Full report - ECE - Cornell University
Contents
1. you guys are always helping me when I have problems 17 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 APPENDIX A User Manual 1 Hardware setup Currently I put all the wire connections on the bread board so all the circuit should be set up as in Figure And then we should connect the microcontroller and the PC through USB cable 2 Run MATLAB code Before we run the MATLAB code we should check Device Manager to see which serial port we are using to connect the microcontroller Then we should go to the fifth line of the MATLAB scripts and change com8 to the serial port we are using After that we can run our MATLAB code The first thing we can see is the time length of this experiment as shown in Figure 10 Command Window Please type in the time length of this data collection fx Time length in minutes Figure 10 Prompt line of time length We should type in how long we want to collect data Notice that the user must type in an integer in this procedure Then the MATLAB will send the current state of the whole system as shown in Figure 11 18 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Command Window Please type in the time length of this data collection Time length in minutes 2 The current values of P diff dP MA delta Gain and Bias are as follows P diff 0 000000 dP MA 0 000000 delta 0 000000 Gain 0 000000 Bias 02. Figure 3 There are several variables I need to change or monitor in this project Parts of them are calculated for calibrating the bioreactor by using MATLAB And the rest of the variables are set every time we want to change the state of the bioreactor They are as follows Name Description Need to change P diff This is the pressure difference between high tank and low tank Y which is used for controlling the pump dP MA Moving Average of the pressure This parameter and delta help N P diff to determine the upper and lower pressure thresholds for the pump Bias Pressure bias This is calculated by the former designer for N eliminating the noise thres The threshold pressure of the aorta pressure When the pressure Y of aorta pressure reaches this value the valve will open delta This variable is multiplied by dP MA every time when the Y microcontroller compares the pressure difference Gain This variable is multiplied by the measured pressure difference by N Microcontroller for comparing the expected P diff Table 1 Key variables and the descriptions Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Turn pump on and off The four transducers send PP based on certain out current signal pressure difference ee S 4 Microcontroller reads Microcontroller sends signal from the four the value of the four transd
3. Ihe format of the name of the saved file is Year Month Day Hour Minute Iimelength fe gt Figure 14 File format In this way we can guarantee that there will never be two files which have the same name and we can use the data to do further analysis 20 Microcontroller Control System for Heart Valve Bioreactor Microcontroller All from lab Kang Li k1694 APPENDIX B Parts Number Part Name Quantities ATmega 1284P chip 1 Prototype Board 1 Resistors Several USB cable 1 Junction Box x 2 Parts number are all from Grainger Quantities Parts Number Part Name 2 6X063 LEVITON Wall Switch 1 Pole Toggle Brown 2 6A702 LEVITON Receptacle 20A 125V 5 20R 2P 3W 1PH 2 6XC61 RACO Box Plastic 2 Gang 2 1LXT1 HUBBELL WIRING DEVICE KELLEMS Wall Plate 2Gang Nylon lvory 2 6C900 OMRON Relay Solid State 4 5XFP9 NO BRAND NAME ASSIGNED Extension Cord 6ft 16 3 13A SJT Black 21 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 APPENDIX C Source Code pump trt 28 c This script is written for MENG Project Heart Valve Bioreactor by Kang Li kI694 Cornell University define F CPU 16000000UL Hinclude trtSettings h Hinclude trtkernel 1284 c Hinclude lt avr interrupt h gt Hinclude lt avr pgmspace h gt Hinclude lt stdio h gt include lt stdlib h gt Hinclude lt string h gt Hinclude lt avr sleep h gt Hdefine begi
4. diff 150 mmHg Pdiff 150 mmHg 150 100 E E 50 Aorta E D High Tank ui u o Low Tank a 50 Ventricle 100 10 15 20 25 30 Time s Figure 9 3D printed heart valve pressure waveform when P diff 150 mmHg 16 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Conclusion designed a microcontroller control system for the heart valve bioreactor It can control the flow of the whole system based on the specified parameters and collect data in MATLAB The future work could be that we can design our own prototype board instead of using bread board so the whole system could be more compact And also we can build several parallel TEHV chambers instead of just one Acknowledgement I would like to thank my advisor Bruce Land for all his instruction His advice of junction box really make the project much safer And he taught me how to change the clock frequency to make the TRT run for much longer time All these things make the project much easier for me to accomplish And I also want to thank all the team members in our bio print team especially Laura She is always so patient and kind When I started to participate in this project I know nothing about the machenism of heart valve and the bioreactor She told me how to start and what goal we should achieve When I have questions she always explains to me no matter how stupid the question is And also for Alain Dan and Duan
5. seconds FontWeight bold FontSize 10 Color 1 1 0 ylabel Ventricle Pressure in mmHg FontWeight bold FontSize 10 Color 1 1 0 title Ventricle Pressure FontSize 15 Color 1 1 0 figureHandle4 figure NumberTitle off Name Aorta Pressure Color 0 0 0 Visible on axesHandle4 axes Parent figureHandle4 YGrid on YColor 0 9725 0 9725 0 9725 XGrid on XColor 0 9725 0 9725 0 9725 Color O O 0 xlim O timeout used ylim 0 120 scaler 388 2081 hold on plotHandle4 plot axesHandle4 i real Ventricle 1 1 Marker LineWidth 1 Color O 1 0 xlabel Time in seconds FontWeight bold FontSize 10 Color 1 1 0 ylabel Aorta Pressure in mmHg FontWeight bold FontSize 10 Color 1 1 0 title Aorta Pressure FontSize 15 Color 1 1 0 PropName1 1 YData PropName1 2 Color PropName1 3 XData 32 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 PropName2 1 YData PropName2 2 Color PropName2 3 XData PropVal1 1 2 0 1 0 PropVal1 2 2 0 1 O PropVal2 1 2 0 1 0 PropVal2 2 2 0 1 OJ start to collect data and plot the real time waveform for i 2 timeout used sample rate fprintf fid c r s pause 0 001 f test fscanf fid s if isempty f test amp amp f test 1 H end end i real z
6. some of the registers to implement this ADC The first register is ADMUX I set the first two bits to 01 which means the reference voltage is 5V And I set Bit 5 to 1 to left adjust the result of the conversion And for Bits 4 0 I set 0b00000 to 0b00011 in the state machine because I need to use channel 0 to channel 4 and I don t need to add gain to the output The second register which is also very important is ADCSRA The most significant bit of ADCSRA is ADEN I set it to 1 to enable the ADC The second most significant bit of ADCSRA is ADSC I set this bit to 1 to indicate the start of ADC When the conversion is complete it returns to zero So can also use this bit to test if the conversion is done and then start the next conversion After the conversion the data is stored in ADCH I load the value to the corresponding variable after 11 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 the conversion The ADC procedure is implemented in pump control subroutine design a state machine to read four channels of the ADC and send out the pump control signal The state machine is as follows DIFFERENCE In this state we measure the values of the pressure of high tank and low tank I use a while loop while ADCSRA amp 1 ADSC to wait for ADC After this loop the value in ADCH can be used So I load the value to variable P tank H which stores the value of high tank pressure Then I set the A
7. 000000 Threshold Aorta Pressure 388 208100 amp cokolololokoleolololoolololololololoolololeoleololokololololelololololololololololololololololololololelololojolololeolooloit Do you want to change the current values fx Please input 1 or 0 1 for changing values Figure 11 The current state of the whole system These information is sent back from the microcontroller If we want to change the state we should type in 1 otherwise we should type in O After we type in 1 the MATLAB will guide us to change the values of some key variables as shown in Figure 12 Command Window The current values of P diff dP MA delta Gain and Bias are as follows P diff 0 000000 dP MA 0 000000 delta 0 000000 Gain 0 000000 Bias 0 000000 Ihreshold Aorta Pressure 388 208100 xXololokololelokololololokololelokololololololololololololololorolololorololololololololololeolololololololololeoloolololelojoioleit Do you want to change the current values Please input 1 or 0 1 for changing values Please input the value of P diff the default value is 100 P diff 100 Please input the value of delta the default value is 1 delta 1 Please input the value of the threshold aorta pressure the default prssure 77 5723989 mmHg thres P diff 100 000000 delta 1 000000 threshold aorta voltage 77 572399 Is this correct Please input 1 or 0 1 for correct Figure 12 Change the values of key variables Afte
8. DC registers as follows ADMUX 1 REFSO 1 lt lt ADLAR 0b00001 ADCSRA 1 ADSC The first line indicates the channel is changed to channel 1 Pin A1 and the reference voltage is 5V and the result is left adjusted The second line starts another ADC procedure Then I load the value of ADCH to P tank L which stores the pressure of the low tank After that I also need to set the channel to channel 2 Pin A2 I also set two variables called HighTank total and LowTank total to eliminate the noise of the ADC I set a count and every time we enter this state DIFFERENCE the count will increment by 1 If the count reaches 50 the microcontroller will compare the value of HighTank total and LowTank total by this sentence deltaP float HighTank total float LowTank total 50 Gain See Table 1 for details The value of variable Gain is set from the MATLAB and protected by TRT since it is used in two tasks After this calculation can use deltaP to control the pump If deltaP P diff delta dP MA we should turn on the pump The variables P diff delta and dP MA are also set from MATLAB and protected by TRT If deltaP gt P diff delta dP MA we should turn off the pump VENTRICLE This state only reads the data of Pin A2 And the microcontroller will load the value of ADCH to variable P ventricle and change the channel to channel 3 Pin A3 AORTA This state reads the data of Pin A3 The microcontroll
9. Microcontroller Control System for Heart Valve Bioreactor A Design Project Report Presented to the School of Electrical and Computer Engineering of Cornell University In Partial Fulfillment of the Requirements for the Degree of Master of Engineering Electrical and Computer Engineering Submitted by Kang Li k1694 MEng Field Advisor Bruce Robert Land Degree Date January 2015 Abstract Master of Engineering Program School of Electrical and Computer Engineering Cornell University Design Project Report Project Title Microcontroller control system for heart valve bioreactor Author Kang Li kl694 Abstract The project team of Butcher Lab has developed a bioreactor culture system to mimic the cardiac cycle for the invitro conditioning of 3D printed tissue engineered heart valve conduits designed a microcontroller control system to control the flow of the whole system and collect data sent from transducers This will help the bio print team to investigate cell and construct function under dynamic physiological conditions and do further research I designed a microcontroller control system for the heart valve bioreactor using ATmega 1284P microcontroller It can control the flow of the whole system based on the specified parameters and collect data in MATLAB This will help Butcher Lab do further analysis Executive Summary This project continues the design and development of a cyclic flow heart valve bioreactor
10. O 1 ADLAR 0b00000 27 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 ADCSRA 1 lt lt ADEN 1 lt lt ADSC 7 channel_flag DIFFERENCE P_tank_H 0 P_tank_L 0 P_aorta 0 P_ventricle 0 P diff 0 delta 0 dP MA 0 Gain 0 Bias 0 time squarewave 0 thres 0 count 0 T 0 ini uart trt_uart_init stdout stdin stderr amp uart_str trtInitkKernel 300 trtCreateSemaphore SEM_RX_ISR_SIGNAL 0 uart receive ISR semaphore trtCreateSemaphore SEM STRING DONE 0 user typed enter trtCreateSemaphore SEM_SEND 1 trtCreateSemaphore SEM_INPUT 1 trtCreateSemaphore SEM_SQUARE 1 trtCreateTask PC_communication 300 SECONDS2TICKS 0 15 SECONDS2TICKS 0 25 amp args 0 trtCreateTask pump_control 300 SECONDS2TICKS 0 01 SECONDS2TICKS 0 015 amp args 1 sei end 28 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Heart valve MCU m clc clear clean the screen and workspace load CalibTransducer mat load the calibration parameters close all close all the figures delete instrfindall delete all the instruments fid serial com8 6 open serial port s BytesAvailableFcnMode byte set the parameters of the serial port s InputBufferSize 5000 s BytesAvailableFcnCount 10 s BaudRate 9600 s BytesAvailableFcn 8 my callback s Timeout 3000 fopen fid fp
11. ad of the AC output of the solid state relay the live line connects one of the exposed lead of the wall socket eventually And the 6 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 neutral line of the power plug directly connects the other exposed lead of the wall socket And the ground line of the power plug connects both of the ground lead of the wall switch and the wall socket The low voltage input side of the solid relay switch connects the microcontroller through a 3 5mm audio cable So if the microcontroller signal is high 5 volts the AC output of the solid state relay conducts So the load the pump or the two way solenoid valve of the AC circuit can be energized I Wall AC AC Live AC Neutral AC Ground Solid State Rela Y Junction Box MCU GND MCU Signal Figure 6 Circuit Diagram of Junction Box In this way I keep all the high power circuit inside the junction box so that the system is very safe And also the wall switch can cut the circuit off in case of dangerous situation Hardware for microcontroller The outputs of the four transducers are all currents which are in the range of 4 20 mA But the built in ADC of ATmega 1284P can only convert voltage to digital signal So put a 250 O resistor in serial with each transducer The microcontroller measures the voltage drop between the two 7 Microcontroller Control System for Heart Valve Bioreactor Kang Li
12. amp 1 ADSC 23 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 P tank H ADCH ADMUX 1 REFSO 1 lt lt ADLAR 0500001 ADCSRA 1 ADSC HighTank total P tank H wait for ADC done while ADCSRA amp 1 ADSC P tank L ADCH Reference voltage is 5V Write one to ADLAR to left adjust the result Select the PINA1 ADC1 as analog input ADMUX 1 REFSO 1 lt lt ADLAR 0b00010 ADCSRA 1 lt lt ADSC LowTank total P tank L count if count gt 50 begin count 0 trtWait SEM INPUT deltaP float HighTank total float LowTank total 50 Gain trtSignal SEM INPUT HighTank total 0 LowTank total 0 load the values sent from MATLAB and protect the variables using TRT trtWait SEM INPUT P diff P dP MA C delta D Gain G Bias B thres T trtSignal SEM_INPUT if P diff AP MA delta are all zeros don t start the pump if P diff gt 0 dP MA gt 0 delta gt 0 begin if deltaP lt P diff delta dP MA begin SET PORTD 2 turn on the pump trtwait SEM SEND pumpsSignal 1 trtSignal SEM SEND end if deltaP gt P diff delta dP MA 24 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 begin CLR PORTD 2 turn off the pump trtwWait SEM SEND pumpsSignal 0 trtSignal SEM SEND end end else begin CLR PORTD 2 end end channel f
13. e uint32 t deadline void args Identifies a function to the kernel as a thread The parameters specify a pointer to the function the desired stack size the initial release time the initial deadline time and an arbitrary data input structure The release time and deadline must be updated in each task whenever trtSleepUntil is called The task structures are statically allocated Be sure to configure MAXNBRTASKS in the kernel file to be big enough When created each task initializes 35 bytes of storage for registers but stack size minimum is around 40 bytes If any task stack is too small the system will crash uint32 ttrtCurrentTime void Get the current global time in timer ticks void trtSleepUntil uint32 t release uint32 t deadline Puts a task to sleep by making it ineligible to run until the release time After the release time it will run when it has the nearest deadline Never use this function in an ISR The deadline release time should be greater than the execution time of the thread between trtSleepUntil calls so that the kernel can meet all the deadlines If you give a slow task a release time equal to its deadline then it has to execute in zero time to meet deadline and nothing else can run until the slow task completes void trtCreateSemaphore uint8 t semnumber uint8 t initval Creates a semaphore with identifier semnumber and initval initial value Be sure to Microcontroll
14. e the value of the protected variables begin parse the received string p strchr cmd P cmd c strchr cmd C cmd d strchr cmd D cmd g strchr cmd G cmd b strchr cmd B cmd t strchr cmd T cmd stricpy P str cmd p 1 c p stricpy C str cmd c 1 d C stricpy D str cmd d 1 g d stricpy G_str cmd g 1 b g stricpy B str cmd b 1 t b stricpy T_str cmd t 1 strlen cmd t 26 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 trtWait SEM INPUT load the values to corresponding variables sscanf P str f amp P sscanf C str f amp C sscanf D str f amp D sscanf G str f amp G sscanf B str f amp B sscanf T str 26d amp T trtSignal SEM INPUT end if cmd 0 s send the package to PC begin trtwait SEM SEND fprintf stdout 96s sendData trtSignal SEM SEND end if cmd 0 c check the current state of the whole system begin trtWait SEM INPUT fprintf stdout rP_diff fdP_MA fdelta fGain fBias fThres d n P diff dP MA delta Gain Bias thres trtSignal SEM INPUT end end end void initialize void begin CLKPR 1 lt lt CLKPCE CLKPR 1 lt lt CLKPSO 1 lt lt CLKPS1 set divide by 8 PINA is input DDRA 0x00 PORTA 0x00 PIND is output DDRD Oxff PORTD 0x00 PINC is output DDRC Oxff PORTC 0x00 ADMUX 1 REFS
15. er Please type in 1 or O 1 for correct If the user types in O the whole procedure of changing values will start over again if the user types in 1 MATLAB will send the new value to the microcontroller and starts to collect data The format of the string which MATLAB sends to the microcontroller is oPXXXfCXXXDXXXGXXXBXXXTXXX and this string will be parsed in microcontroller Start to collect data and plot the real time waveform of the four transducers After changing the value of the key variables we can collect data now I use a for loop to do the data collection Instead of letting the microcontroller send data continuously I design a simple handshaking protocol because MATLAB is very bad at dealing with memory control and it may flush the memory if we don t control the data transfer The first thing is that MATLAB sends a character s to the microcontroller The microcontroller recognizes the character and then sends back a string whose format is HXXXLXXXVXXXAXXXUX This string contains the value of the four transducers High tank Low tank Ventricle Aorta and the pump signal high or low MATLAB will parse the string and send values to the corresponding variable And then MATLAB plots the gn S points in the figure After finishing plotting MATLAB will send again and start the whole procedure again until it reaches the length of the time period we set In this way the whole procedure of data collection is under contro
16. er Control System for Heart Valve Bioreactor Kang Li k1694 configure MAXNBRSEMAPHORES in the kernel file to be big enough The identifier number is 1 based so the first semaphore you define should be numbered 1 void trtWait uint8 t semnumber Adds one to the semaphore If another thread is waiting on the semaphore and has a nearer deadline a context switch will occur You can use this function in an ISR void trtSignal uint8 t semnumber Returns the count of the specified semaphore before it is decremented If the semaphore has a nonzero value the value is decremented Your task must check the return value This function does not block You can use this function in an ISR Table TRT function and description from TRT introduction page of ECE 4760 2 Internal ADC of ATmega 1284P use the built in Analog to Digital Converter of ATmega 1284P This ADC is a 10 bit successive approximation ADC In this project I only use the first 8 bit for the ADC I use four input pins of the chip AO A3 and the internal reference voltage is 5V I use single ended conversion for all the four By the external circuits make the voltage of the input pin is in the range 0 5V So the calculation of ADC is as follows Vin ADC x255 5V For example if the input voltage of Pin AO is 3 4V the microcontroller will store 173 19 which is 10101101 in register ADCH after the Analog to Digital Conversion need to set
17. er will load the value of ADCH to variable 12 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 P aorta and change the channel to channel 0 Pin AO And also the microcontroller will control the two way solenoid valve in this state If P aorta is bigger than the threshold value variable thres the microcontroller will send an open signal to the valve Otherwise the microcontroller will send a close signal In this state the microcontroller also put the four variable in a page whose format is H 3dL 3dV 3dA 3dU 1d This is used for sending data to MATLAB MATLAB Part use MATLAB to communicate with the microcontroller and collect data It is fairly easy to set up the serial port in MATLAB The basic steps of the MATLAB code are as follows 1 Load the calibration parameters of the bioreactor These parameters which are essential for the bioreactor control were created by the former students during the calibration time of the whole bioreactor system They are in the form of mat file So we can load them directly Close all the peripheral of the computer and open the serial port Before we open the serial port of the computer we need to make sure all the instruments are deleted by using delete instrfindall Then we can open the serial port by the command fid serial com8 fopen fid Otherwise MATLAB may get the runtime error Check the current state of the microcontrolle
18. for use in culturing and conditioning of tissue engineered heart valves in the Butcher Lab in BME department The bioreactor can simulate the flow between left ventricle and aorta of the heart to mechanically stimulate the cells of the tissue engineered aortic semi lunar heart valve My part in this project is to design a microcontroller control system for the heart valve bioreactor It can control the flow of the whole system based on the specified parameters and collect data in MATLAB I use the built in ADC of ATmega 1284P microcontroller The microcontroller reads the signal of four pressure transducers high tank low tank ventricle and aorta And the microcontroller has to control one pump and one solenoid valve The pump is turned on off based on the pressure difference between high tank and low tank if the pressure difference exceeds the upper threshold the pump will stop working if the pressure difference is smaller than the lower threshold the pump will start working The two way solenoid valve is controlled based on the pressure of aorta If the pressure of aorta exceeds the threshold the valve will be open otherwise it will be closed And I built two junction boxes for controlling the pump and the two way solenoid valve The junction boxes can connect the low power and the high power by using relay switch It can make the project safe to use In this way we can control the flow inside the microcontroller to mimic the actual flow in the
19. heart valve system of human The values of the thresholds differ every time we run the bioreactor use MATLAB to communicate with the microcontroller MATLAB sends different commands to the microcontroller and the microcontroller will give feedback based on the commands The user can check the current state of the whole system change the values of the parameters and collect data using MATLAB During data collection MATLAB will plot real time wave forms of the four transducers After finishing the data collection MATLAB will store the data for further analysis The future work could be that we can design our own prototype board instead of using bread board so the whole system could be more compact And also we can build several parallel TEHV chambers instead of just one Content Content Introduction seeseenesneennennennennevnnennennennnvnnennennennnennennennnsnnennennennnennennennennnennennennnvenennennennneeneenennsseneenee 1 Hish rag MOTIpu perse D MR 4 Hardwar design seedede ree Ud oeuvre Ud ene eV ae eeu Ud oe eo eua eeu Sen oe ara aes en eno Dee siss 6 SOPEWANE MOSIOM E M M 9 Microcontroller Part 9 1 TRT Tiny Real Time seseevensevvenennenneneenennennenseneenenneneeneenennenneneenennennenneneenennenneneenennennenee 9 2 Internal ADC of ATmega 1284P eeossovessvvenvsvenesvesssvvennevennsvesenvsssnvesnnesenesseneseessnesenneses 11 MATLAB Part seeseesesveve
20. i real 1 H find f test H L find f test L V find f test V A find f test A U find f test U High tank i real 1 str2double f_test H 1 L 1 scaler 388 2081 Low tank i real 1 str2double f_test L 1 V 1 scaler 388 2081 Ventricle i real 1 str2double f test V 1 A 1 scaler 388 2081 Aorta i real 1 str2double f test A 1 U 1 scaler 388 2081 PumpSignal i_real 1 str2double f test U 1 length f test 1 200 PropVal1 1 1 High_tank 1 i_real PropVal1 1 3 1 i_real sample_rate PropVal1 2 1 PumpSignal 1 i_real PropVal1 2 3 1 i_real sample_rate set plotHandle1 PropName1 PropVal1 set plotHandle2 YData Low_tank 1 i_real XData 1 i_real sample rate PropVal2 1 1 Low_tank 1 i_real PropVal2 1 3 1 i_real sample_rate PropVal2 2 1 PumpSignal 1 i_real PropVal2 2 3 1 i_real sample_rate set plotHandle2 PropName2 PropVal2 set plotHandle3 YData Ventricle 1 i real XData 1 i real sample rate set plotHandle4 YData Aorta 1 i real XData 1 i real sample rate 33 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 timelength timeout used 60 savefile is the name of the saved file savefile sprintf d 2d 2d 962d 2d d year now month now day now hour now minute now timelength cprintf 1 0 1 nV The format of the name of the saved fi
21. k1694 leads of the resistor I need four ADCs in this project So the GND of the microcontroller should connect one lead of each resistors and PIN AO PIN A3 connects the other lead of each resistor PIN D2 connects the junction box which controls the pump and PIN CO connects the junction box which controls the two way solenoid valve The whole setup is shown in Figure 7 Aorta Pressure Transducer SINGLE u ES CHAMBER 2 por SETUP W PACING d eg irsk AORTA FEEDBACK pete i CONTROL LEGEND 3 Media L Air I ke ser Water Pins Diagramfor SN ul timerrelay NE ae 3 v Engineered k Heart Valve Electronic Component List 8 pin High Tank Low Tank Pressure socket Pressure Pressure Transducer Transducer transducer transmitter DC Diaphragm Pump AC CablesTo valve i 3 port solenoid valve AC 120VAC BN pee 2portsolenoid valve AC Pressurized Shunt gt Reservoir Capacitance Tank High mount Relayswitch 250 Ohm resistor en EEE gt To the two way solenoid valve power Timer relay and socket Microcontroller M Protective Resistance I N 330 ohms each resistor i t i i i i H iH i i i resistor 2500hms i PE T i USB cable to computer Pn Figure 7 Hardware setup for Heart Valve Bioreactor Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Sof
22. l Notice that we have gn S to use pause function between sending s and receiving the string even when we only need a really short pause Otherwise the real time waveform will stuck and the whole waveform will appear after we finish collecting data Save the data of the four transducers for further analysis 14 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 The last step is that we save the data to a mat file for further analysis The data we want to save is High tank Low tank Ventricle and Aorta And then we delete all the other internal variables At last MATLAB will print a pink information telling the user what format of the saved data is 15 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Result and Analysis The microcontroller system is used for collecting data in out lab We can use these data to do further analysis This is just a simple example Figure 8 shows the porcine heart valve pressure when P diff equals 150 mmHg and the applied aorta pressure equals 0 Figure 9 shows the 3D printed heart valve pressure when P diff equals 150 mmHg and the applied aorta pressure equals 0 We can compare these two figures to check if the printed valve satisfies our demand 125 Aorta MA 100 Ventricle MA Pressure mmHg Pdiff setting 150mmHg No AP Time sec Porcine 2 27 2014 Figure 8 Porcine heart valve pressure waveform when P
23. lag VENTRICLE break case VENTRICLE wait for ADC done while ADCSRA amp 1 ADSC P ventricle ADCH Reference voltage is 5V Write one to ADLAR to left adjust the result Select the PINA3 ADC3 as analog input ADMUX 1 REFSO 1 lt lt ADLAR 0b00011 ADCSRA 1 ADSC channel flag AORTA break case AORTA when energized while ADCSRA amp 1 ADSC P aorta ADCH if P aorta thres begin CLR PORTC 0 open the two way solenoid valve end else begin SET PORTC 0 close the two way solenoid vale the valve is closed end Reference voltage is 5V Write one to ADLAR to left adjust the result Select the PINAO ADCO as analog input ADMUX 1 REFSO 1 lt lt ADLAR 0500000 25 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 ADCSRA 1 ADSC trtwait SEM SEND put the four variables in a package sprintf sendData H 3dL 3dV 3dA 3dU 1d P tank HP tank L P ventricle P aorta pumpSignal trtSignal SEM SEND channel flag DIFFERENCE break end rel trtCurrentTime SECONDS2TICKS 0 01 dead trtCurrentTime SECONDS2TICKS 0 011 trtSleepUntil rel dead end end void PC communication void args begin char cmd 40 P str 10 C str 10 D str 10 G str 10 B str 10 T str 10 int p c d g b t while 1 begin fscanf stdin 96s cmd if cmd 0 o chang
24. le is Year Month Day Hour Minute Timelength VnYr save the four vectors to a mat file save savefile High tank Low tank Ventricle Aorta clear all the internal variables clear f f1 H LA V over timelength timeout used send packett Average clear figureHandle1 figureHandle2 figureHandle3 figureHandle4 clear plotHandle1 plotHandle2 plotHandle3 plotHandle4 clear axesHandle1 axesHandle2 axesHandle3 axesHandle4 clearii real check check flag s savefile timeout f test clear Square current Square used Square location scaler clear Bias used Gain total P diff used PropName1 PropName2 PropVal1 PropVal2 clear R Calib R used Ua Transducer b Transducer dP MA dV MAR Use delta used close the serial port fclose fid delete fid clear fid 34
25. ller system is needed for controlling the flow of the bioreactor The flow diagram is shown in Figure 2 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 The bottom circuit is composed of a chamber with the membrane a pump a high pressured tank and a low pressurized tank There are two solenoid valves which allow us to control the pulse rate The pump is controlled by the pressure difference of the high pressured tank and the low pressurized tank And the solenoid valve is controlled by the timer relay Only water circulates in this bottom circuit The top circuit is composed of a chamber with the membrane a Tissue Engineered Heart Valves TEHV chamber an air tank a media reservoir and a two way solenoid valve The air tank is used for pressurizing the TEHV chamber to maintain a constant value of aorta pressure The two way solenoid valve is controlled by the pressure of aorta If the pressure of aorta reaches the threshold value the valve will be open BIOREACTOR PROCESS FLOW DIAGRAM DYC ne Aorta Pressure K m 3 Transducer Solenoid Valve Air Tank Ventricle L 4 Pressure Transducer Check Valve Media Reservoir Capacitance Membrane Low Tank Pressure Transducer HighTank Pressure Transducer High Pressure Tank Pump Low Pressure Tank Figure 2 Bioreactor Process Flow Diagram Microcontroller Control System for Heart Valve Bioreact
26. lue of P diff dP MA delta Gain Bias and threshold of the aorta pressure transducer The format is P_diff fdP_MA fdelta fGain fBias fThres d This string will be parsed in MATLAB 2 o If the first character of the string is o operation which means the user wants to change the value of the key variables PC communication will parse the following string of the command and load the value to the corresponding variables which are used in the pump control task gn S 3 s If the first character of the string is send which means the PC is collecting data 9 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 and needs the microcontroller to send the data of the four transducers and the pump signal PC communication will package the demanding data into a string and send it back to PC through serial port The format of the string is H963dL963dV963dA963dU961d and it will be parsed in MATLAB on PC These two tasks may access the same variables at the same time So the TRT will manage these accesses by using semaphore The main functions I use in this project is as follows Function Description void trtinitKernel uint16 tidletask stack Sets up the kernel data structures The parameter is the desired stack size of the idle task For a null idle task a stack size of 80 should be sufficient void trtCreateTask void fun void uint16 t stacksize uint32 treleas
27. n define end serial communication library Don t mess with the semaphores itdefine SEM_RX_ISR_SIGNAL 1 Hdefine SEM STRING DONE 2 user hit enter Hinclude trtUart h Hinclude trtUart c define DIFFERENCE 11 define AORTA 12 define VENTRICLE 13 define READ U N U gt gt N amp 1u define SET U N void U 1u lt lt N define CLR U N void U amp 1u lt lt N define FLIP U N void U 1u lt lt N define SEM SEND 3 define SEM INPUT 4 define SEM SQUARE 5 Hdefine T OVERFLOW 500 UART file descriptor 22 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 putchar and getchar are in uart c FILE uart str FDEV SETUP STREAM uart putchar uart getchar FDEV SETUP RW int args 2 unsigned char P tank H P tank L double P diff int count double deltaP double delta double time squarewave dP MA Gain Bias int thres T float P C D G B unsigned char P aorta P ventricle unsigned char channel flag long HighTank total LowTank total int pumpSignal char sendData 14 void initialize void int main void begin initialize set sleep mode SLEEP MODE IDLE sleep enable while 1 begin CLR PORTD 1 sleep cpu end end void pump control void args begin uint32 t rel dead while 1 begin switch channel flag begin case DIFFERENCE wait for ADC done while ADCSRA
28. nnenseneenennennenseneunennensenennennenneneeneenennenneneenennennennenennennenneneenennennenneneenennenneneene 13 Result and IPIE EE 16 In n 17 Acknowledgement 17 APPENDIX User Manual esoseoreeneenesnnenneenennennnennennennsvnnennennennnvnnennennennnveneenennsnnneeneenennssnnenneen 18 1 Hardware setup i icsssicccscscsstecesecesscsstsesticrccescosscesedeacsestessucestansccssscesucestinstcesecestcesdinescests 18 2 Run MATLAB code ceseenvenvvenvenennnvnnvnnennennnnnnennennennnennennennevenennennennnennennennsvnnennennennnennenne 18 APPENDIXB Parts Number seseereenenvvnnveneenennevnnennennennsvnnennennennevenennennennnvenennennesnnveneenenneseneeneen 21 APPENDIX C Source Code c sssseereeneenssnnvnnennennsnnnennennennnnnnennennennnvnnennennennneenennennesnneeneenennssnnenneen 22 pump ttf 28 6 ds 22 Heart valve MCU M EN oni 29 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Introduction This project continues the design and development of a cyclic flow heart valve bioreactor for use in culturing and conditioning of tissue engineered heart valves in the Butcher Lab The bioreactor has to simulate the flow between left ventricle and aorta of the heart to mechanically stimulate the cells of the tissue engineered aortic semi lunar heart valve Figure 1 Heart Valve Bioreactor The microcontro
29. or Kang Li k1694 Pdiff 150 mmHg Pump off 150 Pump on I 100 u E 50 N IN Y N N 5 Aorta 5 0 High Tank a Valve closed Valve open 2 Low Tank a 50 Ventricle 100 10 15 20 25 30 Time s Figure 3 Example of Pump and Solenoid Valve control procedure We can see one example of pump and solenoid valve control procedure in Figure 3 The pump is turned on off based on the pressure difference between high tank and low tank if the pressure difference exceeds the upper threshold the pump will stop working if the pressure difference is smaller than the lower threshold the pump will start working The two way solenoid valve is controlled based on the pressure of aorta If the pressure of aorta exceeds the threshold the valve will be open otherwise it will be closed Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 High Level Design I use ATmega 1284P microcontroller in this project I use the built in Analog to Digital Converter to read the signal from the four transducers and control the pump based on the pressure difference of high tank and low tank and control the two way solenoid valve based on the pressure of aorta I also use MATLAB to communicate the microcontroller with the PC I collect data and plot real time waveforms using MATLAB I also use TRT Tiny Real Time to implement multitasking on the microcontroller The High Level Design diagram is shown in
30. r After we open the serial port we can communicate with the microcontroller through USB cable First thing we want to know is what kind of state the microcontroller or the bioreactor is So we can send a check signal which is a single character c in my design to the microcontroller The microcontroller receives the check signal and sends back a piece of information containing the current state The format of the information is P diffxXxXdP MAXXXdeltaXXXGainXXXBiasXXXThresXXX Then MATLAB parses the information by using strfind function And finishing parsing this information MATLAB will print out the parsed information in the command window So the user will check the current state of the whole system Please check User Manual for screen captures 13 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Set the value of the key variables through user interface and send them to microcontroller Since we get the information of the state we might want to change it to satisfy the demand of this period of data collection After printing out the state of the microcontroller MATLAB will ask the user Do you want to change the current values If the user types in O the state won t change and the MATLAB starts collecting data If the user types in 1 MATLAB will prompt the user to change the state of the system After finishing changing the value MATLAB will print out the value which the user just typed in and ask the us
31. r we check the desired value of the key variables we should type in 1 if all the 19 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 values are correct otherwise we should type in O and start the whole procedure over again After we determine the value of the key parameters MATLAB will start to collect data MATLAB will plot the real time waveforms of the four transducers as shown in Figure 13 f MATLAB BI High Tank Pressure 20 X o Bl Low Tank Pressure S BG File Edit View Insert Tools Desktop Window Help xj RR 2 9 s i 0B HOME File Edit View Insert Tools Desktop Window Help a T ENESEXEE TP BENE o lt gt a Current Foli Nat this df Bl Aorta Pressure Bl Ventricle Pressure File Edit View Insert Tools Desktop Window Help QOS6E8 R SAC9RAL B0E File Edit View Insert Tools Desktop Window Help x O6Gas s AAV9R4 8 08 m values g valul Figure 13 Real time Waveforms of four transducers We can monitor the pressures by these real time waveforms After we reached the time length of this experiment MATLAB will store the four vectors of the values of the four pressures in a mat file and prompt a pink line to tell the user what format of the saved data is as shown in Figure 14 Do you want to change the current values Please input 1 or 0 1 for changing values 0
32. rintf n t t t tGain f Gain current fprintf n t t t tBias f Bias current fprintf n t t t tThreshold Aorta Pressure f Thres current 29 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 forintin TNS KN NST NN fprintf rDo you want to change the current values n ask the user to change value check flag input Please input 1 or 0 1 for changing values if check flag 0 finish input flag 0 while finish input flag 0 fprintf AnPlease input the value of P diff the default value is 100 n P diff input P_diff if size P_diff 0 P_diff_used 100 else P_diff_used P_diff end fprintf AnPlease input the value of delta the default value is 1 n delta input delta if size delta 0 delta used 1 else delta used delta end fprintf AnPlease input the value of the threshold aorta pressure the default prssure 77 5723989 mmHg Mn thres input thres if size thres 0 Thres_used 77 5723989 else Thres_used thres end fprintf P diff f delta f threshold aorta voltage f nls this correct n P_diff_used delta_used Thres_used finish input flag input Please input 1 or 0 1 for correct n if finish input flag 0 clear delta P diff finish input flag thres break end end else P diff used P diff current delta used delta current Thres used Thres current 30 Microcontroller Cont
33. rintf Please type in the time length of this data collection n prompt the user to type in the data length timeout input Time length in minutes timeout_used timeout 60 convert minutes to seconds fprintf fid c n check scaler 5 255 393 3217 convert the units to mmHg sample_rate 44 samples second while isempty check check 1 P check the current state of the whole system check fscanf fid s P_diff_location strfind check P_diff parse the string dP MA location strfind check dP_MA delta location strfind check delta Gain location strfind check Gain Bias location strfind check Bias Thres location strfind check Thres P diff current str2double check P diff location 6 dP MA location 1 dP MA current str2double check dP MA location 5 delta location 1 delta current str2double check delta location 5 Gain location 1 Gain current str2double check Gain location 4 Bias location 1 Bias current str2double check Bias location 4 Thres location 1 Thres current str2double check Thres location 5 length check scaler 388 2081 end fprintf AnThe current values of P diff dP MA delta Gain and Bias are as follows display the current state fprintf n t t t tP_diff f P diff current fprintf n t t t tdP_MA f dP MA current fprintf n t t t tdelta f delta current fp
34. rol System for Heart Valve Bioreactor Kang Li k1694 end R Use 250 Gain total a_Transducer R Calib R Use 5 255 Bias used b Transducer Thres convert round Thres used 388 2081 393 3217 255 5 send packet sprintf P9606 2fC9606 3fD96dG9606 3fB9606 3fT96d P diff used dP MA delta used Gain total Bias used Thres convert fprintf fid o s r send packet send the new value to microcontroller clear P diff current dP MA current delta current clear the internal variables clear Gain current Bias current clear P diff location dP MA location delta location clear Gain location Bias location Thres current initialize the vectors initialize the vectors Low tank zeros timeout used sample rate 1 High tank zeros timeout used sample rate 1 Ventricle zeros timeout used sample rate 1 Aorta zeros timeout used sample rate 1 PumpSignal zeros timeout used sample rate 1 i real 1 set the figure handles figureHandle1 figure NumberTitle off Name High Tank Pressure Color 0 0 0 Visible on axesHandle1 axes Parent figureHandle1 YGrid on YColor 0 9725 0 9725 0 9725 XGrid on XColor 0 9725 0 9725 0 9725 Color O 0 0 xlim 0 timeout used ylim 0 120 scaler 388 2081 hold on plotHandle1 plot axesHandle1 i_real High_tank 1 1 g i_real PumpSignal 1 1 r Marker LineWidth 1 xlabel Time in
35. seconds FontWeight bold FontSize 10 Color 1 1 0 ylabel High Tank Pressure in mmHg FontWeight bold FontSize 10 Color 1 1 0 title High Tank Pressure FontSize 15 Color 1 1 0 figureHandle2 figure NumberTitle off Name Low Tank Pressure Color 0 0 0 Visible on axesHandle2 axes Parent figureHandle2 YGrid on YColor 0 9725 0 9725 0 9725 31 Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 XGrid on XColor 0 9725 0 9725 0 9725 Color O 0 0 xlim O timeout used ylim 0 120 scaler 388 2081 hold on plotHandle2 plot axesHandle2 i_real Low_tank 1 1 g i_real PumpSignal 1 1 r Marker LineWidth 1 xlabel Time in seconds FontWeight bold FontSize 10 Color 1 1 0 ylabel Low Tank Pressure in mmHg FontWeight bold FontSize 10 Color 1 1 0 title Low Tank Pressure FontSize 15 Color 1 1 0 figureHandle3 figure NumberTitle off Name Ventricle Pressure Color 0 0 0 Visible on axesHandle3 axes Parent figureHandle3 YGrid on YColor 0 9725 0 9725 0 9725 XGrid on XColor 0 9725 0 9725 0 9725 Color O 0 0 xlim O timeout used ylim 0 120 scaler 388 2081 hold on plotHandle3 plot axesHandle3 i real Ventricle 1 1 Marker LineWidth 1 Color 0 1 0 xlabel Time in
36. tware design Microcontroller Part 1 TRT Tiny Real Time use TRT Tiny Real Time to implement the multi tasking on the microcontroller TRT is a real time kernel which was written by Dan Henriksson and Anton Cervin technical report Aso see the ECE 4760 webpage about TRT This kernel has some characteristics which make it very suitable for this project Multitask can run on the same ATmega 1284P microcontroller chip Every task has its own release and dead time The scheduling algorithm is Earliest Deadline First EDF There are semaphores to protect shared resources e g memory or the UART which are used by more than one task In this project create two task using Tiny Real Time pump control and PC communication The task pump control is reading the signal sending from the four transducers continuously And it control the pump based on the pressure difference between high tank and low tank And it also controls the two way solenoid valve based on the pressure of the aorta transducer The task PC communication is reading the serial port If it receives command sending from the serial port it will parse the command and react correspondingly There are three different commands based on the first character of the string They are as follows 1 c If the first character of the string is c check which means the PC want to check the current state of the microcontroller PC communication will send back a string which contains the va
37. ucers signals to MATLAB Microcontroller check the Microcontroller reads the current state of the command system Users send different MATLAB display the command to current state or plot the microcontroller using MATLAB real time waveform Figure 4 High Level Design Microcontroller Control System for Heart Valve Bioreactor Kang Li k1694 Hardware design Junction Box I need to use microcontroller to control the pump and solenoid valve which are both driven by 110V wall AC But the output of the microcontroller is 5V DC So I need junction boxes which contain a relay switch to control the AC circuits Figure 5 Junction boxes The major parts of the junction box include solid state relay wall switch and wall socket The circuit diagram is shown as in Figure 6 The junction has a power plug which can be put in any wall socket This plug provide the power of the junction box The wall socket and wall switch are on the surface of the junction box The plug of the pump or the solenoid can be put in the wall socket And the wall switch can cut off the AC circuit in case of emergency situation In this way we can energize the pump or the two way solenoid valve Inside the junction box the AC live line first goes into one exposed lead of the wall switch Then it comes out from the other lead of the wall switch and goes into one exposed lead of the AC output of the solid state relay After coming out from the other le
Download Pdf Manuals
Related Search