the Overview video image window i Live FPA image window j Pop up menu of the live FPA image k Color intensity scale for the live FPA image When you activate the video mode interface figure 15 the Video Setup dialog box a appears automatically in the upper corner on the left Use this dialog box to define among other things the measurement mode and set the illumination the brightness the contrast and the color To close this dialog box click on the X button in the upper right corner of the dialog box If you want to open the Video Setup dialog box once again right click on
19. SIIS Hz Figure 10 Specifying a variable Scanner Velocity Values smaller than 100 cause an error status that is indicated by a red back ground of the entry field and the error message Velocity should be bigger than 100 The error message appears when you position the cursor on the red entry field Note The reason why the lower limit value has been set to 100 is the unstable control of the scanner movement with smaller scanner velocity values Scanner velocity Variable Hz D BE DS Figure 11 Scanner Velocity Value is too small Also the allowable maximum scanner velocity value has been limited it has to be smaller than 80 of the specified frame rate of the FPA detector Otherwise an error status is displayed as well by a red background of the entry field and an error message Check Signal The Check Signal page of the Continuous Scan FPA Measurement dialog win dow differs significantly from corresponding page of the Measurement dialog window 12 OPUS FPA Bruker Optik GmbH Measurement Parameters In the oscilloscope display the intensity values of all pixels i e detector ele ments of the FPA detector are displayed versus the pixel number See figure 12 This kind of display allows you to recognize immediately pixels with a too high signal intensity You can set the signal level optimally by chang ing the parameters Frame Rate Offset and Gain See figure 13a FPA Detector Setup Frame rate Hz
20. art FPA Back ground Measurement button in the Continuous Scan FPA Measurement dialog window on the Basic page figure 9 After the sample measurement the acquired background spectrum is used for the calculation of the result spectra e g transmissions spectra absorptions spectra or reflection spectra This measurement is not a video assisted measurement i e the video mode interface window does not appear 4 4 Continuous Scan Measurement using FPA Detector To start the sample measurement directly click on the Start FPA Measurement button in the Continuous Scan FPA Measurement dialog window on the Basic page figure 9 In case a background spectrum has been acquired before the result spectra e g transmission spectra absorption spectra or reflection spectra can be calculated after the completion of the sample measurement This is done by dividing the sample spectra by the background spectrum Note that the back ground measurement and the sample measurement have to be performed using the same measurement parameters except the parameter Scan Time This mea surement is not a video assisted measurement i e the video mode interface window does not appear 4 5 Kinetic Measurement using FPA Detector When you click on the Start Kinetic FPA Measurement button in the Continu ous Scan FPA Measurement dialog window on the Basic page figure 9 N individual measurements are started with N being the number of scans you have specifie
21. considerably high data rate If the data are read out at the FPA detector with 80 of the maximum frame rate as usual the data rate is 23 6 MByte sec in case of a FPA detector with 64 x 64 pixel and a maximum frame rate of 3773 Hz or 40 25 MByte sec in case of a FPA detector with 128 x 128 pixel and a maximum frame rate of 1610 Hz See the following table Pixel number off Frame Rate Bytes Frame Data Rate FPA detectors Hz KByte MByte sec 64 x 64 0 8 x 3773 8 23 6 128 x 128 0 8 x 1610 32 40 25 To ensure these data rates without frame loss during a continuous measurement the computer ought not to perform other operations than acquiring data More over the data acquisition ought not to be interfered by other programs and ser vices or mouse or keyboard inputs To ensure an undisturbed data acquisition make sure that the following conditions are fulfilled e The computer ought not to be integrated into a LAN e No additional software programs ought to be installed on the com puter e Close all services that are not required e During data acquisition do not press any mouse key or keyboard but ton In case of continuous scan measurements using the FPA detector the FPA images are digitized collected and accumulated between two mirror positions This reduces the measurement time considerably but at the same time it makes high demands on the PC because a continuous minimum data transfer rate has t
22. d In this measurement mode the specified number of scans is not used for averaging in order to reduce the noise The acquired individual spectra are arranged one after the other in a 3D file This measurement mode is suitable for the analysis of samples that change during the measurement e g chemical reac tions This measurement is not a video assisted measurement i e the video mode interface window does not appear 26 OPUS FPA Bruker Optik GmbH Displaying the Measurement Results 4 6 Displaying the Measurement Results For displaying the results of a measurement using the FPA detector the soft ware package OPUS 3D is required Immediately after the measurement you can display the results in an 3D window At that time however the spectra are displayed versus the pixel number and not as intensity over the detector surface because during the measurement no trace has been generated that assigns an intensity value to each pixel Therefore the measurement result does not yet contain a trace block After the measurement you have to generate such a trace block using one of the OPUS Evaluate functions e g integration quantitative analysis identity test factorization To display the intensity over detector sur face drag and drop the trace block and not the AB or TR block into the 3D window In case the trace block is the result of a kinetic measurement there is an additional combo box in the 3D window allowing to select the
23. deo image or the overview video image two slightly different pop up menus appear Their functions are described in detail in the OPUS VIDEO Manual At the bottom of the main window there is a help button g providing informa tion about the OPUS software The Jmage drop down list h contains all video images acquired so far and shows which of the images is currently displayed 4 2 2 Pop up Menu of the Live FPA Image When you right click on the live FPA image the following pop up menu figure 16 appears Measurement Start Measurement Setup FPA Detector Setup FPA Image A Bad Pixels gt Detector regions A Figure 16 Pop up Menu Item Measurement Starting a Measurement To start a measurement select in the pop up menu the function Measurement gt Start Measurement As a result the following dialog box appears Bruker Optik GmbH OPUS FPA 17 Continuous Scan Measurements using FPA Detector xi Background MAP Sample J Pixel binning Direct command ee Send Figure 17 Measure Dialog Box This dialog box allows you to start either a background measurement a sample measurement or a mapping sample measurement When you activate the Pixel Binning check box 2 x 2 4 x 4 and so on neighboring pixels can be put together to one big pixel This measure reduces the image noise and the result file size however it also worsens the image resolution The Direct command fi
24. ector with 64 x 64 detector elements for example pixel 0 0 is in the left lower corner and pixel 63 63 in the right upper corner Bruker Optik GmbH OPUS FPA 23 Continuous Scan Measurements using FPA Detector Clear list of bad pixels Clears all entries in the list of bad pixels Save list of bad pixels Saves the list containing the position of the bad pixels and activates the pixel correction Correct bad pixels Activates or deactivates the automatic pixel correction Detector Regions This menu item allows the automatic recognition of contiguous regions in the live FPA image of which the intensity values do not exceed or fall below the defined limit values If a sample has regions with different intensities for exam ple the concentric rings becoming weaker outwards as shown in figure 28 you can define an upper and a lower limit value To do this select in the pop up menu the function Detector regions Define new regions Measurement A ZO 501x353 Setup FPA Detector gt Setup FPA Image b Bad Pixels A Show saved regions Figure 28 Pop up Menu Item Detector Regions As aresult the following dialog box appears 24 OPUS FPA Bruker Optik GmbH Video assisted continuous Scan Measurement using FPA Detector Define Detector regions x Select all pixels larger than threshold H 4854 r Select all pixels smaller than threshold Cancel 50x535 Figure 29 Define
25. ed step scan measurements for example deselect all entries beginning with PAD First click on OK button and then on the Save Setting button in the Optic Setup and Service dialog window figure 1 3 2 Setting up the Imaging Device The imaging device is the combination of the available optics microscope IMAC the capture device video frame grabber with analog or digital camera the x y stage and the FPA frame grabber card To set up the imaging device select in the Measure menu the Optic Setup and Service function and click on the Devices Options tab Activate the Imaging Device check box and click on the Setup button See figure 3 6 OPUS FPA Bruker Optik GmbH Setting up the Imaging Device IV High Pass Filter Setup IV Imaging device Setup IV Low Pass Filter Setup ES Correlation mode Setup Setup Result Spectrum x Optical Bench Devices Options Interferometer AQP Export Options Service Optic Communication V Source Setup IV Use login operator name J Beamsplitter Setup I Automatic Accessory Recognition V Optical filter Setup I Gain Switch Gain b Aperture Setup I Multiplexed data I Iris aperture IV Wait for devices ready Setup T Polarizer setup J PLL Laser Multiply b Channel Setup I User signals I Sample changer Setup I AGP with Digital Filters IV Detector Setup IV Ext synchronisation Sonde Setup b Preamplifier gain Setup T Mapping device Setup b Velocity Setup I Trans
26. eld is intended for entering commands e g MOT commands for controlling certain mirrors and sending them to the optics Clicking on the Background button opens the following dialog box x Start Measurement Cancel Figure 18 Background Dialog Box This dialog box allows you to optimize the FPA parameter settings to start a background measurement or to return to the previous dialog box figure 17 by clicking on the corresponding button If data blocks like Transmission or Absorption are to be generated during the measurement you first have to perform a background measurement Note that the background measurement and the following sample measurement have to be performed with the same FPA parameter settings This applies especially for the parameter Pixel Binning 18 OPUS FPA Bruker Optik GmbH Video assisted continuous Scan Measurement using FPA Detector Clicking on the Optimize button opens the following dialog box HR xi Manual or automatic optimization Automatic Cancel Figure 19 Optimize Dialog Box This dialog box allows either a manual or an automatic optimization of the FPA parameter settings In case of an automatic optimization several test measure ments are performed with a low resolution The results of these test measure ments are used to determine the optimal FPA parameter values In case of a manual optimization the FPA Detector Setup dialog box figure 12 appears in wh
27. f the result data block transmission or absorption are done automatically after the measurement Note To display the generated 3D file you first have to close the video mode interface For information about displaying manipulating and evaluating the spectra of a 3D file refer to the OPUS 3D Manual When you click on the MAP Sample button in Measure dialog box figure 17 the following dialog box appears x Map positions in X Y E a Optimize Start Measurement Automatic gain offset selection BG before each a sample Figure 21 MAP Sample Dialog Box This dialog box allows you to perform several measurements in succession mapping measurement and to assemble the acquired spectra to a 3D image provided your microscope is equipped with a computer controlled sample stage Define the measurement positions by entering the desired number of individual measurements in x and y direction The result is a rectangular measurement grid with the actual stage position being the lower left measurements position in the grid The complete grid of measurement positions is displayed in the over view video image window provided you have defined a sufficiently large over view video image and can be shifted belatedly Like in case of individual measurements it is recommended to perform the background and the sample measurements with the same FPA parameter set tings i e not to optimize these settings once again But also in th
28. field the number of measurements that are to be performed and averaged at each mirror position Note that the higher this value is the less the noise and the longer the measurement time become We rec ommend a value between 10 and 50 A higher value e g higher than 100 does not improve the signal to noise ratio significantly any more because step scan measurements are sensitive to vibration Therefore repeat the measurement several times instead of using a high coadd count value 30 OPUS FPA Bruker Optik GmbH Video assisted step scan Measurement using FPA Detector The Stabilization Delay after Stepping is a wait time of the system allowing the mirror to stabilize after it has moved to a new position Enter a value between ca 10 and 20ms Acquisition In case of step scan measurements select in the Acquisition mode drop down list only the option Single sided or Double sided and do not select the options Single Sided Forward Backward or Double Sided Forward Backward FT Select in the Phase Correction mode drop down list either the option Power No Peak Search or Mertz No Peak Search to prevent that the interferogram maxi mum peak is searched for each interferogram separately Otherwise in case of a weak signal the peak position of several interferograms may be found too far away from the desired position As a consequence of this the spectra will be incompatible and the spectra calculation will be canceled Note that the
29. gnal intensity is closing the aperture in such a way that only 50 of the light impinges on the detector elements Set the parameter values Gain and Offset in such a way that the signal intensity values are not above 15 of the maximum value 16383 in oscilloscope window and not below 15 of the minimum value 0 In this case you need not switch between the IR and the VIS mode xj x 16383 16383 Pare rate H2 Frame rate Hz 3773 584961 3773 584961 Integration msec Integration msec 0 104750 E 0 104750 E b Enable TZ Enable Offset Gain Offset Gain al b eite GE ZE H See 8192 Sync None gt 8192 Sync None z E Superframe A v Superframe A e P D Line delay Line delay Li m ro mo A D delay A D delay _ pae 6 a Detector bias Detector bias p SA EE dE bedezi IEE 0 Cancel 0 Cancel Pixel number 4096 a Pixel number 4096 Figure 13 a Optimal Signal Intensity b IR beam does not impinge on the Detector VIS 14 OPUS FPA Bruker Optik GmbH Video assisted continuous Scan Measurement using FPA Detector FPA Detector Setup x Frame rate Hz 203 977570 E Integration msec z IV Enable Offset Gain ep Syne None Superframe Ja gt Line delay x EEE 8192 Detector es b E OK Cancel Pixel number 4036 Reset Date of Evacuation Figure 14 Signal in case of Detector Overload Select in the drop down list Sync synchronization
30. he variable Velocity Bruker Optik GmbH OPUS FPA 9 Configuring the Hardware If the list already includes an entry for a variable velocity 1 Variable Hz select it Otherwise you have to add such an entry by clicking on the Add new item button and selecting it afterward For devices that are connected to the PC via Ethernet you need not to set up a variable velocity 10 OPUS FPA Bruker Optik GmbH Measurement Parameters Continuous Scan Measure ments using FPA Detector Select in the Measure menu the Continuous Scan FPA Measurement function As aresult the corresponding dialog window opens See figure 9 Continuous Scan FPA Measurement E x Advanced Optic PU Acquisition FT XY Stage Check Signal Experiment Load HYPERION FPA GLOBAR XPM Operator name Administrator Sample name HYPERION FPA Sample form GLOBARTRANSMISSION Path C 4NWE DEMO BIOMED HYPERION FPA File name HYPERIONFPA Imaging device Hyperion3000 E Objective 15 x IR X Start Video Assisted Continuous Scan FPA Measurement Start FPA Background Measurement Start FPA Measurement Start Kinetic EEA Measurement Figure 9 Continuous Scan FPA Measurement Basic 4 1 Measurement Parameters Most pages of this dialog window Advanced Optic Acquisition and FT are identical to a great extend to the corresponding pages of Advanced Measure ment dialog window For information about these measurement parameters
31. ich you can enter the desired parameters manually See section 4 1 Mea surement Parameters When you click in the Measure dialog box figure 17 on the Sample button you can either first optimize the FPA parameter settings or start the sample measurement See the following figure Sareko x Start Measurement Cancel e Automatic gain offset selection Figure 20 Dialog Box Sample If the already acquired background spectrum is to be used for the calculation of transmission spectra or absorption spectra it is advisable not to optimize the FPA parameter settings once again In this case the background measurement and the sample measurement have to be performed using the same parameter settings especially the same frame rate value An exception are the uncritical parameters Gain and Offset These parameters can be optimized automatically once again by activating the Automatic gain offset selection check box It is use ful to optimize these parameters at this point as normally the signal with sample sample measurement is usually smaller than the signal without sample back ground measurement Bruker Optik GmbH OPUS FPA 19 Continuous Scan Measurements using FPA Detector To start the actual sample measurement click on the Start Measurement button During the measurement the live video image is faded out and after measure ment it is faded in again If desired the spectra calculation and the generation o
32. ient recorder Setup se e Save Settings Cancel Help Figure 3 Setting up the Imaging Device The Devices Options dialog box figure 4 appears This dialog box contains all imaging devices you have set up so far If you want to set up a new imaging device click on the Add new item button and enter a character string having the following syntax number lt equals sign lt description of the imaging device e g 1 Hyp3000mitFPA Note You can enter any number you like However make sure that a number is assigned only to one imaging device in the list When you define a description of the imaging device take into consideration that this description can be used as file name x Imaging device HYP3000mitFPA Setup _ RamanScope Cancel ltem UP Item DOWN Edit Item Add New Item Delete Item Restore Factory Defaults Figure 4 Dialog Box Devices Options Imaging Device To set up an imaging device first click on the entry in question and then on the Setup button next to the entry field See figure 4 The Setup for Imaging Device dialog box appears Bruker Optik GmbH OPUS FPA 7 Configuring the Hardware Setup for Imaging Device HypSOOOMRFPA x m Hyp3000MitFP4 Options Video Options Microscope Device AN Capture Device A Available Objectives Id Video Input Channel Id Electronic Options Ay Video Camera A Optical Options A Image Format
33. is case the uncritical parameter settings Gain and Offset can be optimized automatically once again before the sample measurement Optionally a new background spectrum can be acquired at each measurement position This option however doubles the measurement time During the measurement the live video image is faded out and you can observe in the live video image window the progress of the mapping measurement Measurement positions that have already been measured are displayed in green 20 OPUS FPA Bruker Optik GmbH Video assisted continuous Scan Measurement using FPA Detector The measurement position in process is displayed in yellow and the still unproc essed positions are gray See the following figure After the completion of the measurement close the video mode interface Unprocessed Measure ment Positions Measurement Position in Progress Processed Measure ment Positions Figure 22 Mapping Measurement in Progress Setting up the FPA Detector To set the FPA detector parameters manually select in the pop up menu the function Setup FPA Detector Show Control Panel Measurement gt SSS e d E Setup FPA Detector Show Control Panel Moye Scanner to Maximum IR Intensity Setup FPA Image JA Find Settings automatically Bad Pixels Detector regions Figure 23 Pop up Menu Item Setup FPA Detector As a result the FPA Detector Setup dialog box figure 12 appears This dialog box
34. ital Filters IV Detector Setup IV Ext synchronisation Sonde Setup IV Preamplifier gain Setup I Mapping device setup IV Velocity Setup IV Transient recorder Setup IV High Pass Filter Setup E Imaging device Setup b Low Pass Filter Setup Correlation mode setup Setup Result Spectrum Save Settings Cancel Help Figure 1 Setting up the Transient Recorder The dialog window Devices Options figure 2 opens Click on the Add new item button and enter for example 8 F PA pcdig dll You can define any num ber you like however the number e g 8 at the beginning of the row should occur only once in the list And you can specify also any name you like e g FPA1 However the supplement in brackets pcdig dll is of crucial impor tance as it invokes the function library that is necessary for the FPA detector operation In case the supplement in brackets is misspelled the program library for FPA frame grabber can not be found The supplement is not case sensitive Bruker Optik GmbH OPUS FPA 5 Configuring the Hardware x Transient recorder ESTO bed M3 PAD82 M4 PAD1232a Item UP MS5 PAD1232b ME P D1232c Item DOWN MO intemal ADC M8 FPA1 prod Edit Item Add New ltem Delete Item Restore Factory Defaults Figure 2 Setting up the Transient Recorder It is recommended to select only those transient recorders which the PC is actu ally equipped with If there are no PAD boards available for time resolv
35. meters refer to the OPUS Reference Manual Bruker Optik GmbH OPUS FPA 29 Step Scan Measurement using FPA Detector Basic Select in the Jmaging device drop down list the option you have set up before as described in chapter 3 A field with a yellow background indicates that the FPA detector has to be evacuated as soon as possible For information about evacuating the FPA detector refer to the HYPERION User Manual Recorder Setup FPA Step Scan Measurement x E Basic Recorder Setup Advanced Optic E Acquisition FT xy Stage Device FPA po Sampling Repetition coadd count 1 Experiment Stabilization delay after stepping 40 ms Figure 31 FPA Step Scan Measurement Recorder Setup Enter in the field Device the transient recorder FPA detector you have set up before as described in section 3 1 As the software attempts to initialize the FPA detector the FPA frame grabber card has to be installed and connected already to the switched on detector When you click on the Setup button next to the field the FPA Detector Setup dialog box appears See figure 12 This dialog box allows you to set the FPA detector signal in such a way that the dynamic range of the A D converter is used in the best possible way without cutting off the upper or lower signal inten sity values For more information refer to chapter 4 section 4 1 subsection Check Signal Enter in the Repetition coadd count
36. nd click on the Devices Options tab Activate the Velocity check box and click on the Setup button See figure 7 b Velocity Setup I Transient recorder Setup I High Pass Filter Setup IT Imaging device Setup b Low Pass Filter Setup Correlation mode Setup Setup Result Spectrum x Optical Bench Devices Options Interferometer AOP Export Options Service Optic Communication V Source Setup IV Use login operator name I Beamsplitter Setup JT Automatic Accessory Recognition IV Optical filter Setup I Gain Switch Gain IV Aperture Setup J7 Multiplexed data I Iris aperture IV Wait for devices ready Setup T Polarizer Setup I PLL Laser Multiply IV Channel Setup I User signals I Sample changer Setup J AGP with Digital Filters IV Detector Setup IV Ext synchronisation Sonde Setup IV Preamplifier gain Setup I Mapping device Setup EEE e e Save Settings Cancel Help Figure 7 Setting up the Velocity As a result the following dialog box opens xi e W 1 Variable Hz 1 1 2 2 KHz bed v dedi 3 0 KHz edi 4 0 KHz Item UP dd 5 0 KHz 5 5 7 5 KHz ltem DOWN EE 10 0 KHz bd dei 20 0 KHz ETE Ee 40 0 KHz MIS 9 60 0 KHz Add New Item 10 10 80 0 KHz 11 11 100 0 KHz Delete Item 12 12 130 0 KHz 13 13 140 0 KHz 14 14 150 0 KHz i Restore Factory Defaults Figure 8 Selecting t
37. ndex Numerics 3D image 20 3D window 27 34 A A D delay 15 Acquisition processor 9 12 29 B Background measurement 18 26 Background spectrum 19 20 26 Bad offset pixel 23 Bad pixel 23 33 Band width 3 C Computer controlled x y stage 1 3 Continuous scan measurement 4 11 26 D Data rate 4 Detector bias 15 Detector element 1 13 23 25 Detector evacuation 15 Detector matrix 25 Detector region 24 33 F False color palette 22 False color RGB 22 FPA detector 3 5 8 11 12 13 15 21 23 30 32 FPA frame grabber card 3 5 6 30 FPA image 4 23 33 Frame rate 4 12 13 33 G Gain 14 19 20 23 33 Grayscale 22 I Imaging device 6 7 11 Integration 33 Integration time 13 Interferogram 12 15 25 31 32 33 Inverted grayscale 22 IR mode 14 33 K Kinetic measurement 26 L LANG controller 3 Line delay 15 Live FPA image 17 21 24 31 Live FPA image window 16 Live video image 20 Live video image window 16 17 20 LSTEP board 3 M Mapping measurement 20 N Noise 23 O Offset 14 19 20 23 33 Oscilloscope 23 Overview video image 17 Overview video image window 16 20 P Pixel binning 18 R RAM storage capacity 3 Resolution 3 S Signal intensity 13 14 22 30 32 33 Step scan measurement 4 9 29 31 33 T Trace block 27 Transient recorder 5 6 25 30 V Variable velocity 9 10 12 Video mode interface 15 16 26 31 Video assisted
38. ner movement In case of accumulating measurements all raw data are buffered and averaged in the RAM so that they need not read in again from the hard disk after the mea surement This involves a considerable saving of time During this kind of mea surement a huge amount of data is generated which needs to be buffered in the RAM In the following table the required RAM storage capacity depending on the pixel number the resolution and the band width is listed The listed values hold true for the acquisition mode Double Sided Forward Backward Sagi do Resolution em Band Width cmt Ea Sie capacity 64 x 64 2 15800 1792 64 x 64 2 7900 903 64 x 64 2 3950 460 64 x 64 4 3950 240 128 x 128 2 1580 7167 128 x 128 E 7900 3614 128 x 128 2 3950 1838 128 x 128 4 3950 950 A logical conclusion drawn from this fact is that the PC should be equipped with a RAM having the highest possible storage capacity But without addi tional provisions Windows however can at most manage only a memory address space of 2 GByte So a RAM storage capacity of 2 GByte is a reason able upper limit In the above table the cases marked by an asterisk can be real ized with a 2 GByte RAM Bruker Optik GmbH OPUS FPA 3 Hardware Requirements In case of kinetic measurements the generated raw data are not buffered and averaged in the RAM but they are written on the hard disk in real time This implies a
39. o be ensured Especially the newer FPA detectors are suitable for continuous scan measurements as they allow frame rates of several KHz Optics Step scan measurements using a FPA detector require a spectrometer that is equipped with the step scan option In case of this measurement mode each mirror position is approached separately to accumulate and read out the images of the FPA detector This measurement mode does not make high demands on the clock frequency which however leads to longer measurement times 4 OPUS FPA Bruker Optik GmbH Setting up the Transient Recorder Configuring the Hardware 3 1 Setting up the Transient Recorder After the installation of the FPA frame grabber card in the PC you have to setup this card in OPUS under Transient recorder To do this select in the Mea sure menu the function Optic Setup and Service The dialog box Optic Setup and Service opens Click on the Devices Options tab Activate the Transient recorder check box figure 1 and click on the Setup button x Optical Bench Devices Options Interferometer AQP Export Options Service Optic Communication Source Setup b Use login operator name J Beamsplitter Setup I Automatic Accessory Recognition IV Optical filter Setup I Gain Switch Gain IV Aperture Setup I Multiplexed data I Iris aperture IV Wait for devices ready Setup Polarizer Setup I PLL Laser Multiply IV Channel Setup I User signals J Sample changer setup I AQP with Dig
40. sity is sufficient but neither the upper nor the lower signal values are cut off Bruker Optik GmbH OPUS FPA 13 Continuous Scan Measurements using FPA Detector Offset The parameter Offset is used to shift the signal in y direction The Offset value is set optimally when the signal intensity is as high as possible with no sample in the optical path in case of background measurement and when the signal intensity is as low as possible with an interrupted IR beam e g by switching to the VIS mode or by placing an IR nontransparent material in the optical path Gain If the signal intensity is not sufficient after increasing the integration time you can amplify the signal using the parameter Gain Note however that in case of a too high signal amplification the noise increases to the same degree Ensure that the detector is not overloaded In the IR mode the signal intensity values should not be above 50 of the maximum value 16383 in oscilloscope window In the VIS mode the signal intensity values should not fall below 10 of the maximum value 16383 in the oscilloscope window Note In case of step scan measurements in the IR mode the signal intensity val ues should not be above 15 of the maximum value 16383 in the oscilloscope window and in the VIS mode the signal intensity values should not fall below 10 of the maximum value 16383 in the oscilloscope window Another possibility of optimizing the si
41. specially bad offset pixels i e pixels of which the signal is too low or too high are easily discernible in the live FPA image You can mark these pixels interactively by clicking on them using the mouse To do this select in the pop up menu the function Bad Pixels gt Mark bad pixels with mouse Measurement Setup FPA Detector gt Setup FPA Image Clear list of bad pixels Save list of bad pixels v Correct bad pixels Detector regions Figure 27 Pop up Menu Item Bad Pixels As a result the marked pixels are displayed in the maximum color of the cor responding display option See description above Then the intensities values of these marked pixels are not used but substituted by the values of intact neigh boring pixels This however leads to a reduction of the spatial resolution in the area of these pixels but only the elimination of extreme intensity values makes a meaningful display and evaluation of the measurement data possible Note The positions of the bad pixels are stored in a file in the OPUS directory with the name FPA_ lt serialnumber gt bad with lt serialnumber gt being the serial number of the FPA detector The text file includes the row and column position of the bad pixels and can be edited using a text editor if required The numbering of the positions is done from the left to the right column and from the lower to the upper row beginning with zero In case of a FPA det
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