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1. MA A B DRO mx minm e mE RO mx BEEN d ed E 73 Digital Bool este 3 m s 3 ict i pe i Pc ict x ic de S Be e vee x n USAS SEI RA GARA DAI AA DAA AA AANA LADD AAA AAA ALAS AAA AAA AA AA ALIA AA AAA AA AA AA AA AA AA AA AAAS ADIDAS E Dev ijportojineti FI a 3 nit for read a digital channel Pin 52 on Dag card onnect to s 2 The idea is use two Read Digital Channel modules to start and stop the timer These modules read digital signals from sync 1 and sync 2 When the scanning begins syncl turns to high and the case loop executes the clock outside the while loop is fixed and the clock inside the while loop counts until the scanning 1s finished which means sync 2 turns to high After the while loop has executed the program subtracts the inner clock with the outer clock to obtain the time difference To get the time in seconds it is necessary to divide by 1000 because the values from the clocks are in milliseconds A global Stop VI 1s used to stop the other while loop in counting pulses module so they can be synchronized with each other The principle of the program Read Digital Channel 1s shown in the figure on next page 19 Boolean Data Read OK message warnings Y Lines DAC mx DAG mx one channel for all lines Y zz gt Digital Input hd Digital 1D Bool 1Chan 1Samp E status stop E ES m This program reads a digital signal from a line s and returns the v2. 0 to 39 999 Depending where the cursor is this part of the program will take only the values which the cursor lays on the ntensity Graph currently and cut of all other values The intensity usually has a large dynamic range so it is necessary to make it visible on the graph the solution is to let the y axis be 20 larger than the largest value and 20 smaller than smallest value 54 50 45 Amplitude n 25 20 14 4 gi I I l I I I I I I I I 5500 5510 5520 5530 5540 5550 5560 5570 5580 5590 5599 Time XY Graph Plot 0 i 26 5 3 Buffered Counter at 1 spot When the user examines the image there ought to be one spot which the user wants to examine closer After the laser has moved to this point with DeltaSlewXY command the user can run this program to see how the intensity is changed during a time interval This will be intensity over time I t Figure below shows how the program is implemented ed True v we iin semana sea 1000 Init for generates pulses e values at the same poin digital channel sync 1 H DAG mx esl Dev i portO line15 v ele Digital Bool iLine 1Point Ho JRO mx Dev 1 ctrO E AE C 8 timeout 20 00 OK message warning Init for the counting ounter 1D U32 NSamp ultiple of taos at 1 point E This program is very similar to Buffered Counter with small differences it needs only to count the number of pulses during a time interval and
3. 100 ticks and it will be 100 of x per a line then the total time is 100 x 100 10 000 ticks and it is below 30 000 ticks So far so good The problem is when the user want to have 400 v 500 x or 600 c the total time will be in example 100 x 400 2 40 000 ticks and it exceed the limit of 30 000 ticks The technique is to split the scanning into 2 parts look at the picture below Start Stop End Ot From Start to Stop is 20 000 ticks and it is less than 30 000 ticks so it s ok after the laser reached Stop it will immediately go to End point and it will take 20 000 ticks By doing this way it will not be any conflict with the limitation of SC 2000 This technique will work up to 60 000 ticks if the user wants to scan with a total time of 70 000 ticks then it will not work and the user must change some parameter because 70 000 2 35 000 which exceed the limit 70 000 3 23333 3 and SC 2000 cannot handle decimal numbers 5 2 Buffered Counter This program is the biggest and the most important part of this project it contains several modules which together will perform the following steps 1 Estimate how much time it will take to perform a page scan 2 Calculate the time that has elapsed for a page scan It will show the time when scanning 1s finished 3 Count number of pulses from the detector during a specific interval and plot number of pulses on an Intensity Graph image Each dot on the Intensity Graph
4. V 2 000 h 000k F start Hz Time s Time s T 3 Plot 9 Vbias stop V 12 000 1 000k Fstop Hz 1 600 gt Vbias points Er cst 5 F points 1 800 sd Measurement Partene m d Plot 1 maximum voltage 4 000 _ 2000 E e E 3 2 000 P Plot 3 i o m Measurement xs i A zu e 9007 i Plot 4 Fit Plot 3 Vosc V 0 050 scan delay ms 2600 START MESSUREMENT mi STOP save slopes moa per Lennon d number of averaging j TI I 1 1 1 Plot 4 x ct 0 0 500 0 1000 0 1500 0 2000 0 F 1 1000 0 1500 0 2000 0 Plot 5 Time s Time s I9 in 5 1 Capacity F Plot 6 Measurement pe T T pe faul our OOE O fe g pH me en N a 23 I Capacitance desired inflection point 5 7n 2 400 2 600 1 1 1 1 f da dr di V bias V 2 800 BA EE TE ET EE Et TD varprraapirragp ras prar npr tr erar qu ws y bias UE CURT SE and 10 0 TETTERE ER Dos pos 0 044 p 044 Exc Front panel Controls can be push buttons knobs switches or other input device Indicators can be graphs LEDs and other output displays The connector pane is used when the programmer wants to use a VI as a sub VI it is here the programmer defines input and output of the subVI It correspondes to parameters when calling a function in textbased programming A subVI corresponds to a subroutine 3 3 Confocal Microscope Before explaining how a confocal microscope works
5. allows one to visualize deep into cells and tissues By having the pinhole the microscope is able to eliminate out of focus light which gives it much better resolution The best thing is it can build up a very clean 3 D image by using the pinhole to eliminate out of focus light 4 Materials 4 1 Overview Confocal microscope s main parts are laser photodetector objective lens and mirrors When scanning over an area only the mirrors move and the rest of the microscope are fixed The mirrors are mounted on a board called SC2000 Digital Scan Controller from GSI Lumonics this SC2000 can be programmed in order to control the mirrors movement When a photon hits the photodetector a short TTL pulse is generated from the photodetector and we need to count the number of pulses coming from the detector This can be done with a Data Acquisition card DAQ card which has a built in counter 4 2 SC 2000 Digital Scan Controller 4 2 1 System Overview The Scan Controller is a small intelligent system that is used to control GSI Lumonics SAX family of scanner servo amplifiers and associated equipment It can work in either a stand alone configuration or it can work together with a host computer Below are the basic components of a complete system 1 One or two axes of SAX Galvo micropositioning 2 One SC2000 Scan Controller 3 Cabling 4 Power Supply 5 A host computer for setup and optionally for operation including software 6 O
6. corresponds to a spot on the sample 4 Generate a command which moves the laser to a particular point on the sample that the user wants to examine closer This command is called DeltaSlewXY and is a string in Labview which the user can copy and paste in the Command Line Interface 5 Save the result as a binary file 6 Change the intensity with cursors and see how the intensity 1s changed along the x axis and y axis 18 Implementation of these tasks in Labview 1 To estimate how much time it will take for a page scan it 1s not enough to sum all the time in the assembler program other time parameters must be considered for example a delay caused by software commands or delay from the galvo response The delay from the software command is 315usec and the delay from the galvo response 1s 250usec The table below shows the estimated values and the simulating value for 100x100 200x200 and 300x300 points respectively Number of points Theoretical values Simulated value 100x100 30 sec 30 sec 200x200 107 sec 106 sec 300x300 230 sec 229 sec The theoretical values are values that were calculated with respect to the delays and laser movement before scanning The simulated values are the time from the beginning to the end of scanning 2 When the scanning is complete it is interesting to know how much time has elapsed The implementation of this task 1s showed in the figure below OK message warnings Y Ol Moy Error
7. 007 to May 2008 at Chemical Physics Lund University I would like to thank my supervisors Tomas Jansson at Electrical Measurement and Ivan Scheblykin at Chemical Physics for their help and guidance The reason for me having this project was I found LabView programming was fun and when this project came up I thought this 1s the chance to enter deeply into LabView Lund May 2008 Giang Vu 3 Introduction 3 1 Background and purpose In the Chemical Physics department the use of fluorescence technique is very common and it uses as a part of this confocal microscope This kind of microscope gives several advantages over a traditional microscope for example it is able to reproduce a 3 D image This department has bought a confocal microscope with software enclosed and what they needed was a program for computer control of the microscope and the data acquisition which will be discussed later The requirement of this project was to develop software that can manage the whole operation from scanning to analysing data The software for both the microscope and the DAQ card was implemented in Labview 3 2 LabView LabView Laboratory Virtual Instrumentation Engineering Workbench is a graphical programming language from National Instruments When programming in Labview the user place symbols and wire them together instead of typing in text as traditional programming language like C Java Visual Basic etc Therefore it is easier to program even for
8. 8100 or 50079 8000 pins Mates with GSI supplied J6 serial cable Temp Gnd Temp Y J3 sync 1 out sync 2 out 2 Temp Y connector sync 3 out sync 4 out Sync GND sync 5 in E sync in Mate with sync in 8 Molex 51021 0800 shell sync8 in Q Molex 50079 8100 or 50079 8000 pins Sax X Axis sync cal 9 in i sync cal 10 in sync cal ll in J8 sync cal 12 in i X FBPOS X PFBPOS SERVO RDY SERVO ENB t TEMP OK t GND Command Command lt hJ 02 4 ODS CO FBPOS PFBPOS SERVO_RDY SERVO_ENB Sync Cal connector Y Command Y Command Mates with Mate with Molex 51021 1500 shell Molex 51021 0800 shell Molex 50079 8100 or 50079 8000 pins Molex 50079 8100 or 50079 8000 pins h 60 amp Cn NO Figure 3 4 2 2 Command Line Interface The Command Line Interface software is provided together with Scan Controller the software was programmed in LabView environment It allows users to communicate with the Scan Controller quickly and easily It is used primarily as an environment for designing and programming as stand alone application and for system evaluation Command Line Interface is easy to use for understanding of functionality and capabilities of Scan Controller Once the functionality and limitations of the Scan Controller are understood it is much easier for the user to do the programming Figure 4 shows Command Line Interface software gt Command line interface prod
9. I would like to go through some principles which together build up the microscope 3 3 1 Fluorescence Florescence is a process where a substance sends out light with a different wavelength than the light it absorbed earlier For example if you shine blue light on some molecules it will cause the electrons of the molecules to jump to a higher energy state top black line in the picture Some of the energy is lost internally maybe in form of heat representing squiggly red arrow When the electrons jump back to the ground state the molecule emits green light that contains lower energy than blue light ab fork high Cut y phos Cm it lower dob y luhn ground 1a te One of the advantages of flourescence for microscopy is that you can attach the dye molecules to your sample and therefore only that part of the sample can be seen by the microscope 3 3 2 The pinhole Picture below shows how the lens focus light from a focal point to another point the light is represented by a blue line The red line 1s light from other point than the focal point but still get imaged by the lens of microscope at Fen eiv f A Screen p vi Ql Jr pin hol e MS IN d y The idea with the pinhole is to block light that 1s not from focal point Normally the excitation light illuminates whole sample so the entire sample is fluorescing at the same time If we build up an 1mage with light from all points at the same time th
10. O mx p Ste Fa al E zs ss zw Idle State CO Pulse Freq Implicit 7 1321 status IO 0 00 EE i LJ The figure below shows how the initial state of the counter has implemented as a sub VI It contains the necessary parts like Duplicate Count Prevention and addresses of Source and Gate Continuous Samples Y Low Frequency with 1 Counter Y Counter s a HN DAQ mx B lt D AQmx CI ds TX rs Ps E LER Dev 1 PFI32 v e dock ample cock amp DeviPFISS Pin 9 on DAO card timebase counter Source Pin 2 on DAO card 4 23 Now we have all the parts to make this counter program to work The figure below shows how the program was made 1000 e tao in time 2 31325E 5 Ip gt triggering time ticks 4 m i DAUMX IA mx JAG mx am 55 Mela IHT 2 zv A A A ee T pE Init for read a digital channel sync 1 i Pin 22 on Daq card DAG mx gui m I Dev iportOfine15 er igi Hs Dev 1 ctrO LN 1 ount on pin 2 on DAQ W Tnm AV e first value in the vector is to short that s why program delete the first value This is the main part of the Buffered Counter program When sync 1 turns to high the case loop and the for loop will execute and the counter VI counts the number of pulses coming from the Source It returns all the values as an array but since the first value 1s not correct it must be deleted from the array In order to p
11. The first result of the measurement is not an accurate representation because it is a measure of the number of edges of the SOURCE signal between the beginning of the measurement and the first rising edge of the GATE Therefore the first value is unreliable and should be discarded The figure below shows a three period measurement but only the last two are correct the first value can be removed easily in the LabView program 20 Counter Armed I I GATE Li LI Lj gt LALA AL ALAA AL SOURCE MN E 1 h3 NE Counter Value 3 1 2 3 1 1 2 i Buffer discard 3 2 discard 3 2 lidiscarnd E z E Duplicate Count When a Source signal is slow or non periodic and there is not a single pulse during a period of the Gate then no value will be inserted in the buffer This situation is duplicate counting This kind of behaviour is not desirable in this project because the counter is expected to count the number of pulses coming from the Source in each period of Gate no matter how many pulses there are even there are no pulses In other word if there are no pulses the buffer should register number zero Duplicate Count Duplicate Count Prevention Duplicate Count Prevention is used in buffered counter applications like measuring frequency or period It is necessary to use when the application has slow or non periodic signals as it ensures the right values are inserted in the buffer Normally t
12. al source is 20 MHz or less To enable duplicate count prevention in NI DAQmx you can set the channel property node to Enable Duplicate Count Prevention b Programming Active Channels v Measurement I O Analog Input b Analog Output b Digital Input gt Digital Output gt b b b L DAQmx Data Acquisition ome y Counter Input Counter Output General Properties Pulse Width Two Edge Separation Semi Period J General Properties D Channel Node Counter Timebase gt PJ J More b Count Output State Timing Node Triggering Node Read Node Terminal Count Reached 77 gt Counter Timebase Master Timebase Divisor VA I v Advanced gt Data Transfer and Memory gt Write Node DAQ Assist Real Time gt i gt gt J Duplicate Count Prevention ied Se Prescaler S Nass Dev Config Task Config ctrl Advanced Placea DAQmx Channel Property Node and select Counter Input General Properties gt More gt Advanced gt Duplicate Count Prevention as shown in Figure above 22 When implementing this counter task the GATE will be software timed which means a pulse train will be sent to the GATE and the counter will count the number of rising edges that occur on SOURCE between each pair of active edges of GATE Figure below shows the principle of how to send a pulse train to a specific address Frequency Wait for the user to press the stop button DELH L OS Counter s DAG mx DAG mx DRO mx DR
13. alue in boolean format Note that all Read Digital Channel has been made as a subVI to save space Note that when a Start Task VI after Digital Input 1s used a Clear Task VI must also be used to stop the task 1f necessary and to release any resources the task reserved In this case Clear Task VI 1s placed after the while loop 3 This part of Buffered Counter 1s constructing a program which counts the number of pulses in a specific time interval and plots it in an ntensity Graph so that every point x y on the sample corresponds to a dot on the Intensity Graph image The image 1s the intensity over coordinates I x y First several important ideas will be explained so the reader can understand why the program was implemented in this way Property Node gets reads and or sets write properties of a reference Below are some examples of Property Nodes The DAQmx System Property Node can return the available devices tasks or channels on the current computer The DAQmx Device Property Node can return device settings like bus type or serial number The DAQmx Channel Property Node can be used to read or writes properties of a channel Buffered Period Measurement is a technique that measures the number of periods in a specific time interval between rising or falling edges of a pulse Each time the GATE input becomes high the counter begins to counts number of periods on the SOURCE input and the values are inserted in the buffer
14. an optical imaging technique that has high resolution and can be used to detect individual fluorescing molecules It is commonly used in biology medicine and materials research A confocal microscope system contains scanning mirrors objective lens laser and detector The laser beam is directed by 2 scanning mirrors and it will be focused by an objective lens onto the sample and the emitted fluorescent light is collected by a photodetector In order to obtain an 1mage of the sample the laser beam 1s scanned along the x y axis and the intensity 1s function of the coordinate I x y When a photon hits the photodetector a short TTL pulse 1s generated In order to obtain light intensity we need to know the number of photons TTL pulses over a fixed time interval for example 10 ms This has been realized with a National Instruments Data Acquisition DAQ card model NI 6602 which contains 8 high frequency counters This master thesis 1s about developing a LabView software to control the scanning and the DAQ card It is divided into four different programs the first for controlling the mirrors the second is for plotting the intensity on a graph and save the data in a binary file the third is for counting the number of pulses on one specific spot and the last is for analysing data 2 Acknowledgements This master thesis is the last part of my education to Master of Science in Electrical Engineering This project has been performed from October 2
15. are 100 values in 1 D array then the size is 100 8 800 bytes 1f the matrix is 100x100 then the size is 10 000 8 80 000 bytes The conclusion is the matrix size is much larger than D array In case that the file is a matrix and is represented as 1 D array then a For loop Shift Register and Build Array will be used to convert this array to matrix and then plot it on ntensity Graph as it did Buffered Counter If the file is a 1D array then it is easy to plot on a XY graph 28 6 Results and Discussion The result was functioning programs which meets all the requirements the simulations gave expected behaviours and values The hardest thing was synchronizing the scanning and the counting because the number of time intervals on a line could exceed the maximum time allowed in SC2000 but fortunately this problem could be solved in software After running Buffered Counter and a matrix was saved then the Read Binary File program was opened to read that matrix the pictures from the Intensity Graph and XY Graph from both programs look identical which means the programs work as they should Since the program for controlling the mirrors was implemented in assembler code and the rest in LabView the use of programs for entire operation from scanning to analysing data was a somewhat lengthy procedure because these programs are used separately After this project I have learned much more about Labview since many problems came up when I implemented thes
16. e programs I could either troubleshoot by myself or ask Tomas for assistance but it 1s a good idea to ask application engineers from National Instruments on their discussion forum they are very professional and could answer most questions Concerning improvement of the implementation much has already been done But I think there are room for improvement because The Buffered Counter and the Read Binary File have block diagrams which are larger than the screen and it 1s maybe not desirable parts of program can be implemented as subVI to save space One more thing is if someone can figure out how to implement the scanning program in LabView then it would make it easier for the user to use the programs since they are more automated and better synchronized with each other 29 7 References SC 2000 User Manual http en wikipedia org wiki Fluorescence http mesh kib ki se swemesh show swemeshtree cfm Mesh No H01 671 606 552 6 65 amp tool karolinska http en wikipedia org wiki Labview http Zone ni com devzone cda tut p 1d 3536 From NI discussion forum http forums ni com n1 board message board id 170 amp message id 3 14546 http forums ni com ni board message board 1d 1 70 amp thread 1d 3 12369 http forums ni com ni board message board 1d 250 amp message 1d 34548 30
17. en the background would be hazy What we want to do is look only at the light from the focal point and this can be done by adding a pinhole so all light passes from the focal point but light from other point is blocked 3 3 3 Dichromatic mirror A Dichromatic mirror is a mirror that reflects light shorter than a certain wavelength but passes light longer than that wavelength 3 3 4 The microscope Now we have all concepts to build a confocal microscope A laser is used to provide the excitation light since it 1s necessary to obtain high intensity The blue light reflects by a dichromatic mirror and hits two scanning mirrors that are mounted on motors These mirrors are used to scan the laser beam across the sample Dye in the sample fluoresces and emits green light the light take the same way back but get through the dichromatic mirror and is focused onto the pinhole A detector measures the light that passes through the pinhole a SEY camns a9 mirrors I ae detector pinhole mer OS Cope 17 Sample The light from the sample does not give the whole picture because the laser does not cover up entire sample only from one point to another While the laser scans across the sample the detector collects emitting light from these points and builds up an image of the sample The limitation of the microscope is the scanning mirrors the faster the better Confocal microscopy has several advantages over conventional optical microscopy it
18. fer data to the computer A DAQ card normaly contains both ADC and DAC which mean the DAQ card is able to have analogue digital as input as well as output channels There are five components to be considered when building a basic DAQ system Figure5 Transducers and sensors Signals Signal conditioning DAQ hardware Driver and application software Data Acquisition and Analysis Hardware National Instruments Personal Software Computer Figure 5 Data Acquisition System 12 In this project a photon detector is connected to a DAQ card this photon detector generates digital pulses and sends it directly to the DAQ card and therefore no other external transducers and signal conditioning 1s needed 4 3 1 Digital Signals Unlike an analogue signal which is continuous and can take on any value with respect of time a digital signal 1s a discrete signal and has two possible levels high and low A TTL transistor to transistor pulse defines the signal is low when it is between OV to 0 8V and high when 2V to 5V The useful information that you can measure from a digital signal 1s the state and the rate Figure 6 Figure 6 Primary Characteristics of a Digital Signal State The state of a digital signal is simply the level of the signal on or off high or low Monitoring the state of a switch open or closed 1s the most common way to use digital signals Rate The rate of digital signal measures h
19. function as second program but the difference is this is not a page scan the laser stay at one specific point and the program will count the number of pulses and plot it in a Waveform Graph intensity over time I t The last program is for analysing data 16 5 1 Scanprogram generation Assemble programming The scan program is divided into two assembler programs the first for setting the SC 2000 into the default state start position sync channel etc The second program is for performing page scan which will be explained in next section These programs do not run separately the first program functions as a main program and calls the second program which functions as a sub program just like in Pascal or C Since these programs will be saved as a text file then they can be implemented in Labview the idea is to create a whole scanning program in string constants and then use Search and Replace String VI to replace these constants with desired parameters Page scan The objective of this project is to scan over an area and it is natural to scan this area as figure below show start End oY oo The laser beam moves from start point to end point and in this time the SC 2000 board will turn on syncl and gives the DAQ card permission to count Since the laser shuttle 1s not available and an extern laser is used so it cannot be turned off the laser will be switched on all the time The scanning will look l
20. he counter starts to count when the Gate is high and if a pulse coming from the Source if there is no pulse on the Source then it will not count With duplicate count prevention enabled the counter synchronizes both Source and Gate signals to the maximum 80MHz internal DAQ card timebase By doing this the counter detects edges on the Gate even if there is no pulse on the Source and the count value changes synchronously with the timebase 21 Counter detects rising Gate edge Counter value increments only one time for each Source pulse The first edge of timebase 1s used to increase the counter if there are pulses on the Source and all other edges of timebase are ignored The picture above shows the synchronization between Gate Source and timebase The counter arms when the Gate becoming high and start counting when an edge of timebase is raised If no pulses are detected on the Source during a period the counter will register the value 0 For NI STC II and NI TIO boards using duplicate count prevention reduces the maximum frequency of the Source to quarter of the maximum timebase frequency 80Mhz Duplicate count prevention should only be used if the frequency of the Source signal is 20 MHz or less Duplicate count prevention should only be used in the following situations e Counter measurements e The counter Source is using an external signal in this project the TTL pulses from photodetector e The frequency of the extern
21. ike this instead Start End The laser beam moves from the start point to the end point and then backs to start point again and finally moves to the next line During the time when the laser beam moves back from end point to start point and to the next line the DAQ card shall not count The whole operation continues until it reaches the number of desired lines An assembler program is a simple text file and can be downloaded to SC 2000 17 In order to control the mirrors laser movement there are two parameters to be specified the coordinates and the time The coordinates have a range between 32000 and 32 000 the time have the ranges 32 000 ticks and 32 000 ticks and 1 tick corresponds approximately 23 usec A programs or a command will not work if these coordinates or time exceeds their maximal values For simplicity 30 000 will be considered as the maximum In this project the main task is to count the number of pulses during a specific coordinate and time interval for example the full range of coordinates 1s 5000 and the time interval is 100 ticks Note here that the coordinates and the time are independent of each other and the coordinate is not a problem because the interval never exceeds the limit since only small samples will be scanned only time is an 1ssue here When a scanning program is created the user must specify how many time interval let us call it v will be on a line for example x
22. ing Enviroment for understanding SC 2000 commands Use for development of stand alone application e Library of LabView VIs Contains library of command blocks which can be incorporated into the users LabView program e VisualBasic Assembler Convert English Language commands to machine code binary on a command or file basis Perform error checking and returns flags In this project LabView will not be used to control SC 2000 because the manufacture did not provide any example or documentation instead Command Line Interface will be used as a stand alone application LabView will only be used to generate the assembler code for controlling the mirrors There are 4 inputs and 4 outputs on the SC 2000 board which can be used to synchronize with the DAQ card In order to complete the whole operation from scanning to analysing the data it must be divided in four different programs and each program contains several parts that together meet the specification for that program All of the programs are implemented in LabView even though the program which controls SC 2000 is in assembler 1 Scanprogram generation 2 BufferedCounter 3 BufferedCounter at 1 spot 4 Read binary file The first program is for generating a scanning program a text file and this scanning program will be downloaded 1n SC 2000 The second program 1s the main program which counts the number of pulses and plots it in an ntensity Graph image The third program has the same
23. lot on an ntensity Graph all the arrays must be converted to a matrix It can be done by using a Build Array VI and a Shift Register Together they build arrays to a 2 D array When 2 D array is received it is connected to an Array To Matrix to convert it into a matrix and then it 1s ready to be plot on the ntensity Graph 4 After a page scan sometimes the user wants to examine a specific spot on the sample In order to do that the laser must move to this point and stay there The task 1s to generate a string text so the user can copy and paste it in the Command Line Interface The figure below shows how it has been implemented as a subVI otal range of a line Rates Ue DBL I X ae E LER E gt Add to 0 5 to get laser dot UM babe in the middle of spot 10 KE gt 5 On the ntensity Graph there are two cursors and one of them is used for this purpose When a cursor moves on the ntensity Graph a Property Node will return the position of X and position of Y from 0 to number of t 1 Let us say the total range of a sample is 30 000 and there are 100 intervals on the sample deltaX and deltaY will be 30000 100 3000 which means every interval is 3000 To get the position on x axis and y axis the following formula is used x Cursor X 0 5 deltaX and y Cursor Y deltaY After the positions are received it will be converted to string with Number to Decimal String VI and then added with other string constants to build up a com
24. mand string This is done with Concatenate Strings VI 24 5 After scanning it is important to save the data so it can be analysed later This part of the program saves the result as a binary file The figure below shows how it was implemented Modes TM M MN Nek NNNM nter Filename This case loop is for saving a file ieee si ss ns ns ANN La X Close file and check for errors Simple Error Handler vi LS KIKIER Pd 0101 line SSD 0 0 28 08 28 08 8 08 8 en 28 221 08 01 E 01 0 08 0 08 TTT T 2 08 8 8 8 5028288288288 NNN NNN o 8 10 08 08 408 401 40 401 40 40 40 40 40 208 0 T T T T T T T T T 208 08 T T 0 20 0 LILI 0 LILI Ron on on on III INE KAKA o o o A M E S S OS S S M ME ME MU MES MU MO MO MO RO MO M RO M RO Ne RN e Ne e e e e e e e Re E Ree Re Ree Re Re tt Re Re Ne it e e e e e e Mee tt Ree Re ttt ii M Ne Re M e m e e e EE Re Re Re Re Re ee ee eee Re ee e e e e Re d Nrite data to file By default data is written in a 8 byte Little Endian Format To change formats onvert the array of data to another epresentation and change the Byte Order enum This part was implemented as sub VI The case loop is needed to make sure the program saves the data after scanning and not during the scanning This part is quite standard procedure and can be found in Labview examples First use a File Dialog VI to select location and name of file to save and then use Open Creative Replace File VI to open new file and
25. ow large portion of a signal occurs with respect to time for example an MP3 file that is created has a bit rate setting of 128 kbit s 4 3 2 DAQ Hardware DAQ hardware functions as the link between the computer and sensor detector etc It normally use as a device that converts incoming analogue signals to digital signal so that the computer can interpret them but there are other functions available Analogue Input Output Digital Input Output Counter Timers Multifunction a combination of analogue digital and counter operations on a single device 13 National Instruments offers several hardware platforms for data acquisition The most common available platform is the desktop computer National Instruments offers several type of DAQ hardware for different purposes PCI DAQ boards that plug into any desktop computer PXI CompactPCI is a more robust modular computer platform specifically for measurement and automation applications PXI is ideal for mid to large size applications Compact FieldPoint 1s designed for industrial control the NI Compact FieldPoint programmable automation controller PAC offers the flexibility and ease of a PC and the reliability of a programmable logic controller PLC NI has also DAQ devices for portable or handheld measurements the DAQ devices are connected via USB to a laptops or PocketPC PDAs Figure 7 Desktop er 2 re PXI Rugged and Modular Portable Fig
26. plot the result on a Waveform Graph Note that the result is a 1D array 5 4 Read Binary File All the counter programs save the results as a binary file so it can be analysed later with another software However it 1s better to be able at least to see saved images with LabView This program is for that purpose the front panel is almost identical with the Buffered Counter program For example when this program runs to analyse a file which contains a matrix all the graphs should look like the Buffered Counters graphs right after this matrix 1s received from a scanning The front panel looks like the front panel of Buffered Counter but the implementation is different figure below shows how it was implemented 1OO0000000000000000000000000000000000000000000000000000000000000000000000000000000000000000 MW Tye ve R wu HIT pessrcemcntmcaanscsksedmM UMEN INMMUN True vU E Data Type DBL f Biot del Simple Error Handler vi Byte Order OOOO0O000000000000000000000000000000000000000000000000000000000000000000000000000000000000G6C This picture is not complete this show only the most important part of this program The other part is the same as 6 in Buffered Counter 2 When a file is saved in binary format Labview does not contain any information if it is a matrix or not the values are considered as a 1D array One way to get around this problem is to use a Get File Size VI to determine which type it 1s If there
27. set it for write Use Write to Binary File to save the data and then close file 6 This part of the program is for changing the intensity with respect to a specific region and see how the intensity changes along the x axis and y axis There are two cursors used to frame the specific area and with one click on a button the Intensity Graph will change the intensity scale with respect to this region Next figure shows how to change the intensity it takes x y position from cursor I and subtract with x y position from cursor 0 which gives an area that both cursors have frame in Then take the maximum and minimum value in this area and use a property node of the Intensity Graph to rescale it Intensity Graph 2 using cursor 0 d cursor 1in Intensity Graph 25 The last part of Buffered Counter program 1s to let the user to move one of the cursors and mark a spot and see how the intensity changes on the x axis and y axis which cross this point This means the graphs will show the values of 1D array with number of 1 elements for example number of t can be 100 200 or 300 and so on Figure below shows how it was implemented This for change x and y axis in XY Graphs so it show b XScale Minimum where the cursor 1 in the Intensity oN ae I The idea is first to convert the matrix to a 1D array which contains all the values for example 100x100 10 000 and this array has index from 0 to 9999 if it is 200x200 40 000 then the array has index from
28. software Control of a Confocal Microscope Giang Vu Scan Mirror Galvanometer Galvano NA Scan Mirror Closely Spaced raner eam Scanning Mirrors Bovine Pulmonary Artery Endothelial Cells BPAE Line Master Thesis in Electrical Engineering 30 hp Oct 2007 Jun 2008 Department of Measurement Technology and Industrial Electrical Engineering Department of Chemical Physics Supervisors Tomas Jansson Associate Professor Lund Institute of Technology Lund Ivan Scheblykin Associate Professor Lund University Contents EN JE NN NE 3 2 Akio WICU SEINE sisarien n an a e Shobasesieabanieieadeaseniaiernes 4 T rr 5 3 1 Backeround atid purpose siii ete pE eres 5 SDMA AT NE S 5 3 9 Confocal Microscope redere 6 TIE 6 DANNE 7 3 9 3 DICHPOMANC NT NS are 7 NNN J NN 9 1 KO Uomo EEE ENER EEE SE NR SN 9 4 2 SC 2000 Digital Scan Controller eee 9 d NS SUSI VCINde EE ESN EE DUEEGE 9 42 2 Command Line het EE sveaerne 11 4 2 Assemble L nn save 12 A y DIG ACMS NOs pre 12 2 5 T Dibital SN a T A OA RRE 13 4 3 7 DAO HardWare aasenso sette nde een 13 4 3 3 Driver and Application Software cccccccceccsesceseeeseesseseeeees 14 J RN MN 16 5 1 Scan program generatiQIP saa 17 PT 18 5 3 Buffered Counter at 1 spot spess e Puts d erts eadia 27 TR Bede 27 o Resultand DISCUSSION ae 29 Jede CIN E act pense ees ee CMM MEM MEL 30 1 Abstract Confocal fluorescence microscopy is
29. the user with less programming experience Labview is commonly used for data acquisition instrument control and industrial automation because of an extensive support for instrumentation hardware Labview is available in different operating system as Windows Mac Unix and Linux Every Labview program has three components a block diagram a front panel and a connector pane Block diagram is the main part of the program it is here the user do the programming the program is built up by placing and connecting VI s symbols together The picture below shows an example of a block diagram IE Signal Generator vi Block Diagram File Edit Operate Tools Browse Window Help c m ome bal P oe 13pt Application Font visa A gt gt Simulate Signal Sine Amplitude K Simulate Signal2 Triangle p Sh ae Waveform Chart gt Frequency ld Phase Simulate Signal3 3 8 Waveform Chart Waveform Chart 1 Simulate Signal4 Sawtooth P Block diagram The front panel is where the programmer creates the user interface defines input and output data by using controls and or indicators directory Fitestidatal filename sioz j 2 txt Equivalent circuit model Capacitancec NM CR X Capacitance s lcr a7 Po scan Capacitance c Capacitance s Plot 2 Plot 3 Plot 4 Plot 5 Plot 6 Plot 7 I I 1 ES 1 am 1 i 1 z 1 0 0 500 0 1000 0 1500 0 2000 0 B 500 0 1000 0 1500 0 2000 0 Plot 8 Vbias start
30. ther system components interfaced to the Scan Controller The Scan Controller can be programmed either with GSI Lumonics supplied Lab View interface or customer designed host side software By interfacing directly to the position command position feedback and binary communication of the axis servos the Scan Controller has full position control of the system and position feedback It allows also the host computer to read galvo temperature status and calibration information Besides the system has also interlock which means a device used to help prevent a machine from damaging itself by stopping it when something unsusal happens Figure and Figure 2 on next page show overview of the system Standard scan Controller Serial Port SAX Figure 1 Scan Controller with host computer Scan Controller TTTTTT T Switches can control program execution in standalone operation Figure 2 Typical standalone system The Sync Cal connector provides access to the synchronization calibration I O as well as the pixel clock output of the Scan Controller Figure 3 on next page shows Scan Controller layout pin out and connector part numbers In this project only sync 1 out and sync 2 out will be needed to communicate with DAQ card 10 J7 Temp Gnd V RTS RS4850ut Temp X TXD RS46Sout 5V in out Pwr connector Temp X connector Mates with Molex 51021 0400 shell serial interface connector Molex 50079
31. uction vi Scan Controller ComConfig Command Line id y FreeFlashSpace interface FreeRAMSpace Version 2 07 11 4 2 3 Assemble language With Command Line Interface the user has two different ways to write a motion program for the SC 2000 this Scan Controller accepts either a motion program language that consists of a binary machine language or assembler language It is very easy for the programmer to use assembler language because it consist of English language commands for controlling axis motion it requires only that the programmer has basic English knowledge If the programmer chooses assembler language then the programs can be typed into a text file with a text editor such as WordPad There are two basic operating modes in the Scan Controller Vector mode is used to control X and Y axis galvos to move both X and Y direction Raster mode is used to control a selected single axis Vector commands can differ from raster commands by writing a xy suffix For example SlewXY is a vector command and Slew is a raster command 4 3 Data Acquisition Data acquisition means collecting signals from measured source and process the signal and present on a PC Before it was common that measurements was done on stand alone instruments like multi meters oscilloscopes counters etc but nowadays it have become more important to gather measured data and present it on a PC A Data Acquisition Card is used to measure the signal and trans
32. ure 7 DAQ Hardware Options from NI In this project National Instruments PCI 6602 will be used 4 3 3 Driver and Application Software Driver Software Driver Software that usually comes with the DAQ hardware it allows the operating system to recognize the DAQ hardware Without software to control or drive the hardware the DAQ device will not work properly A good driver offers high and low level access 14 Application Software The application layer can be an environment that you build an application that meet your own criteria or it can be a configuration based program with preset functionality Depend on your application s complexity you can choose an application software that is appropriate for the purpose NI has three development environment software that make it possible to design complete system of instrumentation acquisition and control applications as mention before only LabView will be used in this project LabVIEW with graphical programming methodology LabWindows M CVT M for traditional C programmers Measurement Studio for Visual Basic C and NET With the introduction of NI SignalExpress it is possible to use configuration based software to build up a program and the user does not need to do the programming The disadvantage 1s that the program become slower 15 5 Implementation There are three different types of command programming software available for SC2000 e Command Line Interface Learn
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