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1. Figure 2 Drawings for scanner housing These are the drawings that make up the assembly It is easy to see that there are a lot of little details in the design of all three of the major parts The difficulty that was run into in designing this was that after all was done on paper going out and getting an estimate on actually making it deemed to be rather troublesome due to the functionality of the CNC dealing with the square corners and 45 degree chamfer on the inside wall Some revision had to be done before getting an accurate estimate As simple as the design already stands trying to make it simpler would exclude some of the key features that are needed in our plate scanner to get it to run efficiently Right now were considering a more economical and rapid fabrication just to begin refining the turbidostat and all its various functions 2 2 CIRCUIT BOARDS In order to make measurements of the optical density of the individual wells two different circuit boards are being created one board for the 24 photodiodes and one board for the 24 LEDs Photodiode Circuit Board Figure 3 Dimensional Picture of Photodiode Board The photodiode circuit board will be screwed into the lid of our enclosure using stand offs and predrilled holes in both the board and the lid Figures al and a2 in Appendix A show the components that will be used in both of these boards Figure a2 shows a higher level representation with 3 shift registers th
2. This milestone was very important as it sets the stage to test our modeling behavior and design specifications Difficulties we still need to overcome include the following list i2 The drilling out of the housing unit to desired size Soldering and incorporating circuits with housing unit Arduino to PI controller to Liquid handler communication 3to 8 decoder second current driver and shift registers used for the control signals to the block code set up for the microcontroller Testing to determine any further problems This next week will be very important in completing and implementing our design for testing and also determine what flaws we need to overcome 13 APPENDIX A HARDWARE SCHEMATICS A04 Aig A24 bos OEZ4 VA MC74HC138ADTR2G V TSSOP 16 e UO gt eo mM a C8_Z_138 0 1uF 3 groups of 8 chips For each group 5 inputs 1 Ein 3 lines to select which chip is being controlled 2 total 9 5 lines to Arduino pwr gnd OE 1 for de selected chips ICs 1 For OE pins 74xx138 active low decoder unselected pins high 2 For outputs connect together OE must be low on at most 1 chip at a time 3 For SO S1 pins connect together all chips at same sensitivity 4 For S2 S3 pins connect together Sheet Photodiode 0 Sheet Photodiode 7 photodiod e sc IOUT OUTs can be tied together because OEZ puts OUT in a high Z state File 8 sensors sch Sheet Group Z o
3. ARDUINO SOFTWARE The Present Test Code The following is a description of the code that we currently have set up on our Arduino Mega board This is by no means a finalized version of the code that we have and will certainly be changed by the final product What we have so far is the basic code that is needed to test the readings of the photodiode which are taken in the LEDs turning on and off as needed and the drawing of the correct amount of current Appendix B shows the code that 1s currently on our Arduino Mega This code utilizes many of the registers used on the Atmel ATmegal280 microcontroller to set up various interrupts timers counters and more We decided that working more low level with the microcontroller instead of using the Arduino development code would be more desirable because it would give us access to the interfaces of the microcontroller and would give us more control over our code The code that is shown in appendix B utilizes an external counter on pin 47 TCNTS5 that counts the low to high transitions on the incoming digital signal This pin is hooked up to the output of the photodiode and is counted until the interrupt service routine ISR is fired as defined in the upper portion of the code This ISR is set up to fire when Timer 4 reaches a certain value which was calculated to be 8000 in order for the interrupt to fire approximately every second When this interrupt fires the counter value which corresponds to
4. to units in which the liquid handler knows how much solution to extract and replace 5 Create two arrays one with amount of solution to extract and another with how much nutrients to add 6 Wnte these values to two separate files Bele e The basic code of a PI controller 1s integrator state num wells 0 while 1 for each well W error read well W ref integrator state W integrator state W error u W kp error ki integrator_state W output u wait The while loop keeps going as long as there is data coming from the Arduino file Since there are 24 wells num wells will equal 24 Inside the loop the read_well W ref gives the error calculated and will be used when the respective proportional and integral gains are applied to find the needed output u w of the controller This value will then be sent through the calculation and inserted into the array of values After this program is executed the liquid handler will read those files to perform the actual controlling of the bacterial growth 5 0 CONCLUSIONS The work for this project has been divided up irregularly with each member contributing when difficulties arise Generally though Peter Harker has been building the housing unit and system modeling Max Holloway has been working on the arduino set up and software design with Evan Dreveskracht working on interfacing the liquid handler and soldering Much of our meetings involve help from our various advisors as well
5. Turbidostat Hardware and Software Design MS 4 600 nm LEDs By Peter Harker Maxwell Holloway Evan Dreveskracht Table of Contents Introduction ccc cece cece ccc cececececcecucuceeuecenss Hardware 2 1 Scanner Assembly Design 2 2 Circuit Boards cc cc cece cece ce eere eee 2 3 Gripping Mechanism 0 cece cece ee eens System Model Discritized 0 ccc ccc cece eee eens Software Implementation 4 1 Arduino Software een 4 2 PI Controller Software CONCIUSIONS cece cece cee cccecececcecucucuceccucucucs EDO is crass Goes aici lated teens TO 28 DUC D E ceste Era uen Pee anaes 1 INTRODUCTION For the fourth milestone we are focusing on the main components of our hardware and software design and discussing our choices for each These designs are the must fundamental aspects of this project and give an overview of our project as a whole Our hardware includes the scanner housing circuit boards and liquid handler This week and part of next we will be focusing on completion of the scanner housing and circuit board specifically which will be determined on shipping times and CNC mill availability For the software of our system we will explain the Arduino and PI controller code Further incorporating the PI controller code with the liquid handler is also needed but will be incorporated after our syst
6. Using this enables us to place and remove the lid as shown in figure 1 without the use of a servo motor This is important since our turbidostat will have to perform two main functions every 15 minutes which are take readings lid on and extract and refill wells lid off Another function which will be performed once a day will be the exchanging of plates which lies inside the housing unit The gripper will also be utilized in that way In order to accomplish this there will be lots of calibrating involved to ensure that the gripper picks up and drops off in exactly the right position There are options in the liquid handler software which allows you to step to a gripping position and save the position to memory 3 SYSTEM MODEL DISCRITIZED In our last couple reports we showed what our controller would do in a continuous control setting In reality our system acts more discretely then continuous since our sample time is once every 15 minutes This means that although bacterial growth is continuous our controller assumes one value of optical density every 15 minutes It does not take into account that the bacteria population is still growing What we want to see is how close our system model is to a real life setting and if our controller is good enough Zero Order Bacteria Population x on Hold1 Band Limited White Noise Integral Gain Integrator2 NN 1 3 fh a 1 fu s E Desired Population Satu
7. at will take in serial data and will send out parallel controls to for each block Each of these blocks consist of eight photodiodes that all use the same control lines The AO Al and A2 control signals sent into the blocks are used to control a 3 to 8 decoder that selects the output enable lines of one of each of the photodiodes so that one of these are being read at one time The SO S1 S2 and S3 control lines control the sensitivity and frequency scaling of the photodiodes Controls SO and S1 are used to control the sensitivity using the following table 1x Figure 4 Effects of S0 and S1 on the Photodiode L H L H H Controls S2 and S3 control the frequency according to the following table 5 fo SCALING divide by Figure 5 Effects of S2 and S3 on the Photodiode The following list shows the components that are used for the photodiode circuit board 3 Shift Registers 74L 595 1 Buffer 74LS541 3 3 to 8 Decoders 74L S138 24 Photodiodes Light to Frequency Converters TSL230 LED Array Circuit Board Figure 6 Dimensional Picture of the LED Board The LED array circuit board will be screwed into the bottom plate of the enclosure that we created using stand offs and predrilled holes in both parts Figure a3 in appendix A shows the schematic for the LED board In this schematic you can see that there are two integrated circuits ICs that are connected to the grou
8. ble gt 0O char c Serial read ULnES X on D7 ewirteh c case o 18 on 1 Case ET long m millis while Serial available amp amp millis j if Serial available Serial print e Serial print in tOTLUTDM char LEDbit Serial read O IC LEDD lt O LEDDLt gt 7 4 LOCU if on LEDs BV LEDbit telse LEDS amp v BV LEDD1IL TLC SetByte LEDs Serial print o Serial print LEDbit DEC Serial print 3 cerial println LEbDs BIN void SPI shifts uints t data SPDR data while SPSR amp BV SPIF vord TLC SevBylce uince L darte SPI shift8 data TILO LE PORT BV TLC LE TLC Lis PORT a BV ILC LE youd SPI inrt i OPCR BV MSTR BYV SPE SPSR BV SPI2X 19
9. em and readings are working properly 2 HARDWARE The turbidostat design project consists mainly of hardware design and programming the hardware to do what we want it to do There are two main categories for which the hardware is made up of that is the plastic housing unit and the printed circuit boards containing the surface mounted LED s and photodiodes To design and make these have consumed a considerable amount of time but when finished we will have a fully functional plate scanner ready to read optical densities in a 24 big well plate 2 1 SCANNER ASSEMBLY DESIGN Figure 1 Scanner assembly where printed circuit boards top and bottom and plate center will sit This 1s currently the design we hope to use for our plate scanner We have been running into some issues financially in getting it made with the budget we have In order to achieve the best quality paying someone to mill it on a CNC is far too expensive which caught us by surprise The other option is to rapid prototype or use a 3D printer but our customer has concerns about the precision of the printer and there is also that same price issue in getting it made that way The likely solution that we came up with will be to use the CNC located in the SOS lab on the third floor of the electrical engineering building
10. f 8 Light Sensors Figure a1 Components Inside Each Box of Eight Photodiodes 14 Sheet Group of 8 Light Sensors 1 SER BF our QUT BF SRCLK_BF RCLK_BF D sensors sc ouTc_OUT2_BF DDDODDOOD TO mmococou27 D zL ile 8 sensors sc OuTG_OUT3_BF D D ODDODOOD0 I cCc mmuo ouz e g ile 8 sensors sc 74 8541 CONN 10 University of Washington EE449 Spring 2010 File photodiodes sch Sheet Title Photodiodes for the Mini Plate Reader for the Liquid Handler t Board for the Photodiodes ircui Figure a2 High Level Schematic of C 15 LED15 10 CONN P ld 2 22 LED Vr ext 1 26V VG T lout Vr ext Rext 15 3 CM 1 d VG is 127 128 0 992 on startup CM is 1 at startup ss N 20 1mA 1 25V 9310hms 15 at startup g 2 SCK 3 OE ED2 21 C OE ED2 TLC5926 U 23 R EXT a z o ba University of Washington EE449 Spring 2010 File leds sch 2V 2V 0 1uF 0 1uF Bypass caps for the TLCs Sheet Title LEDs for the Mini Plate Reader for the Liquid Handler Size A4 Date 22 apr 2010 KiCad E D A eeschema 20100406 SVN R2508 final Id 1 1 a ee HANS ooo le eee LED y d bal x A MOSI 2 a 5 SCK 3 510 LE ED1 4 LE ED1 9 P OE ED2 21 C OE ED2 7 R5 TLC5926 5 U ox OEN ED2 23_ p_ext B2 1 e N it Board
11. ircul Figure a3 Schematic for the LED C 16 APPENDIX B ARDUINO CODE AS IS HARDWARE SETUP PE6 Photodiode pulse input enabled SOFTWARE SETUP t 115200 baud serial General tips purputs the digital input wath pull up resistor 1 most of the macros are defined in http www nongnu org avr libc user manual modules html Z Vi Dan ig 1 lt Dub LO Ben bie Dy BYU Lo Seu Dit d BVi4 3 Idioms for setting bits eg 0x0 0x10 lf set biti in REG BV bitl1 REG Je BVIDILL BV iD1L2 4 Idioms for clearing bits REG amp BV bitl clear bitl REG amp BV bitl BV bit2 0 16 REG set bitl and bit2 in REG in REG If Clear brtl and bat in REG 5 Use ninti ty ince ty winti ty nints t sro Iinetead of int char is an B bit microcontroller possible This a include lt avr interrupt h gt include lt inttypes h gt SO Use Tinte C Of NDS Lt whenever fdefine fdefine fdefine fdefine fdefine fdefine fdefine fdefine fdefine fdefine fdefine define fdefine fdefine fdefine Ginco t TLC LE TLC LE PORT TLC LE DDR TLC OE TLC OE PORT TLC OE DDR TLC SDI TLC SDI PORT TLC SDI DDR TLC CLK TLC CLK PORT TLC CLK DDR PHOTOD OUT PHOTOD PORT PHOTOD DDR LEDs PBO PORTB DDRB PLO PORTL DDRL pE2 77 51 PORTB DDRB PB1 PORTB DDRB PL2 PORTL DDRL yr 99 49 Jf 82 Jf 4T TIMER1 COMPA vect fi
12. nds of the 24 LEDs These ICs are current drivers that are used to provide a constant current that 1s the same for all of the lights This current 1s referenced using an external resistor on pin 23 and also using the following equation IOUT target 1 25 V Rext x 15 We want 20 1 mA and are using a 931 Q resistor to accomplish this We had to use two different current driver ICs because the maximum amount of LEDs that can be hooked up 6 to one of these components is 16 and we need to hook up 24 In order to set up our circuit correctly we daisy chained two of the ICs so that both drivers can be controlled through on serial output The basic way that one of these drivers works is by taking in serial data on pin 2 a clock on pin 3 that clocks the data input a latch signal on pin 4 that sets the current data set up to the outputs and an output enable on pin 23 How this is connected to the Arduino board will be addressed with more specifics in the next section The following list shows the components that are used for the photodiode circuit board 2 Current Drivers TLC5926 24 LEDs HLMP EJ10 XZODD ND Digikey Part Number 2 0 1 uF Capacitors For Noise Control 2 3 GRIPPING MECHANISM Figure 7 Use of gripper to pick up plate and re locate it One of the solutions to facilitating this design project was to use make use of the gripper This is one of the functions of the liquid handler located in the SOS lab
13. ration Zero Order Integrator X x n u gt Hold Product reson Gan T LLLA a Integrator1 N x n u Generator Nutrient Input u Fresh Media n Zero Order Hold2 Figure 8 Simulink model with zero order holds and pulse generator to achieve discrete characteristics Bacteria population top Fresh media center Controller output or Nutrients bottom Figure 9 Desired population 0 Figure 11 Desired population 1 2 In discretizing our system to take into account the large sample time we found that our proportional and integral gains were a little to high By adjusting these gains we achieved reasonable results 4 SOFTWARE IMPLIMENTATION The implementation of software for our turbidostat will be done on 3 separate devices and will entail 3 separate programs with 3 separate programming languages The issue we struggled with was how to interface all of these together in order to achieve a fully functional turbidostat without any significant time delay or data acquisition errors The obvious solution to that predicament was to allow for each program to write to a text file so that the program requesting data would be able to read in the file The devices and programs we will be using are the Arduino mega which provides its own programming language the liquid handler which provides its own program and language 9 and the PC which will carry out the liquid handler software and our PI controller code written in java or C 4
14. res every 1 second see setup ISR TIMERA COMPA vect ninco E oun TONES 05 sea ds oerial printlnicount DIES enable interrupts DEC 17 void setup Serial begin 115200 Serral println hz s Make sure OE is high initially TLC OR PORT BV CTLC OR Pin Setup ILC SDI DDR BV CLC SDI TLC OE DDR BV TLC OB TLC LE DDR BV TLC LE ILC CLK DDR p BVUDDC CLR Pin setup PHOTOD DDR amp BV PHOTOD OUT PHOTOD PORT BV PBOTOD OUT enable pull up resistor on PES T3 TIMER1 setup to fire the TIMERI COMPA vect interrupt every 1 second WGMn 3 0 0b1111 fast PWM mode OCRnA top CSn 2 0 0b101 clock counter at F CPU 1024 prescaler at 1024 TCCRAA BV WGM41 _BV WGM40 TCCR4B BV WGM43 _BV WGM42 TIMSK4 BV OCIE4A enable COMPA interrupt OCR4A 8000 15624 1024 16e6 15625 steps 1 second per interrupt note that the register should be set to steps TCNT4 0 TCCR4B BV CS42 BV CS40 start timer prescaler at 1024 TIMER3 setup to count pulses on the T3 pin rising edge WGMn 3 0 0b0000 normal mode f CSn 2 0 blli glock on rising edge of T3 TONTS O TCCRSA 993 TCCR5B BV CS52 BV CS51 BV CS50 f initialize all LEDs to off SPI init TLC setBytetl set OE to low TLC OE PORT amp BV TLC OE sext void loop if Serial availa
15. the frequency of the signal since it is printed every second is printed to the serial console Additionally we can accept user input from the console to turn LEDs on and off through the current driver which will be explained more in depth below We have connected one current driver IC with eight LED outputs we are using a slightly different Texas Instrument that drives only 8 LEDs instead of 16 however the concept is the same to the microcontroller using an SPI interface This interface allows serial input to be taken in by the current driver in the form of 8 bits which then select which LEDs should be on and off As shown by figure 5 10 OE ED2 T1 IL LE ED1 0 i 0d SDI mn at Iu l l 00g OUTO tt ttt tH OUTT OUT2 1 9 I I off OUT 1331113411 1 d I SDI Figure 12 Timing Diagram for Current Driver Test Chip TLC5916 We have set up an interface in the serial monitor where the user can type o or P followed by a number to turn an LED on or off respectively For example if ol is typed into the console then LED 1 is turned on If f1 is typed into the console then that same LED 1s turned off This allows us to verify that the LEDs are working as they should use the current drivers Planned Code That Will Be Implemented Now that we have the building blocks of the code set up 1 e the photodiodes are being read and the LEDs are being
16. turned on and off through the current driver we will have to use these building blocks to create our final code Portions that are left that are yet to be implemented are the 3 to 8 decoder the second current driver and the shift registers used for the control signals to the blocks These changes will be very easy to implement The 3 to 8 decoder is very easy to control and only needs 3 input lines a binary value to select which output will be a low signal while the others are high The shift registers use the same concept as the current drivers and we will be running USART interfaces as SPI to control these The second current driver only requires that we hook up the serial data out of the first current driver to the serial data in of the second Then we will have to change our SPI function slightly to send the first 8 bits through to the second chip before latching When our final circuit comes we will begin testing the code on our final board and verify that everything 1s working as should be 11 4 2 PI CONTROLLER SOFTWARE The PI controller software will be written 1n java and will perform our closed loop feedback control system implementation The basic functions this program will be carrying out are Execute the plate scanner program on Arduino and read in the data saved to file Create an array of current optical densities read in from text file sent by Arduino send each OD through the PI control loop Perform a calculation from OD

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