simple spectro https:/github.com/hackuarium/simple-spectro - - PowerPoint PPT Presentation

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simple spectro https:/github.com/hackuarium/simple-spectro - - PowerPoint PPT Presentation

Feb 02, 2024 550 likes •1.9k views

simple spectro https:/github.com/hackuarium/simple-spectro https://hackuarium.github.io/simple-spectro http://www.hackuarium.ch Supported by oceane@patiny.com florian@patiny.com luc@patiny.com DIY biology Do It Together biology and more

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simple spectro

https:/github.com/hackuarium/simple-spectro https://hackuarium.github.io/simple-spectro http://www.hackuarium.ch

  • ceane@patiny.com

florian@patiny.com luc@patiny.com

Supported by

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DIY biology Do It Together biology and more …

Meet us every Wednesday evening, 7.30pm-10.30pm

@Hackuarium

www.hackuarium.ch

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3D printing Milling Injection molding Breadboard PCB PCBA Microcontroller Data analysis Chemistry Biology Environment

Electronic Mechanic Software Applications Project

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Agenda

  • 1. General overview
  • 2. Electronics
  • 3. Mechanics
  • 4. Programming
  • 5. Experiments
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1

General overview

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Spectrophotometer ?

I0 I

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Beer-Lambert law

  • A: absorbance
  • T: transmittance
  • I0: intensity of the light
  • I: intensity of the light after the cell
  • L: length of the cell
  • c: concentration (M)
  • 훆: molar attenuation coefficient

A = - log (T) = - log (I / I0) = 훆 L c

I0 I

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RGB led ?

Available spectra

Type Name R G B W

Show the spectra of the 4 leds: R : red led G : green led B : blue led W : white, represented as a black line Z : background E : experimental A : absorbance T : transmittance

Tracking information

Chart Wavelength (nm) Intensity chart 565 488.25 chart-1 565 6,247.63 chart-2 565 262.75 chart-3 565 6,355.63 Name Comment red pH:1.37 E red pH: 1.50 E red pH: 1.64 E red pH: 1.77 E red pH: 1.87 E red pH: 1.92 E red pH: 1.97 E red pH: 2.00 E red pH: 2 14 E

Spectra

  • Filter

Smooth 8 Normalize Experiment

Save

Name Concentration

Concentration in mM

Comment

Test RGB Acquire

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2

Electronics

Arduino …

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Classical approach

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Arduino platform

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https://www.adafruit.com/?q=breakout

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A solution : use of shields

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May become a little bit complex …

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We tried this approach

  • Arduino MEGA
  • Extensions board for halloween

decoration

  • "This is what is need for my

bioreactor"

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Can we make our own Arduino ?

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Legoino : master board

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Legoino : extensions

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Arduino Leonardo

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Arduino platform

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Microcontroller : ATMEGA32U4

  • 32 kb of programmable flash memory
  • 2.5 kb SRAM (Static random-access memory)
  • 1 kb EEPROM (Electrically Erasable Programmable Read-

Only Memory)

  • Operating voltage: 2.7v to 5.5V
  • 8 (min 2.7V) / 16 (min 4.5V) MHz
  • 26 I/O, 12 x 10bits ADC
  • USART, I2C, USB, SPI
  • 2 x 16bits Timer / Counter
  • 4 x PWM 16 bits, 6 x PWM 11 bits

4 CHF

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Microcontroller : ATMEGA32U4

Datasheet

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Making your own PCB

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www.pcbway.com - www.seedstudio.com

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PCB production

  • $5 for 5 to 10 PCBs 10x10cm
  • + shipping … $10 to $25
  • Numerous suppliers
  • http://www.pcbway.com (currently my preferred one)
  • http://www.seedstudio.com
  • http://www.elecrow.com
  • https://oshpark.com - $5 for 3 per square inch
  • You need Gerber Files
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www.pcbway.com ⚠ combine shipping

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eagle

https://www.autodesk.com/products/eagle/ Opensource alternative: KiCad
 http://kicad-pcb.org/

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Schematic

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USB

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LCD

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Light to frequency - TSL 237

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Exercise

  • Download the project
  • https://github.com/hackuarium/simple-spectro
  • In eagle
  • Open Schematic: tutorial/eagle/tutorial.sch
  • Add 3 leds with corresponding resistors on pins A0, A1 and A2
  • Board
  • Routing
  • Check
  • Create Gerber files
  • Check Gerber : https://gerber-viewer.easyeda.com/
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Soldering the PCB

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PCBA

Printed Circuit Board Assembly

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www.elecrow.com

  • Free components list
  • https://www.elecrow.com/pcb-assembly-p-366.html
  • 120 SMD capacitors
  • 235 SMD resistors
  • Provider: https://lcsc.com/
  • In Eagle:
  • ‘attr’, add LCSC Part # (or free components)
  • ‘run ULP ➡ bom’, export as CSV
  • ‘export ➡ mount SMD’ : export .mnb and .mnt
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www.elecrow.com

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Through holes components

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  • 1. Solder pins on LCD screen
  • 2. Check the screen !!!!
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1 2 3 4 5

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6 7

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3

Mechanics

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Various strategies

Laser cutting ✔ fast and cheap ✘ limited shapes (2D) 3D printing ✔ any shape ✘ slow ✘ not that cheap Milling ✔ perfect quality ✘ cost ✘ time Molding ✔ cheap for large series ✘ setup cost ✘ time

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3D printing

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You need an STL file

https://github.com/Hackuarium/simple-spectro/tree/master/CAD/open-box

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The cost of 3D printing

  • Printer 1000 CHF
  • Case 50g: 3 CHF
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https://www.shapeways.com/

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Laser cutting

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The cost of laser cutting

  • Machine 2000 CHF
  • Plexiglas 3mm: 70 CHF / m2
  • https://roehmschweiz.ch/fr/produits/plaques/plexiglas/gs-allround/
  • MDF 3mm: 10 CHF / m2
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Milling

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Aluminum case

  • Aluminium milling
  • Black anodizing
  • Logo laser engraving
  • ISO 10303 (STEP file, Standard for

the Exchange of Product model data)

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https://www.mfg.com

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  • full.step
  • 20

pcs

  • EUR 1140,00
  • 14 calendar-days production time
  • full.step
  • 50

pcs

  • EUR 2245,00
  • 16 calendar-days production time
  • full.step
  • 100 pcs
  • EUR 3625,00
  • 20 calendar-days production time
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Molding

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Molding

http://www.emold.net/

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Generating the files

Alternatives to Fusion 360

https://www.autodesk.com/products/fusion-360

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FreeCAD

  • 2D
  • 3D
  • open-source
  • STL file (Standard Triangle

Language)

  • https://www.freecadweb.org
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OpenSCAD

  • 2D
  • 3D
  • open-source
  • command line
  • http://www.openscad.org
  • full integration in FreeCAD
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OpenSCAD

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OpenSCAD

https://en.wikibooks.org/wiki/OpenSCAD_User_Manual/Transformations#minkowski

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Exercise

  • Create a millable box with 4 holes

for the screws

  • http://www.openscad.org/

cheatsheet/

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4

Programming

https://www.arduino.cc/en/Main/Software

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Arduino: the basics

Install the software:

https://www.arduino.cc/en/Main/Software

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Arduino IDE (Integrated Development Environment)

Verify Upload New Open Save Serial monitor Tabs

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Select the right Arduino

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Select the connected Arduino

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Arduino IDE: setup and loop

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Blink

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Testing the LEDs

Exercise: Create an RGB sequence

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More advanced

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Microcontroller : addressing pins

  • 3 registers: DDRx, PORTx, and PINx
  • DDRx: 0=INPUT, 1=OUTPUT
  • PORTx:
  • INPUT: pull-up if 1
  • OUTPUT: 1: drive pin HIGH, 0, drive pin LOW
  • PINx: toggle the pin
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DDRB: input / output ?

7 6 5 4 3 2 1

DDRB = (1 << DDB4) | (1 << DDB0);

DDR: Data direction register

7 6 5 4 3 2 1

1 bit shift

  • r

7 6 5 4 3 2 1

1 1

7 6 5 4 3 2 1

1

| = DDRB =

Initial:

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Microcontroller : ATMEGA32U4

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Microcontroller : addressing pins

// pin 0 and 4 of PORT B to output DDRB = (1 << DDB4) | (1 << DDB0); // drive pin 0 and 4 of PORT B to HIGH PORTB = (1 << PB4) | (1 << PB0);

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Microcontroller : ATMEGA32U4

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Debug using Serial.println

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Test all the functionalities

Exercise: Test LCD display

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Multithread

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Scalable way of programming

  • Tabs
  • NilRTOS (multi-thread)
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Multithread with Shared parameters

Parameters

getParameter(x) setParameter(x, value) setAndSaveParameter

  • A
  • B
  • C
  • …

Parameters accessible from all the Thread and saved in EEPROM.

ThreadLcd

Process allowing to control the simple- spectra from a LCD display

ThreadTemperature ThreadBattery ThreadSerial

General process allowing communication

  • ver Serial (Bluetooth, Zigbee, Lora, …)

ThreadAcquisition

Process taking care of the acquisition based

  • n the parameters
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A COLOR_1 Red value for sample 1 B COLOR_2 Green value for sample 2 C COLOR_3 Blue value for sample 3 D COLOR_4 UV value for sample 4 E COLOR_5 Not used 5 F BLANK_1 Red value for blank 6 G BLANK_2 Green value for blank 7 H BLANK_3 Blue value for blank 8 I BLANK_4 UV value for blank 9 J BLANK_5 Not used 10 K BEFORE_DELAY Delay before taking blank 11 L FIRST_DELAY Delay between blank and first experiment 12 M INTER_DELAY Delay between experiments 13 N NUMPER_EXP Number of experiments 14 O NEXT_EXP Next experiment, 0 blank and then for kinetic 15 P WAIT Current time to wait 16 Q NUMBER_ACQ number of acquisition of 100ms that will be taken 17 R INVERT_ROTARY invert rotary direction 18 S BATTERY battery voltage (hundredths of volt) 19 T TEMPERATURE temperature (hundredths of degree) 21 V ACTIVE_LEDS as a binary code (red, green, blue, uv, temperature, battery)

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Connecting to spectro

Serial monitor

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Arduino IDE (Integrated Development Environment)

  • h: help
  • s: display all current settings
  • K: get current delay
  • K5: set current delay to 5s
  • d: data
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Plot data

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Experiments5

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E131 in Gummy blue sharks

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Left: known [ ], right: Haribo

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Absorbance versus concentration

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OD versus time

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Determine [] of E131

  • Mother solution:
  • 10mg of E131 in 25mL of water
  • Diluted solutions
  • 0 mL ➡ 5 mL of mother solution in 20mL of water
  • 0, 0.5, 1.0, 1.5, 2.0, 2.5, 3.0, 3.5, 4.0, 4.5, 5.0 mL

Analyse data

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What’s next ?

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Hardware

  • Electronic
  • reduce power consumption (we went from 5mA to 250µA)
  • hard reset (to check, now software reboot)
  • Mechanics
  • Good solution for the screen (glued plexiglass)
  • Stability / reproducibility
  • https://hackuarium.github.io/simple-spectro/
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Applications

  • determination of pH ?
  • kinetic reaction
  • bacteria growth versus temperature
  • various bacteria
  • consortium growth
  • mercury water contamination using

quantum dots

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Carbon quantum dots

  • Prof. Eric McLamore, University of Florida
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Results

  • Prof. Eric McLamore, University of Florida
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