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Overview:

This repository contains the instructions/code/files for the assembly and operation of the LEDbyXample photoreactor. LEDbyXample is designed for automation and self-driving labs (SDLs), like those at the Acceleration Consortium in Toronto. Although it is designed for 8 mL (2 dram) vials that can be placed inside by a robotic arm with gripper, the 3d-printed design files are easily altered for use with larger vials. Most components, including for the LEDs (~1W to be suitable for photochemistry) are modular and easy to swap.

Authors:

Owen Alfred Melville, Staff Scientist
Monique Ngan, Automation Technician
Acceleration Consortium
Last Updated 2024-10-22

Why LEDbyXample?

Low Cost: Existing photoreactors on the market are quite expensive. One of the cheapest, the Pioreactor, costs about $340 USD ($460 CAD). There is no need for such a large price. The main parts for the LEDbyXample photoreactor cost about $80 USD, with additional electronic components from kits costing another $80 USD. Many of these additional parts are small electronic components that users may already have, and the kits provide more parts than are required by the reactor. Many of the components could also likely be sourced for cheaper as long as the builders are able to perform their own quality control checks.

Automation Friendly: LEDbyXample is designed to work with automation and self-driving labs. Vials can be release inside the reactor by a robotic arm with a gripper. Automation of the stirring rpm and LED intensity is controlled through a custom python script and uses a Raspberry Pi Pico which can be commanded through a USB cable. Wireless support for the Pico is available but not documented in this project.

Skill Development: LEDbyXample is made largely from scratch. This allows builders to develop their DIY skills (3D printing, electronics prototyping, microcontroller use). It contains clear build instructions with photos, links to videos, and clear part lists with links. The Python code used to communicate with the microcontroller is designed to be clear and easily modified.

Modular / Customizable: LEDbyXample is designed to be modular, with components (LEDs, fans, bases) that can be easily removed or swapped. The 3D printed parts that comprise the physical reactor can be modified to accomodate for different vial sizes.

Summary of Steps:

  1. Order the required items
  2. 3D Print the required parts
  3. Assemble the photo-reactor
  4. Operate the photo-reactor

Tools Required For This Project:

Skills required For This Project:

Step 1: Order the Required Items:

The majority of the components for this project are electronic.

Materials Required:

These materials are required for the photoreactor. You would need to purchase more to make additional photoreactors. Note, only 1x Fan and 1x Fan Board are strictly needed for stirring. The active cooling Fan and Fan Board are optional. The total cost with 2 LED modules and 1 active cooling (fan) module is $82.80 USD.

Item Supplier Part number Number Cost (USD) Total Cost (USD)
Raspberry Pi Pico WH PiShop 402-1 1 9.8 9.8
Grove Shield for Pico Digikey 1597-103100142-ND 1 6.25 6.25
Fan Control Board Digikey 1528-4808-ND 2 7.99 15.98
Square Fan (20mm Diameter) Digikey 2223-CFM-2006CF-060-078-22-ND 2 11.06 22.12
Grove to Fan Board Connectors Digikey 1528-4528-ND 2 2.83 5.66
Power Barrel Connector Digikey PJ-102AH 1 1.02 1.02
Power Supply Digikey L6R06H-050 1 5.31 5.31
LED Stars (Green) Digikey LST1-01H06-GRN1-01 2 6.41 12.82
NPN Transistor Digikey 1727-4252-1-ND 2 0.56 1.12
USB Cable for Pico Digikey DH-20M50056 1 2.72 2.72
Total Cost (USD) $82.80
Total Cost (CAD) $115.53

Materials Required - Kits:

These materials come in kits, so you may not need them if you already have similar materials. They can be used for multiple reactors or other projects.

Item Supplier Cost (CAD)
Prototype PCB Board Amazon Canada 21.99
Nyodenium Magnets 6mm x 2mm Amazon Canada 9.99
Heat Sinks Amazon Canada 10.99
Resistors Amazon Canada 17.99
Solder Seal Connectors Amazon Canada 16.99
4-Pin Connectors Amazon Canada 21.99
2-Pin Connectors Amazon Canada 10.77
Total Cost (USD) $79.29
Total Cost (CAD) $110.71

Generic Materials Required

Photo of Materials


Step 2: 3D Print the Parts:

All the 3D printed parts can be printed with 0.2 mm layer height and a 0.4 mm nozzle. For prototyping or low-temperature reactors, PLA filament can be used. For higher temperatures or shorter wavelength (blue,violet,UV), ASA can be used. Since ASA tends to warp, I recommend using glue stick on the print bed.

File Name Purpose Printing Considerations Number Required Customization Potential
LED_holder.stl Holds LED + Heat Sink None 1 per LED
blank_holder.stl Blocks Window None 1 per unblocked window
fan_base.stl Holds Fan + Magnets Tree Supports from base only 1 Change inset for larger fan
fan_holder.stl Holds Cooling Fan Tree supports from base only Only if cooling desired
reactor_shield.stl Holds Vial Tree supports from base only 1 Change circle diameter for larger vial
screw_base.stl Connects reactor to base None 1 Change screw pattern for different base

Step 3: Assemble the Photoreactor:

The 3D printed parts are modular. When assembled, they should look like this:

Step 3a: Assemble the LED Holders

The LED Holder takes the 3D printed insert, and adds in a heat sink and a ~1W LED with attached wires to be controlled by the microcontroller.

Parts Required:

Steps:

  1. Take your LED star, it should have two large soldering pads labelled + and -
  1. Clean the LED star pads using rubbing alcohol (isopropanol) and a tissue
  2. Tricky step Alert Attach a red wire to the + labelled pad on the right of the star, and tape it down away from the pad to keep it in place. Heat up your soldering iron in a well ventilated area, then place it over the wire. Using your non-dominant hand, feed solder to the pad from different directions, allowing it to flow onto the pad. Once the solder has covered the whole pad, carefully remove the soldering iron and replace it in its holder. The wire should be encased in solder that has made a strong bind with the pad. If after 2 minutes, gentle pressure on the solder pushes it off the pad, you may need to clean the pad and repeat the process. For tips on this process, see this video (Time Stamp 4:30) https://www.youtube.com/watch?v=H-82av4zQKY&ab_channel=MrTroutDT

https://github.com/user-attachments/assets/7bd34561-cb51-4cb3-8f49-8e8b69328b1f

  1. Repeat the last process using a black wire and the - labelled pad on the right of the star. Ensure the contact has been well made after completion
  1. Remove the adhesive from the heat sink, and slide it into the 3D printed LED holder. Note that the spikes of the heat sink point outwards, towards the thinner side. The flat side of the heat sink should point inwards towards the thinner side.
  1. Carefully feed the red and black wire through the hole at the bottom of the LED holder. If your wires will not fit, you can use a sharp knife to cut open the channel. As you feed the wires through, you may need to bend them so you can position the LED in a central location on the heat sink.
  1. If you wanted a permanent setup, you could wire these red and black ends straight to your LED board (Step 3c). However, to make them removable/swappable, the wires need connectors. I recommend getting a set of pre-wired connectors with red and black wires at the non-connector end. Take the red wire from your LED and the red wire from the connector, and place them in a solder seal connector so that the bare ends of the wires are touching and under the "solder" of the connector. Use your heat gun to carefully heat up the solder seal connector from different angles. First the plastic will melt, sealing the wires together, then you will see the solder spreading from the central area, which should create a proper connection between the two wires. Let the connection cool. To check that the wiring has been made correctly, you can use a multimeter, comparing the LED pad to the appropriate pin in the connector. Use this youtube video for guidance: https://www.youtube.com/watch?v=bvDk3HzS7lM&ab_channel=SkillBuilder
  1. Repeat the last step to connect the black wires.

Congratulations, you have created your LED holder, which can slide in and out of the photoreactor! You can create as many of these as you have LEDs that you want to use

Step 3b: Assemble the Fan Base

The fan base holds a fan with magnets to allow for magnetic stirring.

Parts Required:

Steps:

  1. Thread the wires through the hole near the center of the fan base, with the black side of the fan facing up.
  1. Carefully pull on the wires and wiggle the fan into the center square.
  1. Using super glue or double-sided tape, carefully place the magnets on the top of the fan.

  1. Attach the connectors: You can wire the fan to a 4-pin connector using the optional kit or an alternative.

    Using Optional Kit: Using the same technique as in Step 3a - 7, use solder seal connectors to extend the length of the fan wires by attaching them to pre-crimped wires from the electrical connector kit. Then, connect each wire to the connector head. When inserted correctly, the ends of the wire should be fully contained inside the plastic connectors, and fit snugly in place.

Using Other Connectors: If you have a pre-wired connector with 4 wire leads, you can use that instead of the connector kit. Using the same technique as in Step 3a - 7, use solder seal connectors to connect the fan wires to your pre-wired 4-pin connector.

Congratulations, you have created your Fan Base which is used to stir a magnetic rod in the reactor

Step 3c: (Optional) Assemble the Fan Holder

The fan holder holds a fan to actively cool the reactor vial. The cooling capacity of the current setup is unknown, and it is possible a larger or a stronger fan is required. This will be investigated for future versions of the photoreactor.

Parts Required:

Steps:

  1. Thread the wires through the hole near the bottom of the fan holder, with the black side of the fan facing out.
  1. Carefully pull on the wires and pull the fan into its slot.
  1. Using the same technique as in Step 3a - 7, use solder seal connectors to extend the length of the fan wires by attaching them to pre-crimped wires, then carefully insert the pre-crimped wires into the connector head. Alternatively, if you have a pre-wired connector with 4 wire leads, you can use that instead.

Congratulations, you have created your Fan Holder which is used to cool the reactor

Step 3d: Assemble the LED Board

The LED Board uses transistors to control the on/off status of the LEDs, with the signal to the transistor coming from the Rasperry pi. It also has a power inlet port to power the LEDs separately from the Pi, as they draw quite a bit of current. In the future, an LED board could be purchased to directly control the LED, including its intensity, something not currently possible with this design. The design described here controls 2 LEDs at a time, but it could be extended to control more LEDs at once.

Parts Required:

Steps:

  1. Mount the power board and solder in a 1000 Ohm resistor between the power and ground sides. This creates a power port. The GND side represents your ground, and 5V your high voltage.
  2. Solder the circuit diagram above. For now, leave the open circles with text labels. The power supply and 1000 Ohm resistor are already completed in step 1. For the NPN transistors, the drawing below shows the schematic. Pin 1 (base) goes to the 330 Ohm resistor, and eventually to the RPi GPIO Pin. This acts like a switch for this LED. Pin 2 (collector) goes towards the LED and the power supply. Pin 3 (emitter) goes to ground.
  1. Solder wires into the open circles that connect to the RPi GPIO pins. The other end of the wire can be bare or an open pin. We will connect these to the RPi in a later step.
  2. Solder wires into the open circles that connect to the LED. For clarity, you can use red wires to go towards the power supply, and black wires towards the transistors. These wires should be at their other end connected to the complementary connectors that you used in Steps 3a-7 and 3a-8. These are meant to connect and disconnect the LED holders so you can change them.
  3. Solder a black wire from the ground/- terminal. The other end of the wire can be bare or an open pin. We will connect this wire to the RPi Ground Pin in a later step, to ensure a common ground.
  1. (Optional): To add more LED outputs, add more of this section of the circuit diagram, connected in the same way. If you add many more LEDs, you may require a power supply that is rated for higher current.

Congratulations, you have created your LED Board which is used to control the reactor LEDs

Step 3e: Assemble the Fan Board

The Fan Board uses pre-made fan control boards to control the RPM of the fans. It connects to the Rasperry pi and to a separate power supply. The current design is for 2 fans (1 cooling, 1 stirring) but could be easily be extended for use with more fans.

Parts Required:

Steps:

1a. (Optional) Mount the power board and solder in a 1000 Ohm resistor between the power and ground sides. This creates a power port. The GND side represents your ground, and 5V your high voltage. 1b. Alternatively, you can connect the 5V using a wire to the 5V section of the LED board or to the 5V Pin in the Pico. This means one less power supply, but will draw power either from the LED power supply or from the Pico (which you don't want to draw too much from).

  1. Solder the circuit diagram above. Solder wires into the open circles for the fan power (red) and ground (black). These will go to the 4-pin connector to the fan.
  2. For each Fan Control Board, solder wires into the "FAN" (blue) and "TACH" (yellow) ports, the other ends will go to the 4-pin connector to the fan.
  3. For each Fan Control Board, attach a Grove to Fan Board Connector. This will connect to the RPi.
  4. Take the power (red), ground (black), tach (yellow), and fan (blue) wires and connect them to a 4-pin connector that complements the one you created for your fans in step 3b-4.

Congratulations, you have created your Fan Board which is used to control the reactor Fans

Step 3f: Combine the Electronics

We need to connect the boards to the raspberry pi, which controls them. Optionally, you can choose to house them in the 3D printed holder, the parts of which you would need to print. This housing is only to keep the electronics tidy, and is not needed.

Parts Required:

Steps:

  1. Place the Raspberry Pi into the Grove Shield. This requires some force so that it goes in all the way.
  2. Common ground: Take the wires directed towards "RPi Ground" from the Fan and LED Boards and connect them to any open pin on the Raspberry Pi Pico labelled GND.
  3. Signal wires (LEDs): Take the wires directed towards "RPi GPIO Pin 0" and "RPi GPIO Pin 1" from the LED board and connect them to the Raspberry Pi Pico in the corresponding Pins ("GP0" and "GP1")
  4. Signal wires (Fans): Take the Grove-to-stemma connectors from the fan boards and connect them to the top-right corner slots on the Raspberry Pi Pico (with the USB connector oriented up).


Optional: Add the electronics to a housing

The electronics housing can be used to house the Raspberry Pi Pico and auxillary electronics. The holders for the auxillary electronics will fit the 60x40 mm PCB boards. They can be printed according to the instructions below. For the material you can use PLA but the snapping mechanism on the snap lid may work better with PETG.

File Name Purpose Printing Considerations Number Required Customization Potential
Pico Holder_MainBody.stl Holds the Pico Flat side down 1
Pico Holder_Main_Lid.stl Lid for Main Unit Flat side down 1
Aux_Module.stl Holds LED/Fan Board Flat side down 2 Could change to hold different sized PCB
Pico Holder_Port_Door_Default.stl Blank door for Aux Unit Flat side down 0 Can add ports
Pico Holder_Port_Door_Open_Ports.stl Custom door for Aux Unit Flat side down 2
Pico_Aux_Lid_Snap.stl Lid for Aux Unit Flat side down 2
Pico Holder_Port_Door_Honeycomb Honeycomb door for Aux Unit Flat side down 2

Instructions:



Congratulations, you have finished assembling the electronics!

Step 3g: Assemble the Reactor

Parts Required:

Steps:

  1. Connect the electrical connectors for each LED and fan to the electrical setup.


  1. Assemble the reactor parts. The LED holder, blank holders, and fan holders should slot easily into the 4 slots on the sides of the reactor shield. The reactor shield slots onto the fan base, which slots onto the screw base. The screw base has slots for fastening the base of the reactor. These could be modified to attach the reactor to a different base or with different screws.


Congratulations, you have fully assembled the LEDbyXAmple photoreactor!

Step 4: Operate the Photoreactor:

To operate the photoreactor, we will need to use a Python script that connects to the RPi Pico. The script can be used to control the RPM of the fan (with some constraints) and to turn the LEDs on and off as needed.

Step 4a: Installations

Steps:

  1. Install a code editor, we recommend VSCode.
  2. Install Python on your computer if it is not already installed.
  3. Install Micropico extension in VScode
  4. Connect the RPi Pico to your computer using the Usb B Micro B to Usb A Cable, while pressing the BOOTSEL button on the Pico. A file directory for the Pico should show up in your file explorer.
  5. Flash the Raspberry Pi by downloading the MicroPython UF2 file for Pico W into your computer and moving the file to the directory of the Raspberry Pi. The file directory should disappear after this and disconnect it from your computer.
  6. Open a new “micropico vPERL” terminal in VS code
  7. When the Raspberry Pi is connected it should show a success message in green text.

VS Code - Raspberry Pi Connected

Step 4b: Python Scripts

Steps:

  1. Download the python scripts from this github repository, including photo_reactor.py and reactor_test.py and the "lib" folder with the drivers for the fan boards
  2. In VSCode, “Configure project” for the folder that contains the lib folder, photo_reactor.py & reactor_test.py files
  3. Upload the project to Raspberry Pi by right clicking on folder containing all the project files & select “Upload project to Pico”
  4. To run the test code, select reactor_test.py file & right click to choose “Run current file on Pico”

NOTE: Do not look directly at your LEDs! We recommend using blue-light blocking glasses and never looking directly at the emitted light

Step 4b: Operation

The LEDbyXample photoreactor currently has two functions: Switch on/off the LEDs (could have up to 4 in one reactor) and initialize/set the rpm of the fans (both for stirring and cooling).

Functions:

  1. add_fan ( fan ) takes in the SoftI2C address with two pins that are associated with controlling the fan, these numbers will change depending on which slot you put your fans in on the pico board
  2. add_led ( pin ) takes in the GPIO pin number for a specific LED to set it up for operation
  3. turn_on_led ( index ) turns on the LED with the specified index
  4. turn_off_led ( index ) turns off the LED with the specified index
  5. set_led_brightness (index, duty_cycle) Set the brightness of an LED to between 0 and 100 (duty_cycle) using pulse width modulation.
  6. initialize_fan ( index, starting_duty_cycle) attempts to turn on fan with specific index, it will try different duty cycles until it is able to measure an rpm (sometimes the initial duty cycle is insufficient when there is a load like a stir bar in a thick liquid. Note that the fan may not initialize if the stir bar is too close or too far away from the magnets. This matters more if you are using a different vial than the 2 dram (8 mL) vial this reactor was designed for. This function returns the duty cycle that was sufficient to activate the fan.
  7. set_fan_rpm (index, target_rpm, duty_cycle) This attempts to get the specified fan to reach a specific rpm, starting with the specified duty cycle. It may not maintain that rpm, but will keep the same duty cycle, which is returned by the function.
  8. hold_fan_rpm (index, target_rpm, target_time, duty cycle) This attempts to adjust the input duty cycle to maintain a target rpm for a specific time period. This means adjusting the duty cycle up and down slightly as needed.

Future Steps

  1. Increase the physical robustnest of the design, preventing the pieces from falling over when wires are tugged.
  2. Measure the temperature of the reactor using a thermocouple or an IR probe/camera.
  3. Measure the spatial uniformity of the LED emission in the reactor.
  4. Use feedback control to increase cooling fan speed when temperature rises. This might require a stronger cooling fan.